# Patent

## Title
Compositions and methods for bacterial lysis and neutral lipid production

## Abstract

The present invention is directed to a cyanobacterium that produces neutral lipids or alkanes. Such neutral lipids or alkanes may be used for biofuel production.

## Background
REFERENCE TO SEQUENCE LISTING
A paper copy of the sequence listing and a computer readable form of the same sequence listing are appended below and herein incorporated by reference. The information recorded in computer readable form is identical to the written sequence listing, according to 37 C.F.R. 1.821 (f).
FIELD OF THE INVENTION
The invention encompasses a cyanobacterium that produces neutral lipids or alkanes. Such neutral lipids or alkanes may be used for biofuel production.
BACKGROUND OF THE INVENTION
The search for alternative fuel sources continues to be a high priority. Photosynthetic bacteria, such as the cyanobacteria, potentially provide a source of lipids that are relatively easy to harvest. The lipids may then be converted to biofuel. To increase the efficiency of the system, however, it would be beneficial to use a bacterial strain that produced lipids that are readily converted to a biofuel, such as neutral lipids. Hence, there is a need in the art for a photosynthesizing bacterium that produces high concentrations of neutral lipids or hydrocarbons like alkanes.
REFERENCE TO COLOR FIGURES
The application file contains at least one photograph executed in color. Copies of this patent application publication with color photographs will be provided by the Office upon request and payment of the necessary fee.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 depicts the native lipid comparisons in wild-type Synechocystis. Monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), and sulphoquinovosyl-diacylglycerol (SQDG), were compared using UV absorbance (Rel A205, at the wavelength of 205 nm; and Rel A211, at the wavelength of 211 nm) and MS (mass spectrum) relative area (Rel A-MS). The subtypes of lipids are shown on the X axis, for example, ‘16, 18:3’ means a DGDG molecule with a saturated C16 fatty acid and a C18 fatty acid with 3 double bonds. All the other lipid amounts were shown as relative amounts compared to the absorbance peak or MS area of 16, 18:3.
FIG. 2 depicts lipid metabolism in Synechocystis. Red suns indicate pathways toward TAG, which are in consideration for over-expression or introduction from other organisms. Yellow stop signs indicate pathways away from TAG, which are in consideration for knocking out (i.e., elimination).
FIG. 3 depicts intracellular lipid inclusions in prokaryotes and general structures of the lipids. (A) Cell of R. eutropha H16 accumulating PHB inclusions; (B) cell of R. opacus PD630 from late stationary growth phase accumulating large amount of TAG inclusions; (C) cell of A. calcoaceticus ADP1 with three spherical WE inclusions; (D) Acinetobacter sp. strain HO1-N accumulating small rectangular WE inclusions; (E) Acinetobacter sp. strain M1 accumulating large, disclike WE inclusions. Bars, 0.2 μm. Cited from (Walternann and Steinbuchel 2005).
FIG. 4 depicts biosynthetic funtions of the wax ester synthase (WS)/acyl-CoA:diacylglycerol acyltransferase (DGAT) (WS/DGAT) enzyme identified in A. baylyi sp. ADP1.
FIG. 5 depicts suggested models for the formation of PHA inclusions in bacteria. (A) The ‘micelle’ model; (B) the ‘budding membrane’ model. Cited from (Walternann and Steinbuchel 2005).
FIG. 6 depicts the construction of triglyceride-producing Synechocystis strains SD201, SD202 and SD203. The primers used in the construction can be referred to in Table 9.
FIG. 7 depicts TLC analysis of the total lipids of SD210 and SD202 grown in BG-11 medium and high carbon-to-nitrogen BG-11 medium (CN210 and CN2O2), where 10 mM glucose was added to BG11 to increase carbon from 0.19 mM (0.2 mg/l NaCO3) to 60.19 mM, and NaNO3 was decreased from 3 g/L to 0.03 g/L. On the most right and left lanes TAG with three C16:0 serves as control. The arrows indicate overproduced TAGs from the total lipid extracts.
FIG. 8 depicts the genetic genealogy tree of constructing Green Recovery strains.
FIG. 9 depicts culture lysis of the Green Recovery strains induced by CO2 limitation.
FIG. 10 depicts cell membrane permeability created in the Green Recovery strains by CO2 limitation.
FIG. 11 depicts a plot of the relationship between membrane permeability (revealed by Sytox staining) and cell viability (revealed by CFU) during Green Recovery after CO2 limitation.
FIG. 12 depicts plots of membrane damage of different SD strains after CO2 limitation with 1/4 and 1/16 dilution of the original culture. A) SD256; B) SD257; C) SD237; D) WT.
FIG. 13 depicts a plot of membrane damage of SD256 after CO2 limitation under different conditions. Normal means the CO2 limited cultures were rotated at 100 rpm under continuous illumination (140 μmol photons m−2 s−1); low light means the CO2 limited cultures were rotated at 100 rpm under illumination (20 μmol photons m−2 s−1); dark means the CO2 limited cultures were rotated at 100 rpm under illumination (2 μmol photons m−2 s−1); sitting means the CO2 limited cultures were shaken only once per day before sampling and under illumination (140 μmol photons m−2 s−1).
FIG. 14 depicts a gas chromatography plot of the analysis of the FFA samples extracted by hexane from the SD237 culture after CO2 limitation. The retention time and the types of released FFAs are marked on the peaks.
FIG. 15 depicts the fatty acid profiles of SD strains. All the cultures were grown to about 4×108 cells/ml at 30° C. For wild-type, the columns show the fatty acid profile of total membrane lipids. For SD237, the columns show the released FFA profile by Green Recovery, which is similar to that of wild-type with abundant unsaturated fatty acids. For SD232, the columns show the profile of secreted FFAs, which are highly saturated with significant amounts of C12:0 and C14:0. For SD239 before (Green Recovery), the columns show the profile of secreted FFAs before CO2 limitation, which is similar to that of the FFA secretion strain SD232. For SD239 after (Green Recovery), the columns show the profile of all the FFAs contributed by SD239 after CO2 limitation, which is a mixture of secreted FFAs (e.g., C12:0 and C14:0) and released FFAs (e.g., C18:2 and C18:3).
FIG. 16 depicts FFA yields of SD256 and SD237 during Green Recovery. Ten CO2-limiting flasks with 16 ml cultures were set in the same conditions on day zero for each strain. Every day, the whole cultures in duplicate flasks were extracted by hexane for FFA yields. The cell membrane damage was observed after SYTOX staining, and the permeable cell percentages are indicated above the columns.
FIG. 17 depicts the alkane biosynthesis pathway in cyanobacteria.
FIG. 18 depicts a phylogentic tree of alkane biosynthesis genes in cyanobacteria. Of these alkane biosynthesis genes, ten genes from Synechococcus sp. PCC 7942, Prochlorococcus marinus subsp. Pastoris str. CCMP 1986, Nostoc punctiorme PCC 73102, Thermosynechococcus elongatus BP-1, and Gloebacter violaceus PCC 7421, were chose for alkane overproduction in Synechocystis PCC sp. 6803.
FIG. 19 depicts GC analysis of the alkane production in SD294 culture.
FIG. 20 depicts GC analysis of alkane production and release of alkane by Green Recovery in the SD303 culture. A, GC analysis of a culture of SD303, which has been grown for 3 day with a cell density of 3×108 cells/ml. B, GC analysis of the SD303 culture after Green Recovery induced by CO2 limitation.
FIG. 21 depicts the construction of stationary-phase-autolysis strains SD111 and SD112. The isiA and isiB locus are shown at the top of the figure, indicated by two leftward pink arrows, which are controlled by the isiA promoter (PisiA), Fur box (brown box), and antisense RNA (IsiR, red arrow). A DNA fragment for transformation including flanking region 1, P22 lysis cassette (13, 15, and 19), kanamycin resistance cassette (KmR), and flanking region 2 are spliced together by overlapping PCR, and transferred into SD100 (6803 wild type) and SD202 (a neutral lipid production strain) by homologous double crossover exchange to result in SD111 and SD112.
FIG. 22 depicts the autolysis response of SD111 on Fe-deficient BG-11 plates. Upper four plates, >103 SD111 6803 cells were grown on the BG11 plates containing different concentrations of Fe, i.e., 20 μM (1×Fe in BG-11), 4 μM (0.2×Fe in BG-11), 3 μM (0.15×Fe in BG-11), 2 μM (0.1×Fe in BG-11); lower four plates, >104 wild type 6803 cells were grown on the same BG-11 plates containing different concentrations of Fe.
FIG. 23 depicts the Stationary-phase-autolysis of SD111 when grown in BG-11 medium. The first autolysis period is in exponential growth phase when the cell density is between 107-107.5 cells/ml, the second autolysis period is in stationary growth phase when the cell density is above 108 cells/ml. The drop and fluctuation of CFU in these two periods suggested that the old cells were undergoing self-lysis.
FIG. 24 depicts the biodiesel biosynthesis pathway. TE, thioesterase; ACL, acyl-CoA ligase; ATF, acyl transferase.
FIG. 25 depicts the GC analysis (A) of secreted FFA (B) and FAEE (C) of induced SD251 culture supplemented with ethanol.
FIG. 26 depicts TEM images of wild-type (A), SD201 (B) and SD202 (C). The white vacuoles inside the cell indicate the presence of neutral lipid droplets.



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides a cyanobacterium capable of producing neutral lipids. In certain embodiments, the cyanobacterium additionally comprises the regulated expression of a nucleic acid encoding a protein capable of hydrolyzing the lipid membranes, allowing at least one enzyme to degrade the cellular lipid membranes and the peptidoglycan layer of a bacterial cell wall. Such degradation allows for ready harvesting of the neutral lipids, which may be useful for developing biofuels.
I. Neutral Lipids
One aspect of the present invention encompasses a cyanobacterium capable of producing neutral lipids. As used herein, the phrase “neutral lipids” refers to non-polar lipids. Non-limiting examples of neutral lipids may include triacylglycerol (TAG), steryl esters (SEs), wax ester (WE), fatty acyl methyl ester (FAME), fatty acyl ethyl ester (FAEE) and poly(3-hydroxybutyrate) (PHB). Generally speaking, neutral lipids lack charged groups and are therefore unable to integrate into bilayer membranes in substantial amounts. They serve as intracellular storage molecules for sterols, free fatty acids, and diacylglycerols (DAGs).
In some embodiments, a cyanobacterium capable of producing neutral lipids comprises a nucleic acid sequence encoding a neutral lipid synthase. Generally speaking, a neutral lipid synthase is a synthase that aids in the expression of one or more neutral lipids. Neutral lipid synthases may be found in other prokaryotic or eukaryotic species. For instance, the first wax ester synthase (WS) as well as acyl-CoA:diacylglycerol acyltransferase (DGAT) (WS/DGAT) enzyme was identified in A. baylyi sp. ADP1, and its gene (atfA) was cloned into E. coli by Kalscheuer and Steinbüchel (2003 J. Biol. Chem. 287: 8075-82). This bacterium possesses only a single WS/DGAT enzyme. Numerous atfA homologs, however, can be found among the available genome databases of actinomycetes, especially in those of Mycobacterium, Rhodococcus and Streptomycetes. In particular, Mycobacteria possess a large number of conserved proteins with high homologies to the A. baylyi sp. ADP1 AtfA. By way of non-limiting example, 15 atfA homologous genes were identified and characterized in M. tuberculosis H37Rv. Genes with high homologies to the Acinetobacter sp. ADP1 atfA were also identified in the genome databases of several Gram-negative strains, including marine bacteria like Hahella chejuensis, psychrophilic strains like Psychrobacter sp. and Polaromonas sp. and even in Bradyrhizobium japonicum. Hence, suitable neutral lipid synthases may be derived, for example, from Acinebacter baylyi, Rhodococcus opacus, Rhodococcus ruber, Ralstonia eutropha, Streptomyces coelicolor, Norcardia sp., or Mycobacterium smegmatis. In one embodiment, the TAG synthase encoded by the atfA gene from Acinebacter baylyi is a non-limiting example of a neutral lipid synthase. Alternatively, suitable neutral lipid synthases may be synthesized in vitro based on a wild-type sequence derived from a prokaryotic or eukaryotic organism. Methods of introducing a nucleic acid sequence encoding a neutral lipid synthase to a cyanobacterium are known in the art and detailed in the examples.
In other embodiments, a cyanobacterium capable of producing neutral lipids comprises a nucleic acid sequence encoding a lipid body protein. Typically a lipid body protein aids in storing the neutral lipids within the cyanobacterium. A non-limiting example of a lipid body protein is a PHA inclusion protein such as PhaC, PhaZ, PhaR, and phasins such as PhaP1. Additionally, proteins associated with TAG inclusions have been referred to as granule-associated proteins (GAP) and exhibit apparent molecular masses ranging from to 31 kDa. By way of non-limiting example, in R. opacus PD630, these were GAP15, GAP17, GAP20, GAP26, and GAP31, with the numeration indicating the apparent molecular weight (Kalscheuer et al. 2001 Arch. Microbiol. 177:20-28.)
The nucleic acid encoding PhaP1 may be cloned from Ralstonia eutropha. Methods of introducing a nucleic acid sequence encoding a lipid body protein to a cyanobacterium are known in the art and detailed in the examples.
In certain embodiments, a cyanobacterium of the invention may lack a functional lipase that catalyzes the hydrolysis of a neutral lipid. For instance, a cyanobacterium may lack a functional lipase encoded by a lipA nucleic acid. Methods for modifying a cyanobacterium to lack a functional lipase are known in the art and may include deletion mutations and insertion-deletion mutations. In one embodiment, a cyanobacterium that lacks a functional lipase may comprise a nucleic acid cassette inserted into the coding region of lipA. For instance, the cassette may comprise a nucleic acid sequence encoding a neutral lipid synthase or a nucleic acid sequence encoding a lipid body protein. In certain embodiments, the cassette may comprise PpsbAII atfA phaP1.
II. Release of Fatty Acids from Cellular Membranes
Another aspect of the invention encompasses the discovery that the regulated expression of a nucleic acid encoding a protein capable of hydrolyzing the lipid membranes to free fatty acids may be used to disrupt the cells and release intracellular neutral lipids. Hence, in one embodiment, the invention encompasses a cyanobacterium comprising an inducible promoter operably-linked to a nucleic acid encoding a first protein capable of hydrolyzing the lipid membranes of the bacterium and at least one endolysin protein. In another embodiment, the invention encompasses a cyanobacterium comprising a first nucleic acid, wherein the first nucleic acid comprises a first inducible promoter operably-linked to a nucleic acid encoding a first protein capable of hydrolyzing the lipid membranes of the bacterium; and a second nucleic acid, wherein the second nucleic acid comprises a second promoter operably-linked to a nucleic acid encoding at least one endolysin protein.
In certain instances, the invention encompasses a cyanobacterium comprising more than one integrated nucleic acid construct of the invention. For instance, the invention may encompass a cyanobacterium comprising a first inducible promoter operably-linked to a nucleic acid encoding a first protein capable of hydrolyzing the lipid membranes of the bacterium, a second inducible promoter operably-linked to a different nucleic acid encoding a first protein capable of hydrolyzing the lipid membranes of the bacterium, and at least two endolysin proteins. In a further embodiment, the nucleic acid sequences encoding the endolysin proteins may be operably linked to a constitutive promoter.
Methods of making cyanobacterium of the invention are known in the art. Generally speaking, a cyanobacterium is transformed with a nucleic acid construct of the invention. Methods of transformation are well known in the art, and may include electroporation, natural transformation, and calcium chloride mediated transformation. Methods of screening for and verifying chromosomal integration are also known in the art.
In one embodiment, a method of making a cyanobacterium of the invention may comprise first transforming the bacterium with a vector comprising, in part, an antibiotic resistance marker and a negative selection marker. Chromosomal integration may be selected for by selecting for antibiotic resistance. Next, the antibiotic strain is transformed with a similar vector comprising the target genes of interest. Chromosomal integration of the target genes may be selected for by selecting for the absence of the negative marker. For instance, if the negative marker is sacB, then one would select for sucrose resistance. For more details, see Kang et al., J. Bacteriol. (2002) 184(1):307-12, hereby incorporated by reference in its entirety.
(a) Nucleic Acid Constructs
The present invention encompasses a nucleic acid construct that, when introduced into a bacterium, may be used in a method for inducing the degradation of lipid membrane or the peptidoglycan layer of a bacterial cell wall. In one embodiment, the nucleic acid comprises an inducible promoter operably-linked to a nucleic acid sequence encoding a first protein capable of hydrolyzing bacterial lipid membranes into free fatty acids. In another embodiment, the nucleic acid comprises an inducible promoter operably-linked to a nucleic acid sequence encoding a first protein capable of forming a lesion in a bacterial lipid membranes. In yet another embodiment, the nucleic acid comprises a promoter operably-linked to at least one endolysin. In another embodiment, the nucleic acid comprises an inducible promoter operably-linked to both a nucleic acid sequence encoding a first protein and a nucleic acid sequence encoding at least one endolysin. In still another embodiment, the nucleic acid comprises an inducible promoter operably-linked to a nucleic acid sequence encoding a first protein and a second promoter operably-linked to a nucleic acid sequence encoding at least one endolysin. Each component of the above nucleic acid constructs is discussed in more detail below.
Methods of making a nucleic acid construct of the invention are known in the art. Additional information may be found in Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989)
i. Promoters
A nucleic acid construct of the present invention comprises a promoter. In particular, a nucleic acid construct comprises a first inducible promoter. In some embodiments, a nucleic acid also comprises a second promoter. When a nucleic acid comprises a first and a second promoter, the promoters may read in opposite directions, or may read in the same direction.
A. First Inducible Promoter
In certain embodiments, a nucleic acid of the invention encompasses a first inducible promoter. Non-limiting examples of inducible promoters may include, but are not limited to, those induced by expression of an exogenous protein (e.g., T7 RNA polymerase, SP6 RNA polymerase), by the presence of a small molecule (e.g., IPTG, galactose, tetracycline, steroid hormone, abscisic acid), by absence of small molecules (e.g., CO2, iron, nitrogen), by metals or metal ions (e.g., copper, zinc, cadmium, nickel), and by environmental factors (e.g., heat, cold, stress), and by growth phase. In each of the above embodiments, the inducible promoter is preferably tightly regulated such that in the absence of induction, substantially no transcription is initiated through the promoter. Additionally, induction of the promoter of interest should not typically alter transcription through other promoters. Also, generally speaking, the compound or condition that induces an inducible promoter should not be naturally present in the organism or environment where expression is sought.
In one embodiment, the inducible promoter is induced by limitation of CO2 supply to the cyanobacteria culture. By way of non-limiting example, the inducible promoter may be variant sequences of the promoter sequence of Synechocystis PCC6803 that are up-regulated under the CO2-limitation conditions, such as the cmp genes, ntp genes, ndh genes, sbt genes, chp genes, and rbc genes.
In one embodiment, the inducible promoter is induced by iron starvation or by entering the stationary growth phase. By way of non-limiting example, the inducible promoter may be variant sequences of the promoter sequence of Synechocystis PCC6803 isiA gene. In some embodiments, the inducible promoter may be variance sequences of the promoter sequence of cyanobacterial genes that are up-regulated under Fe-starvation conditions such as isiA, or when the culture enters the stationary growth phase, such as isiA, phrA, sigC, sigB, and sigH genes.
In one embodiment, the inducible promoter is induced by a metal or metal ion. By way of non-limiting example, the inducible promoter may be induced by copper, zinc, cadmium, mercury, nickel, gold, silver, cobalt, and bismuth or ions thereof. In one embodiment, the inducible promoter is induced by nickel or a nickel ion. In an exemplary embodiment, the inducible promoter is induced by a nickel ion, such as Ni2+. In another exemplary embodiment, the inducible promoter is the nickel inducible promoter from Synechocystis PCC6803. In another embodiment, the inducible promoter may be induced by copper or a copper ion. In yet another embodiment, the inducible promoter may be induced by zinc or a zinc ion. In still another embodiment, the inducible promoter may be induced by cadmium or a cadmium ion. In yet still another embodiment, the inducible promoter may be induced by mercury or a mercury ion. In an alternative embodiment, the inducible promoter may be induced by gold or a gold ion. In another alternative embodiment, the inducible promoter may be induced by silver or a silver ion. In yet another alternative embodiment, the inducible promoter may be induced by cobalt or a cobalt ion. In still another alternative embodiment, the inducible promoter may be induced by bismuth or a bismuth ion.
In some embodiments, the promoter is induced by exposing a cell comprising the inducible promoter to a metal or metal ion. The cell may be exposed to the metal or metal ion by adding the metal to the bacterial growth media. In certain embodiments, the metal or metal ion added to the bacterial growth media may be efficiently recovered from the media. In other embodiments, the metal or metal ion remaining in the media after recovery does not substantially impede downstream processing of the media or of the bacterial gene products.
In one embodiment, the nucleic acid comprises a metal or metal ion inducible promoter operably-linked to a nucleic acid sequence encoding a first protein capable of hydrolyzing a bacterial lipid membranes. In another embodiment, the nucleic acid comprises a metal or metal ion inducible promoter operably-linked to both a nucleic acid sequence encoding a first protein and a nucleic acid sequence encoding at least one endolysin. In yet another embodiment, the nucleic acid comprises a metal or metal ion inducible promoter operably-linked to at least one endolysin. In still another embodiment, the nucleic acid comprises a metal or metal ion inducible promoter operably-linked to a nucleic acid sequence encoding a first protein and a second promoter operably-linked to a nucleic acid sequence encoding at least one endolysin.
B. Second Promoter
Certain nucleic acid constructs of the invention may comprise a second promoter. The second promoter may be an inducible promoter, or may be a constitutive promoter. If the second promoter is an inducible promoter, it may or may not be induced by the same compound or condition that induces the first inducible promoter. In one embodiment, the same compound or condition induces both the first and the second inducible promoters. In another embodiment, the first inducible promoter is induced by a different compound or condition than the second inducible promoter. Non-limiting examples of inducible promoters that may be used are detailed in section I(a)(i) above.
Constitutive promoters that may comprise the second promoter are known in the art. Non-limiting examples of constitutive promoters may include constitutive promoters from Gram negative bacteria or a Gram negative bacteriophage. For instance, promoters from highly expressed Gram negative gene products may be used, such as the promoter for Lpp, OmpA, rRNA, and ribosomal proteins. Alternatively, regulatable promoters may be used in a strain that lacks the regulatory protein for that promoter. For instance Plac, Ptac, and Ptrc may be used as constitutive promoters in strains that lack LacI. Similarly, P22 PR and PL may be used in strains that lack the P22 C2 repressor protein, and λ PR and PL may be used in strains that lack the λ C1 repressor protein. In one embodiment, the constitutive promoter is from a bacteriophage. In another embodiment, the constitutive promoter is from a Salmonella bacteriophage. In yet another embodiment, the constitutive promoter is from a cyanophage. In some embodiments, the constitutive promoter is a Synechocystis promoter. For instance, the constitutive promoter may be the PpsbAII promoter or its variant sequences, the Prbc promoter or its variant sequences, the Pcpc promoter or its variant sequences, and the PrnpB promoter or its variant sequences.
In one embodiment, a nucleic acid of the invention comprises a metal or metal ion inducible promoter operably-linked to a nucleic acid sequence encoding a first protein and a second constitutive promoter operably-linked to a nucleic acid sequence encoding at least one endolysin. In another embodiment, a nucleic acid of the invention comprises a metal or metal ion inducible promoter operably-linked to a nucleic acid sequence encoding a first protein and a second inducible promoter operably-linked to a nucleic acid sequence encoding at least one endolysin.
ii. First Protein
A nucleic acid construct of the invention also comprises a sequence encoding at least one first protein. Generally speaking, a first protein is a protein capable of degrading the lipid membranes into free fatty acid and release intracellular neutral lipids. For instance, the first protein may be a lipolytic enzyme that is able to hydrolyze acylglycerols. In one embodiment, the first protein may be a lipolytic enzyme that hydrolyzes diacylglycerols, including MGDG (monogalactosyl diacylglycerol), DGDG (digalactosyl diacylglycerol), PG (phosphatidylglycerol), and SQDG (sulfoquinovosyl diacylglycerol). In another embodiment, the first protein may be a lipase that hydrolyzes triacylglycerols. In yet another embodiment, the first protein may be a lipolytic enzyme that hydrolyzes monoacylglycerols. In still yet another embodiment, the first protein may be a lipolytic enzyme from a bacterium, e.g., Staphylococcus hyicus. In a further embodiment, the first protein may be a lipolytic enzyme from a fungus, e.g., Fusarium oxysporum. In one embodiment, the first protein may be a lipolytic enzyme from an animal, e.g, guinea pig.
In other embodiments, a first protein is a protein capable of hydrolyzing the lipid membranes that provides the endolysin access to the peptidoglycan layer of the cell wall. In these embodiments, the first protein may be a bacteriophage protein. For instance, the first protein may be a bacteriophage holin protein. In one embodiment, the first protein is a holin from a bacteriophage that infects gram-negative bacteria. In another embodiment, the first protein is a holin from a bacteriophage that infects gram-positive bacteria. In certain embodiments, the first protein is a holin from a cyanophage. In one embodiment, the first protein is a holin from a bacteriophage that infects Synechocystis. In another embodiment, the first protein may be from a bacteriophage that infects Salmonella. In still another embodiment, the first protein may be from a P22 phage. For example, the first protein may be gene 13 of the P22 phage. In yet another embodiment, the first protein may be from a λ phage. For example, the first protein may be encoded by gene S of the λ phage. In still another embodiment, the first protein may be from an E. coli phage. For instance, the first protein may be encoded by gene E of E. coli phage PhiX174. In certain embodiments, a nucleic acid of the invention may comprise at least two holins. In one embodiment, a nucleic acid may comprise a holin from P22 and a holin from λ phage. For instance, the nucleic acid may comprise gene 13 and gene S.
Additionally, a first protein may be a holin described above with at least one, or a combination of one or more, nucleic acid deletions, substitutions, additions, or insertions which result in an alteration in the corresponding amino acid sequence of the encoded holin protein, such as a homolog, ortholog, mimic or degenerative variant. For instance, a first protein may be a holin described above encoded by a nucleic acid with codons optimized for use in a particular bacterial strain, such as Synechocystis. Such a holin may be generated using recombinant techniques such as site-directed mutagenesis (Smith Annu. Rev. Genet. 19. 423 (1985)), e.g., using nucleic acid amplification techniques such as PCR (Zhao et al. Methods Enzymol. 217, 218 (1993)) to introduce deletions, insertions and point mutations. Other methods for deletion mutagenesis involve, for example, the use of either BAL 31 nuclease, which progressively shortens a double-stranded DNA fragment from both the 5′ and 3′ ends, or exonuclease III, which digests the target DNA from the 3′ end (see, e.g., Henikoff Gene 28, 351 (1984)). The extent of digestion in both cases is controlled by incubation time or the temperature of the reaction or both. Point mutations can be introduced by treatment with mutagens, such as sodium bisulfite (Botstein et al. Science 229, 1193 (1985)). Other exemplary methods for introducing point mutations involve enzymatic incorporation of nucleotide analogs or misincorporation of normal nucleotides or alpha-thionucleotide by DNA polymerases (Shortle et al. Proc. Natl. Acad. Sci. USA 79, 1588 (1982)). PCR-based mutagenesis methods (or other mutagenesis methods based on nucleic acid amplification techniques), are generally preferred as they are simple and more rapid than classical techniques (Higuchi et al. Nucleic Acids Res. 16, 7351 (1988); Vallette et al. Nucleic Acids Res. 17, 723 (1989)).
In addition to having a substantially similar biological function, a homolog, ortholog, mimic or degenerative variant of a holin suitable for use in the invention will also typically share substantial sequence similarity to a holin protein. In addition, suitable homologs, ortholog, mimic or degenerative variants preferably share at least 30% sequence homology with a holin protein, more preferably, 50%, and even more preferably, are greater than about 75% homologous in sequence to a holin protein. Alternatively, peptide mimics of a holin could be used that retain critical molecular recognition elements, although peptide bonds, side chain structures, chiral centers and other features of the parental active protein sequence may be replaced by chemical entities that are not native to the holin protein yet, nevertheless, confer activity.
In determining whether a polypeptide is substantially homologous to a holin polypeptide, sequence similarity may be determined by conventional algorithms, which typically allow introduction of a small number of gaps in order to achieve the best fit. In particular, “percent homology” of two polypeptides or two nucleic acid sequences is determined using the algorithm of Karlin and Altschul [Proc. Natl. Acad. Sci. USA 87, 2264 (1993)]. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul, et al. (J. Mol. Biol. 215, 403 (1990)). BLAST nucleotide searches may be performed with the NBLAST program to obtain nucleotide sequences homologous to a nucleic acid molecule of the invention. Equally, BLAST protein searches may be performed with the XBLAST program to obtain amino acid sequences that are homologous to a polypeptide of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST is utilized as described in Altschul, et al. (Nucleic Acids Res. 25, 3389 (1997)). When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) are employed. See http://www.ncbi.nlm.nih.gov for more details.
In one embodiment, a nucleic acid of the invention comprises a metal or metal ion inducible promoter operably-linked to a nucleic acid sequence encoding a P22 phage holin. In another embodiment, the nucleic acid comprises a metal or metal ion inducible promoter operably-linked to both a nucleic acid sequence encoding a P22 phage holin and a nucleic acid sequence encoding at least one endolysin. In yet another embodiment, the nucleic acid comprises a metal or metal ion inducible promoter operably-linked to a nucleic acid sequence encoding a P22 phage holin and a second promoter operably-linked to a nucleic acid sequence encoding at least one endolysin.
iii. Endolysin
In some embodiments, a nucleic acid of the invention comprises at least one endolysin. In other embodiments, a nucleic acid of the invention comprises at least two endolysins. In yet another embodiment, a nucleic acid of the invention comprises at least three endolysins. In still another embodiment, a nucleic acid of the invention may comprise at least four endolysins. As used herein, “endolysin” refers to a protein capable of degrading the peptidoglycan layer of a bacterial cell wall. Generally speaking, the term endolysin encompasses proteins selected from the group consisting of lysozyme or muramidase, glucosaminidase, transglycosylase, amidase, and endopeptidase. Exemplary endolysins do not affect the cell until after the first protein creates lesions in the lipid membranes. Stated another way, the accumulation of endolysins in the cytosol of a bacterium will typically not substantially impair the growth rate of the bacterium. In another exemplary embodiment, the endolysin has a high enzymatic turnover rate. In yet another exemplary embodiment, the endolysin is from a gram positive bacteria. Because the cell walls of gram positive bacteria typically have a thicker peptidoglycan layer, an endolysin from a gram positive bacteria might be expected to have a higher enzymatic turnover rate.
In one embodiment, at least one endolysin is from a bacteriophage. In certain embodiments, suitable endolysins may be from phages detailed in section I(b) above in reference to the first protein. In another embodiment, at least one endolysin is from a Salmonella bacteriophage. In yet another embodiment, at least one endolysin is from a P22 phage. In still yet another embodiment, at least one endolysin is from a λ phage. In an alternative embodiment, at least one endolysin is gp19 from a P22 phage. In another alternative, a nucleic acid of the invention comprises gp19 and gp15 from a P22 phage. In some embodiments, at least one endolysin is R from a λ phage. In other embodiments, a nucleic acid of the invention comprises R and Rz from a λ phage. In certain embodiments, a nucleic acid of the invention comprises gp19, gp15, R, and Rz.
Additionally, an endolysin may be a protein described above with at least one, or a combination of one or more, nucleic acid deletions, substitutions, additions, or insertions which result in an alteration in the corresponding amino acid sequence of the encoded endolysin protein, such as a homolog, ortholog, mimic or degenerative variant. Such an endolysin may be generated using recombinant techniques such as those described in section I(b) above in reference to a first protein. In addition to having a substantially similar biological function, a homolog, ortholog, mimic or degenerative variant of an endolysin suitable for use in the invention will also typically share substantial sequence similarity to an endolysin protein. In addition, suitable homologs, ortholog, mimic or degenerative variants preferably share at least 30% sequence homology with an endolysin protein, more preferably, 50%, and even more preferably, are greater than about 75% homologous in sequence to an endolysin protein. Alternatively, peptide mimics of an endolysin could be used that retain critical molecular recognition elements, although peptide bonds, side chain structures, chiral centers and other features of the parental active protein sequence may be replaced by chemical entities that are not native to the endolysin protein yet, nevertheless, confer activity. Percent homology may be calculated as described in section I(b) above.
iv. Additional Components
In certain embodiments, nucleic acids of the invention may further comprise additional components, such as a marker, a spacer domain, and a flanking sequence.
A. Markers
In one embodiment, a nucleic acid of the invention comprises at least one marker. Generally speaking, a marker encodes a product that the host cell cannot make, such that the cell acquires resistance to a specific compound, is able to survive under specific conditions, or is otherwise differentiable from cells that do not carry the marker. Markers may be positive or negative markers. In some embodiments, a nucleic acid of the invention may comprise both a positive marker and a negative marker. In certain embodiments, the marker may code for an antibiotic resistance factor. Suitable examples of antibiotic resistance markers may include, but are not limited to, those coding for proteins that impart resistance to kanamycin, spectromycin, neomycin, geneticin (G418), ampicillin, tetracycline, and chloramphenicol. Additionally, the sacB gene may be used as a negative marker. The sacB gene is lethal in many bacteria when they are grown on sucrose media. Additionally, fluorescent proteins may be used as visually identifiable markers. Generally speaking, markers may be present during construction of the strains, but are typically removed from the final constructs. Proteins can also be marked by adding a sequence such as FLAG, HA, His tag, that can be recognized by a monoclonal antibody using immunological methods. In some embodiments, a marker may be a unique indentifier of a genetically modified cyanobacterium.
B. Spacer Domain
Additionally, a nucleic acid of the invention may comprise a Shine-Dalgarno sequence, or a ribsome binding site (RBS). Generally speaking, a RBS is the nucleic acid sequence in the mRNA that binds to a 16s rRNA in the ribosome to initiate translation. For Gram negative bacteria, the RBS is generally AGGA. The RBS may be located about 8 to about 11 bp 3′ of the start codon of the first structural gene. One skilled in the art will realize that the RBS sequence or its distance to the start codon may be altered to increase or decrease translation efficiency.
C. Flanking Sequence
Nucleic acid constructs of the invention may also comprise flanking sequences. The phrase “flanking sequence” as used herein, refers to a nucleic acid sequence homologous to a chromosomal sequence. A construct comprising a flanking sequence on either side of a construct (i.e. a left flanking sequence and a right flanking sequence) may homologously recombine with the homologous chromosome, thereby integrating the construct between the flanking sequences into the chromosome. Generally speaking, flanking sequences may be of variable length. In an exemplary embodiment, the flanking sequences may be between about 300 and about 500 bp. In another exemplary embodiment, the left flanking sequence and the right flanking sequence are substantially the same length. For more details, see the Examples.
v. Plasmids
A nucleic acid construct of the invention may comprise a plasmid suitable for use in a bacterium. Such a plasmid may contain multiple cloning sites for ease in manipulating nucleic acid sequences. Numerous suitable plasmids are known in the art.
III. Overproduction of Acyl-CoA
The critical substrate for neutral lipids synthesis is acyl-CoA. The A. baylyi sp. ADP1 WS/DGAT is able to transfer acyl-CoA to diacylglycerol to produce TAG, and also able to transfer acyl-CoA to methanol or ethanol to produce FAME or FAEE respectively. However, cyanobacteria do not possess the acyl-CoA synthesis pathway, and thus do not have a significant amount of acyl-CoA in the cell for the production of neutral lipids. In contrast, cyanobacteria normally use acyl carrier proteins (ACP) as the intermediate acyl carriers for fatty acid synthesis and metabolism.
To overproduce acyl-CoA in cyanobacteria, free fatty acids have to be released from acyl-ACP by thioesterases. In this invention, thioesterases are from bacteria and plants, e.g, tesA gene and its variants, and fatB genes and their variants. Then the free fatty acids have to be ligated to Coenzyme A by acyl-CoA ligases (ACL). In this invention, ACL genes are from bacteria (e.g., fadD from E. coli), and from yeast (e.g., faa2 from Saccharomyces cerevisiae). Acyl-CoA is the right substrate to produce an acyltransferase (e.g., WS/DGAT) to trans-esterify with an alcohol for a neutral lipid such as triaclyglycerols (TAG here after), fatty acly methyl esters (FAME hereafter), or fatty acyl ethyl esters (FAEE hereafter).
A bacterium of the invention may comprise an alteration that enables the synthesis of at least one acyl-ACP thioesterase (hereinafter TE). Methods of altering a bacterium to synthesize a TE are known in the art. For instance, a bacterium may be altered to express a nucleic acid encoding a TE. Such a nucleic acid may be operably linked to a regulated promoter or a constitutive promoter. In certain embodiments, a bacterium may synthesize one, two, three, four or five TEs. A nucleic acid encoding a TE may be chromosomally integrated, or may be expressed on an extrachromosomal vector. Suitable vectors are known in the art. Similarly, methods of chromosomally inserting a nucleic acid are known in the art. For additional details, see the Examples.
In some embodiments, a bacterium may synthesize a TE that is restricted to the cytosol of the bacterium. For instance, in one embodiment, a bacterium of the invention may synthesize a variant of TesA that is restricted to the cytosol of the bacterium. By way of non-limiting example, a bacterium may synthesize *TesA. The expression of a nucleic acid encoding TesA may be regulated or constitutive. For instance, the nucleic acid may be operably linked to an inducible promoter. Non-limiting examples of a suitable inducible promoter include PnrsB, PcmpA, PisiA, PsigE, PlrtA, or PsbD2. PnrsB is nickely inducible, PcmpA is inducible by CO2, PisiA is inducible under low Fe conditions, PsigE is inducible during the stationary phase, PlrtA is dark inducible, and PsbD2 may be induced by strong light.
Alternatively, the nucleic acid encoding a TE may be operably linked to a constitutive promoter, such as PpsbA2, Pcpc, Prbc, PpetB, PpsaAB, PhspA, or PsigA.
Other TE enzymes are known in the art and may be used in the present invention. For instance, a TE from Cinnamomum camphorum, Umbellularia californica, or Cuphea hookeriana may be used. In another embodiment, a TE outlined in WO 2009/076559 may be used.
The selection of the TE may be determined by the desired chain length of the resulting free fatty acid. For instance, see Example 13 below. In one embodiment, a TE with a preference for shorter free fatty acids may be used. For instance, a TE with a preference for C16, C14, C12, C10 or C8 fatty acids may be used.
A nucleic acid encoding a TE may be modified for high-level expression in a bacterium of the invention. As used herein, “modified” refers to an alteration of a nucleic acid sequence that results in a change in the level of transcription of a nucleic acid sequence, or that results in a change in the level of synthesis of encoded protein. For instance, in one embodiment, modify may refer to altering the start codon of a nucleic acid sequence. Generally speaking, a GTG or TTG start codon, as opposed to an ATG start codon, may decrease translation efficiency ten-fold. In another embodiment, modify may refer to altering the Shine-Dalgarno (SD) sequence of a nucleic acid sequence. The SD sequence is a ribosomal binding site generally located 6-7 nucleotides upstream of the start codon. The SD consensus sequence is AGGAGG, and variations of the consensus sequence may alter translation efficiency. In yet another embodiment, modify may refer to altering the distance between the SD sequence and the start codon. In still another embodiment, modify may refer to altering the −35 sequence for RNA polymerase recognition. In a similar embodiment, modify may refer to altering the −10 sequence for RNA polymerase binding. In an additional embodiment, modify may refer to altering the number of nucleotides between the −35 and −10 sequences. In an alternative embodiment, modify may refer to optimizing the codons of the nucleic acid sequence to alter the level of translation of the mRNA. For instance, non-A rich codons initially after the start codon of a nucleic acid sequence may not maximize translation of the corresponding mRNA. Similarly, the codons of the nucleic acid sequence may be altered so as to mimic the codons from highly synthesized proteins of a particular organism. In a further embodiment, modify may refer to altering the GC content of the nucleic acid sequence to change the level of translation of the corresponding mRNA. In still another embodiment, a nucleic acid may be optimized by altering the nucleic acid such that the ability of the encoded protein to form efficient enzyme complexes is affected.
IV. Methods
Yet another aspect of the invention encompasses a method for degrading the peptidoglycan layer of a bacterial cell wall to aid in the release of neutral lipids from the cyanobacterium. Generally speaking, the method comprises inducing the first promoter in a cyanobacterium of the invention that produces neutral lipids, such that the first protein is expressed. Methods of inducing a promoter are well known in the art. For more details when the promoter is induced by a metal or metal ion, see the Examples. The first protein, by forming lesions in the lipid membranes, allows the endolysin to degrade the peptidoglycan layer of a bacterial cell wall. The endolysin may be operably-linked to the first promoter, or alternatively, the endolysin may be operably-linked to a second promoter, as detailed above.
The second promoter may be an inducible promoter, or a constitutive promoter. In some embodiments, the second promoter is a constitutive promoter. In these embodiments, the endolysin(s) are expressed and accumulate in the cell, but are inactive because they do not have access to the peptidoglycan layer of the cell wall. After the induced expression of the holin(s), the endolysin(s) has access to the peptidoglycan layer of the cell wall, and subsequently, may degrade the peptidoglycan layer of the cell wall.
In other embodiments, the second promoter is an inducible promoter. The inducible promoter may be induced by a different compound or condition than the first promoter. In these embodiments, expression of the endolysin(s) may be induced first, with the subsequent induction of the holin(s) via the first promoter.
In certain embodiments, the peptidoglycan layer of the cell wall is substantially degraded in less than 12 hours, less than 10 hours, less than 8 hours, less than 7 hours, less than 6 hours, less than 5 hours, or less than 4 hours. In one embodiment, the peptidoglycan layer of the cell wall is substantially degraded in less than 6 hours.
After the peptidoglycan layer of a cell wall is degraded, the remaining lipid membranes may be further disrupted to release the neutral lipids of the cell into the media.
DEFINITIONS
The term “cell wall”, as used herein, refers to the peptidoglycan layer of the cell wall. Stated another way, “cell wall” as used herein refers to the rigid layer of the cell wall.
The term “operably-linked”, as used herein, means that expression of a gene is under the control of a promoter with which it is spatially connected. A promoter may be positioned 5′ (upstream) of a gene under its control. The distance between the promoter and a gene may be approximately the same as the distance between that promoter and the gene it controls in the gene from which the promoter is derived. As is known in the art, variation in this distance may be accommodated without loss of promoter function.
The term “promoter”, as used herein, may mean a synthetic or naturally-derived molecule which is capable of conferring, activating or enhancing expression of a nucleic acid in a cell. A promoter may comprise one or more specific transcriptional regulatory sequences to further enhance expression and/or to alter the spatial expression and/or temporal expression of same. A promoter may also comprise distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. In some embodiments, activators may bind to promoters 5′ of the −35 RNA polymerase recognition sequence, and repressors may bind 3′ to the −10 ribosome binding sequence.
The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventors to function well in the practice of the invention. Those of skill in the art should, however, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments that are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention, therefore all matter set forth or shown in the accompanying drawings is to be interpreted as illustrative and not in a limiting sense.
EXAMPLES
The following examples illustrate various iterations of the invention.
Example 1
Lipid Content of Synechocystis Sp. PCC 6803
The cyanobacterium Synechocystis sp. PCC 6803 (“Synechocystis” or “6803” hereafter) was selected as the model microorganism to produce biodiesel in tube-like photobioreactors after genetic modification to increase the production of lipids and facilitate lipid recovery. The virtues of Synechocystis, such as rapid growth rate, environmental adaptability and ease of genetic modification, make this cyanobacterial strain a promising solar energy collector for future convertible energy production. However, in exploring the feasibility of technical routes for growth in the field bed photobioreactor with production of lipids for ease of conversion to biofuels, it was realized that several challenges would have to be addressed. The first problem was the natural lipid content of Synechocystis. According to results of HPLC-MS analyses, the main lipid contents are polar lipids (Wada and Murata 1990) such as glyco-lipids (monogalactosyldiacylglycerol, MGDG and digalactosyldiacylglycerol, DGDG), sulfo-lipids (sulphoquinovosyl-diacylglycerol, SQDG), and phospho-lipid (PG) as shown in FIG. 1. These polar lipids are the components of membranes (glyco-lipids and sulfo-lipids for the photosynthesis thykaloid membranes and phospholipids for the cell membranes), which would not form lipid drops in a polar solvent within the cells. In addition, the sugar, sulfate or phosphate molecules would cause problems in the downstream refinery processes in the production of biofuels.
The following examples describe the genetic changes engineered into Synechocystis to anticipate problems in downstream processing and refining into biofuels. Synechocystis was genetically engineered to store these neutral lipids in lipid drops or lipid bodies. Once the lipids are sequestered, their yields can be accumulated; once the lipids are accumulated, they could be easily recoverable. In addition, to facilitate the lipid recovery process, a nickel inducible lysis system for Synechocystis was developed. Briefly, as previously reported, we introduced a set of lysis genes from bacteriophages into the Synechocystis sp. PCC 6803 genome and placed them downstream of a Ni2+ sensing and tightly regulating element, so that expression of the lysis genes would be induced by addition of Ni2+. By combining these two systems in Synechocystis, neutral lipid production and nickel controllable lysis, a neutral lipid releasing Synechocystis recombinant was achieved, which would increase the production efficiency of lipids more readily modifiable into biofuels.
Example 2
Genetic Engineering of Synechocystis for TAG Production
Most lipids in Synechocystis are glyco-lipids (DGDG and MGDG) constituting photosynthesis thykaloid membranes (FIG. 1), and there are also some phospho- and sulfo-lipids. All of these lipids are polar membrane lipids. Storage neutral lipids such as in the form of triglycerides are rarely found in Synechocystis. As shown in FIG. 2, no triglyceride synthesis gene was identified in the genome of Synechocystis sp. PCC 6803. Also, the basic triglyceride signals obtained by HPLC-MS were only low-level noise. In plants and animals, energy is stored in the form of neutral lipids, mainly TAG (Dyer and Mullen 2008). Neutral lipids have a higher energy content than membrane lipids, which is the basis of interest in this form of lipid by energy companies.
From diverse petroleum polluted soils and water habitats, several groups of prokaryotes that accumulate neutral storage lipid compounds such as poly(3-hydroxybutyrate) PHB, triacylglycerol (TAG) and wax ester (WE) in their lipid bodies have been identified (Alvarez and Steinbuchel 2002; Walternann, Hinz et al. 2005). As shown in FIG. 3, (Walternann and Steinbuchel 2005), bacteria such as Rhodococcus opacus, Rhodococcus ruber, Ralstonia eutropha, Streptomyces coelicolor, Norcardia sp., and Mycobacterium smegmatis, store neutral lipids as lipid bodies in their cells. As shown in FIG. 4, the final step in WE and TAG biosyntheses in the bacterium Acinetobacter baylyi sp. ADP1 is catalyzed by a promiscuous (multifunctional) enzyme, which exhibits both WE synthase (WS) and diacylglycerol (DAG):acly-CoA aclytransferase (DGAT) activities (Kalscheuer and Steinbuchel 2003; Walternann, Stoveken et al. 2007).
The TAG synthase gene (atfA) was cloned from Acinetobacter baylyi sp. ADP1, which encodes a promiscuous (multifunctional) enzyme (WS/DGAT) exhibiting both WE synthase (WS) and diacylglycerol (DAG):acly-CoA aclytransferase (DGAT) activities (Kalscheuer and Steinbuchel 2003). It was the first prokaryotic WS/DGAT enzyme, not related to any known acyltransferase enzyme families in eukaryotes. Its acyltransferase activities were successfully expressed in yeast (Kalscheuer, Luftmann et al. 2004) and E. coli (Kalscheuer, Stolting et al. 2006). It should be noticed that the substrates for TAGs are DAG and acly-CoA, which are also the substrates for the DGDG, MGDG, SQDG and PG, so the substrates for TAGs should be abundant in Synechocystis cells. For the purpose of neutral lipid production, the TAG synthase gene from A. baylyi sp. ADP1 was introduced into the Synechocystis genome. A gene encoding a prokaryotic lipid body protein, a phasin (PHA inclusion protein) PhaP1, was also introduced into the Synechocystis genome. The phaP1 gene was cloned from Ralstonia eutropha H16. PhaP1 is able to target and bind to intracellular TAG inclusions in other oil bacteria and provides an anchor to other target proteins (Hanisch, Walternann et al. 2006). As shown in FIG. 5, it was reported that the non-specificity of PhaP1 could be utilized to help the formation of TAG-containing lipid bodies.
In addition, the putative Synechocystis lipase gene (lipA, sll1969) was interrupted by inserting the genes for the lipid-producing operon cassette PpsbAII atfA phaP1 in the coding region of lipA. The gene encodes an enzyme with acetyltransferase and hydrolase activities, which catalyzes the hydrolysis of TAGs. The construction of the strains SD201 and SD202 containing the genes for the lipid-producing cassette inserted into the coding region of lipA in opposite orientations are shown in FIG. 6 and Table 1. In this regard, the PpsbAII promoter is a constitutive and active promoter in Synechocystis. The detailed methods of the constructions are described in Example 20.







TABLE 1







The Synechocystis strains used or developed for this invention












Parent



SD #
Genotype
plasmid
Description/Derivation





SD100
Synechocystis sp. PCC 6803

From Dr. Wim Vermaass' lab,



wild type

School of Life Science, Arizona





State University


SD101
ΔnrsBA21::PnrsB20 13 19 15 KmR
SD100
This is a testing strain obtained by




pψ101
transforming SD100 with pψ101 to





make sure that the lysis genes from





bacteriophage would work in





cyanobacteria.


SD102
ΔnrsBAC11::PnrsB21 13 KmR
SD100
This is an intermediate strain



sacB
pψ102
obtained by transforming SD100





with pψ102, with a Kmr-sacB





cassette, which can be replaced by





further insertion.


SD104
ΔnrsBAC11::PnrsB22 13
SD102
Nickle inducible lysis strain.



Inv(PpsbA223 19 15)-23
pψ104
Obtained by transforming SD102





with pψ104. The P22 genes 15 and





19 (endolysin) were placed under a





constitutive promoter (PpsbAll) in





opposite orientation of the holin





gene.


SD106
ΔnrsBAC11::PnrsB24 13 S R Rz
SD102
Nickle inducible lysis strain.




pψ106
Obtained by transforming SD102





with pψ106. Lysis genes S, R, Rz





from E. coli phage λ were inserted





after P22 gene 13.


SD107
ΔnrsBAC11::PnrsB25 13 RBS S R
SD102
Nickle inducible lysis strain.



Rz
pψ107
Obtained by transforming SD 102





with pψ107. A RBS sequence





(ribosome binding site) was





inserted before lysis genes S, R,





Rz.


SD111
PisiA26::13 19 15 KmR
SD100
Stationary autolysis strain, stocked.




pψ111
The lysis genes will befully





induced at the first 5 days of the





stationary growth phase, slightly





induced at exponential growth





phase (104-4.5 cells/ml), also fully





induced at Fe deficiency (Fe <2 μM,





1/10 BG-11





concentration). Note that PisiA is





a strong promoter in E. coli. The





cassette 13 19 15 KmR was





inserted in between PisiA26 and isiA,





so no mutation in sequence, but





the isiA express should be





interrupted.


SD121
ΔnrsBAC11::PnrsB27 13 19 15
SD102
Nickle inducible lysis strain. Nickel




pψ121
controlling P22 lysis cassette strain


SD122
ΔnrsBAC11::PnrsB28 S R Rz
SD102
Nickle inducible lysis strain. Nickel




pψ122
controlling lambda lysis cassette





strain


SD123
ΔnrsBAC11::PnrsB29 13 TT
SD102
Nickle inducible lysis strain.



PpsbA223 19 15
pψ123
Strategy 2 strain using P22





lysozymes. TT means translational





terminator.


SD124
ΔnrsBAC11::PnrsB29 13 TT
SD102
Nickle inducible lysis strain.



Inv(PpsbA223 19 15)-23
pψ124
Strategy 2 strain using P22





lysozymes, different orientation for





constitutive lysis cassette


SD128
ΔnrsBAC11::PnrsB29 13 TT
SD102
Nickle inducible lysis strain.



PpsbA231 15
pψ128
Strategy 2 strain using P22





endolysin


SD129
ΔnrsBAC11::PnrsB29 13 TT
SD123
Nickle inducible lysis strain.



PpsbA223 19 15
pψ228
Strategy 2 strain using P22



Δsll1951-15::sacB KmR

lysozymes With S-layer deletion.





Can not be constructed, suggesting





that S-layer can not be deleted





under a background of constitutive





expression of the endolysin genes.


SD200
ΔlipA22::sacB KmR
SD100
Intermediate strain for Optimization




pψ200
Strategy 1, to enable insertion of





foreign genes at the lipA locus


SD201
ΔlipA22::PpsbA231 atfA RBS phaP
SD200
Neutral lipid producing strain,




pψ201
stocked.





The phaP here is directly PCRed





from the bacteria, in which the





original gene is assigned as phaP1.


SD202
ΔlipA22::Inv(PpsbA231 atfA RBS
SD200
Neutral lipid producing strain,



phaP)-32
pψ202
stocked


SD203
ΔlipA22::PpsbA231 atfA RBS phaP
SD201
Neutral lipid producing strain



ΔnrsBAC11::PnrsB22 13
pψ104
SD104 + SD 201, a double mutant



Inv(PpsbA223 19 15)-23

strain, which can release TAG oil





drops after Ni2+ addition. Stocked.


SD204
ΔlipA22::Inv(PpsbA231 atfA RBS
SD205
Neutral lipid producing strain



phaP)-32
pψ104
SD104 + SD202, a double mutant



ΔnrsBAC11::PnrsB22 13

strain, which can release TAG oil



Inv(PpsbA223 19 15)-23

drops after Ni2+ addition. Stocked.





Unstable


SD205
ΔlipA22::sacB KmR
SD104
SD104 + SD 200, Intermediate



ΔnrsBAC11::PnrsB22 13
pψ200
strain for SD 203, 204 and 211. To



Inv(PpsbA223 19 15)-23

insert foreign gene at ΔlipA22





locus. For SD211 construction


SD206
slr1704-50::sacB KmR
SD100
Intermediate strain for Optimization




pψ206
Strategy 2, SD209. The foreign





genes will be inserted at the





slr1704 locus.


SD207
Δ(slr1993-slr1994)-14::sacB
SD100
Intermediate strain for SD210,



KmR
pψ207
optimization Strategy 4, deleting





the PHA synthesis genes


SD208
ΔlipA22::Prbc34 aftA69 RBS pha-
SD200
Neutral lipid producing strain.



68
pψ208
Optimized SD201 using new





codons. Optimization Strategy 1. At





the same locus.





aftA69 pha-68 are two synthesized





genes based on the codon





optimization of aftA and phaP.


SD210
Δ(slr1993-slr1994)-14:.Prbc34
SD207
Neutral lipid producing strain



aftA69 RBS pha-68

Optimization Strategy 4 for oil





production stability, deleting the





PHA synthesis genes


SD211
ΔlipA22::Prbc34 aftA69 RBS pha-

Neutral lipid producing strain with



68

nickel inducible lysis. SD208 + SD



ΔnrsBAC11::P22 13 Inv(PpsbA223

104, Optimized oil producing stain



15 19)-23

with Nickel inducing lysis.


SD212
Δ(slr1993-slr1994)-14::Prbc34
SD210
SD210 + SD206, intermediate



aftA69 RBS pha-68

strain for double mutant SD213.



slr1704-50::sacB KmR




SD213
Δ(slr1993-slr1994)-14::Prbc34
SD212
SD210 + SD209, double mutant



aftA69 RBS pha-68

with two copies of aftA69.



slr1704-50::Prbc34 aftA69 RBS





pha-68




SD214
Δaas-23::sacB KmR
SD100
Deletion of slr1609




pψ213



SD216
Δaas-23::PpsbA236 tesA136
SD214
FFA secretion strain. E. coli ‘tesA




pψ216
gene fused with an HA tag is driven





by PpsbA2, with the same orientation





of Paas, as the deleted aas gene.


SD217
Δaas-23::Inv(PpsbA236 tesA136)-
SD214
FFA secretion strain. E. coli ‘tesA



44
pψ217
gene fused with an HA tag is driven





by PpsbA2, with the opposite





orientation of Paas, as the deleted





aas gene.


SD218
Δ(slr1993-slr1994)-14::Pcpc37
SD207
FFA secretion strain. From SD207,



accBC27(Ec)Prbc38 accD(Ec)
pψ218
overexpression E. coli accBCDA



RBS accA30(Ec)

genes in Syn at the locus deleting





genes for PHB synthesis.


SD219
ΔnrsBAC11::PnrsR35 tesA136
SD215
FFA secretion strain. SD215 +



Δ(slr1993-slr1994)-14::sacB
pψ207
S4KS deleting PHB synthesis



KmR

genes slr1993 and slr1994


SD220
Δaas-23::PpsbA236 tesA136
SD216
FFA secretion strain. SD216 +



Δ(slr1993-slr1994)-14::sacB
pψ207
S4KS deleting PHB synthesis



KmR

genes slr1993 and slr1994


SD221
Δaas-23::Inv(PpsbA236 tesA136)-
SD217
FFA secretion strain. SD217 +



44
pψ207
S4KS deleting PHB synthesis



Δ(slr1993-slr1994)-14::sacB

genes slr1993 and slr1994



KmR




SD222
ΔnrsBAC11::PnrsB35 tesA136
SD219
FFA secretion strain. SD219 +



Δ(slr1993-slr1994)-14::Pcpc37
pψ218
EcoACCs overproduction



accBC27(Ec) Prbc38 accD(Ec)





RBS accA30(Ec)




SD223
ΔnrsBAC11::PnrsB35 tesA136
SD219
FFA secretion strain. SD219 +



Δ(slr1993-slr1994)-14::Pcpc39
pψ225
SynACCs overproduction



accB RBS accC70 Prbc40 accD





RBS accA




SD224
Δaas-23::PpsbA236 tesA136
SD220
FFA secretion strain. SD220 +



Δ(slr1993-slr1994)-14::Pcpc37
pψ218
EcoACCs overproduction



accBC27(Ec) Prbc38 accD(Ec)





RBS accA30(Ec)




SD225
Δaas-23::PpsbA236 tesA136
SD220
FFA secretion strain. SD220 +



Δ(slr1993-slr1994)-14::Pcpc39
pψ225
SynACCs overproduction



accB RBS accC70 Prbc40 accD





RBS accA




SD226
Δaas-23::Inv(PpsbA236 tesA136)-
SD221
FFA secretion strain. SD221 +



44
pψ218
EcoACCs overproduction



Δ(slr1993-slr1994)-14::Pcpc37





accBC27(Ec) Prbc38 accD(Ec)





RBS accA30(Ec)




SD227
Δaas-23::Inv(PpsbA236 tesA136)-
SD221
FFA secretion strain. SD221 +



44
pψ225
SynACCs overproduction



Δ(slr1993-slr1994)-14::Pcpc39





accB RBS accC70 Prbc40 accD





RBS accA




SD228
ΔnrsBAC11::PnrsB tesA136
SD223
FFA secretion strain. SD223 +



Δ(slr1993-slr1994)-14::Pcpc39
pψ228
deletion of genes for S-layer



accB RBS accC70 Prbc40 accD





RBS accA





Δsll1951-15::sacB KmR




SD229
Δaas-23::PpsbA236 tesA136
SD225
FFA secretion strain. SD225 +



Δ(slr1993-slr1994)-14::Pcpc39
pψ228
deletion of genes for S-layer



accB RBS accC70 Prbc40 accD





RBS accA





Δsll1951-15::sacB KmR




SD230
Δaas-23::Inv(PpsbA236 tesA136)-
SD227
FFA secretion strain. SD227 +



44
pψ228
deletion of genes for S-layer



Δ(slr1993-slr1994)-14::Pcpc39





accB RBS accC70 Prbc40 accD





RBS accA





Δsll1951-15::sacB KmR




SD231
ΔnrsBAC11::PnrsB35 tesA136
SD228
FFA secretion strain. SD223 +



Δ(slr1993-slr1994)-14::Pcpc39
pψ230
deletion of genes for S-layer +



accB RBS accC70 Prbc40 accD

short chain TEs The B1 and B2



RBS accA

mean these are mutated fatB



Δsll1951-15::PpsbA210

genes. Since these were codon-



fatB161(Uc) Prbc41 fatB262(Ch)

optimized genes they were





“mutated”.


SD232
Δaas-23::PpsbA236 tesA136
SD230
FFA secretion strain. SD225 +



Δ(slr1993-slr1994)-14::Pcpc39
pψ230
deletion of genes for S-layer +



accB RBS accC70 Prbc40 accD

short chain TEs



RBS accA





Δsll1951-15::PpsbA210 fatB16 (Uc)





Prbc41 fatB262(Ch)




SD233
Δaas-23::PpsbA236 tesA136
SD232
FFA secretion strain. On the basis



Δ(slr1993-slr1994)-14::Pcpc39
pψ102
of SD232, an intermediate strain for



accB RBS accC70 Prbc40 accD

inserting genes under the control of



RBS accA

Ni inducible promoter.



Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





ΔnrsBAC11::PnrsB21 13 KmR





sacB




SD234
Pcmp16::KmR sacB RBS
SD100
An intermediate strain for inserting




pψ234
genes under the control of Pcmp


SD235
Δaas-23::PpsbA236 tesA136
SD232
On the basis of SD232, an



Δ(slr1993-slr1994)-14::Pcpc39
pψ234
intermediate strain for inserting



accB RBS accC70 Prbc40 accD

genes under the control of Pcmp



RBS accA





Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





Pcmp16::KmR sacB RBS




SD236
ΔnrsBAC11::PnrsB42 fol RBS shl
SD102
Nickel controlling lipolysis genes




pψ236



SD237
Pcmp43::fol RBS shl RBS
SD234
Green Recovery strain. CO2




pψ237
limitation controlling lipolysis genes


SD238
Δaas-23::PpsbA236 tesA136
SD233
SD232 + Nickel controlling lipases



Δ(slr1993-slr1994)-14::Pcpc39
pψ236




accB accC70 Prbc40 accD accA





Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





ΔnrsBAC11::PnrsB42 fol RBS shl




SD239
Δaas-23::PpsbA236 tesA136
SD235
Green Recovery plus FFA



Δ(slr1993-slr1994)-14::Pcpc39
pψ237
secretion strain. SD232 + CO2



accB RBS accC70 Prbc40 accD

controlling lipases



RBS accA





Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





Pcmp43:: fol shl RBS




SD240
Δaas-23::PpsbA236 tesA136
SD232
On the basis of SD232, an



Δ(slr1993-slr1994)-14::Pcpc39
pψ240
intermediate strain for inserting



accB RBS accC70 Prbc40 accD

genes at the cyanophycin synthesis



RBS accA

gene deletion site.



Δsll1951-15::PpsbA210





fatB161(Uc) Prbc40 fatB262(Ch)





Δ(slr2001-slr2002)-17::KmR





sacB




SD241
ΔlipA22::Inv(PpsbA231 atfA phaP)-
SD202
On the basis of SD232, an



32
pψ207
intermediate strain for inserting



Δ(slr1993-slr1994)-14::sacB

genes at the PHB synthesis gene



KmR

deletion site.


SD242
ΔlipA22:: Inv(PpsbA231 atfA phaP)-
SD241
2nd neutral lipid exploration. Acyl-



32
pψ242
CoA overexpression on the basis of



Δ(slr1993-slr1994)-14::Pcpc

SD202 (WS/DGAT



fadD(Ec) PpsbA236 tesA136

overproduction). The fadD(Ec) here





is a real acyl-CoA synthetase gene





(fadD) introduced from Ecoli.





Failed in transformation by lethality,





for the first time, suggesting that





the atfA, fadD and tesA genes





cannot be put together in 6803.


SD243
Δaas-23::PpsbA2 tesA136
SD240
Further optimization for C8 C10



Δ(slr1993-slr1994)-14::Pcpc39
pψ243
shorter chain fatty acid production



accB RBS accC70 Prbc40 accD

and deletion of genes for



RBS accA

cyanophycin synthesis, on the



Δsll1951-15::PpsbA210

basis of SD232



fatB161(Uc) Prbc41 fatB262(Ch)





Δ(slr2001-slr2002)-17::PpsbA211





fatB262(Ch)




SD244
PsbtA18::sacB KmR RBS
SD100
Intermediate strain for CO2




pψ244
controlling,





The sacB Kmr cassette was





inserted between PsbtA and sbtA.





There is a duplicated RBS for the





downstream sbtA gene.


SD245
Pcmp16::Pcmp43 fol RBS shl RBS
SD237
Intermediate strain for CO2



PsbtA18::sacB KmR RBS
pψ244
controlling,





Parent SD237


SD246
Δaas-23::PpsbA236 tesA136
SD239
FFA secretion strain with Green



Δ(slr1993-slr1994)-14::Pcpc39
pψ244
Recovery. Intermediate strain for



accB RBS accC70 Prbc40 accD

CO2 controlling,



RBS accA

Parent SD239



Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





Pcmp43::fol RBS shl RBS





PsbtA18::sacB KmR RBS




SD247
Δaas-23::PpsbA236 tesA136
SD243
Intermediate strain for SD250



Δ(slr1993-slr1994)-14::Pcpc39
pψ102
On the basis of 243, an



accB RBS accC70 Prbc40 accD

intermediate strain for inserting



RBS accA

genes under the control of Ni



Δsll1951-15::PpsbA210

inducible promoters.



fatB161(Uc) Prbc41 fatB262(Ch)





Δ(slr2001-slr2002)-17::PpsbA211





fatB262(Ch)





ΔnrsBAC11::PnrsB21 13 KmR sacB




SD248
Δaas-23::PpsbA236 tesA136
SD243
Intermediate strain from SD243



Δ(slr1993-slr1994)-14::Pcpc39
pψ248
On the basis of SD243, an



accB RBS accC70 Prbc40 accD

intermediate strain for inserting



RBS accA

genes at the penicillin binding



Δsll1951-15::PpsbA210

protein 2 (PBP2) gene deletion site.



fatB161(Uc) Prbc41 fatB262(Ch)





Δ(slr2001-slr2002)-17::PpsbA211





fatB262(Ch)





Δslr1710-19::KmR sacB




SD249
Δaas-23::PpsbA236 tesA136
SD248
FFA secretion strain. 5th generation



Δ(slr1993-slr1994)-14::Pcpc39
pψ249
modification strain



accB RBS accC70 Prbc40 accD

SD243 with PBP2 deletion and Cc



RBS accA

FatB1 (C14:0) overproduction



Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





Δ(slr2001-slr2002)-17::PpsbA211





fatB262(Ch)





Δslr1710-19::PpsbA210





fatB163(Cc)




SD250
Δaas-23::PpsbA236 tesA136
SD248
3rd neutral lipid exploration



Δ(slr1993-slr1994)-14::Pcpc39
pψ250
Put FadD and WS/DGAT on the



accB RBS accC70 Prbc40 accD

basis of SD243



RBS accA

Cannot be constructed, failed in



Δsll1951-15::PpsbA210

transformation by lethality, for the



fatB161(Uc) Prbc41 fatB262(Ch)

second time, suggesting that the



Δ(slr2001-slr2002)-17::PpsbA211

atfA, fadD and tesA genes cannot



fatB262(Ch)

be put together in 6803.



Δslr1710-19::PpsbA244 atfA Pcpc45





fadD(Ec)




SD251
Δaas-23::PpsbA236 tesA136
SD247
3rd neutral lipid exploration backup,



Δ(slr1993-slr1994)-14::Pcpc39
pψ251
Controllable synthesis of FadD and



accB accC70 Prbc40 accD accA

WS/DGAT on the basis of SD243



Δsll1951-15::PpsbA210 fatB161





(Uc) Prbc41 fatB262(Ch)





Δ(slr2001-slr2002)-17::PpsbA210





fatB262(Ch)





ΔnrsBAC11::PnrsB46 atfA Pcpc45





fadD(Ec)




SD252
PsbtA46::gpl RBS
SD244
Green Recovery strain. GPL




pψ252
controlled by PstbA. I duplicated a





RBS for sbtA if the ribosome can





come down through gpl for sbtA.


SD253
Pcmp43::fol RBS shl RBS
SD245
Green Recovery strain.



PsbtA46::gpl RBS
pψ252
Combination of SD252 and SD237


SD254
Δaas-23::PpsbA236 tesA136
SD246
Green Recovery strain with FFA



Δ(slr1993-slr1994)-14::Pcpc39
pψ252
secretion. Combination of SD252,



accB accC70 Prbc40 accD accA

SD237 and SD232



Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





Pcmp43::fol RBS shl RBS





PsbtA46::gpl RBS




SD256
Pcmp47::fol RBS
SD234
Green Recovery strain. 1ST CO2




pψ256
limitation test strain for Fol





individually


SD257
Pcmp48::shl RBS
SD234
Green Recovery strain. 1ST CO2




pψ257
limitation test strain for Shl





individually


SD258
Pcmp49::gpl RBS
SD234
Green Recovery strain. 1ST CO2




pψ258
limitation test strain for Gpl





individually


SD260
Pcmp43::fol RBS shl RBS
SD245
Green Recovery strain. Looking for



PsbtA50::gpl RBS 13 19 15 RBS
pψ260
a faster lysis rate.


SD262
Δaas-23::PpsbA236 tesA136
SD246
Green Recovery strain. Fast



Δ(slr1993-slr1994)-14::Pcpc39
pψ260
autolysis FFA secreting strain.



accB RBS accC70 Prbc40 accD





RBS accA





Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





Pcmp43::fol RBS shl RBS





PsbtA50::gpl RBS 13 19 15 RBS




SD273
Δaas-23::PpsbA236 tesA136
SD269
Acyl-CoA overexpression strain.



Δ(slr1993-slr1994)-14::Pcpc39
pψ273
SD243 + S22Pa2FAA2PcpcFadD



accB RBS accC70 Prbc40 accD

faa138 is a synthesized gene for



RBS accA

Faa2p from Saccharomyces



Δsll1951-15::PpsbA210

cerevisiae, a long chain fatty acyl-



fatB161(Uc) Prbc41 fatB262(Ch)

CoA synthetase accepts a wider



Δ(slr2001-slr2002)-17::PpsbA211

range of acyl chain lengths than



fatB262(Ch)

Faa1p, preferring C9:0-C13:0;



Δslr2132-22:: PpsbA212 faa138

involved in the activation of



Pcpc45 fadD(Ec)

endogenous pools of fatty acids.





fadD(Ec) is the acyl-CoA ligase





from E. coli.


SD274
Δaas-23::PpsbA236 tesA136
SD269
FFA secretion strain. SD243 + Ptrc



Δ(slr1993-slr1994)-14::Pcpc39
pψ274
tesA137



accB RBS accC70 Prbc40 accD

See how Ptrc works in 6803.



RBS accA





Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





Δ(slr2001-slr2002)-17::PpsbA211





fatB262(Ch)





Δslr2132-22:: Ptrc tesA137




SD277
Δaas-23::PpsbA236 tesA136
SD256
FFA secretion strain. SD249 + Ptrc



Δ(slr1993-slr1994)-14::Pcpc39
pψ274
tesA137



accB RBS accC70 Prbc40 accD

See how Ptrc works in 6803.



RBS accA





Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





Δ(slr2001-slr2002)-17::PpsbA211





fatB262(Ch)





Δslr1710-19::PpsbA210





fatB163(Cc)





Δslr2132-22:: Ptrc tesA137




SD278
Δaas-23::PpsbA236 tesA136
SD235
FFA secretion strain with Green



Δ(slr1993-slr1994)-14::Pcpc39
pψ256
Recovery. SD232 + SD256



accB RBS accC70 Prbc40 accD





RBS accA





Δsll1951-15::PpsbA210





fatB161(Uc) Prbc41 fatB262(Ch)





Pcmp47::fol RBS









Example 3
Increasing the TAG Production by Optimizing Strain Construction and the Cyanobacteria Growth Conditions
To increase the TAG production in 6803, two strategies were applied in this invention. The first is to insert an optimized WS/DGAT gene, which sequence has been codon optimized for the maximum protein synthesis in 6803. The second is to adjust the strain growth conditions.
For the first strategy, the Acinetobacter baylyi sp. ADP1 WS/DGAT gene atfA has been codon edited based on the codon bias of the highly expressed 6803 genes, also based on the secondary mRNA structure prediction that will eliminate the possible stem-loop structures, which would lead to shorter mRNA half lives. The redesigned gene was assigned as aftA69. In the redesigning, aftA69 was constructed as a part of the neutral lipid producing cassette Prbc34 aftA69 RBS pha-68, where Prbc34 is the promoter of 6803 rbc operon, RBS is ribosome binding site, and pha-68 is a redesigned from Ralstonia eutropha gene PhaP1. This cassette Prbc34 aftA69 RBS pha-68 was inserted into a site close to slr1704-50 to generate SD209 slr1704-50::Prbc34 aftA69 RBS pha-68. In another strain SD210, this cassette Prbc34 aftA69 RBS pha-68 was inserted into replace the PHB synthesis genes slr1993 and slr1994 to generate strain SD210 Δ(slr1993-slr1994)-14::Prbc34 aftA69 RBS pha-68. The detailed methods of the constructions are described in Example 11. The detailed strain constructions are described in Table 1.
The lipid profiles of the neutral lipid constructions are listed in Table 2 where the membrane lipids (PG, SQDG, MGDG, and DGDG) and the produced TAGs are measured by HPLC-MS. According to Table 1, the TAGs only count for 0.10% in WT, but the TAG percentages increased to 0.57%, 0.72% and 0.56% in the first generation TAG strains SD201, SD202, and SD203 respectively, and the TAG percentages kept increasing to 1.77% and 2.20% in the second generation strains SD209 and SD210 respectively. This result showed the success of increasing neutral lipid production by genetic optimization.
For the second strategy, the strain SD210 was grown in a high carbon-to-nitrogen medium, as most bacteria with TAG accumulation drastically increased the number of the TAG bodies and lipid content in the high carbon-to-nitrogen medium. For adjusting the carbon-to-nitrogen ratio, 10 mM glucose was added to BG11 to increase carbon from 0.19 mM (0.2 mg/l NaCO3) to 60.19 mM, and NaNO3 was decreased from 3 g/L to 0.03 g/L, which resulted a carbon-to-nitrogen ration increase of 31700 fold. The lipid profiles of SD210 grown in the high carbon-to-nitrogen medium is also shown in Table 2 (column CN210). According to Table 2, the TAG percentage of SD210 increased from 2.20% to 2.83% when cultivated in high carbon-to-nitrogen medium. The TLC (thin layer chromatography) analysis of SD210 also indicated that SD210 was capable of producing TAGs and the production was higher when this strain was cultivated in high carbon-to-nitrogen medium (FIG. 7).







TABLE 2







TLC analysis of the total lipids of SD210 and SD202 grown in BG-11 medium and high carbon-


to-nitrogen BG-11 medium (CN210 and CN202), where 10 mM glucose was added to BG11 to increase carbon


from 0.19 mM (0.2 mg/l NaCO3) to 60.19 mM, and NaNO3 was decreased from 3 g/L to 0.03


g/L. On the most right and left lanes TAG with three C16:0 serves as control. The arrows


indicate overproduced TAGs from the total lipid extracts.















LIPID TYPE
m/z
WT
SD201
SD202
SD203
SD209
SD210
CN210



















PG
16-16:2
717.5
ND
ND
ND
ND
7.50
5.82
0.00



16-16:1
719.49
220.37
43.82
64.44
33.22
37.62
29.85
17.29



16-16:0
721.5
136.45
17.72
41.27
15.18
35.63
11.93
89.33



16-18:0
749.54
0.00
0.00
0.00
0.00
0.00
0.00
167.68


SQDG
16-16:3
787.47
21.00
39.35
226.68
36.50
167.03
60.08
0.00



16-16:0
793.51
3815.98
2324.70
4452.16
1718.27
3165.24
1420.43
1968.27



16-17:2
803.5
54.59
179.14
62.99
142.91
40.70
149.97
0.00



16-17:1
805.51
97.51
373.64
173.61
517.96
33.84
341.61
67.76



16-17:0
807.53
39.99
168.99
48.52
214.00
18.81
97.00
104.79



16-18:0
821.54
0.00
47.92
20.56
38.68
23.98
7.61
917.57


MGDG
16-16:2
749.52
146.61
50.79
63.16
30.05
43.59
24.01
0.00



16-16:1
751.53
796.91
155.08
413.08
124.59
147.57
91.40
32.24



16-16:0
753.55
581.16
93.74
306.03
92.14
184.38
71.17
388.23



16-18:1
779.56
515.08
97.27
314.55
129.03
43.72
57.43
170.99



16-18:0
781.58
0.00
0.00
0.00
0.00
0.00
0.00
695.36


DGDG
16-16:1
913.59
129.10
79.84
105.47
74.40
41.37
50.92
0.00



16-16:0
915.59
192.78
129.59
135.92
147.92
ND
ND
832.66



16-18:0
943.63
ND
ND
ND
ND
ND
ND
75.00














Total membrane
6747.53
3801.58
6428.42
3314.86
3990.97
2419.23
5527.16
















Triglycerides
16-16-16:2
825.69
1.32
4.42
2.960
1.778
1.27
1.77
1.35



16-16-16:1
827.71
1.67
7.38
8.171
3.278
7.85
6.21
7.95



16-16-16:0
829.73
1.32
4.05
14.036
3.556
27.33
12.76
33.10



16-16-18:0
857.76
0.94
2.49
13.416
3.374
18.59
16.01
54.45



16-16-18:1
883.77
1.26
3.24
2.785
4.976
10.33
13.37
33.80



16-16-18:0
885.79
0.15
0.38
5.408
1.415
6.36
4.20
30.35














Total TAGS
6.67
21.97
46.78
18.38
71.74
54.32
161.00


TAG/Total (%)
0.10
0.57
0.72
0.55
1.77
2.20
2.83
















Chl a
NA

1779.90
1850.10
1899.90
1389.90
1850.10
1140.00
ND









Example 4
Combining the Lipid Producing Ability and Inducible Lysis Ability into Synechocystis 
A number of nickel inducible lysis SD strains were designed and constructed (Table 1). They showed significant cell lysis after addition of nickel to the cell cultures (Table 3). Of these SD strains, SD101 was made first to determine whether the phage-encoded lysis system would work in cyanobacteria. This preliminary design was named Strategy 1, and that is one of the reasons the kanamycin-resistance marker was not removed. For the next step, Strategy 2 was designed to try to achieve a more rapid cell disruption at lower Ni2+ concentrations than needed to induce lysis with the Strategy 1 strain. Strategy 2 (SD104) was designed to over express the endolysin genes (P22 19 15) under a strong Synechocystis constitutive promoter PpsbAII, while the Ni2+ inducible control was used for expression of the holin gene (P22 13). It was hoped that before induction of expression of the holin gene, the endolysins are accumulated in cells, but they cannot reach their substrates in the peptidoglycan layer of the cell wall. Once the holin gene 13 is expressed to produce holes in the lipid membranes from within, the endolysins now can gain access to the peptidoglycan cell wall layer and trigger the lysis process. The detailed strain constructions are described in Table 1.
As shown in Table 3, the lysis rate of the Strategy 2 strain is higher than that of the Strategy 1 strain. The results for SD204 suggest that the TAG-producing strain is able to be lyzed for TAG release by the nickel inducible lysis system.







TABLE 3







Comparison of different lysis strategies














Mutation
Lysis




Doubling
Rates to Ni2+
Rates


Strain
Lysis Strategies
Time
Resistance
(%/


SD No.
Descriptions
(hour)
(10−7/generation)
hour)














SD100
Wild type Synechocystis
8.65
—
—


SD101
Strategy 1, only use
9.8
1.39
10.05



phage P22 lysis






cassette





SD104
Strategy 2, control P22
11.20
0.93
15.5



holin gene (13), while






constitutively expressing






endolysin genes (19 and






15)





SD204
Combination of SD104
14.21
1.02
16.5



and SD 202, capable of






both TAG production






and nickel inducible






lysis









Example 5
Constructing a CO2-Limitation Inducible Lipolytic Enzymes System for ‘Green Recovery’
The following example describes how to develop a ‘Green Recovery’ system for cyanobacteria. With the Green Recovery system, no nickel addition is necessary for induction of lysis. The lysis and release of lipids will be induced by CO2 limitation of the culture. This invention involves lipolytic enzymes that are able to hydrolyze the fatty acyl chains from the membrane lipids (e.g, PG, MGDG, DGDG, and SQDG) for free fatty acids, so that on the lipolytic degradation of the cell membranes (both cytoplastic and thylakoid), the overproduced neutral lipid will be released with the free fatty acid from the membrane lipids producing a lipid mixture.
We previously developed a nickel inducible lysis system for cyanobacterium Synechocystis sp. PCC 6803, which is able to induce the phage lysis genes to break down the cell walls by adding nickel as an inducer. However, this system does not release the cyanobacterial lipids as an easily-recoverable form like triacylglycerols or free fatty acids. Cyanobacterial lipids are mainly in the form of diacylglycerols as the components of membranes, including MGDG (monogalactosyl diacylglycerol), DGDG (digalactosyl diacylglycerol), PG (phosphatidylglycerol), and SQDG (sulfoquinovosyl diacylglycerol). To utilize the lipids in the cyanobacterial biomass, we developed a ‘Green Recovery’ system, where inducible lipolytic enzymes degrade the membrane lipids into free fatty acids (FFA hereafter) with the collapse of cell. The Green Recovery system controls the lipolytic genes with CO2-limitation inducible promoters, which will switch on the lipolytic genes by stopping CO2 aeration instead of adding eco-unfriendly nickel.
The lipolytic enzymes (EC 3.1.1) hydrolyzing the carboxylic ester bonds to release the fatty acids from the diacylglycerols include galactolipase and phospholipase B. Galactolipase (EC 3.1.1.26) catalyzes the hydrolysis of galactolipids, such as DGDG and MGDG by removing one or two fatty acids. Phospholipase B is an enzyme with a combination of both PLA1 (EC 3.1.1.32) and PLA2 (EC 3.1.1.4) activities; that is, it can cleave acyl chains from both the sn-1 and sn-2 positions of a phospholipid. For the purpose of fatty acid recovery from membrane lipids, we will test the performances of three lipolytic enzymes (from bacteria, fungi, and herbivorous animal digestive juice) in 6803. First, the lipase from Staphylococcus hyicus (Shl) is unique among the bacterial lipases in that it has a very broad substrate spectrum ranging from triacylglycerol lipids of various chain lengths to phospholipids and lysophospholipids. Second, the modified fungal phospholipase from Fusarium oxysporum (Fol) exhibited emerging galactolipase activity as well as increased phosopholipase activity. Third, guinea-pig lipase (Gpl, also called GPLRP2, guinea-pig pancreatic lipase-related protein 2) from the digestive juice of guinea-pig shows the highest galactolipase ever found, and plays a dual role in the digestion of galactolipids and phospholipids, the most abundant lipids occurring in plant thylakoid membranes.
We will use a 6803 inorganic carbon (Ci) limitation response mechanism to develop an inducible transcription system regulated by CO2. Cells of 6803 aerated with CO2-free air for 30 min in the light depleted the total Ci to near zero levels (McGinn et al., 2003). Under these conditions, transcripts for the three inducible Ci uptake systems, ndhF3, sbtA, and cmpA genes, showed near-maximal mRNA abundance at 15 min under Ci limitation. By utilizing their promoter sequences to control the lipase genes, Green Recovery of fatty acids could be initiated by CO2 limitation by stopping aeration of the biomass. Gas supply to the photobioreactor is easy to regulate, and limiting the CO2 supply will be an economical and eco-friendly method to initiate lipid hydrolysis.
Another advantage of the Green Recovery system emerges when combined with the cyanobacterial FFA secretion system. The FFA secretion avoids the energy intensive biomass processes (i.e., concentration and extraction) by directly recovering the secreted FFA from the culture medium. However, the FFA secreting system still requires substantial biomass to achieve cost-effective FFA production, which means a significant amount of fixed carbon has to be converted and stored as lipid membranes. It is expected that the Green Recovery system will convert the lipids into FFAs in the potential spent cyanobacterial biomass generated by the FFA secreting system, and also will cause cell lysis and release the unsecreted intracellular FFAs. With this combination approach, the secreted FFAs, unsecreted FFAs and the membrane FFAs will incorporate and be recovered by one single separation.
Example 6
Green Recovery Strain Construction and Test
Three groups of strains were constructed for Green Recovery (Table 1, FIG. 8). The first group consists of four strains (SD256, SD257, SD258, and SD252) to evaluate performances of three lipolytic enzymes and two CO2 responsive promoters in 6803. The second group consists of three strains (SD237, SD252, and SD260) which contain multiple lipolytic enzymes as well as lysozymes (13, 19, and 15) from Salmonella bacteriophage P22 to achieve faster lysis responses to CO2 limitation, and to evaluate the optimal strategy for maximum lipid recovery. The third group consists of three strains (SD235, SD239 and SD246) that incorporate the lipid recovery system into FFA secreting strain (SD232) to evaluate the Green Recovery of FFA after FFA secretion. The genotypes of the experimental strains and their parent strain and intermediate strains are listed in Table 1, and their genealogy is shown in FIG. 8. The growth of the strains is comparable to the wild type, with doubling times of about 9 hours.
The Green Recovery of some of the strains has been tested for cell lysis and fatty acid release. FIG. 9 showed that the Green Recovery strain cultures significantly lysed after CO2 limitation in flasks at the cell densities of 0.4-3.0×109 cells/ml. As shown in FIG. 10, two Green Recovery strains SD256 and SD257 demonstrated significantly increased membrane permeability after CO2 limitation as revealed by Sytox staining. The 6803 wild-type (SD100) cells also showed membrane damages at high cell density and CO2 limitation conditions. However, when a native lipase gene lipA (slr1969) is deleted from wild type strain 6803 to result in SD200, this lipA deficient strain showed a much lower level of membrane damage at high cell density and CO2 limitation conditions. This suggests that the wild type 6803 cells have a background autolysis at high cell density because of the native lipase gene(s), but in the Green Recovery strains in which exogenous lipolytic genes are controlled by CO2 limitation inducible promoters, the inducible membrane destruction is much stronger than the background autolysis.
The membrane destruction and release of fatty acids into the culture of the Green Recovery strains after CO2 limitation are shown in Table 4. Based on the data in Table 4, the Green Recovery strains SD256 and SD257 released significantly increased fatty acid amounts from cell membranes (11.5 and 10.3×10−15 g/cell, respectively) after CO2 limitation compared to the amount of the wild-type strain (SD100, 6.3×10−15 g/cell). Also, the background fatty acid release was dramatically reduced in the lipA deficient strain SD200, which suggests that the native lipase gene or genes caused the background membrane fatty acid release and high cell density autolysis. It is expected that the Green Recovery system can be more precisely controlled by changing the native promoter of lipA gene into a CO2 limitation inducible promoter.







TABLE 4







CO2 limitation inducible membrane destruction and release


of fatty acids in the Green Recovery strains.













Strain
SD100
SD200
SD237
SD256
SD257
SD258





Description
Wild
ΔlipA22::sac
Pcmp43::fol
Pcmp47::fol
Pcmp48::shl
Pcmp49::gpl



Type
B KmR
RBS shl
RBS
RBS
RBS





RBS


Initial cell
1.37
3.42
1.96
1.92
1.69
4.03


density (1012


cells/L)


FFA/cell
6.3 ± 1.1
0.79 ± 0.23
7.5 ± 2.1
11.5 ± 1.9
10.3 ± 0.7
1.9 ± 0.1


(10−15 g)


Time (day)
3.42
4.2
2.6
1.5
2.23
3.34


until 50%


lysis after


CO2 limitation









Example 7
Conditions for Green Recovery
We tested several optimal conditions for Green Recovery, such as cell density of the cultures (FIG. 11), intensity of illumination (FIG. 12), and agitation of the cultures (FIG. 13). It was observed that the membrane damage was faster and FFA release was higher after 1/4 dilution (about 108 cells/ml) than at the original cell density (about 109 cells/ml) (Table 5 and FIG. 11). Light is essential for Green Recovery, which is negligible in the dark (less than 2 μmol photons m−2 s−1), and much slower in low light (20 μmol photons m−2 s−1) than in higher light levels (140 μmol photons m−2 s−1) (FIG. 12). A probable explanation for these observations is that energy from photosynthesis is required for gene expression, synthesis and function of lipase enzymes. Because of self-shading, photosynthetic cells have a higher metabolic activity at low cell density than at high cell density. This is consistent with the higher FFA yields that we observed at low cell concentrations (Table 5). The intensity of agitation did not affect the rate of lysis; for example, continuous rotation at 60 rpm/min and intermittent shaking (once per day) produced similar membrane damage curves (FIG. 13).







TABLE 5







Membrane damage and FFA yields of SD strains for Green Recovery














Starting cell
Membrane

FFA yield



Genetic
density
damageb
Recovered
(10−12 mg/


Strain
Descriptiona
(CFU/ml)
(%/day)
FFAc (mg/L)
cell)
















SD100
Wild Type
3.2 × 109

8.9
16.5 ± 2.5 
 5.1 ± 0.8


SD200
ΔlipA::sacB KmR
3.4 × 109

2.5
 2.7 ± 1.1
 0.8 ± 0.3


SD256
Pcmp::fol
1.6 × 109

35.1
19.3 ± 1.0 
12.4 ± 0.6 




3.9 × 108 
(1⁄4)d
94.7
 5.5 ± 0.7
14.0 ± 1.8 


SD257
Pcmp::shl
2.9 × 109

33.8
22.7 ± 1.0 
 7.9 ± 0.4




7.2 × 108 
(1⁄4)d
83.4
 5.7 ± 1.2
 8.0 ± 1.7


SD237
Pcmp::fol RBS shl
1.5 × 109

45.2
23.6 ± 1.1 
15.7 ± 0.7 




3.8 × 108 
(1⁄4)d
91.3
10.6 ± 0.1 
28.0 ± 0.4 


SD258
Pcmp::gpl
3.0 × 108

9.4
 5.2 ± 0.6
17.4 ± 2.0 


SD252
Psbt::gpl
3.5 × 108

13.5
 3.1 ± 1.4
 8.8 ± 4.1


SD239
Δslr1609::PpsbA2 ‘tesA
5.8 × 108

56.7
 23.6 ± 0.02e
 40.7 ± 0.03e



Δ(slr1993-slr1994)::



44.6 ± 2.8f
76.8 ± 4.7f



Pcpc accBC Prbc



21.0 ± 2.8g
36.1 ± 4.7g



accDA








Δsll1951::*PpsbA2 UC








fatB1 Prbc Ch fatB2








Pcmp::fol RBS shl







SD254
Δslr1609::PpsbA2 ‘tesA
7.3 × 108

34.5
45.1 ± 0.4e
61.7 ± 0.5e



Δ(slr1993-slr1994)::



63.6 ± 0.4f
87.2 ± 0.5f



Pcpc accBC Prbc



18.6 ± 0.4g
25.4 ± 0.5g



accDA








Δsll1951::*PpsbA2 Uc








fatB1 Prbc Ch fatB2








Pcmp::fol RBS shl








Psbt::gpl







SD262
Δslr1609::PpsbA2 ‘tesA
8.9 × 108

67.3
47.0 ± 0.7e
52.8 ± 0.8e



Δ(slr1993-slr1994)::



73.4 ± 1.4f
82.5 ± 1.5f



Pcpc accBC Prbc



26.5 ± 1.4g
29.7 ± 1.5g



accDA








Δsll1951::*PpsbA2 Uc








fatB1 Prbc Ch fatB2








Pcmp::fol RBS shl








Psbt::gpl RBS 13 19








15





aDetailed genetic information is described in Table S1.


bMembrane damage was detected by SYTOX staining. The damage rates (%/day) were estimated from starting time point to the 50% permeable cell time point, when over 99.9% cells were dead. If the permeable cell percentage did not drop to 50%, the damage rates were estimated over the entire experimental period.


cRecovered FFAs were extracted by 10 ml hexane from 16 ml cultures after four days of CO2 limitation.


dThe data for 1/16 dilutions were similar to the data for 1⁄4 dilutions.


eThe secreted FFAs before CO2 limitation.


fTotal FFAs after CO2 limitation, including secreted FFAs and released FFAs.


gFor combination strains, released FFAs were calculated by subtracting the total amount from the secreted amount.






Example 8
Green Recovery for FFAs
Gas Chromatography (GC) showed that a significant amount of FFAs were released by lipolytic degradation of the membrane lipids (FIG. 14 and Table 5). Green Recovery FFA yield of 36.1×10−12 mg/cell were measured in SD239, compared to 200×10−12 mg FFA/cell secreted by an FFA-secretion SD277 grown in the same conditions. The FFA yields of Green Recovery were closely related to the membrane damage even under different conditions (Table 5). GC also showed that the profile of the released FFA was close to the fatty acid profile of the 6803 membrane lipids with abundant unsaturated fatty acids (FIG. 15), suggesting that the released FFAs were degraded from membrane lipids. FFA release occurred concomitantly with membrane damage during Green Recovery, and the released FFA amount reached the maximum when most cells became permeable to the SYTOX stain (FIG. 16).
Example 9
Green Recovery with FFA Secretion
The FFA-secretion strains that harbor the Green Recovery system (SD239, SD254 and SD262 in Table 5) are still able to release membrane lipids as FFAs at rates faster than non-FFA-secretion strains following CO2 limitation. GC analysis showed that the profile of the FFAs overproduced by acyl-ACP thioesterases by FFA-secretion strains was different from the profile of the membrane-released lipids. The FFAs recovered from overproducing strains are highly saturated and rich in C12:0 and C14:0, whereas FFAs obtained via the Green Recovery system contained substantial amounts of unsaturated fatty acids and only a small portion of C12:0 and C14:0, which is the same composition observed in membrane lipids (FIG. 15). The released FFA amount from membrane lipids is similar to the amount of secreted FFA from thioesterases (Table 5, SD239). As anticipated, the FFAs recovered from the combination strains (e.g., SD239 and SD262) after CO2 limitation was a mixture of the overproduced FFAs and the released membrane FFAs.
Example 10
Application Discussions
The Green Recovery system was designed for production of scalable and cost-effective renewable biofuels in photobioreators. Productive photobioreators require aeration systems to supply the photosynthetic microorganisms with CO2. Lipid recovery from biomass by limiting CO2 supply is clearly an efficient and effective method. The system we describe here does not require traditional biomass processes, such as cell harvesting, dewatering, cell disruption, solvent extraction or inducer molecules like those employed in our previous inducible cyanobacteria lysis system, thus considerably reducing the cost of lipid recovery. Since continuous agitation is not required for Green Recovery (FIG. 13), this system only needs sunlight and possibly intermittent agitation to convert biomass into FFAs. Another advantage of Green Recovery is that lipolytic enzymes convert diacylglycerols in the membranes into FFAs, which due to their low density and low solubility in water are easier to harvest and refine than the diacylglycerol lipids. Although it was reported that the guinea pig lipase Gpl had the strongest galactolipase activities ever identified, our experiment showed that Gpl was not as effective as the others in 6803 (Table 5). We speculate that the compromised performance of Gpl in 6803 was due to different lipid substrates in cyanobacteria and plants or improper protein folding of an animal protein in a cyanobacterial protein synthesis system. We anticipate that Green Recovery would provide the same advantages when applied in other microbial bioreactors such as algae, E. coli, and yeast.
Green Recovery exhibits other advantages when combined with the previously described cyanobacterial FFA secretion system. The FFA secretion system avoids the energy intensive biomass processes such as concentration and extraction by directly recovering the secreted FFA from the culture medium. However, the FFA secretion system still requires substantial biomass to achieve cost-effective FFA production, which means a significant amount of fixed carbon has to be converted and stored as lipid membranes. It is expected that the Green Recovery system will recover the membrane lipids in the potential spent cyanobacterial biomass generated by the FFA secretion system, and also will cause cell lysis and release of the unsecreted intracellular FFAs. To our surprise, incorporation of the Green Recovery system into the FFA secretion strains resulted in an increased damage rate upon CO2 limitation (Table 5, SD239 and SD262). We postulate that secretion of FFAs through the cytoplamstic membranes creates some lesions in the membranes which facilitate the contact of lipolytic enzymes to the acyl glycerol ester bonds. These findings demonstrate the practical combination of the FFA-secretion system and Green Recovery in photobioreactors, where the old cultures or the spent biomass can be utilized for extra FFA yield. We believe that cyanobacterial biofuel will be instrumental in developing a carbon neutral source of sustainable fuels.
Example 11
Alkane Biosynthesis in Cyanobacteria
Alkanes, the major constituents of gasoline, diesel, and jet fuel, are naturally produced by diverse species. Alkanes have been reported in a diversity of microorganisms, and the most consistent reports are from the cyanobacteria. An alkane biosynthesis pathway from cyanobacteria was well known (FIG. 17). The pathway consists of an acyl-acyl carrier protein reductase and an aldehyde decarbonylase, which together convert intermediates of fatty acid metabolism to alkanes and alkenes. The aldehyde decarbonylase is related to the broadly functional nonheme diiron enzymes. Heterologous expression of the alkane operon in Escherichia coli leads to the production and secretion of C13 to C17 mixtures of alkanes and alkenes. These genes and enzymes can now be leveraged for the simple and direct conversion of renewable raw materials to fungible hydrocarbon fuels.
Example 12
Alkane Genes in Cyanobacteria
With bioinformatics analysis, we found the phylogenetic relationship of the alkane production genes in cyanobacteria as shown in FIG. 18. From these alkane production genes, we chose ten alkane biosynthesis genes from five cyanobacterial species (i.e, Synechococcus sp. PCC 7942, Prochlorococcus marinus subsp. Pastoris str. CCMP 1986, Nostoc punctiorme PCC 73102, Thermosynechococcus elongatus BP-1, and Gloebacter violaceus PCC 7421) for overexpression in Synechocystis PCC sp. 6803. The strain constructions are listed in Table 6. Some of these alkane overproduction strains are built on the base of a Green Recovery strain such as SD237, so that they are able to release intracellular alkanes with CO2 limitation.







TABLE 6







Alkane overexpression strain constructions.









Alkane




Strains
Genotype
Alkane gene sources





SD293
Δsll1951-15::PpsbA210 orf1593
Synechococcus 7942



orf1594
(original)


SD294
Pcmp43::fol RBS shl RBS
Synechococcus 7942



Δsll1951-15::PpsbA210 aac (7942)
Nostoc 73102



Ptrc adc (73102)



SD295
Pcmp43::fol RBS shl RBS
Synechococcus 7942



Δsll1951-15::PpsbA210 orf1593
(original)



orf1594



SD298
Pcmp43::fol RBS shl RBS
Synechococcus 7942



Δ(slr1993-slr1994)-14:: PpsbA210
Nostoc 73102



aac (7942) Ptrc adc (73102)



SD303
Pcmp43::fol RBS shl RBS
Synechococcus 7942



Δ(slr1993-slr1994)-14:: PpsbA210
Nostoc 73102



aac (7942) Ptrc adc (73102)




Δsll1951-15:: PpsbA210 orf1593




orf1594



SD307
Pcmp43::fol RBS shl RBS
Synechococcus 7942



Δ(slr1993-slr1994)-14:: PpsbA210
Nostoc 73102



aac (7942) Ptrc adc (73102)
Thermosynchococcus BP-1



Δsll1951-15:: PpsbA210 orf1593




orf1594




Δ(slr2001-slr2002)-17::P psbA210




Ptrc aac (BP-1) Ptrc adc(BP-1)



SD308
Δ(slr2001-slr2002)-17:: P psbA210
Thermosynchococcus BP-1



Ptrc aac (BP-1) Ptrc adc(BP-1)



SD309
Δ(slr2001-slr2002)-17::EHC1 Ptrc
Prochococcus 1986



aac (1986) Ptrc adc(1986)



SD310
Δ(slr2001-slr2002)-17::EHC1 Ptrc
Gloebacter 7421



aac (7421) Ptrc adc(7421)









Example 13
Alkane Overproduction in Genetic Modified Synechocystis SD Strains
As shown in Table 6, nine strains were constructed for expressing the alkane biosynthesis genes from Synechococcus sp. PCC 7942, Prochlorococcus marinus subsp. Pastoris str. CCMP 1986, Nostoc punctiorme PCC 73102, Thermosynechococcus elongatus BP-1, and Gloebacter violaceus PCC 7421. Alkane biosynthesis was detected in their cultures. The GC analysis of the alkane production in SD294 culture was shown in FIG. 19, with a Heptadecane yield of 1.5 mg/L and 83.3×10−13 mg/cell, which is a 55.5 fold increase from wild-type SD100 (with a yield of 1.5×10−13 mg/cell) (Table 7).







TABLE 7







Alkane production in genetically modified Synechocystis SD strains













Strains
WT
SD293
SD294
SD295
SD298
SD303
















Gene

Syn7942
Syn7942
Syn7942
Syn 7942
Syn 7942


sources and

(original)
Nostoc 73102
(original)
Nostoc 73102
Nostoc 73102


modification

ΔS-layer
ΔS-layer
ΔS-layer
ΔPHB
ΔS-layer





Green Recovery
Green Recovery
Green Recovery
ΔPHB








Green Recovery


Cell density
6.5
4.3
1.8
1.4
1.4
3.0


on Day 5


(CFU 108/mL)


Heptadecane
0.1
0.6
1.5
0.9
0.36
0.83


(C17:0) (mg/L)


10-13 mg/cell
1.5
14.0
83.3
64.3
25.7
27.7









Example 14
Alkane Overproduction with Green Recovery
One alkane overproduction strain SD303 (Pcmp43::fol RBS shl Δ(slr1993-slr1994)-14::PpsbA210 aac PX adc Δsll1951-15::PpsbA210 orf1593 orf1594) was constructed on the base of a Green Recovery strain SD237, by overexpressing the alkane biosynthesis genes from Nostoc punctiorme PCC 73102 and Synechococcus sp. PCC 7942. The experiment showed that this strain is able to produce alkanes and undergo Green Recovery when induced by CO2 limitation. As shown in FIG. 20, a culture of SD303 was grown to a cell density of 3×108 cells/ml, GC analysis showed that 0.17 mg/L of heptadecane was detected in the culture medium. After Green Recovery induced by CO2 limitation for 3 days, 0.9 mg/L of heptadecane were released into the culture medium, also a significant amount of free fatty acids were generated by Green Recovery (FIG. 20). This experiment showed that Green Recovery is able to release the alkanes which are retained inside the cell, and also to produce free fatty acids for biofuel production.
Example 15
Constructing a Stationary-Growth-Phase Autolysis System in 6803
The following example describes how to construct a stationary-growth-phase autolysis system in 6803, so that the neutral lipid cyanobacterial cells are able to autolyze for neutral lipid release when the culture enters stationary-growth-phase. This stationary-growth-phase autolysis system can also be induced to undergo cell lysis by iron starvation in the culture.
According to the microarray data by Jamie et al [Jamie S. F. et al, 2007 Arch Microbiol 187:265-279], the transcription of approximately 10% of the genes in the 6803 wild type were different in the stationary growth phase, compared to the exponential growth phase. Among the highly up-regulated genes for stationary phase, the isiA gene has its own promoter, and its iron deficiency-dependent regulation mechanism is well documented. At least three mechanisms are involved in the up regulation of the isiAB operon [Ulf, D., et al, 2006 PNAS 103:7054-7058]. (1) depression of ferric uptake regulator Fur (encoded by sll0567) on the Fur box in the promoter (+163-+186); (2) a 90 bp region upstream of the −35 box carrying a positive acting element is essential for full induction activity under iron-deplete conditions; (3) an internal antisense RNA repressor (isiR, a cis-encoded antisense RNA transcribed from the noncoding strand) is abundant under iron-replete conditions but not under iron limitation.
The invention is to fuse the isiA promoter with the P22 lysis cassette. However, the isiA promoter is strong in E. coli without the repressors present in 6803, so the entire correct plasmid containing the PisiA-P22 13 19 15 cassette is lethal after transfer to host E. coli cells. To avoid lethal amplification of the PisiA-P22 13 19 15 DNA cassette in E. coli, DNA molecules specifying the PisiA-P22 13 19 15 cassette to be transformed into Synechocystis were directly created by over-lapping PCR. As shown in FIG. 21, the whole transformation unit, including flanking regions F1 and F2, the P22 lysis cassette and KmR, was created by overlap PCR splicing, and transferred into SD100 (6803 wild type) and SD202 (a neutral lipid production strain) by homologous double crossover exchange to generate SD111 and SD112, respectively.
As shown in FIG. 22, SD111 grew normally on a BG-11 plate, grew slower on a 0.2×Fe BG-11 plate (4 μM Fe), grew into colonies and then autolysed on a 0.15×Fe BG-11 plate (3 μM Fe), but did not grow on 0.1× (and lower Fe concentration) BG-11 plates (2 μM Fe and lower). When grown in 1.0 concentration BG-11 medium, SD111 showed two autolysis periods (FIG. 23), the first autolysis period is in exponential growth phase when the cell density is between 107-107.5 cells/ml, the second autolysis period is in stationary growth phase when the cell density is above 108 cells/ml. The drop and fluctuation of CFU in these two periods suggested that the old cells were performing self-lysis. In strain SD112, the stationary-phase-autolysis is incorporated into the TAG-producing strain SD202, so that the overproduced TAGs will be released from the old lysing cells into the culture medium.
Example 16
Acyl-CoA Overproduction in Cyanobacteria
The following example describes how to increase the essential substrate for neutral lipid synthesis-acyl-CoA. The primary neutral lipid synthetase identified so far (like the WS/DGAT described above) are acyl-transferases which utilize acyl-CoA as acyl donor instead of acyl-ACP (FIG. 4). However, in cyanobacteria, the majority acyl carried molecules are acyl-ACPs instead of acyl-CoA. By increasing the acyl-CoA level, it is expected to resolve the bottleneck of neutral lipid synthesis, and thus drastically increase the yield of neutral lipid production in cyanobacteria.
Acyl-CoA overproduction in cyanobacteria is based on free fatty acid overproduction. As shown in FIG. 24, the major acyl carrier molecules in cyanobacteria are acyl-ACPs, to convert acyl-ACPs into acyl-CoA, the acyl chains first need to be decoupled from acyl-ACPs as FFAs by a thioesterase (TE hereafter), and then to be activated as fatty acyl CoA by an acyl CoA ligase (ACL hereafter).
In our previous research, we have already inserted thioesterase genes from E. coli and plants into 6803, which resulted in the overproduction and secretion of FFAs. ACL is the first-step enzyme for the β-oxidation pathway, which ligates FFA with Coenzyme A for fatty-acyl-CoA. In E. coli, ACL is encoded by fadD. There are many other functional ACL genes in yeast and other heterotrophic microorganisms.
The TE genes were introduced into 6803 successively in the strains SD216, SD225, SD232, SD243, SD249 and SD277 (Table 1). Starting with SD243 and its SD247 derivative, an ACL overexpression cassette Pcpc45 fadD(Ec) is inserted to yield SD251 to overproduce acyl-CoA, where Pcpc45 is the promoter of the 6803 cpc operon, and fadD(Ec) is the fadD gene from E. coli. To further increase the acyl-CoA synthesis, an artificial operon PpsbA212 faa138 Pcpc45 fadD(Ec) was inserted into SD243 to result in SD273 with two ACLs. In SD273, faa138 is a synthesized gene for Faa2p from Saccharomyces cerevisiae, a long chain fatty acyl-CoA synthetase that accepts a wider range of acyl chain lengths than Faa1p, preferring C9:0-C13:0; involved in the activation of endogenous pools of fatty acids. fadD(Ec) is the acyl-CoA ligase from E. coli. The detailed strain constructions are described in Table 1.
Example 17
Biodiesel-Producing Cyanobacteria
The following example describes how to produce neutral lipids FAME and FAEE—the components of biodiesel on the basis of the acyl-CoA overproducing strains.
In our previous research, we genetically modified cyanobacterium 6803 to overproduce and secrete free fatty acids (FFA hereafter). Fatty acids are energy molecules that can be chemically converted into liquid fuels such as alkanes or fatty acyl esters. However, fatty acids cannot be used as biofuel, and an extra chemical reaction is required to convert them into lipid transportation fuels. Thus we are planning to introduce fatty acyl ester synthesis pathways into the FFA-secreting 6803 to have 6803 produce fatty acyl esters such as fatty acyl methyl ester (FAME hereafter) or fatty acyl ethyl ester (FAEE hereafter).
Biodiesel, the primary renewable alternative to diesel, is consumed at greater than 2 billion gallons per year, and is composed of FAME or FAEE derived from the chemical transesterification of plant and animal oils. FAME or FAEE can be directly used in diesel combustion engines They are chemically more stable than FFAs as they do not form fatty acid cation precipitations like FFA. FAME and FAEE are liquids at room temperature with very low solubility in water, so they are easily recovered from an aqueous photobioreactor (PBR hereafter). They are also biologically more stable than FFAs as most bacteria are able to consume FFAs through the β-oxidation pathway, but this fatty acid consuming pathway cannot degrade FAME or FAEE.
On the basis of acyl-CoA overproducing strains, SD251 and SD237 for example, another substrate for synthesis of FAME or FAEE is a short alcohol, e.g., methanol or ethanol, respectively. The biosynthesis pathway for methanol is present in some methane bacteria, but the pathway is uncommon, complicated and needs methane for the substrate. Therefore we will focus on biosynthesis of ethanol, which is simple and well studied. It is reported that exogenous expression of pyruvate decarboxylase and alcohol dehydrogenase genes will enable bacteria like cyanobacteria and E. coli to produce ethanol from pyruvate. At the first trial stage, we will provide the cyanobacterial cells short alcohols by adding methanol and ethanol into the culture, and we plan to introduce the ethanol pathway into 6803 later so that ethanol addition is not necessary any more.
To have 6803 produce FAME or FAEE, the whole metabolic pathway (FIG. 24) needs to be introduced into 6803. We need to introduce TE genes to uncouple FFA from acyl-ACP, to introduce and overexpress ACL genes to transfer FFA to fatty acyl-CoA, and to introduce the atfA gene to synthesize FAME or FAEE with short alcohols.
However, when we attempted to overexpress fadD and tesA (Pcpc fadD(Ec) PpsbA236 tesA136) on the background SD202 (ΔlipA22:: Inv(PpsbA231 atfA phaP)-32), no transformant colonies could be obtained. In another trial, when we attempted to add atfA and fadD (PpsbA244 atfA Pcpc45 fadD(Ec)) onto SD243 (an FFA overproduction strain), the transformation failed again as no transformant colonies grew out. These two failures seemed to suggest that these three pathway genes cannot be overexpressed in 6803 at the same time. The detailed strain constructions are described in Table 1.
To avoid the transformation difficulty, we made SD251 on the basis of SD243 (Table 1). The genotype of SD251 is Δaas-23::PpsbA236 tesA 136, Δ(slr1993-slr1994)-14::Pcpc39 accB accC70 Prbc40 accD accA, Δsll1951-15::PpsbA210 fatB161 (Uc) Prbc41 fatB262(Ch), Δ(slr2001-slr2002)-17::PpsbA210 fatB262(Ch), ΔnrsBAC11::PnrsB46 atfA Pcpc45 fadD(Ec).
In SD251, fadD(Ec) is overexpressed by promoter Pcpc45, while the aftA gene is controlled by the Ni inducible promoter PnrsB46. This strain is successfully constructed. It is thought that with the addition of Ni2+, the aftA gene will be turned on, and with the further addition of alcohols the induced WS/DGAT will esterify acyl-CoA with alcohol to yield FAME or FAEE.
To test this idea, a 200 ml SD251 culture ( ̃1011 cells) was divided into five cultures of 200 ml. For aftA gene induction, 10 mM NiSO4 was added. For alcohol addition, 1 ml absolute alcohol was added on the first day and 2 ml alcohol was added everyday after the first day. After 72 h about 170 ml cultures were left in the five flasks. To each whole culture, 3 g NaCl and 3 ml H3PO4 was added and the culture extracted with 20 ml acetyl acetate. After 30 min shaking (200 rpm) at 37° C., the cultures were centrifuged, and the 3 ml acetyl acetate phase was dried for GC analysis. The treatment and GC results are shown in Table 8. As an example, the GC curve for sample D is shown in FIG. 25.
The results in Table 8 show that SD251 is able to produce and secrete FAME and FAEE with nickel induction and addition of alcohols. However, the FAE secretion is only about 0.5% of that of FFA. The similar chain length pattern suggests that the FAEs are converted from the FAAs. This experiment has been performed twice with similar results each time. We tried to analyze the intracellular FAEs, but some lipids in the Folch extraction interfered with C18:3 peaks, so we have to optimize the GC methods for the intracellular FAEs.
To increase the conversion ratio of FAEs from FFAs, it is planned to increase the synthesis of ACL and WS/DGAT. Besides E. coli fadD, another ACL (FAA2 from yeast) gene was synthesized after codon optimization, and is being inserted into SD243. CoA is a big group, so acyl-CoA is not supposed to be easily secreted out of cells, and will accumulate inside the cells. After ACL overproduction, the atfA gene will be tested for inducible expression (e.g., by the control of PisiA, PnrsB, Psbt, or Pcmp) and for constitutive expression. With the increase in acyl-CoA amount, the aftA gene can be constitutively expressed in 6803 in the presence of TEs and ACLs. In the future, the ethanol synthesis pathway will be introduced into 6803, so it will produce FAEE without addition of ethanol.







TABLE 8







FFA and FAE production of SD251 Culture with Different Treatments









Treatments













A
B
C
D
E





Induction
None
None
10 mM
10 mM
10 mM





NiSO4
NiSO4
NiSO4


Alcohol
None
Methanol
None
Methanol
Ethanol


GC: Total 
6.21
4.72
5.60
5.39
5.29


secreted FFA







(mg)







GC: Total
0
0.017
0.004
0.026
0.031


secreted







FAME/FAEE







(mg)







FFA yield
243.7
185.0
219.7
221.3
207.5


(mg/L/72 h)







.FAE yield
0
0.66
0.15
1.01
1.20


(mg/L/72 h)









Example 18
Combining Green Recovery with FAEE Production
On the basis of SD251, inserting the Green Recovery cassett Pcmp43:fol RBS shl RBS (as in SD237) will enable the resulting strain to undergo Green Recovery at CO2 limitation. The resulting strain will produce FAME/FAEE with induction by Ni and addition of methanol or ethanol (as in SD251), and will undergo Green Recovery to release intracellular FAME/FAEE when the culture is limited for CO2, also Green Recovery will convert about 50% membrane lipids into free fatty acids for biofuel production (as in SD237).
Example 19
Bacterial Strains, Culture Media and Growth Conditions
All SD strains are derived from Synechocystis sp. PCC 6803 and listed in Table 1. SD strains were grown at 30° C. in modified BG-11 medium (34) under continuous illumination (50 μmol photons m−2 s−1) and bubbled with 1% CO2-enriched air. The details for growing an SD culture from a colony descended from a single cell are described in Example 12. For plating and transformant selection, 50 μg/mL kanamycin or 4.5% (w/v) sucrose is added to 1.5% agar plates (w/v). All of our strains are maintained as concentrated cultures in BG-11 medium with 20% glycerol and stored at −80° C.
Example 20
Genetic Manipulation for Cyanobacterium 6803
Methods for DNA manipulation are standard. The primers for constructions and genotype verifications are listed in Table 9. DNA sequences were analyzed in the DNA Sequence Laboratory at Arizona State University. Gene segments are synthesized at Genscript (Piscataway, N.J., USA). The nucleic acid sequences of non-6803 genes were redesigned by codon optimization based on the codon frequencies of highly expressed 6803 genes (Table 10). Also stem-loop hairpins in the predicted mRNA secondary structure were removed to smooth the transcription and to stabilize mRNA by prolonging its half-life. Multiple gene modifications are applied into SD strains by using a sacB-KmR cassette.
We optimized the current genetic modification techniques for 6803 gene deletion, insertion and substitution. Suicide vectors harboring a positive selection marker (e.g., KmR) and a counter selection marker (e.g., sacB) are widely applied in a two-step gene deletion and insertion for 6803 without leaving any drug marker residuals.
i. Transformation of Suicide Vectors Containing sacB-KmR Cassette.
About 106 SD cells in 10 μl BG-11 medium are mixed with 400 ng suicide vector DNA containing the sacB-KmR cassette and incubated for 5 h. Then the mixtures were plated onto a filter membrane (Whatman PC MB 90MM 0.4 μm) layered on a BG-11 agar plate. After segregation on the BG-11 plate for about 24 h, the membrane carrying the cyanobacteria was transferred onto a BG-11 plate containing 50 μg/mL of kanamycin. Generally, the colonies appear 4-5 days later. Individual colonies are restreaked with a sterile loop onto a kanamycin BG-11 agar plate and a 4.5% sucrose BG-11 agar plate. Those patches growing on a kanamycin BG-11 agar plate and not growing on a 4.5% sucrose BG-11 agar plate have the correct insertions with the sacB-KmR cassette.
ii. Transformation with Markerless Constructs.
To replace the sacB-KmR selective marker with target gene segments, about 106 sacB-KmR cells in 10 μl BG-11 medium are mixed with 400 ng suicide vector DNA containing the target genes and incubated for 5 h. The mixtures are inoculated into 2 mL buffered BG-11 medium and grown for 3-4 days. 1 mL inoculation is plated onto a 4.5% sucrose-containing BG-11 agar plate. Generally, the colonies appear 5-8 days later. Individual colonies are restreaked onto a kanamycin BG-11 agar plates and a 4.5% sucrose BG-11 agar plates. The patches growing on sucrose plates and not growing on kanamycin plates are positive candidates for further evaluation by PCR.
iii. Confirmation of Replacement.
Cells from a colony are resuspended in 2 μl water in a 200 μl PCR tube. The cell suspension is frozen at −80° C. for 2 min, and then thawed in a 60° C. water bath. This freeze-thaw cycle needs to be performed three times. 1 μl frozen-thawed cell suspension is used as the PCR template for a 30 μl PCR reaction including the primers specific for the inserted gene segments or the deleted region.
When a foreign gene is introduced into 6803, it may cause adverse effect on the growth and be subjected to gene loss or modification, since any cell losing the genetic alteration will likely have a higher growth rate to eventually take over the population. The genetic stability of foreign genes in 6803 is therefore tested by growing a culture of the strain with periodic dilution and subculturing for at least two months. After this time, the cells from the culture are plated onto BG-11 agar plates to obtain single isolated colonies. One hundred single colonies are picked and tested for all genetic attributes and confirmed for the presence of the foreign gene by PCR as described above. The percentage of positive colonies in the culture reflects the genetic stability of the foreign gene. Genes found to be unstable can be modified to eliminate non-functional hydrophobic domains that often are responsible for poor growth due to association with and impairment of lipid membranes function.







TABLE 9







Primers used in this study








Primer Name
Sequences (5′ to 3′)










consturction of pψ101








SynL-S-SacI
GCgAgcTcCAGACGACTACGGGCAAAG


SynL-A-to-P22
ATGTTTTTCTGGCATCACACCACCTCAAATTGGG


P22-S-to-SynL
TTGAGGTGGTGTGATGCCAGAAAAACATGATCT


P22-A-SacII
gaccGcGGTTATTTTAAGCACTGACTCC


KR-S-SacII(-)
GGccGcGGAAAGCCACGTTGTGTCTCA


KR(-)-A-to-Syn
ACCCCCTGGGGCAGAAAGCCACGTTGTGTCTCA


SynR-S-to-KR(-)
ACAACGTGGCTTTCTGCCCCAGGGGGTTTCTTGA


SynR-A-BamHI
GGgAtcCGTTGGTTAGCCAAGAGAATC


 







consturction of pψ102








P2213-A-NdeI
GACATATGTTACTGCTGATTTGCATCATCGA


SynR-S-XbaI
gaTCTAGACACATTGCTCCTTTTGTGCGTAA


SynR-A-SacII
gaCCGCGGAACTAATGGCTTGGGCTAGGTATA


 







Consturction of pψ121








SynL-S-KpnI
GAGGTACCGCCAATTGCAGACGACTACG


SynR-S-XbaI
GATCTAGACACATTGCTCCTTTTGTGCGTAA


SynR-A-SacII
GACCGCGGAACTAATGGCTTGGGCTAGGTATA


Syn-right-A-SphI
aGGCAtgCGTTGGTTAGCCAAGAGA


P22-A-to-F1
GCACAAAAGGAGCAATGTGttattttaagcactgactcc


F1-S-to-P22
tcagtgcttaaaataaCACATTGCTCCTTTTGTGCG


SynR-A-F2
CAAACTAATGGCTTGGGCTAGGTATAGCT


 







Consturction of pψ122








F1-A-to-LMD
catgtttttctggCATCACACCACCTCAAATTGGG


LMD-S-to-F1
AGGTGGTGTGATGccagaaaaacatgacct


LMD-A-to-F2
ACAAAAGGAGCAATGTGctatctgcactgctcattaata


F2-S-to-LMD
agtgcagatagCACATTGCTCCTTTTGTGCGT


SynR-A-SacII
gaCCGCGGAACTAATGGCTTGGGCTAGGTATA


 







Consturction of pψ123 and pψ124








tP4-S
atCATATGaagacaaacgaaagcccccacctagcgtcatgccgggtggggg



ctttttcatCTGCAGta


tP4-A
TACTGCAGATGAAAAAGCCCCCACCCGGCATGACGCTA



GGTGGGGGCTTTCGTTTGTCTTCATATGAT


tP4-A-PstI
CTGCAGATGAAAAAGCCCCCACC


pA2-S-BamHI
gaGGATCCTAATTGTATGCCCGACTATT


pA2-A-to-P2219
actgctgatttgcatCATTTGGTTATAATTCCTTATG


P2219-S-to-pA2
GAATTATAACCAAATGatgcaaatcagcagtaacgg


P2215-A-BamHI
gaGGATCCttattttaagcactgactcct


lambdaS-S-NdeI
gaCATATGccagaaaaacatgacctgt


 







Construction of pψ126








S2F1-S-HindIII
AGaagcTTTGTGGCCCAACAATTGGT


S2F2-A-EcoRI
GTGAAtTCTGTAAGCAGTTAGAGTGGCCC


S2-segS-400
CGGTCTACTCCGGTTAAATCCCCTAACG


S2-segA-400
CCACAGCCCCAACAATAAGCAAGAT


 







Construction of pψ127








lambdaS-S-NdeI
gaCATATGccagaaaaacatgacctgt


lambdaS-S-NdeI-RBS
gaCATATGaggaGGTGTGatgccagaaaaacatgacc


pA2-A-to-R
actgctgatttgcatCATTTGGTTATAATTCCTTATG


R-S-to-pA2
GAATTATAACCAAATGatgcaaatcagcagtaacgg


 







Construction of pΨ214








FadD-F1-A
TAA ACT CTG TAG GCC AGC GGC AA


FadD-F1-S
CGT CAA TGC CTA GAC CTA GCA GTA CC


FadD-F2-S
AAG GAT TTC CGT TTT ATC CCA GCA CCA


FadD-F2-A
GTA ATT GCC ACA GAC AAG CGT ATT CGG


KS-NdeI
ACC ATA TGC ATC CTA GGC CTA TTA ATA TTC CGG


KS-BamHI
GAA TTA GGA TCC GTC GAC CTG CAG G


 







Construction of pΨ215








NiF1-S-EcoRI
GAgAA TTc CAG ACG ACT ACG GGC AAA G


NiF1-A-toTesA
AAC GTG TCC GCC ATC ACA CCA CCT CAA ATT G


TesA-S-toNiF1
GAG GTG GTG TGA TGG CGG ACA CGT TAT TGA T


TesA-A-toNiF2
CAA AAG GAG CAA TGT GTT ATT TGT CAT CAT CGT



CTT


NiF2-S-toTesA
GAT GAT GAC AAA TAA CAC ATT GCT CCT TTT GTG CG


NiF2-A-BamHI
ACG GAT CCG CAA GCA GTG AAA GAT AG


 







Construction of pΨ216








TesA-S
CAAATGGCGGACACGTTATTGATTCTG


TesA-A
CTT TGT AGT CTG AGT CAT GAT TTA CTA AAG GCT G


Test-S-to-pA2
ATTATAACCAAATGGCGGACACGTTA


pA2-S
TCCCCATTGCCCCAAAATACATCC


pA2-A-to-TesA
CAA TAA CGT GTC CGC CAT TTG GTT ATA ATT CCT TA


 







Construction of pΨ207








S4F1-S-PstI
GActgcAGGTCATTGCCGATAAAGTTG


S4F1-A-XbaI
AGtctagATAATGTACAGGTCAAGCTGGTCT


S4F2-S-SacI
GAgagcTCATTGACACCGAAATGACTTTGG


S4F2-A-EcoRI
GAGAATTCTTTGCATTTCCGAAACCACCC


S4F2-S-XbaI
GATCTAGAATTGACACCGAAATGACTTTGG


S4F2-A-KpnI
GAGGTACCTTTGCATTTCCGAAACCACCC


 







Construction of pΨ223








Pcpc-S
TAG GCT GTG GTT CCC TAG GCA ACA GT


Pcpc-A-to-SynB
TCC GTA AAG TTA ATA GCC ATT GAA TTA ATC TCC



TAC TTG AC


SynB-S-to-Pcpc
AGG AGA TTA ATT CAA TGG CTA TTA ACT TTA CGG



AAC TGC G


SynB-A-to-SynC
CAT TGA ATT AAT CTC CTC TAG GGT TTA ATC CAC



ATT AGG GTT


SynC-S
CCT AGA GGA GAT TAA TTC AAT GCA ATT CGC CAA



AAT TTT AAT TGC


SynC-A
CTC TCC ATT GAC CTA GGG TGT TAA ATG CTC TTC G


SynC-S-to-SynB
GTG GAT TAA ACC CTA GAG GAG ATT AAT TCA ATG



CAA TTC GC


SynC-A-to-Prbc
CTT TAC TTA TGG CAA TGC TCT CCA TTG ACC TAG



GGT GTT


Prbc-S
AAC ACC CTA GGT CAA TGG AGA GCA TTG CCA T


Prbc-A-to-SynD
CAA TCA AAT AGA GAC ATC TAG GTC AGT CCT CCA



TAA AC


SynD-S-to-Prbc
AGG ACT GAC CTA GAT GTC TCT ATT TGA TTG GTT



TGC C


SynD-A-to-SynA
AGT CCT CCT TAA CCA TCT TGA TTG ACG GAA AT


SynA-S
GAC CTA GAT GAG TAA AAG TGA GCG TCG TGT TTT



TCT


SynA-S-to-SynD
TCA AGA TGG TTA AGG AGG ACT GAC CTA GAT GAG



TAA AAG TGA


SynA-A
TCA TTA CAC CGC CGT TTC TAA AAA TTG ACC CAA



ATG


SynB-S-Seq
CCT TCG GCC ATC AAG AGA ATG CAG AG


SynA-A-Seq
TGA CGC AAC TGT TCA GCC CGA CT


 







Construction of pΨ228








S5F1S
CAC CAC TTT ACC CAT GAC GGA AGG TGG


S5F1A
TGT CTC GGA GTT GCT TAG GGT AAT CAT AGC A


S5F2S
TCG CGA ATT CCT GTT CAT CAA CAA CGG TG


S5F2A
AAA GCT AAA GCG ACT GAG GAA GTG CCA G


 







Construction of pΨ231








Fats-S
AGA TAT CGC GTG CAA GGC CCA GTG


Fats-A
TGA TAT CAT TAA GAG ACC GAG TTT CCA TTG G


 







Construction of pΨ240








S7F1-S
GAC TTC CAA AAC GGC GAT CAA GCC AAC C


S7F1-A
GTC CAT TAG GGG AGT GTC CGC CAA CA


S7F2-S
GGT ACC ATG CAC TGG TGG ATT ACG CC


S7F2-A
GGG AAA TTG TTC CGT TAA CTG TTG ATA TTC CCG GT


 







Construction of pΨ243








ChFatB-s-to-Psba
CTG AAC GAA GGA ATT ATA ACC AAA TGG TGG CTG



CTG CTG CTA GTT C


PsbA-a-to-ChFatB
GAA CTA GCA GCA GCA GCC ACC ATT TGG TTA TAA



TTC CTT CGT TCA G


 







Construction of pΨ248








S9F1S
CAA TAG GAT TCG TAG AGA TTG AGA TAC TCC ATG



GCG T


S9F1A
AGC CTT TTT TGA GGG CTA CCT TTT GGC TGT T


S9F2S
GGC TCC CTA CTT TTA CGG TTA CAT TTT TGG CGA AT


S9F2A
CTA CAA GGA AGC AAT TTG TCG CAT ATA TTG ACC



CCA A


 







Construction of Alkane strains








EHC1S
GAT ATC GTT CGT TAA TTT TTC CCA TCG CTT TTA G


EHC1A
GAT ATC TAA ACT TAG TCT AAG GAT TAA TGA GAG T


EHC2S
ATG ATA TCT GTA ATT TCG TCG AGT CCC AGC CA


EHC2A
TTG TTT CTC CTC TTT AAA ATT ATA CGA GCC GGA T


BP-1-S
AAA TGT TCG GTT TAA TCG GCC ATC TGA CTA GC


BP-1-A
TCT TAG GCA CCA GTC AGC CCA TAA ACA GAC A


Pro1986-S
ATG TTT GGT TTG ATT GGG CAC TCT ACT AGT TTC G


Pro1986-A
TCT TAG GCA CCA GTC AGC CCA TAA ACA


Glo7124-S
AAA TGT TCG GTC TGA TCG GGC ACC TC


Glo7124-A
ATA TCT TAT TGG CGG GGA GCA CTG GC


aar-A
CCA AAT GAA ATT TGG TTT AAT TGG TCA TCT CAC



TAG


1593-s-to-pA2
AAG GAA TTA TAA CCA AAT GCC GCA GCT TGA AGC



CAG CCT T


pA2-a-to-1593
TTC AAG CTG CGG CAT TTG GTT ATA ATT CCT TCG



TTC AGA TT


1594-A
TCA AAT TGC CAA TGC CAA GGG TTG GAA GC


ADC-A
CTG ATA TCT TAA GCA CCG ATC AAC CCG TAG GCA



CT


 







Segregation Checking/Sequencing








FadD-F2-Seq
ATA AGT TTG GGT TAC CAC TGG TCG TTT GAG CTT C


FadD-F1-Sequ
CTTCCCTTCTTCCTTCCATCTGATTATGGT


S4-seg100-S
TGGCTCCCTGACCAATTTTTCGG


S4-seg100-A
CCA GGC AAT TTC CTC CGG TTT ACC


S5100S
TCA TCG TGT TAA CAG CGG TAT GCT TCT AGT CT


S5100A
CAA AGG TAC CGC TAA TAC CTG TAA GTT CTA CGA



GG


S7 Seg 51S
GGG GAT CAA TTG CGT CTC TGT GGC


S7 Seg 90A
CAA AGC GTT GAC CGT GCC AGT TTT TGA C


S9-S68
CCC TAA AAA AAG TCA AAC TAA CCT TTC CCA GGG



TGG


S9-A71
CTT CTT TGG CCA CAT CTT CGC CTA GTA AAT GGT T
















TABLE 10





Synthesized DNA segments















Prbc34 aftA69 RBS pha-68


TTGGCGGGTGTCGGGCTGGCTTAACTATGCGGCATCAGGCAGATTGTACTGAGAGTGCACCATATG


 


AGAATTCCGGATATCTAGAAGCTT


 


CAACGGCTCACAAGCCCAACTAATCACCATTTGGACAAAACATCAGtAATTCTAATTAGAAAGTCC


 


AAAAATTGTAATTTAAAAAACAGTCAATGGAGAGCATTGCCATAAGTAAAGGCATCCCCTGCGTGA


 


TAAGATTACCTTCAGAAAACAGATAGTTGCTGGGTTATCGCAGATTTTTCTCGCAACCAAATAACT


 


GTAAATAATAACTGTCTCTGGGGCGACGGTAGGCTTTATATTGCCAAATTTCGCCCGTGGGAGAAA


 


GCTAGGCTATTCAATGTTTATGGAGGACTGACCTAG


 


atg cgT CCt tta CAC ccg att gat TTC ATc ttT ctg TCC ttG gaG aaa CGt


 


caa caA ccC atg cat gta GGC GGC tta TTC ttg TTC cag att cct gat aac


 


gcc CCC gac acc TTC att caa gat ctg gtg aat gaC atc cgC ATc TCC aaa


 


TCC atT cct GTG CCC CCc ttT aac aat aaa ctg aaC ggT CTG TTC tgg gaT


 


gaG gaT gaG gag ttt gaC tta gat CAC caC ttt cgC CAC att GCC ctg ccC


 


caC cct GGC cgT atT cgG gaa tta tTa att tat atC agC caa gaA cac agt


 


acg ctg CTg gaC cgC GCt aag ccc ttg tgg acc tgT aaC att atC gaa ggC


 


att gaa ggc aat cgt TTC gcc atg tac ttc aaa att caC CAt gcg atg gtc


 


gat ggC GTc GCC GGt atg cgC CTg att gaa aaG TCC ctc tcc cat gat gta


 


ACC gaa aaa agt atc gtg CCC ccC tgg TGC GTG gaA ggC aaa cgG GCt aag


 


cgc tta CGG gaa cct aaa ACt ggt aaa att aag aaa atc atg tct ggt att


 


aaA agT cag CTG caA gcg ACC ccc ACC gtc att caa gaA CTc tcC caA ACC


 


gta TTC aaa gat att ggC cgt aat cct gat CAC GTG TCC agc ttt cag gcg


 


cct TGC tct att ttg aat cag cgt gtg agT TCC TCC CGG cgt ttt GCC GCg


 


caA Agt ttt gac CTG gat cgt ttt cgt aat att gcc aaa TCC ttg aaC gtC


 


acc att aaC gat GTG gta CTG gcg gta TGC tct ggt GCC tta cgt gcg tat


 


ttg atg Tcc caC aat tCC Ctg cct TCC aaa CCC tta att gcT atg GTG CCC


 


gcc tct atC cgG aaC gaT gaC TCC gaC gtc agc aac cgt att acg atg att


 


ctC GCg aat ttg GCC acc cac aaa gat gat cct tta caa cgt CTc gaa att


 


atc cgc cgt TCt GTG caa aac TCC aag caa cgc ttc aaa cgt atg acT agc


 


gaC caA att CTc aat tat agt GCt gtG gta tat ggT cct GCC ggC ctc aac


 


ATT att tct ggc atg atg CCC aaa cgc caa gcc ttc aat ctC GTG atC AGc


 


aat gtT ccC ggT CCC CGc gag CCC CTG tac tgg aat GGC gcc aaa CTG gat


 


GCC ctc tac CCC GCC TCC att gta tta gac ggt caG GCC ttg aat att ACC


 


atg acT tCt taC tta gat aaa TTg gaG cTc GGt ttg att GCT tgT cgt aat


 


GCC ttg CCC CGG atg cag aat tta ctg ACC CAC tta gaa gaa gaa att caa


 


CTc TTC gaa ggT gta att GCg aag cag gaa gat att aaa ACt gcG aat taa


 


GGAGGAATTAAA


 


aTG ATc ctG acc ccC gaG caa gtG GCT GCT gcg caa AAA GCT AAT ctc gaa


 


acC ctg TTc GGT ctg acc acT AAA gcC ttC gaG GGT gtG gaa AAA ctc gtG


 


GAA ctC AAT ctC cag gtc gtG AAA act TCC TTT GCT gaa GGT gtt GAT AAT


 


GCc AAA AAA gcC ctC TCC GCT AAA GAT GCT caA gaa ctg ctC GCT ATc caA


 


GCc GCT GCT GTT cag ccC gtG GCT gaA AAA acc ctC GCT TAT acc cgG cac


 


ctg tat gaa ATT gcC TCC gaa acc cag agc GAA TTT acc AAA gta GCT GAA


 


gct caa ctg GCT gaG GGT TCC AAA AAT GTg caa gcg ctg gtc GAA AAT ctc


 


GCT AAA AAT GCT ccC GCc ggt TCC gaa TCt acc GTT GCT ATT GTT AAA TCC


 


gcC ATc tcc gcC GCc AAT AAT GCc TAc GAA TCC GTg cag AAA gcg acc AAA


 


caa gcg gtc gaa ATT gcC gaa acc AAT TTc cag gct gcC gct acg gct GCT


 


acc AAA gct GCT cag caa GCT agc GCT acg GCT cgt acg GCT acg GCT AAA


 


AAA acg acg gct GCT tga


 


GAATTCCGGATATCTAGAAGCTTG


 


GTCGACTGCAGAGGCCTGCATGAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTAAATT


 


PpsbA2 faa2








TCGCCCCTCTACACAGCCCAGAACTATGGTAAAGGCGCACGAAAAACCGCCAGGTAAACTCTTCTCAACCCCCAAAACGC


 


CCTCTGTTTACCCATGGAAAAAACGACAATTACAAGAAAGTAAAACTTATGTCATCTATAAGCTTCGTGTATATTAACTT


 








CAA


 


ATG GCT GCC CCT GAC TAT GCC TTA ACC GAT TTG ATT GAA AGT GAT CCC CGT TTC GAA TCT


 


TTG AAG ACC CGT TTG GCC GGT TAT ACT AAA GGG TCC GAC GAA TAC ATT GAA GAA CTG TAC


 


TCT CAA TTG CCC CTG ACT TCC TAC CCC CGT TAT AAA ACT TTC TTG AAA AAG CAG GCC GTC


 


GCC ATT AGT AAT CCT GAT AAT GAA GCC GGT TTT TCC TCT ATT TAC CGC TCC TCT CTC TCC


 


AGC GAA AAC CTG GTA TCC TGT GTC GAT AAA AAC TTG CGC ACT GCC TAT GAC CAC TTT ATG


 


TTT AGT GCC CGG CGT TGG CCC CAA CGG GAT TGT CTc GGt AGC CGG CCC ATC GAT AAA GCC


 


ACT GGC ACC TGG GAA GAA ACC TTT CGT TTT GAA TCT TAT AGT ACC GTT TCC AAG CGG TGC


 


CAC AAT ATC GGC TCC GGG ATC TTG TCC CTG GTG AAT ACT AAA CGC AAG CGC CCC TTA GAA


 


GCC AAC GAC TTT GTt GTc GCT ATC CTG TCC CAC AAT AAC CCC GAA TGG ATC TTG ACC GAT


 


TTG GCT TGT CAA GCC TAC AGT TTA ACC AAT ACC GCC CTG TAT GAA ACC CTG GGT CCC AAC


 


ACC TCT GAA TAT ATC CTG AAC TTG ACC GAG GCT CCG ATC CTG ATT TTT GCC AAA TCC AAC


 


ATG TAT CAC GTT CTC AAG ATG GTA CCC GAT ATG AAA TTT GTC AAC ACC TTG GTC TGC ATG


 


GAC GAA CTG ACC CAC GAC GAG TTA CGG ATG TTA AAC GAA AGC TTG CTG CCC GTA AAG TGT


 


AAC TCC CTG AAT GAG AAA ATT ACC TTT TTC AGC CTC GAA CAA GTG GAA CAA GTA GGT TGC


 


TTC AAC AAA ATT CCC GCC ATT CCT CCC ACC CCC GAT TCC CTG TAT ACC ATT AGC TTC ACC


 


AGC GGC ACT ACt GGt CTG CCC AAg GGc GTa GAg ATG TCT CAC CGg AAc ATT GCT TCC GGT


 


ATT GCC TTT GCT TTT AGC ACC TTT CGT ATC CCG CCG GAC AAG CGC AAC CAA CAA CTG TAT


 


GAC ATG TGC TTC CTG CCC TTG GCC CAC ATT TTC GAA CGG ATG GTG ATT GCT TAT GAC TTG


 


GCT ATT GGc TTT GGG ATC GGc TTc CTG CAC AAA CCg GAC CCt ACC GTG CTG GTA GAA GAC


 


TTG AAG ATC CTG AAA CCG TAC GCT GTC GCC CTG GTT CCC CGG ATC CTG ACC CGT TTC GAG


 


GCT GGC ATT AAA AAC GCC CTG GAT AAA AGC ACC GTT CAG CGG AAC GTG GCT AAT ACC ATC


 


CTG GAT AGC AAA TCT GCT CGC TTT ACt GCg CGT GGc GGt CCC GAC AAG TCT ATT ATG AAC


 


TTT TTG GTC TAC CAT CGG GTG CTG ATT GAT AAA ATC CGc GAC AGC CTC GGT TTA TCT AAC


 


AAC AGT TTC ATT ATC ACC GGT AGC GCT CCT ATC AGC AAa GAT ACt CTc CTC TTC TTG CGG


 


TCC GCC CTG GAC ATT GGT ATC CGG CAG GGT TAC GGC CTC ACt GAA ACt TTC GCC GGT GTT


 


TGT CTG TCC GAA CCT TTC GAA AAA GAC GTG GGT TCC TGT GGT GCC ATT GGT ATC TCC GCC


 


GAA TGC CGC CTC AAA TCC GTA CCC GAG ATG GGC TAC CAC GCT GAC AAA GAC CTG AAA GGG


 


GAA TTA CAA ATC CGT GGC CCG CAA GTG TTT GAA CGT TAC TTT AAG AAC CCC AAC GAA ACC


 


AGC AAA GCC GTG GAT CAA GAT GGT TGG TTT AGT ACC GGC GAC GTG GCg TTc ATT GAT GGT


 


AAA GGT CGT ATC TCC GTG ATT GAC CGC GTG AAA AAC TTC TTC AAA CTG GCC CAC GGT GAA


 


TAC ATT GCC CCC GAA AAA ATC GAA AAC ATT TAC TTG AGT TCT TGT CCC TAC ATT ACC CAA


 


ATT TTT GTC TTT GGT GAC CCC CTC AAA ACC TTT TTG GTA GGC ATT GTT GGG GTC GAC GTG


 


GAC GCC GCT CAA CCC ATT TTG GCT GCC AAA CAT CCG GAA GTG AAA ACT TGG ACC AAA GAA


 


GTC CTC GTG GAA AAC CTG AAT CGG AAT AAA AAG CTG CGC AAA GAG TTT CTG AAT AAG ATT


 


AAC AAA TGT ACC GAC GGG TTG CAG GGT TTC GAA AAA TTG CAC AAC ATC AAA GTG GGC CTC


 


GAG CCT CTG ACC TTA GAA GAT GAT GTA GTT ACC CCT ACC TTC AAA ATT AAG CGT GCC AAA


 


GCC TCC AAA TTT TTC AAG GAT ACC TTG GAC CAA CTG TAC GCT GAA GGT AGC TTA GTG AAA


 








gpl


ATG Aaa TTG TTT GCC TGG ACT ATT GGT TTA CTG CTg ctg GCC ACt GTG CGC GGc GCT GAG


 


GTc TGT TAT TCT CAt TTG GGC TGc TTT TCC GAC GAG AAA CCG TGG GCg GGT ACC TCT CAA


 


CGG CCC ATC AAg AGT TTG CCg TCC GAC CCT AAA AAG ATT AAt ACC CGG TTC TTG CTG TAC


 


ACC AAt GAa AAt CAA AAT TCC TAC CAA CTG ATC ACC GCT ACT GAT ATT GCC ACC ATC AAA


 


GCC AGT AAC TTC AAT CTc AAC CGc AAA ACC CGC TTC ATT ATT CAC GGT TTC ACC GAC AGC


 


GGT GAG AAC TCT TGG CTG AGT GAT ATG TGT AAA AAC ATG TTC CAA GTT GAA AAA GTG AAT


 


TGC ATT TGC GTG GAT TGG AAA GGC GGT TCC AAG GCT CAA TAC AGT CAG GCT TCC CAG AAT


 


ATT CGG GTG GTC GGT GCC GAA GTT GCC TAT TTA GTG CAA GTA CTG AGC ACC TCC CTG AAC


 


TAT GCC CCG GAA AAC GTA CAT ATT ATT GGT CAC TCC CTC GGC GCC CAC ACC GCT GGG GAA


 


GCC GGG AAG CGG CTG AAC GGG CTG GTA GGG CGG ATT ACC GGc cTc GAC CCC GCC GAA CCC


 


TAC TTT CAA GAT ACC CCC GAA GAA GTC CGG CTG GAT CCC TCT GAC GCT AAA TTT GTG GAC


 


GTG ATT CAC ACT GAT ATT AGC CCC ATT CTG CCT AGT CTG GGT TTC GGT ATG TCC CAG AAG


 


GTC GGT CAC ATG GAC TTC TTC CCC AAC GGC GGC AAA GAT ATG CCC GGG TGC AAA ACC GGC


 


ATC TCC TGC AAC CAC CAC CGG AGT ATT GAA TAT TAT CAC AGC AGT ATT TTG AAC CCC GAA


 


GGT TTt TTa GGC TAC CCG TGT GCT TCC TAC GAT GAA TTc CAA GAA TCt GGG TGC TTC CCC


 


TGT CCC GCT AAA GGT TGT CCT AAA ATG GGT CAC TTT GCC GAC CAG TAC CCC GGg AAG ACC


 


AAT GCT GTC GAA CAA ACC TTc TTC CTC AAC ACC GGg GCg TCC GAT AAT TTC ACC CGG TGG


 


CGC TAT AAA GTA ACC GTT ACC CTG AGT GGC GAA AAA GAC CCG TCC GGT AAC ATC AAT GTG


 


GCT TTG TTA GGT AAA AAC GGG AAC TCT GCT CAA TAC CAG GTT TTC AAG GGC ACC CTG AAG


 


CCC GAC GCC TCC TAT ACT AAT TCC ATT GAT GTC GAA CTC AAC GTT GGG ACC ATT CAA AAA


 


GTG ACC TTC CTG TGG AAA CGG AGC GGG ATC TCC GTC TCT AAA CCC AAG ATG GGT GCT TCt


 


CGc ATT ACt GTT CAA AGT GGT AAA GAC GGG ACC AAA TAT AAC TTC TGC TCC AGC GAT ATT


 


GTG CAA GAA AAC GTC GAG CAG ACT CTG AGC CCC TGC taa A


 


RBS fol RBS shl


TTCCCAATTTGAGGaGGTGTG


 


ATG GAA GTa TCC CAa GAT CTG TTT AAT CAA TTC AAT CTG TTC GCT CAA TAC TCC GCg GCT


 


GCT TAC TGT GGg AAA AAT AAC GAT GCT CCT GCg GGc ACC AAT ATT ACt TGT ACC GGT AAC


 


GCT TGC CCT GAA GTG GAg AAg GCT GAC GCC ACC TTT TTG TAC AGC TTC GAA GAT AGC GGC


 


GTA GGC GAT GTG ACT GGt TTC cTc GCC TTG GAT AAT ACC AAT AAA TTG ATT GTT CTC TCT


 


TTC CGT GGC agt GAc TCC ATT GAG AAT TGG ATT GCC AAC TTG AAc TTt TGG TTG AAG AAA


 


ATC AAt GAt ATT TGT TCC GGc TGT CGG GGt CAC GAT GGT TTC ACC AGC AGC TGG CGT TCC


 


GTG GCC GAC ACC CTC CGG CAA AAG GTg GAa GAT GCT GTg CGc GAA CAt CCt GAT TAC CGC


 


GTT GTT TTT ACC GGG CAC TCC CTG GGC GGG GCC TTG GCC ACC GTA GCC GGT GCT GAC CTG


 


CGC GGT AAC GGC TAC GAT ATT GAT GTG TTC TCC TAT GGG GCT CCC CGG GTT GGG AAC CGG


 


GCT TTT GCt GAg TTT TTG ACC GTt CAa ACC GGc GGT ACC TTG TAT CGG ATC ACC CAT ACC


 


AAT GAT ATT GTT CCC CGC CTG CCC CCT CGT GAA TTC GGT TAT AGC CAC TCC TCC CCC GAA


 


TAC TGG ATT AAA AGC GGC ACC TTG GTT CCC GTG ACC CGT AAC GAC ATT GTA AAA ATT GAG


 


GGC ATT GAC GCC ACC GGT GGT AAT AAT CAA CCT AAT ATC CCC GAT ATC TTG GCT CAT CTG


 


TGG TAT TTT CAA GCC ACC GAC GCT TGT AAC GCC GGC GGT TTC AGT TAA


 








ATGAAGCCTACCGTTAAAGCTGCTCCCGAGGCTGTTCAGAACCCGGAAAACCCGAAAAACAAGG


 


ACCCCTTTGTGTTTGTGCACGGCTTTACCGGTTTTGTGGGGGAGGTTGCTGCGAAAGGTGAGAA


 


TCACTGGGGCGGCACCAAAGCCAATCTGCGCAACCATTTGCGGAAAGCTGGTTACGAAACCTAC


 


GAAGCCTCCGTATCCGCCTTGGCCTCCAATCACGAACGTGCTGTGGAACTGTACTATTATCTGA


 


AAGGTGGTCGGGTAGACTATGGTGCTGCCCATTCCGAAAAATATGGCCATGAGCGTTACGGGAA


 


AACTTATGAAGGTGTGCTGAAAGATTGGAAACCCGGGCACCCCGTACACTTTATCGGTCATTCC


 


ATGGGTGGTCAGACCATTCGGCTGCTGGAACATTATCTGCGCTTTGGTGATAAAGCCGAAATTG


 


CCTATCAACAACAGCACGGGGGTATTATTAGCGAATTATTTAAGGGCGGTCAAGACAACATGGT


 


GACCTCTATCACTACTATTGCCACCCCTCACAATGGTACCCATGCTTCTGACGATATTGGCAAT


 


ACCCCGACTATCCGGAACATTCTGTATAGCTTCGCCCAAATGTCCAGTCATCTGGGCACCATCG


 


ACTTTGGGATGGACCATTGGGGTTTCAAGCGGAAAGATGGCGAGAGTCTGACCGATTATAATAA


 


GCGGATTGCCGAGAGCAAAATCTGGGATTCTGAAGATACTGGGCTGTATGACCTGACCCGTGAA


 


GGCGCCGAGAAAATCAACCAGAAAACCGAATTGAATCCCAATATCTATTACAAAACCTACACTG


 


GGGTGGCTACCCATGAAACTCAGTTAGGCAAACACATCGCGGACCTCGGCATGGAATTTACCAA


 


AATCCTCACCGGCAACTATATCGGGAGCGTAGACGATATTCTGTGGCGGCCCAATGATGGTTTG


 


GTGAGCGAAATCTCCAGCCAACACCCCAGCGATGAGAAGAACATTTCCGTAGACGAAAACTCCG


 


AACTGCATAAGGGTACCTGGCAGGTCATGCCTACCATGAAAGGGTGGGACCACTCCGATTTTAT


 


TGGTAATGACGCCCTGGATACCAAACACTCCGCCATCGAACTCACCAACTTTTATCATAGCATT


 


TCTGACTACTTGATGCGGATCGAAAAAGCCGAATCTACCAAAAACGCCTAATGATATCGA


 


Ptrc tesA137








ATG AAA GCT GAT ACT CTG TTG ATT TTG GGG GAC TCC TTG TCT GCT GGT TAT CGT ATG TCC


 


GCT AGC GCC GCT TGG CCC GCC TTG CTC AAC GAC AAA TGG CAA AGT AAG ACT TCC GTT GTG


 


AAT GCT TCC ATT AGt GGT GAC ACC AGC CAG CAG GGC CTG GCT CGT CTC CCC GCT CTG CTC


 


AAA CAG CAT CAG CCC CGT TGG GTC CTG GTA GAA CTG GGC GGT AAC GAC GGT CTc CGc GGC


 


TTC CAA CCT CAA CAG ACC GAA CAA ACC CTC CGG CAG ATC TTA CAG GAT GTG AAA GCC GCC


 


AAC GCC GAA CCC CTC CTG ATG CAA ATC CGC CTG CCC GCC AAC TAT GGT CGG CGC TAT AAC


 


GAA GCC TTC AGT GCT ATC TAT CCC AAA CTC GCT AAG GAA TTC GAC GTG CCC CTG CTG CCC


 


TTT TTC ATG GAA GAA GTT TAT CTG AAA CCC CAG TGG ATG CAA GAC GAT GGT ATT CAT CCC


 


AAT CGT GAC GCT CAA CCC TTT ATT GCC GAT TGG ATG GCT AAA CAA TTA CAA CCC CTC GTA


 


AAC CAC GAT TCC GAC TAT AAA GAT GAc GAT GAc AAG TAA gatatcga


 


*PsbA2 UC fatB1 Prbc Ch fatB2








CTCTACACAGCCCAGAACTATGGTAAAGGCGCACGAAAAACCGCCAGGTAAACTCTTCTCAACCCCCAAAACGCCCTCTGTTTACC


 














ATG GCt ACC ACC TCT TTA GCT TCC GCc TTt TGC TCG ATG AAA GCT GTA ATG TTa GCT CGT


 


GAT GGt CGG GGt ATG AAA CCt CGT AGt AGT GAT TTG CAA CTc CGT GCG GGA AAT GCG CCT


 


ACC TCT TTG AAA ATG ATC AAT GGG ACC AAA TTC AGT TAT ACG GAG AGC TTG AAA CGG TTG


 


CCT GAT TGG AGC ATG CTC TTT GCT GTT ATC ACC ACC ATC TTT TCG GCT GCT GAG AAA CAA


 


TGG ACt AAT CTA GAG TGG AAG CCG AAA CCG AAG CTA CCC CAG TTG CTT GAT GAT CAT TTT


 


GGA CTG CAT GGG TTA GTT TTC CGG CGC ACC TTT GCC ATC CGG TCT TAT GAa GTT GGA CCT


 


GAT CGC TCC ACC TCT ATT CTG GCT GTT ATG AAT CAT ATG CAG GAG GCT ACC CTT AAT CAT


 


GCG AAA AGT GTG GGA ATT CTA GGA GAT GGA TTC GGG ACG ACG CTA GAG ATG AGT AAG CGG


 


GAT CTG ATG TGG GTT GTT CGG CGC ACG CAT GTT GCT GTT GAA CGG TAC CCT ACT TGG GGT


 


GAT ACT GTA GAA GTA GAG TGC TGG ATT GGT GCT TCT GGA AAT AAT GGC ATG CGT CGT GAT


 


TTC CTT GTC CGG GAC TGC AAA ACC GGC GAA ATT CTT ACT CGC TGT ACC AGC CTT TCG GTG


 


CTG ATG AAT ACT CGC ACt CGt CGT TTG TCC ACC ATt CCT GAT GAA GTT CGT GGt GAa ATA


 


GGG CCT GCT TTC ATc GAT AAT GTT GCT GTg AAA GAC GAT GAA ATT AAG AAA CTA CAA AAA


 


CTC AAT GAT AGC ACT GCC GAT TAT ATt CAA GGA GGT TTG ACc CCT CGT TGG AAT GAT TTG


 


GAT GTC AAT CAA CAT GTT AAC AAC CTC AAA TAC GTT GCC TGG GTT TTT GAG ACC GTC CCc


 


GAt TCC ATC TTT GAG AGT CAT CAT ATT TCC AGC TTC ACT CTT GAA TAT CGT CGT GAG TGt


 


ACc CGT GAT AGC GTG CTG CGG TCC CTG ACC ACT GTC TCT GGT GGC TCG TCG GAG GCT GGG


 


TTA GTT TGC GAT CAT TTG CTC CAA CTT GAA GGT GGG TCT GAG GTA TTG CGT GCC AGA ACT


 


GAG TGG CGG CCT AAA CTT ACC GAT AGT TTC CGC GGc ATT AGT GTT ATT CCC GCC GAA CCG


 


CGC GTG TAA


 








TCTCGCAACCAAATAACTGTAAATAATAACTGTCTCTGGGGCGACGGTAGGCTTTATATTGCCAAATTTCGCCCGTGGGAGAAAGC


 


TAGGCTATTCAATGTTTATGGAGGACTGACCTAG


 


ATG GTG GCT GCT GCT GCT AGT TCC GCT TTC TTC CCT GTT CCA GCC CCc GGA GCC TCC CCT


 


AAA CCC GGG AAG TTC GGA AAT TGG CCC AGT AGC TTG AGC CCT TCC TTC AAG CCC AAG TCA


 


ATC CCC AAT GGC GGA TTT CAG GTT AAG GCT AAT GAC AGC GCC CAT CCA AAa GCc AAt GGT


 


TCT GCc GTT AGT CTA AAG TCT GGC AGC CTC AAC ACT CAa GAa GAC ACT AGT TCC TCC CCT


 


CCT CCT CGG ACT TTC CTT CAt CAG TTG CCT GAT TGG AGT CGt CTT CTG ACT GCT ATt ACc


 


ACC GTG TTC GTG AAA TCT AAG CGT CCT GAC ATG CAT GAT CGG AAA TCC AAG CGT CCT GAC


 


ATG CTG GTG GAC TCC TTT GGG TTG GAG AGT ACT GTT CAG GAT GGc tTa GTG TTC CGA CAG


 


AGT TTT TCC ATT CGT TCT TAT GAA ATA GGC ACT GAT CGA ACG GCC TCT ATA GAG ACC CTT


 


ATG AAC CAC TTG CAG GAA ACC TCT CTC AAT CAT TGT AAG AGT ACC GGT ATT CTC CTT GAC


 


GGC TTC GGT CGT ACT CTT GAG ATG TGT AAA CGC GAC CTC ATT TGG GTG GTA ATT AAA ATG


 


CAG ATC AAG GTG AAT CGC TAT CCA GCT TGG GGC GAT ACT GTC GAG ATC AAT ACC CGt TTC


 


agC CGG TTG GGG AAA ATt GGT ATG GGT CGC GAT TGG CTA ATT AGT GAT TGC AAC ACC GGA


 


GAA ATT CTT GTA CGG GCT ACG AGC GCG TAT GCC ATG ATG AAT CAA AAG ACG CGG AGA CTC


 


TCC AAA CTT CCA TAC GAG GTT CAC CAG GAG ATT GTG CCT CTT TTT GTC GAC TCT CCT GTC


 


ATT GAA GAC AGT GAT CTG AAA GTG CAT AAG TTT AAA GTG AAG ACT GGT GAc agC ATT CAA


 


AAG GGT CTA ACT CCG GGG TGG AAT GAC TTG GAT GTC AAT CAG CAC GTA AGC AAC GTG AAG


 


TAC ATT GGG TGG ATT CTC GAG AGT ATG CCA ACA GAA GTT TTG GAG ACC CAG GAG CTA TGC


 


TCT CTC GCC CTT GAA TAT CGC CGG GAA TGC GGA CGC GAC AGT GTG CTG GAG TCC GTG ACC


 


GCT ATG GAT CCC TCC AAA GTT GGA GTC CGT TCT CAG TAC CAG CAC CTT CTG CGG CTT GAG


 


GAT GGG ACT GCT ATC GTG AAC GGT GCT ACT GAG TGG CGG CCG AAG AAT GCA GGA GCT AAC


 


GGG GCG ATc agC ACG GGA AAG ACT TCC AAT GGA AAC TCG GTC TCT TAA tgatatca


 


*ppsbA2 Ch fatB2


AGatATcGCGTGCAAGGCCCAGTGATCAATTTCATTATTTTTCATTATTTCATCTCCATTGTCCCTGAAAATCAGTTGT


 


GTCGCCCCTCTACACAGCCCAGAACTATGGTAAAGGCGCACGAAAAACCGCCAGGTAAACTCTTCTCAACCCCCAAAAC


 


GCCCTCTGTTTACCCATGGAAAAAACGACAATTACAAGAAAGTAAAACTTATGTCATCTATAAGCTTCGTGTATATTAA


 








TTATAACCAA


 


ATG GTG GCT GCT GCT GCT AGT TCC GCT TTC TTC CCT GTT CCA GCC CCc GGA GCC TCC CCT


 


AAA CCC GGG AAG TTC GGA AAT TGG CCC AGT AGC TTG AGC CCT TCC TTC AAG CCC AAG TCA


 


ATC CCC AAT GGC GGA TTT CAG GTT AAG GCT AAT GAC AGC GCC CAT CCA AAa GCc AAt GGT


 


TCT GCc GTT AGT CTA AAG TCT GGC AGC CTC AAC ACT CAa GAa GAC ACT AGT TCC TCC CCT


 


CCT CCT CGG ACT TTC CTT CAt CAG TTG CCT GAT TGG AGT CGt CTT CTG ACT GCT ATt ACc


 


ACC GTG TTC GTG AAA TCT AAG CGT CCT GAC ATG CAT GAT CGG AAA TCC AAG CGT CCT GAC


 


ATG CTG GTG GAC TCC TTT GGG TTG GAG AGT ACT GTT CAG GAT GGc tTa GTG TTC CGA CAG


 


AGT TTT TCC ATT CGT TCT TAT GAA ATA GGC ACT GAT CGA ACG GCC TCT ATA GAG ACC CTT


 


ATG AAC CAC TTG CAG GAA ACC TCT CTC AAT CAT TGT AAG AGT ACC GGT ATT CTC CTT GAC


 


GGC TTC GGT CGT ACT CTT GAG ATG TGT AAA CGC GAC CTC ATT TGG GTG GTA ATT AAA ATG


 


CAG ATC AAG GTG AAT CGC TAT CCA GCT TGG GGC GAT ACT GTC GAG ATC AAT ACC CGt TTC


 


agC CGG TTG GGG AAA ATt GGT ATG GGT CGC GAT TGG CTA ATT AGT GAT TGC AAC ACC GGA


 


GAA ATT CTT GTA CGG GCT ACG AGC GCG TAT GCC ATG ATG AAT CAA AAG ACG CGG AGA CTC


 


TCC AAA CTT CCA TAC GAG GTT CAC CAG GAG ATT GTG CCT CTT TTT GTC GAC TCT CCT GTC


 


ATT GAA GAC AGT GAT CTG AAA GTG CAT AAG TTT AAA GTG AAG ACT GGT GAc agC ATT CAA


 


AAG GGT CTA ACT CCG GGG TGG AAT GAC TTG GAT GTC AAT CAG CAC GTA AGC AAC GTG AAG


 


TAC ATT GGG TGG ATT CTC GAG AGT ATG CCA ACA GAA GTT TTG GAG ACC CAG GAG CTA TGC


 


TCT CTC GCC CTT GAA TAT CGC CGG GAA TGC GGA CGC GAC AGT GTG CTG GAG TCC GTG ACC


 


GCT ATG GAT CCC TCC AAA GTT GGA GTC CGT TCT CAG TAC CAG CAC CTT CTG CGG CTT GAG


 


GAT GGG ACT GCT ATC GTG AAC GGT GCT ACT GAG TGG CGG CCG AAG AAT GCA GGA GCT AAC


 


GGG GCG ATc agC ACG GGA AAG ACT TCC AAT GGA AAC TCG GTC TCT TAA tgatatca


 


PpsbA2* Cc fatB1


AGatATcGCGTGCAAGGCCCAGTGATCAATTTCATTATTTTTCATTATTTCATCTCCATTGTCCCTGAAAATCAGTTGT


 


GTCGCCCCTCTACACAGCCCAGAACTATGGTAAAGGCGCACGAAAAACCGCCAGGTAAACTCTTCTCAACCCCCAAAAC


 


GCCCTCTGTTTACCCATGGAAAAAACGACAATTACAAGAAAGTAAAACTTATGTCATCTATAAGCTTCGTGTATATTAA


 








TTATAACCAA


 


ATG AAA ACT ACT TCT CTC GCC TCT GCC TTC TGT TCT ATG AAA GCT GTT ATG CTG GCg CGG


 


GAT GGT CGC GGT ATG AAA CCC CGT TCC AGT GAT CTG CAA TTA CGG GCT GGC AAC GCT CAG


 


ACC TCC TTG AAG ATG ATT AAC GGC ACT AAA TTC AGT TAT ACC GAA TCT TTG AAG AAA CTC


 


CCC GAT TGG AGC ATG TTG TTC GCC GTG ATT ACC ACC ATt TTt AGT GCT GCC GAA AAA CAA


 


TGG ACC AAT CTC GAA TGG AAA CCC AAA CCC AAC CCC CCG CAG CTG CTC GAT GAC CAT TTT


 


GGc CCC CAC GGC TTG GTG TTT CGG CGT ACC TTC GCT ATC CGG TCT TAT GAA GTC GGT CCC


 


GAT CGG AGC ACT TCC ATC GTC GCT GTT ATG AAT CAC TTG CAA GAA GCC GCT TTG AAC CAt


 


GCT AAA tct GTT GGG ATT CTG GGT GAT GGC TTC GGT ACC ACT CTG GAG ATG AGT AAG CGC


 


GAT CTG ATC TGG GTA GTA AAG CGT ACt CAT GTG GCC GTG GAA CGT TAt CCg GCC TGG GGT


 


GAT ACC GTA GAA GTG GAG TGT TGG GTA GGC GCC TCC GGT AAC AAC GGT CGG CGT CAC GAC


 


TTC TTG GTG CGT GAC TGT AAA ACt GGc GAG ATC CTG ACC CGC TGT ACT TCC CTG AGC GTT


 


ATG ATG AAC ACC CGG ACC CGT CGC TTA TCC AAG ATT CCC GAA GAA GTT CGC GGG GAA ATT


 


GGt CCt GCT TTC ATT GAT AAC GTT GCT GTT AAG GAT GAG GAG ATT AAA AAG CCG CAA AAG


 


CTC AAT GAT TCT ACC GCC GAT TAC ATT CAA GGG GGT CTG ACT CCC CGT TGG AAT GAT CTG


 


GAT ATT AAT CAG CAT GTG AAT AAC ATC AAA TAT GTG GAT TGG ATT CTG GAG ACT GTG CCC


 


GAC TCT ATT TTC GAG TCC CAC CAC ATT agc AGT TTT ACC ATT GAA TAT CGT CGC GAA TGT


 


ACT ATG GAC AGT GTT TTG CAA TCC CTG ACC ACC GTC TCC GGC GGT TCC TCT GAA GCT GGC


 


CTG GTG TGC GAA CAC CTC TTG CAA CTC GAA GGC GGT AGT GAA GTg CTc CGt GCC AAG ACC


 


GAA TGG CGG CCC AAA TTG ACC GAC TCC TTT CGC GGG ATT TCT GTG ATT CCC GCC GAA TCC


 


TCC GTC TAA GATATCAT


 


PpsbA2* Cc fatB1


AGatATcGCGTGCAAGGCCCAGTGATCAATTTCATTATTTTTCATTATTTCATCTCCATTGTCCCTGAAAATCAGTTGT


 


GTCGCCCCTCTACACAGCCCAGAACTATGGTAAAGGCGCACGAAAAACCGCCAGGTAAACTCTTCTCAACCCCCAAAAC


 


GCCCTCTGTTTACCCATGGAAAAAACGACAATTACAAGAAAGTAAAACTTATGTCATCTATAAGCTTCGTGTATATTAA


 








TTATAACCAA


 


ATG AAA ACT ACT TCT CTC GCC TCT GCC TTC TGT TCT ATG AAA GCT GTT ATG CTG GCg CGG


 


GAT GGT CGC GGT ATG AAA CCC CGT TCC AGT GAT CTG CAA TTA CGG GCT GGC AAC GCT CAG


 


ACC TCC TTG AAG ATG ATT AAC GGC ACT AAA TTC AGT TAT ACC GAA TCT TTG AAG AAA CTC


 


CCC GAT TGG AGC ATG TTG TTC GCC GTG ATT ACC ACC ATt TTt AGT GCT GCC GAA AAA CAA


 


TGG ACC AAT CTC GAA TGG AAA CCC AAA CCC AAC CCC CCG CAG CTG CTC GAT GAC CAT TTT


 


GGc CCC CAC GGC TTG GTG TTT CGG CGT ACC TTC GCT ATC CGG TCT TAT GAA GTC GGT CCC


 


GAT CGG AGC ACT TCC ATC GTC GCT GTT ATG AAT CAC TTG CAA GAA GCC GCT TTG AAC CAt


 


GCT AAA tct GTT GGG ATT CTG GGT GAT GGC TTC GGT ACC ACT CTG GAG ATG AGT AAG CGC


 


GAT CTG ATC TGG GTA GTA AAG CGT ACt CAT GTG GCC GTG GAA CGT TAt CCg GCC TGG GGT


 


GAT ACC GTA GAA GTG GAG TGT TGG GTA GGC GCC TCC GGT AAC AAC GGT CGG CGT CAC GAC


 


TTC TTG GTG CGT GAC TGT AAA ACt GGc GAG ATC CTG ACC CGC TGT ACT TCC CTG AGC GTT


 


ATG ATG AAC ACC CGG ACC CGT CGC TTA TCC AAG ATT CCC GAA GAA GTT CGC GGG GAA ATT


 


GGt CCt GCT TTC ATT GAT AAC GTT GCT GTT AAG GAT GAG GAG ATT AAA AAG CCG CAA AAG


 


CTC AAT GAT TCT ACC GCC GAT TAC ATT CAA GGG GGT CTG ACT CCC CGT TGG AAT GAT CTG


 


GAT ATT AAT CAG CAT GTG AAT AAC ATC AAA TAT GTG GAT TGG ATT CTG GAG ACT GTG CCC


 


GAC TCT ATT TTC GAG TCC CAC CAC ATT agc AGT TTT ACC ATT GAA TAT CGT CGC GAA TGT


 


ACT ATG GAC AGT GTT TTG CAA TCC CTG ACC ACC GTC TCC GGC GGT TCC TCT GAA GCT GGC


 


CTG GTG TGC GAA CAC CTC TTG CAA CTC GAA GGC GGT AGT GAA GTg CTc CGt GCC AAG ACC


 


GAA TGG CGG CCC AAA TTG ACC GAC TCC TTT CGC GGG ATT TCT GTG ATT CCC GCC GAA TCC


 


TCC GTC TAA GATATCAT


 


EHC1


GAtaTC GTTCGTTAAT TTTTCCCA TCGCTTTTAG


 


TAGATGTAGGCAGATCCAACCATCGGTAAAGTTGATTAG


 


TGTGGCCCAG GCCCATCGCCGGCAGG GATTGGGAAA


 


GTATCACGAATTACACTGCCGTGAAAATTTAACGATATTTTGGACAG


 


GGGAAAGATT GGCGATCGCCGTTGTG GTTAAGCCAG


 


CTAAAAGGCCCACTCGTTAGGACACACGGTGTAAAAAAAA


 


ACAAAATATT TTTGCCCA TTTTTGCGGT


 


CAACTTTGACTGACCAGCTAATTTTGTACACGACTTAGGAGTT


 


TGTAATTTCG TCGAGTCCCA GCCACCCCCGACCC AAGTTTGCTT


 


GCTTTACAAAACTCTCATTAATCCTTAGACTAAGTTTA GAtaTC


 


EHC2


ATGATATC TGTAATTTCG TCGAGTCCCA GCCACCCCCGACCC AAGTTTGCTT


 


GCTTTACAAAACTCTCATTAATCCTTAGACTAAGTTTA


 


ACAAAATATT TTTGCCCA TTTTTGCGGT


 


CAACTTTGACTGACCAGCTAATTTTGTACACGACTTAGGAGTT


 


GGGAAAGATT GGCGATCGCCGTTGTG GTTAAGCCAG


 


CTAAAAGGCCCACTCGTTAGGACACACGGTGTAAAAAAAA


 


GTTCGTTAAT TTTTCCCA TCGCTTTTAG


 


TAGATGTAGGCAGATCCAACCATCGGTAAAGTTGATTAG


 


TGTGGCCCAG GCCCATCGCCGGCAGG GATTGGGAAA


 


GTATCACGAATTACACTGCCGTGAAAATTTAACGATATTTTGGACAG


 


AGCTGTTGACAATTAATCATCCGGCTCGTATAATTTTAAAGAGGAGAAACAA


 


Ptrc adc7421 Ptrc aar7421


gaGATATCGAGCTGTTGACAATTAATCATCCGGCTCGTATAATTTTAAAGAGGAGAAACAA


 


ATGTTCGGTCTGATCGGGCACCTCACCAATTTGTCCCACGCCCAACGGGTTGCCCGCGACTT


 


GGGCTACGACGAATACGCCTCCCACGATTTAGAATTTTGGTGCATGGCCCCCCCCCAAGCCG


 


TTGACGAAATCACTATTACTTCCGTGACCGGTCAGGTGATCCACGGCCAGTATGTAGAGTCCT


 


GTTTTTTACCCGAAATGCTCGCGCAAGGGCGGTTCAAGACTGCTATGCGCAAAATCCTGAACG


 


CCATGGCCCTGGTACAAAAACGGGGTATTGACATTACCGCTTTAGGGGGGTTCAGTAGCATCA


 


TTTTCGAGAATTTTTCCCTCGATAAATTGCTCAATGTGCGTGATATTACCCTCGACATCCAGC


 


GCTTCACCACCGGCAACACTCACACCGCGTATATTTTGTGTCAACAAGTGGAACAAGGTGCGG


 


TACGGTACGGTATTGATCCCGCCAAAGCCACCGTTGCCGTGGTCGGGGCCACCGGTGATATTG


 


GTTCCGCCGTATGCCGCTGGTTGACTGATCGGGCTGGGATCCACGAATTGTTGTTGGTGGCCC


 


GTGACGCTGAACGTCTCGACCGGCTCCAACAAGAACTCGGTACCGGTCGGATTCTCCCCGTGG


 


AGGAGGCCCTGCCCAAAGCGGATATTGTGGTATGGGTGGCTTCCATGAACCAGGGGATGGCTA


 


TCGACCCCGCGGGGCTGCGTACCCCCTGTTTGCTCATCGATGGTGGCTACCCCAAAAACATGG


 


CGGGCACCTTGCAACGGCCCGGCATTCACATTCTGGACGGGGGCATGGTTGAACACTCCTTGG


 


ACATCGACTGGCAGATTATGAGCTTCCTGAATGTGCCGAACCCCGCCCGGCAATTCTTCGCTT


 


GTTTTGCTGAAAGCATGCTGCTGGAATTCGAAGGTTTGCACTTCAACTTTTCCTGGGGTCGTA


 


ACCATATTACTGTAGAAAAGATGGCGCAAATTGGCTCCCTGAGCAAGAAACACGGCTTTCGCC


 


CTTTGTTGGAACCCTCCCAACGCTCCGGTGAACTGGTGCACGGTtaa


 


AGCTGTTGACAAcTgATCATaCGtCTCGTATAATTTTAAAGAGGAGAAACAA


 


ATGAATCGGACCGCTCCCTCCTCTGCCGCTTTGGACTACCGGTCTGATACCTA


 


TCGGGATGCCTATAGCCGCATTAACGCTATTGTCCTCGAAGGTGAACGGGAAG


 


CGCACGCGAATTATTTGACCTTGGCCGAAATGCTGCCCGACCATGCCGAAGCT


 


CTGAAAAAGTTGGCCGCTATGGAAAATCGCCACTTCAAAGGCTTCCAGTCCTG


 


CGCCCGTAATCTCGAAGTGACCCCCGATGATCCCTTCGCGCGTGCGTACTTCG


 


AGCAATTGGATGGCAACTTCCAACAGGCCGCTGCCGAAGGTGACTTGACCACTT


 


GTATGGTCATTCAAGCGCTCATTATTGAATGTTTTGCCATTGCCGCCTATAACG


 


TGTACATTCCTGTCGCCGACGCCTTCGCCCGCAAAGTGACCGAGGGTGTTGTCA


 


AAGACGAGTACACTCATTTAAACTTTGGCCAACAATGGCTGAAGGAACGTTTCG


 


TAACTGTGCGTGAAGGTATCGAGCGTGCCAATGCTCAAAACTTGCCCATTGTTT


 


GGCGCATGCTCAATGCTGTTGAAGCCGATACCGAAGTTTTGCAGATGGATAAGG


 


AAGCCATTGTCGAAGACTTCATGATTGCTTACGGTGAAGCCCTCGGTGATATTG


 


GGTTTAGCATGCGTGATGTGATGAAAATGTCCGCTCGTGGTTTGGCCAGTGCTCCCCGCCAAtaagatatc


 


PpsbA2 aar7942 Ptrc adc73012








CCATTGTCCCTGAAAATCAGTTGTGTCGCCCCTCTACACAGCCCAGAACTATGGT


 


AAAGGCGCACGAAAAACCGCCAGGTAAACTCTTCTCAACCCCCAAAACGCCCTCT


 


GTTTACCCATGGAAAAAACGACAATTACAAGAAAGTAAAACTTATGTCATCTATA


 














ATGaaaTTTGGTTTAATTGGTCATCTCACTAGTTTAGAGCAGGCCCGGGATGTTTC


 


CCGTCGGATGGGTTATGATGAGTACGCCGATCAGGGTTTGGAATTTTGGTCTTCCG


 


CTCCTCCCCAAATCGTTGATGAAATCACCGTTACTTCCGCCACCGGTAAGGTGATC


 


CACGGTCGTTACATTGAAAGTTGTTTCCTGCCCGAAATGTTGGCCGCTCGCCGGTT


 


TAAAACCGCCACCCGTAAAGTGTTGAACGCTATGAGCCACGCTCAGAAACACGGCA


 


TTGATATCTCCGCCCTCGGTGGTTTTACCAGTATCATTTTTGAAAACTTTGATCTC


 


GCTAGTCTCCGTCAAGTGCGGGACACTACCCTGGAGTTTGAACGGTTCACTACTGG


 


CAACACCCATACCGCCTACGTTATCTGTCGTCAAGTTGAGGCCGCTGCGAAAACCC


 


TGGGGATCGATATTACCCAGGCTACCGTTGCCGTGGTAGGCGCCACCGGGGATATC


 


GGTAGTGCTGTTTGCCGGTGGTTAGATCTGAAATTGGGTGTGGGGGATCTCATTT


 


TGACTGCTCGGAACCAGGAACGCCTGGATAATCTGCAAGCTGAATTGGGTCGCGG


 


CAAGATCCTCCCCTTAGAAGCCGCCCTCCCCGAAGCCGATTTCATTGTGTGGGTC


 


GCCTCTATGCCCCAAGGTGTTGTTATTGACCCCGCCACTCTGAAACAGCCTTGTG


 


TTTTGATCGATGGGGGTTACCCTAAAAACCTGGGCTCCAAAGTACAGGGTGAAGG


 


CATCTACGTGCTCAATGGGGGCGTCGTGGAACACTGTTTTGATATCGACTGGCAA


 


ATTATGAGCGCTGCCGAAATGGCTCGCCCCGAGCGTCAAATGTTTGCCTGTTTTG


 


CCGAGGCCATGTTGTTGGAATTCGAAGGGTGGCACACCAACTTCTCCTGGGGTCG


 


CAACCAAATTACCATTGAAAAGATGGAAGCGATCGGCGAAGCCTCTGTGCGTCAT


 


GGTTTTCAGCCCTTGGCTTTAGCCATCtaa


 


GAGCTGTTGACAATTAATCATCCGGCTCGTATAATTTTAAAGAGGAGAAACAA


 


ATGAAACAGCAATTGACCGACCAAAGTAAAGAGCTCGATTTTAAGTCCGAAACCTA


 


TAAAGACGCCTACAGTCGGATCAATGCCATTGTGATTGAAGGTGAACAGGAAGCGC


 


ATGAAAATTACATCACTTTGGCCCAACTGCTCCCGGAGTCCCACGACGAACTGATC


 


CGCTTGTCCAAGATGGAATCCCGGCATAAGAAAGGCTTTGAAGCGTGCGGCCGTAA


 


CCTGGCGGTAACCCCCGACTTACAGTTTGCCAAAGAATTTTTCAGCGGTTTGCATC


 


AAAATTTTCAGACCGCCGCTGCCGAAGGTAAAGTGGTGACTTGCCTGCTCATTCAG


 


TCTCTCATTATCGAGTGCTTCGCGATCGCTGCCTATAACATTTACATCCCCGTTGC


 


TGATGATTTTGCCCGCAAAATCACTGAAGGCGTAGTAAAAGAAGAATACTCCCATT


 


TGAATTTCGGCGAAGTGTGGCTGAAAGAGCATTTCGCTGAATCCAAAGCTGAACTC


 


GAACTGGCCAACCGCCAAAATTTGCCCATTGTTTGGAAAATGCTCAACCAGGTGGA


 


GGGGGATGCCCACACTATGGCCATGGAAAAAGACGCCTTGGTTGAAGATTTTATGA


 


TTCAATACGGTGAAGCCCTCTCCAACATTGGCTTCTCTACCCGGGACATTATGCGC


 


TTGAGTGCCTACGGGTTGATCGGTGCTTAAgatatcag


 


Ptrc adc1986 Ptrc aar1986


gaGATATCGAGCTGTTGACAATTAATCATCCGGCTCGTATAATTTTAAAGAGGAGAAACAA


 


ATGTTTGGTTTGATTGGGCACTCTACTAGTTTCGAAGACGCCAAACGCAAGGCTT


 


CCTTGTTGGGTTTCGATCACATCGCTGATGGCGACTTGGACGTCTGGTGTACCGC


 


CCCCCCCCAGCTGGTAGAAAATGTTGAAGTGAAGAGCGCTAT


 


TGGCATTAGCATCGAAGGTAGTTACATTGATAGCTGTTTTGTT


 


CCCGAAATGTTAAGCCGCTTCAAGACCGCTCGCCGGAAAGTGC


 


TGAATGCTATGGAGTTGGCCCAGAAAAAAGGTATCAATATCAC


 


CGCCTTGGGTGGTTTCACCTCCATTATCTTCGAAAATTTTAAC


 


CTGTTGCAGCACAAACAAATCCGGAACACCTCCCTGGAATGGG


 


AACGTTTTACCACCGGTAACACCCACACCGCGTGGGTGATTTG


 


TCGGCAACTGGAAATGAATGCCCCCAAAATTGGGATTGACTTG


 


AAATCCGCCACCGTGGCGGTGGTGGGCGCCACCGGTGACATTG


 


GCAGCGCCGTTTGTCGCTGGCTGATTAACAAAACCGGCATCGG


 


TGAGTTGTTGTTGGTAGCCCGGCAGAAGGAACCCTTAGATTCC


 


TTACAAAAAGAACTGGACGGGGGCACCATCAAAAATCTGGACG


 


AAGCCCTCCCCGAAGCGGACATTGTGGTGTGGGTCGCCAGTAT


 


GCCCAAGACCATGGAAATCGATGCGAATAACCTGAAACAGCCG


 


TGTTTGATGATTGATGGCGGTTACCCCAAAAACCTGGACGAGA


 


AATTTCAAGGCAACAACATCCATGTTGTAAAAGGTGGTATCGT


 


GCGCTTCTTCAATGACATTGGTTGGAACATGATGGAACTGGCC


 


GAAATGCAGAACCCCCAACGGGAAATGTTTGCGTGCTTCGCCG


 


AAGCTATGATCTTAGAGTTCGAAAAATGTCATACCAACTTCTC


 


TTGGGGTCGGAATAATATTAGTCTGGAAAAGATGGAGTTCATC


 


GGTGCCGCCAGCGTTAAACACGGCTTTTCCGCCATCGGCTTGGA


 


CAAGCACCCCAAAGTGTTAGCCGTCTAA


 


GAaCTGTTGACAATTgATCATCtGaCgCGTATAATTTTAAAGAGGAGAAACAA


 


ATGCAAACCCTGGAAAGCAATAAAAAAACCAACCTCGAAAACAGCATTGATCT


 


GCCCGATTTCACCACCGATAGTTATAAAGATGCCTATAGCCGGATCAACGCCA


 


TCGTGATTGAAGGGGAACAGGAAGCGCACGATAATTATATTTCCTTGGCTACC


 


CTGATCCCCAATGAACTGGAAGAATTAACCAAACTCGCCAAAATGGAACTGAA


 


ACACAAGCGGGGGTTCACCGCCTGCGGGCGCAATCTCGGCGTTCAAGCCGATA


 


TGATCTTCGCCAAAGAATTTTTTAGCAAATTGCACGGTAACTTTCAGGTGGCT


 


TTGAGCAATGGTAAAACCACCACCTGTCTCCTGATTCAGGCGATTCTGATTGA


 


AGCGTTCGCCATTTCCGCTTACCACGTTTATATTCGGGTGGCTGATCCCTTCG


 


CCAAGAAAATCACCCAAGGTGTCGTGAAAGACGAATACTTACACTTGAATTAT


 


GGGCAAGAATGGCTCAAAGAAAATCTCGCCACCTGCAAAGATGAACTCATGGA


 


AGCTAACAAAGTGAATTTGCCCTTAATTAAGAAAATGTTGGATCAAGTTTCCG


 


AGGACGCGAGCGTACTGGCCATGGACCGTGAAGAACTGATGGAAGAATTCATG


 


ATCGCGTACCAGGACACCCTCTTGGAAATCGGCTTGGATAACCGCGAAATCG


 


CTCGGATGGCGATGGCGGCTATCGTGTAAGATATCag


 


PpsbA2 7942orf_1593 Ptrc 7942orf_1594


AGatATcGCGTGCAAGGCCCAGTGATCAATTTCATTATTTTTCATTATTTCATCTCCATTGT


 


CCCTGAAAATCAGTTGTGTCGCCCCTCTACACAGCCCAGAACTATGGTAAAGGCGCACGAAA


 


AACCGCCAGGTAAACTCTTCTCAACCCCCAAAACGCCCTCTGTTTACCCATGGAAAAAACGA


 


CAATTACAAGAAAGTAAAACTTATGTCATCTATAAGCTTCGTGTATATTAACTTCCTGTTAC


 


AAAGCTTTACAAAACTCTCATTAATCCTTTAGACTAAGTTTAGTCAGTTCCAATCTGAACgAAGGAATTATAACCAA


 


ATGCCGCAGCTTGAAGCCAGCCTTGAACTGGACTTTCAAAGCGAGTCCTACAAAGACGCTTAC


 


AGCCGCATCAACGCGATCGTGATTGAAGGCGAACAAGAGGCGTTCGACAACTACAATCGCCTT


 


GCTGAGATGCTGCCCGACCAGCGGGATGAGCTTCACAAGCTAGCCAAGATGGAACAGCGCCAC


 


ATGAAAGGCTTTATGGCCTGTGGCAAAAATCTCTCCGTCACTCCTGACATGGGTTTTGCCCAG


 


AAATTTTTCGAGCGCTTGCACGAGAACTTCAAAGCGGCGGCTGCGGAAGGCAAGGTCGTCACC


 


TGCCTACTGATTCAATCGCTAATCATCGAGTGCTTTGCGATCGCGGCTTACAACATCTACATC


 


CCAGTGGCGGATGCTTTTGCCCGCAAAATCACGGAGGGGGTCGTGCGCGACGAATACCTGCAC


 


CGCAACTTCGGTGAAGAGTGGCTGAAGGCGAATTTTGATGCTTCCAAAGCCGAACTGGAAGAA


 


GCCAATCGTCAGAACCTGCCCTTGGTTTGGCTAATGCTCAACGAAGTGGCCGATGATGCTCGC


 


GAACTCGGGATGGAGCGTGAGTCGCTCGTCGAGGACTTTATGATTGCCTACGGTGAAGCTCTG


 


GAAAACATCGGCTTCACAACGCGCGAAATCATGCGTATGTCCGCCTATGGCCTTGCGGCCGTT


 


TGATCCAGGAAATCTGAATGTTCGGTCTTATCGGTCATCTCACCAGTTTGGAGCAGGCCCGCG


 


ACGTTTCTCGCAGGATGGGCTACGACGAATACGCCGATCAAGGATTGGAGTTTTGGAGTAGCG


 


CTCCTCCTCAAATCGTTGATGAAATC


 


ACAGTCACCAGTGCCACAGGCAAGGTGATTCACGGTCGCTACATCGAATCGTGTTTCTTGCCG


 


GAAATGCTGGCGGCGCGCCGCTTCAAAACAGCCACGCGCAAAGTTCTCAATGCCATGTCCCAT


 


GCCCAAAAACACGGCATCGACATCTCGGCCTTGGGGGGCTTTACCTCGATTATTTTCGAGAAT


 


TTCGATTTGGCCAGTTTGCGGCAAGTGCGCGACACTACCTTGGAGTTTGAACGGTTCACCACC


 


GGCAATACTCACACGGCCTACGTAATCTGTAGACAGGTGGAAGCCGCTGCTAAAACGCTGGGC


 


ATCGACATTACCCAAGCGACAGTAGCGGTTGTCGGCGCGACTGGCGATATCGGTAGCGCTGTC


 


TGCCGCTGGCTCGACCTCAAACTGGGTGTCGGTGATTTGATCCTGACGGCGCGCAATCAGGAG


 


CGTTTGGATAACCTGCAGGCTGAACTCGGCCGGGGCAAGATTCTGCCCTTGGAAGCCGCTCTG


 


CCGGAAGCTGACTTTATCGTGTGGGTCGCCAGTATGCCTCAGGGCGTAGTGATCGACCCAGCA


 


ACCCTGAAGCAACCCTGCGTCCTAATCGACGGGGGCTACCCCAAAAACTTGGGCAGCAAAGTC


 


CAAGGTGAGGGCATCTATGTCCTCAATGGCGGGGTAGTTGAACATTGCTTCGACATCGACTGG


 


CAGATCATGTCCGCTGCAGAGATGGCGCGGCCCGAGCGCCAGATGTTTGCCTGCTTTGCCGAG


 


GCGATGCTCTTGGAATTTGAAGGCTGGCATACTAACTTCTCCTGGGGCCGCAACCAAATCACG


 


ATCGAGAAGATGGAAGCGATCGGTGAGGCATCGGTGCGCCACGGCTTCCAACCCTTGGCATTGGCAATTTGA


 


PpsbA2 aarBP-1 Ptrc adcBP-1








CTGAAAATCAGTTGTGTCGCCCCTCTACACAGCCCAGAACTATGGTAAAGGCGCACGAAAAACC


 


GCCAGGTAAACTCTTCTCAACCCCCAAAACGCCCTCTGTTTACCCATGGAAAAAACGACAATTA


 








TTAATCATCCGGCTCGTATAATTTTAAAGAGGAGAAACAA


 


ATGTTCGGTTTAATCGGCCATCTGACTAGCCTGGAGCATGCGCAGGCCGTAGCCCACCA


 


ATTAGGTTATCCCGAATACGCCGACCAAGGTCTGGAGTTCTGGTGTATGGCGCCCCCCC


 


AAATTGTCGATGAAATTACTGTAACCAGCGTCACCGGCAAAACCATTTACGGCAAATAC


 


GTGGAATCTTGTTTTCTCCCCGAAATGTTGGCCAACCAACGCGTTAAGGCTGCTACCCG


 


GAAAGTTATCAATGCGATGGCGCATGCTCAGAAACATAACATTGATATTACCGCTTTGG


 


GCGGCTTTAGTTCCATCATCTTCGAAAATTTTGATTTGGAGAAGATGAGCCATATTCGT


 


AATATTGAATTGGATTTTCGGCGGTTTACCACCGGTAACACCCACACCGCTTATATTAT


 


TTGCCAACAGATCGAACAAGCGGCTCCCCAAGTGGGCATCGATCTGCGGCAAGCTACCG


 


TTGCCGTGTGCGGTGCTACCGGTGACATTGGGTCTGCGGTATGTCGTTGGCTGAACACC


 


TGCCTCGATGTGCAAGATCTGTTGTTGGTGGCCCGTAATCGTGATCGGCTCTTAGAGTT


 


GCAAGCCGAACTGGGCCGTGGTAAAATTTTAGATTTGATGGAGGCCTTGCCCTTGGCTG


 


ATATTGTGGTATGGGTTGCCAGTATGCCTAAGGGCGTGGAATTGTCCATCGAACAATTG


 


AAACGCCCGAGTCTGATGATTGATGGTGGTTACCCCAAAAACATGGCCACCAAGATTCA


 


ACATCCGCAAATCCATGTTTTGAACGGCGGCATTGTTGAACACGCCTTAGATATTGATT


 


GGAAAATTATGGAAATTGTGAATATGGACGTCCCCTCCCGCCAGATGTTTGCTTGTTTT


 


GCTGAAGCGATGTTGCTGGAATTTGAAGGCTGGCACACCAACTTTTCCTGGGGTCGGAA


 


CCAAATCACCGTGGAAAAGATGCAACAAATTGGGGAAGTATCCCGTAAACACGGTTTCC


 


AACCCTTGTTATTAAACCCCCAATAA


 


GAGCTGTTGACAATTgATCATCaGGaTCGTATAATTTTAAAGAGGAGAAACA


 


ATGACCACCGCCACTGCCACCCCCGTTTTAGACTATCATTCCGATCGGTACAAAGACGCCTACAGTC


 


GCATCAACGCTATTGTCATTGAAGGCGAACAAGAGGCTCACGACAACTATATTGACTTGGCCAAATT


 


GTTGCCCCAACACCAAGAAGAATTAACCCGTTTGGCCAAAATGGAAGCCCGGCATAAGAAGGGTTTC


 


GAAGCTTGCGGGCGCAATTTGTCTGTTACCCCCGATATGGAATTCGCCAAAGCTTTCTTCGAAAAGC


 


TCCGTGCGAACTTCCAACGTGCTCTGGCCGAAGGTAAAACCGCCACCTGCCTCCTGATCCAAGCCCT


 


GATCATCGAATCCTTCGCCATCGCCGCGTACAATATCTACATTCCCATGGCCGACCCCTTTGCCCGT


 


AAAATTACCGAGTCCGTGGTCAAGGATGAATACTCCCATTTAAACTTCGGCGAAATCTGGTTGAAAG


 


AACACTTCGAATCCGTGAAAGGGGAACTGGAAGAAGCCAATCGGGCTAATCTCCCGCTGGTCTGGAA


 


GATGTTGAACCAGGTTGAGGCCGACGCGAAAGTATTAGGGATGGAAAAGGACGCCTTAGTCGAAGAC


 


TTTATGATTCAATACTCTGGTGCCTTGGAAAACATTGGCTTTACCACCCGCGAAATCATGAAGATGT


 


CTGTTTATGGGCTGACTGGTGCCtaaGATATCAG









Example 21
Growth of an SD Culture Started from a Single-Cell Descended Colony
The following example describes how to grow a mutant 6803 culture started from a single cell descended colony.
Part A—Starting from Plates.


    
    
        1. From a single colony on a BG-11 plate use a sterile, 0.7 mm needle to scrape a 7 mm2 patch onto a fresh BG-11 plate. Repeat this until multiple patches have been scraped onto the same plate. These patches can be considered as cells derived from an individual cell, which will be used to inoculate cultures for individual experiments.
        2. Seal plates with parafilm and allow to grow at 31° C. with light at 50 mol photons m−2 sec−1 (Curtiss lab incubator conditions with 3 light bulbs on, the real light intensity will be measured by Michael) with plates face up for at least 2 days, but no more than two weeks.
        3. Using a 2 mm loop, resuspend cells from a single cell derived patch and inoculate the cells using a pipette in 1 ml of fresh BG-11 to an O.D.730 of at least 0.05-0.1 (an O.D. less than 0.05 will result in cell lysis and long lag phase). Vortex the tube until a homogenous solution is achieved (5-15 seconds). Vortexing time will vary depending on the adhesive qualities of each strain.
        4. Grow cells at 31° C. with light at 50 mol photons m−2 sec−1 for 2 days. This culture can be expanded for large-scale experiments as follows in the downstairs Conviron chamber (140 mol photons m−2 sec−1, 30° C.): Dilute the culture into a larger volume down to an O.D.730 of 0.05 or greater. For cultures less than 25 ml place on a shaker under normal growth conditions and agitate at a rate of 200-300 rpm. For cultures greater than 25 ml, bubbling of air is required until the culture reaches a density of at least 1×107 CFU/ml. At this density, air can be exchanged for 1% CO2.
        5. Grow cells at 30° C. with light at 140 mmol photons m−2 sec−1 (basement Conviron conditions) to the desired O.D.730 (for example, OD 0.2-0.4 for transformation of exogenous DNA).

Part B—Starting from Frozen Stock.

        1. Spread frozen stock on a BG-11 agar plate (50 μg/ml Km BG-11 if with KmR/sacB), and grow for 3-7 days.
        2. Using sterile technique, scrape at least 5*106 cells into 1 ml BG-11 media (OD730nm above 0.03). For slow growth strains, scrape at least 2*107 cells (OD730nm above 0.12).
        3. Proceed with step A-4 above. If cell density is high enough, the cells can be grown in 1 ml BG-11 for one day.
    
    


Example 22
Growth and Cell Damage Measurements
Bacterial growth in liquid culture was monitored spectrophotometrically or by flow cytometry and/or by plating. The relationship between 6803 culture optical density and cell density is used for conversion of optical density into cell density during growth. Staining with 5 μM SYTOX Green nucleic acid stain (Invitrogen Molecular Probes, Inc. OR, USA) for 5 min was used to detect damaged cells. Cells were observed under an Axioskop40 fluorescence microscope (Zeiss, Germany). Green cells are sorted in a FACSAria flow cytometer (BD Biosciences, CA, USA) and counted as damaged.
Example 23
Lipids Separation and Measurement
The FFAs in the medium are quantitatively separated from the culture medium by hexane, which is unable to release FFAs and other lipids from intact 6803 cells. One hundred mL of culture is acidified by 2 mL H3PO4 (1M) containing 1 g NaCl, and extracted with 100 mL hexane. For the unsecreted intracellular FFAs, the cells are extracted by the Folch method for total lipids. The FFA samples were analyzed by gas chromatography (GC) analysis.
GC was performed to determine the FFA amount in the hexane extracts. After 6000 g×10 min centrifuge, 5 ml hexane was taken out from the upper organic layer, filled in a glass tube (13×100 mm, Fisherbrand), dried on a nitrogen evaporator (N-EVAP111, Organomation Associates Inc.). The dried samples were then re-dissolved by a known volume of hexane and analyzed by gas chromatography (Shimadzu GC 2010) equipped with a Supelco Nukol capillary column (30 m×0.53 mm×0.50 μm) and flame ionization detector (FID).
For the unsecreted intracellular FFAs, the cells are collected by centrifugation, and extracted by the Folch method for total lipids. The intracellular unsecreted FFA were extracted from the cell pellet after hexane extraction, and calculated with the final cell density.
GC operating conditions were as follows: split ratio 1:5; inject volume 1 μL; helium carrier gas with constant flow rate 30 ml/min; H2 40 ml/min, Air 400 ml/min, make up gas (helium) 5 ml/min; injector and detector temperature 250° C.; and oven temperature started at 150° C. and increased at a rate of 10° C./min to 220° C. and held for 10 min. Each FFA compound was identified by comparing its retention time with that of standard (Sigma, St. Louis, Mo.). Compound concentrations in samples were quantified based on the area under the chromatogram peak in comparison with the standards.
Example 24
Transmission Electron Microscopy Analysis
The triglyceride inclusion droplets in cyanobacterial cells were visualized by transmission electron microscopy (TEM). A specific cell fixation procedure for Synechocystis sp. PCC 6803 and mutant strains is shown below. All steps are at room temperature unless noted. Initial steps may be done in Eppendorf tubes. Typically, the protocol proceeds through the following steps:

    
    
        1. Primary fix, for the fixation of proteins, cells in suspension with 2% glutaraldehyde in 50 mM KH2PO4—K2HPO4 buffer, pH 6.8 for 2 hours or overnight at 4° C. Wash fixed cells, pellet cells, decant fixative, resuspend cells in approx 1 ml of the same buffer, invert tube for a few minutes, and wash 3 times.
        2. Solidify cells in agarose, pellet and decant wash buffer. Resuspend in approx 50-100 μl of buffer. Pipet cells from tube and put on a small piece of parafilm. Add equal vol of 2% agarose (melt, and then cool to near-solidification point). Pipet cells-agarose mixtures. Cut into 4-5 small chunks with lancet or shaver and transfer to a glass vial, wash with buffer, allow sitting for 15 min. Repeat wash two times.
        3. Secondary fix, for the lipid fixation, in 1% osmium tetroxide in KH2PO4—K2HPO4 buffer for 2 h. Remove secondary fix solution. Wash 3 times with buffer, then 3 times with de-ionized H2O, 15 min per step.
        4. Uranyl block stain with 2% aqueous uranyl acetate for 2 hours at room temperature or overnight at 4° C. Wash 3 times with H2O, 15 min each. Remove uranyl acetate. Dehydrate samples through the following ethanol series, 5-10 min each step: 20%, 50%, 75%, 95%, and 100% EtOH 3 times, then in 1:1 EtOH:acetone 2 times. Lead block stain. Incubate 1 h at room temperature in a saturated solution of lead acetate in 1:1 EtOH:acetone. Wash samples 2 times for 15 min in 1:1 EtOH:acetone, then 2 times 15 min in acetone.
        5. Infiltrate with increasing epoxy resin (Spurr's resin, firm mixture) series, 25% increments, using 100% resin 3 times. Place vials on rotary wheel during all these steps. Specifically, 25%, 50% steps minimum of 4 hours; 75% and 100% steps for a minimum of 6 hours.
        6. Polymerization. After 3rd 100% resin step, embed cell-chunks in flat molds using fresh resin. Put in oven at 60° C. for 24-36 hours. The polymerized modes need to be trimmed first and cut into sections in a microtome. Sections on grids would be post stained if necessary, and then can be checked under TE
    
    


The transmission electronic microscopy (TEM) images of SD201 and SD202 (FIG. 26) showing that the TAG-producing Synechocystis strains accumulate significant triglyceride droplets.
Example 25
Optimizing the Codons in Non-6803 Genes for Optimal Expression in 6803
The expression levels of a foreign gene can be optimized for a host cell by changing the gene's low frequency use codons into high frequency use codons. Table 11 shows the codons usage bias for the highly expressed genes in 6803.
Based on the codon usage frequencies, the low frequency use codons were replaced. Codons for the non-6803 genes were also changed to adjust their GC content to around 48%, which is the general GC content for 6803 genes.
Finally, according to the mRNA structures predicted by RNAfold WebServer (rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi), the mRNA secondary structures of the non-6803 genes were optimized to interrupt the stable stem-loop structures by changing the codons, which may impede the translation process of ribosome. After the transcription of a foreign gene in a bacterium, the mRNA might form stem-loop structures, which are readily cleaved by RNase, resulting in degradation of the mRNA.
As stated above, the codon-optimized non-6803 genes were synthesized and cloned into pUC57 by GenScript Corp (NJ, USA). The redesigned and synthesized DNA segments are listed in Table 10.







TABLE 11







Codon usage frequencies in the Top-40 


highly expressed 6803 genes.













Relative %

% within


Codon
Amino Acid
within AA
Codon Count
Total














GCA
A
5.60%
107
0.52%


 


GCC
A
53.30%
1024
5.01%


 


GCG
A
13.10%
252
1.23%


 


GCT
A
28.00%
538
2.63%


 


TGC
C
41.20%
61
0.30%


 


TGT
C
58.80%
87
0.43%


 


GAC
D
49.50%
555
2.72%


 


GAT
D
50.50%
566
2.77%


 


GAA
E
79.60%
1080
5.29%


 


GAG
E
20.40%
276
1.35%


 


TTC
F
52.80%
443
2.17%


 


TTT
F
47.20%
396
1.94%


 


GGA
G
8.60%
151
0.74%


 


GGC
G
31.80%
561
2.75%


 


GGG
G
15.90%
280
1.37%


 


GGT
G
43.80%
773
3.78%


 


CAC
H
68.70%
276
1.35%


 


CAT
H
31.30%
126
0.62%


 


ATA
I
0.60%
8
0.04%


 


ATC
I
42.40%
566
2.77%


 


ATT
I
57.00%
760
3.72%


 


AAA
K
68.90%
713
3.49%


 


AAG
K
31.10%
322
1.58%


 


CTA
L
9.30%
175
0.86%


 


CTC
L
20.50%
386
1.89%


 


CTG
L
23.30%
439
2.15%


 


CTT
L
7.80%
147
0.72%


 


TTA
L
10.50%
197
0.96%


 


TTG
L
28.60%
539
2.64%


 


ATG
M
100.00%
478
2.34%


 


AAC
N
60.10%
475
2.33%


 


AAT
N
39.90%
315
1.54%


 


CCA
P
6.00%
57
0.28%


 


CCC
P
64.10%
607
2.97%


 


CCG
P
11.60%
110
0.54%


 


CCT
P
18.30%
173
0.85%


 


CAA
Q
62.40%
469
2.30%


 


CAG
Q
37.60%
283
1.39%


 


AGA
R
1.90%
20
0.10%


 


AGG
R
2.80%
29
0.14%


 


CGA
R
4.20%
44
0.22%


 


CGC
R
28.00%
294
1.44%


 


CGG
R
36.70%
385
1.89%


 


CGT
R
26.50%
278
1.36%


 


AGC
S
20.70%
224
1.10%


 


AGT
S
13.20%
143
0.70%


 


TCA
S
1.90%
21
0.10%


 


TCC
S
45.30%
491
2.40%


 


TCG
S
4.80%
52
0.25%


 


TCT
S
14.10%
153
0.75%


 


ACA
T
4.30%
48
0.24%


 


ACC
T
69.80%
776
3.80%


 


ACG
T
8.90%
99
0.48%


 


ACT
T
17.00%
189
0.93%


 


GTA
V
17.60%
271
1.33%


 


GTC
V
17.20%
264
1.29%


 


GTG
V
39.50%
608
2.98%


 


GTT
V
25.70%
395
1.93%


 


TGG
W
100.00%
252
1.23%


 


TAC
Y
61.40%
355
1.74%


 


TAT
Y
38.60%
223
1.09%


 


TAA
*
52.60%
20
0.10%


 


TAG
*
47.40%
18
0.09%


 


TGA
*
0.00%
0
0.00%

## Claims

1. A cyanobacterium, wherein the cyanobacterium:
(a) expresses at least one nucleic acid encoding an acyl carrier protein (ACP) thioesterase (TE);
(b) overexpresses one or more nucleic acids encoding an acyl-CoA ligase (ACL); and
(c) inducibly expresses at least one nucleic acid encoding a neutral lipid synthase,
such that the cyanobacterium is capable of synthesizing fatty acyl methyl esters (FAME) or fatty acyl ethyl esters (FAEE) in a culture upon addition of short alcohols to the culture.

2. The cyanobacterium of claim 1, wherein the cyanobacterium further comprises a mutation that disrupts a native functional lipase that catalyzes the hydrolysis of a neutral lipid.

3. The cyanobacterium of claim 2, wherein the lipase is fipA.

4. The cyanobacterium of claim 1, further comprising an inducible promoter operably-linked to a nucleic acid encoding at least one protein capable of hydrolyzing the lipid membranes of the bacterium and at least one endolysin protein.

5. The cyanobacterium of claim 4, wherein the inducible promoter is induced by the lack of CO2.

6. The cyanobacterium of claim 4, wherein the at least one protein capable of hydrolyzing the lipid membranes is selected from the group consisting of galactolipase, phospholipase B, and a lipase.

7. The cyanobacterium of claim 1, further comprising
(a) a first nucleic acid, wherein the first nucleic acid comprises a first inducible promoter operably-linked to a nucleic acid encoding at least one protein capable of hydrolyzing the lipid membranes of the bacterium; and
(b) a second nucleic acid, wherein the second nucleic acid comprises a second promoter operably-linked to a nucleic acid encoding at least one endolysin protein.

8. The cyanobacterium of claim 1, wherein:
(a) the at least on nucleic acid encoding an ACP TE is selected from the group consisting of tesA and fatB;
(b) the one or more nucleic acids encoding an ACL nucleic acid is selected from the group consisting of fadD and faa2; and
(c) the at least one nucleic acid encoding a neutral lipid synthase is selected from the group consisting of atfA and a homolog thereof.

9. The cyanobacterium of claim 8, wherein:
(a) the at least on nucleic acid encoding an ACP TE is tesA operably-linked to a constitutive promoter;
(b) the one or more nucleic acids encoding an ACL nucleic acid is fadD fadA operably-linked to a constitutive promoter; and
(c) the at least one nucleic acid encoding a neutral lipid synthase is atfA operably-linked to an inducible promoter.

10. The cyanobacterium of claim 9, wherein the tesA, fadD and/or atfA nucleic acid is codon-optimized.

11. The cyanobacterium of claim 1, wherein the short alcohol is selected from the group consisting of methanol and ethanol.

12. The cyanobacterium of claim 1, further comprising exogenous expression of pyruvate decarboxylase and alcohol dehydrogenase such that the cyanobacterium is capable of synthesizing fatty acyl ethyl esters (FAEE) in a culture without the addition of ethanol to the culture.

13. A method for releasing neutral lipids from a cyanobacterium, the method comprising
(a) altering the cyanobacterium, wherein the cyanobacterium (i) expresses at least one nucleic acid encoding an acyl carrier protein (ACP) thioesterase (TE); (ii) overexpresses one or more nucleic acids encoding an acyl-CoA ligase (ACL); and (iii) inducibly expresses at least one nucleic acid encoding a neutral lipid synthase, such that the cyanobacterium is capable of synthesizing fatty acyl methyl esters (FAME) or fatty acyl ethyl esters (FAEE) in a culture upon addition of short alcohols to the culture;
(b) introducing into the bacterium a nucleic acid comprising an inducible promoter operably-linked to a nucleic acid, the nucleic acid encoding at least one protein capable of hydrolyzing the lipid membranes of the bacterium and at least one endolysin protein; and
(c) inducing the promoter to express both the protein capable of hydrolyzing the lipid membranes and the endolysin, wherein the protein capable of hydrolyzing the lipid membranes frees fatty acids from the lipid membranes of the cyanobacterium and allows the endolysin to degrade the peptidoglcan layer of the cell wall.

14. The method of claim 13, wherein the neutral lipid synthase is a triglyceride synthase.

15. The method of claim 13, wherein the cyanobacterium comprises a nucleic acid encoding a lipid body protein.

16. The method of claim 13, wherein the lipid body protein is a phasing protein.

17. The method of claim 13, wherein the cyanobacterium further comprises a mutation that disrupts a native functional lipase that catalyzes the hydrolysis of a neutral lipid.

18. The method of claim 13, wherein the inducible promoter is induced by the lack of CO2.