# Patent

## Title
Sphingomonas strains producing greatly increased yield of PHB-deficient sphingan (diutan)

## Abstract

PHB-deficient Sphingomonas strains having improved sphingan yield are provided. Certain of the Sphingomonas strains are diutan-producing strains that exhibit a dramatic improvement in productivity and yield due to a combination of certain genetic modifications that affect PHB and sphingan synthesis. Moreover, the sphingans produced from such strains have superior characteristics including improved filterability, clarity, and improved rheology-modifying characteristics. The sphingans provided are, thus, highly desirable in a variety of commercial and industrial uses, including personal care items, cement applications, and oilfield applications.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application is a divisional application of U.S. application Ser. No. 12/533,649 filed Jul. 31, 2009 entitled “Sphingomonas Strains Producing Greatly Increased Yield of PHB-Deficient Sphingan (Diutan),” which application is related to U.S. application Ser. No. 11/264,268 entitled “High Viscosity Diutan Gums,” filed Nov. 1, 2005, now pending, and U.S. application Ser. No. 11/292,366 entitled “Mutant bacterial strains of the genus Sphingomonas deficient in production of polyhydroxybutyrate and a process of clarification of sphingans and compositions thereof,” filed Dec. 2, 2005, now pending, which is a divisional of U.S. application Ser. No. 09/798,642, filed Mar. 2, 2001, now pending, which claims the benefit of provisional application U.S. Application No. 60/186,433, filed Mar. 2, 2000, which are hereby incorporated by reference in their entireties to the extent that they are not inconsistent with the disclosure herein.


The sequence listing in the file named “68492o705000.txt” having a size of 179,295 bytes that was created Jul. 31, 2009 is hereby incorporated by reference in its entirety.
BACKGROUND
1. Field of the Art
This application generally relates to the construction of PHB-deficient Sphingomonas strains that produce high yields of diutan with improved filterability. In another aspect, this application relates to diutan produced from PHB-deficient Sphingomonas strains that produce high yields of diutan with improved filterability.
2. Description of Related Art
A number of bacteria of the genus Sphingomonas produce polysaccharides called sphingans that have related structures with a generally conserved tetrasaccharide backbone structure and different side chains (ref. no. 1, 6, 7, 8, 10). The sphingans gellan, welan, rhamsan and diutan are produced commercially for use in food, oilfield or personal care applications. The value of sphingan polysaccharides lies in their abilities to modify the rheology of aqueous solutions, i.e., to thicken liquids, suspend solids, stabilize emulsions, or form gels and films.
Sphingans are structurally related to one another, but are not identical. Common members of the genus Sphingomonas and the sphingans they produce include Sphingomonas elodea ATCC 31461, which produces gellan (S-60); Sphingomonas sp. ATCC 31555, which produces welan (S-130); Sphingomonas sp. ATCC 31961, which produces rhamsan (S-194); Sphingomonas sp. ATCC 53159, which produces diutan (S-657); Sphingomonas sp. ATCC 31554, which produces an as yet unnamed polysaccharide (S-88); Sphingomonas sp. ATCC 31853, which produces an as yet unnamed polysaccharide (S-198); Sphingomonas sp. ATCC 21423, which produces an as yet unnamed polysaccharide (S-7); Sphingomonas sp. ATCC 53272, which produces an as yet unnamed polysaccharide (NW-11); Sphingomonas sp. FERM-BP2015 (previously Alcaligenes latus B-16), which produces alcalan (Biopolymer B-16) and the like. A description of the Sphingomonads and the polysaccharides they produce can be found, for example, in U.S. Pat. Nos. 4,377,636; 4,326,053; 4,326,052 and 4,385,123 (for ATCC 31461 and its S-60 polysaccharide); in U.S. Pat. No. 4,342,866 (for ATCC 31555 and S-130); in U.S. Pat. No. 4,401,760 (for ATCC 31961 and S-194); in U.S. Pat. No. 5,175,278 (for ATCC 53159 and S-657); in U.S. Pat. Nos. 4,331,440 and 4,535,153 (for ATCC 31554 and S-88); in U.S. Pat. No. 4,529,797 (for ATCC 31853 and S-198); in U.S. Pat. No. 3,960,832 (for ATCC 21423 and S-7); in U.S. Pat. No. 4,874,044 (for ATCC 53272 and NW-11); in U.S. Pat. No. 5,175,279 (for FERM BP-2015 and B-16), each of which is incorporated by reference herein in its entirety to the extent that they are not inconsistent with the disclosure herein.
One particular sphingan, diutan (also known as heteropolysaccharide S-657), is prepared by fermentation of strain Sphingomonas sp. ATCC 53159 (ref. no. 17). Diutan exhibits unique rheological properties in aqueous solutions including high thermal stability, superior suspension properties, and the ability to generate high viscosity at low concentrations. The diutan polysaccharide imparts significant pseudoplasticity to polar solvents such as water, such that diutan can act as a rheological modifier that is capable of particle suspension, friction reduction, emulsion and foam stabilization, filter cake deposition and filtration control. Consequently, diutan has found industrial utility as a rheological modifier in a variety of contexts, including cementitious systems as disclosed in U.S. Pat. No. 6,110,271, which is incorporated herein by reference in its entirety to the extent that they are not inconsistent with the disclosure herein.
Diutan consists of a repeat unit with a backbone comprised of [→4)-α-L-rhamnose-(1→3)-β-D-glucose-(1→4)-β-D-glucuronic acid-(1→4)-β-D-glucose-(1→] and a two-sugar L-rhamnose side-chain attached to the (1→4) linked glucose residues (ref. no. 2, 7). Two O-acetyl groups are attached per repeat unit to the 2′ and 6′ positions of the (1→3) linked glucose (ref. no. 4).
Progress has been made in elucidating the genetics and biochemistry underlying biosynthesis of diutan and other sphingans. Genes for biosynthesis of sphingans S-88, S-7, and gellan have been identified (ref. no. 5, 12, 13, 15). Genes for several glycosyl transferases of the backbone structure have been analyzed biochemically (ref. no. 11, 14), as have genes gelC and gelE, potentially involved in chain length determination (ref. no. 9). Several of the genes for synthesis of sugar nucleotide precursors have also been elucidated (ref. no. 12). The genetics and biochemistry of polymerization, secretion and control of polysaccharide molecular length are less defined.
A cluster of genes involved in biosynthesis of diutan has been identified that includes genes for glycosyl transferases, genes encoding enzymes for synthesis of a precursor molecule dTDP rhamnose, and genes for secretion of the polysaccharide (ref. no. 3). Plasmids, e.g., pS8 and pX6, containing some of the genes in the aforementioned cluster, were shown to increase the yield of diutan by about 10%, and one plasmid in particular (pS8) was found to significantly improve the rheological properties of diutan from the wild-type strain (ref. no. 18).
Growth conditions typically used for producing diutan and other sphingans also promote production of the internal storage polymer polyhydroxybutyrate (“PHB”), which is generally regarded as an undesirable side-product and is difficult to remove during sphingan preparation. The PHB can form small insoluble particles that interfere with clarity and filterability, limiting the usefulness of the sphingans. For example, the turbidity imparted by PHB particles can limit applicability for household and personal care products in which appearance is critical for consumer acceptance. Moreover, certain oilfield uses require filterability; however, the PHB particles can plug small pores in oil field rock formations, preventing the flow of the sphingan solution and/or the return flow of the crude oil after treating the well. Finally, as PHB synthesis and sphingan synthesis compete for the available carbon source, PHB synthesis can have some adverse effect on sphingan yield.
Accordingly, attempts have been made to eliminate PHB production in sphingan-producing strains. Ref. no. 26 describes a strain of Sphingomonas elodea (a gellan-producing species) that was isolated following chemical mutagenesis. This strain, called LPG-2, has decreased PHB production, but produces gellan of inconsistent quality and yield.
A more targeted approach to eliminating PHB production was undertaken by deletion of a gene required for PHB synthesis, the phaC gene (ref. no. 20). Precise deletion of phaC from a diutan producing strain (ATCC 53159) reproducibly resulted in poor growth and severely reduced diutan productivity (strains NPD3 and NPD6). These strains exhibit increased carbohydrate hydrolysis and accumulation of organic acids, suggesting a critical role for phaC in maintaining normal cellular metabolism. Derivatives with less impaired diutan productivity were subsequently isolated. Two independent derivatives, PDD3 and PDD6, have uncharacterized spontaneous mutation(s) and remain PHB-deficient (ATCC deposit nos. PTA-4865 and PTA-4866, respectively). Though recovery of up to 90% of total diutan yield has been reported (ref. no. 20), this yield was only obtained following a greatly increased culture growth time and has not been consistently reproducible. Under standard growth conditions, diutan productivity and yield by these strains is only approximately half of wild-type levels.
SUMMARY
In view of the foregoing, there is a need to overcome the low sphingan productivity that is characteristic of PHB-deficient strains. The present disclosure addresses this need in the art by providing a genetically modified strain of Sphingomonas which not only lacks PHB production but also provides surprisingly high diutan productivity. Unexpectedly, the plasmids pS8 and pX6—which give only modest improvement in diutan productivity in PHB-producing strain—are now shown to greatly improve diutan productivity in a PHB-deficient strain. The great improvement in diutan productivity was particularly surprising because the plasmids contain genes involved in diutan biosynthesis and are not known to contain any genes that would offset the metabolic deficiency of a PHB-deficient strain. Certain embodiments of these genetically modified strains, described infra, fully overcome the poor yield and low productivity of PHB-deficient strains, while simultaneously attaining the desired filterability and clarity of PHB-deficient sphingans.
Certain embodiments encompass a mutant strain of the genus Sphingomonas having a genetic modification that reduces, or, preferably, substantially or entirely eliminates the production of PHB. In exemplary embodiments, the genetic modification inactivates the phaA gene, phaB gene, phaC gene, or any combination thereof. In another exemplary embodiment, the genetic modification to impair PHB synthesis is obtained by screening or selection for a PHB-deficient organism. The genetic modification that impairs PHB synthesis can reduce or completely eliminate PHB production, and can optionally be conditional, such as conditional induction, suppression, overexpression, knock-out, etc. of a gene involved in PHB synthesis, a gene that suppresses PHB synthesis, or any combination thereof. Optionally, a mutant strain of the genus Sphingomonas having a genetic modification that reduces, or, preferably, substantially or entirely eliminates the production of PHB also includes at least one additional genetic modification that suppresses the poor growth and/or poor diutan productivity of such strains. In an exemplary embodiment, the additional genetic modification can include at least one of the suppressor mutations contained in strains PDD3, PDD6, or both, or a variant of such suppressor mutation(s).
Certain embodiments encompass a method of increasing sphingan production in a host organism, such as an organism of the genus Sphingomonas. Exemplary methods of increasing sphingan production include increasing the expression in the host organism of at least one gene involved in sphingan synthesis. Such genes can be involved in sphingan synthesis, secretion, polymerization, synthesis of precursors, control of polysaccharide molecular length, etc. For example, additional copies of at least one gene involved in sphingan production can be introduced on an extrachromosomal element (such as a plasmid) or can be integrated into the host genome, or both. Such genes can be derived from the host strain or can be homologs derived from another species or strain. Homologs can include functional, structural, or sequence homologs of a gene involved in sphingan production or of a gene having an enzymatic activity the same as or similar to a gene involved in sphingan synthesis. In exemplary embodiments, the genes can be obtained by screening or selection for a Sphingomonas strain having increased sphingan production. Exemplary methods of increasing sphingan production also include introduction of genes involved in sphingan production having modified (non-native) sequences, such as modified promoter or enhancer elements, expression-optimized sequences, etc. Additionally, the native chromosomal copy of at least one gene involved in sphingan synthesis can optionally be deleted, or be replaced by any of the foregoing.
In certain embodiments, an extrachromosomal or integrated sequence element containing at least one gene, such as all of the genes that are contained in the insert in plasmid pS8 and/or pX6, or homolog(s) thereof, can be introduced into a Sphingomonas strain. For example, the at least one gene can include dpsS, dpsG, dpsR, dpsQ, dpsI, dpsK, dpsL, dpsJ, dpsF, dpsD, dpsC, dpsE, dpsM, dpsN, atrD, atrB, dpsB, rmlA, rmlC, rmlB, rmlD, orf7, orf6, orf5, or any combination thereof. In certain exemplary embodiments, the gene(s) include at least one gene encoding a sphingan biosynthetic enzyme, such as a dpsG polymerase. In another exemplary embodiment, such genes encoding a sphingan biosynthetic enzyme can include a dpsG polymerase and a glucose-1-phosphate thymidylyltransferase gene; a dTDP-6-deoxy-D-glucose-3-5-epimerase gene; a dTDP-D-glucose-4,6-dehydratase gene; and a dTDP-6-deoxy-L-mannose-dehydrogenase gene. In another exemplary embodiment, such genes encoding a sphingan biosynthetic enzyme can include a dpsG polymerase and a rhamnosyl transferase IV gene; a beta-1,4-glucuronosyl transferase II gene; a glucosyl isoprenylphosphate transferase I gene; and a glucosyl transferase III gene. In another exemplary embodiment, such a gene encoding a sphingan biosynthetic enzyme can include a dpsG polymerase and one or more of the polysaccharide export genes dpsD, dpsC, and dpsE. In another exemplary embodiment, such a gene encoding a sphingan biosynthetic enzyme can include a rhamnosyl transferase IV gene; a beta-1,4-glucuronosyl transferase II gene; a glucosyl isoprenylphosphate transferase I gene; glucosyl transferase III gene; a glucose-1-phosphate thymidylyltransferase gene; a dTDP-6-deoxy-D-glucose-3-5-epimerase gene; a dTDP-D-glucose-4,6-dehydratase gene; and a dTDP-6-deoxy-L-mannose-dehydrogenase gene. In another exemplary embodiment, such a sphingan biosynthetic enzyme can be selected from the group consisting of a gene encoding a polymerase; lyase; rhamnosyl transferase IV; beta-1,4-glucuronosyl transferase II; glucosyl transferase III; polysaccharide export protein; secretion protein; glucosyl-isoprenylphosphate transferase I; glucose-1-phosphate thymidylyltransferase; dTDP-6-deoxy-D-glucose-3-5-epimerase; dTDP-D-glucose-4,6-dehydratase; dTDP-6-deoxy-L-mannose-dehydrogenase, and any combination thereof. In certain embodiments, any combination of the foregoing genes or homologs thereof can be introduced into a Sphingomonas strain. In one exemplary embodiment, the Sphingomonas strain is a diutan-producing strain, such as ATCC 53159, or a PHB-deficient derivative thereof, such as a phaC deletion strain, such as NPD3, NPD6, PDD3, or PDD6. In another exemplary embodiment, the Sphingomonas strain is derived from Sphingomonas elodea ATCC 31461, Sphingomonas sp. ATCC 31555, Sphingomonas sp. ATCC 31961, Sphingomonas sp. ATCC 53159, Sphingomonas sp. ATCC 31554, Sphingomonas sp. ATCC 31853, Sphingomonas sp. ATCC 21423, Sphingomonas sp. ATCC 53272, Sphingomonas sp. FERM-BP2015, or a PHB-deficient derivative, such as a phaC deletion strain of any of the foregoing, or a phaC deletion strain bearing further mutation(s) that improve growth or sphingan productivity. In an exemplary embodiment, the phaC deletion strain is derived from a gellan-producing strain, such as LPG-2 (ref. no. 26), NPG-1, NPG-2, NPG-3, PDG-1, PDG-3 (ref. no. 20) or a derivative thereof.
In exemplary embodiments, a gene involved in sphingan synthesis can be derived from a homolog of a gene contained in plasmids pS8 or pX6. Such a homolog can be a Sphingomonas homolog, i.e., derived from an organism of the genus Sphingomonas. Exemplary organisms from which Sphingomonas homologs can be derived include Sphingomonas elodea ATCC 31461, Sphingomonas sp. ATCC 31555, Sphingomonas sp. ATCC 31961, Sphingomonas sp. ATCC 53159, Sphingomonas sp. ATCC 31554, Sphingomonas sp. ATCC 31853, Sphingomonas sp. ATCC 21423, Sphingomonas sp. ATCC 53272, Sphingomonas sp. FERM-BP2015, or any combination thereof. In another exemplary embodiment, a gene involved in sphingan synthesis can encode a polypeptide having at least about 70% sequence identity, such as about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity, to a polypeptide sequence of SEQ ID NO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, or 53. In another exemplary embodiment, a gene involved in sphingan synthesis can be encoded by a polynucleotide having at least about 60% sequence identity, such as about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity, to a polynucleotide sequence of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, or 52.
Certain embodiments of the present compositions include a diutan, particularly a PHB-deficient diutan, exhibiting an improvement (relative to diutan produced from a wild-type strain) in a number of different viscosity measurements. Among these are: i) an intrinsic viscosity of greater than about 150, preferably higher than about 155, more preferably higher than about 160 dL/g; ii) a sea water 3 rpm viscosity greater than about 35, such as greater than about 37, such as greater than about 40, such as greater than about 42, such as greater than about 45, such as greater than about 47, such as greater than about 50 dial reading; iii) a sea water 0.3 rpm viscosity greater than about 35,000, such as greater than about 39,000, such as greater than about 40,000, such as greater than about 42,000, such as greater than about 45,000, such as greater than about 48,000, such as greater than about 50,000, such as greater than about 54,000 centipoise (cP); and a PEG low shear rate viscosity greater than about 3500, such as greater than about 3700, such as greater than about 3900, such as greater than about 4000, such as greater than about 4200, such as greater than about 4500, such as greater than about 4700, such as greater than about 5000, such as greater than about 5200, such as greater than about 5500, such as greater than about 5700, such as greater than about 6000 cP.
Certain embodiments of the present strains include a mutant strain of the genus Sphingomonas that is able to produce PHB-deficient diutan at a rate of at least about 0.10 g/L/hr, such as at least about 0.11 g/L/hr, such as at least about 0.12 g/L/hr, such as at least about 0.13 g/L/hr, such as at least about 0.14 g/L/hr, such as at least about 0.15 g/L/hr, such as at least about 0.2 g/L/hr, and/or a yield of PHB-deficient diutan of at least about 12 g/L, such as at least about 15 g/L, such as at least about 16 g/L, such as at least about 17 g/L, such as at least about 18 g/L, such as at least about 19 g/L, such as at least about 20 g/L, such as at least about 21 g/L. For example, certain embodiments can include a mutant strain of the genus Sphingomonas able to produce PHB-deficient diutan at a rate of between about 0.15 g/L/hr and about 0.60 g/L/hr, such as between about 0.16 g/L/hr and about 0.5 g/L/hr, such as between about 0.17 g/L/hr and about 0.4 g/L/hr, such as between about 0.18 g/L/hr and about 0.35 g/L/hr, such as between about 0.19 g/L/hr and about 0.3 g/L/hr, such as between about 0.2 g/L/hr and 0.25 g/L/hr, such as between about 0.21 g/L/hr and about 0.22 g/L/hr. Additionally, certain embodiments can include a mutant strain of the genus Sphingomonas able to produce a yield of PHB-deficient diutan between about 12 g/L and about 30 g/L, such as between about 13 g/L and about 25 g/L, such as between about 14 g/L and about 22 g/L, such as between about 19 g/L and about 21 g/L.
Certain embodiments of the present strains include a mutant strain of the genus Sphingomonas containing a genetic modification that substantially or entirely eliminates the production of PHB and a genetic modification that results in increased production of a sphingan, wherein the mutant strain of the genus Sphingomonas increases the rate of production or yield of PHB-deficient diutan by at least about 50%, such as by at least about 60%, such as by at least about 70%, such as by at least about 80%, such as by at least about 90%, such as by at least about 100%, such as by at least about 110%, such as by at least about 120%, such as by at least about 120%, such as by at least about 130%, such as by at least about 140% relative to a congenic strain containing the genetic modification that substantially or entirely eliminates the production of PHB and lacking the genetic modification that increases the production of a sphingan. For example, the increase in the rate of production or yield of PHB-deficient diutan can be between about 50% and about 200%, such as between about 60% and about 190%, such as between about 70% and about 180%, such as between about 80% and about 170%, such as between about 90% and about 160%, such as between about 100% and about 150%, such as between about 110% and about 140%, such as between about 120% and about 130%.
In certain embodiments, one or more copies of specific DNA sequences are introduced within certain Sphingomonas strains to provide increased biosynthetic production of high viscosity diutan polysaccharide that is essentially free of PHB. The engineered bacteria containing such genes for increased production produce significantly greater amounts of PHB-deficient diutan polysaccharide compared to non-engineered bacteria and create diutan with the aforementioned resultant high viscosity properties.
The DNA can be delivered into bacteria of the genus Sphingomonas in multiple copies (via plasmid, other known manner) or increased expression of the genes via a suitable method, e.g., coupling to a stronger promoter. After insertion of the DNA into the target bacteria, the production of diutan can be determined by fermenting the engineered bacteria and comparing the yield in terms of amount produced and quality produced. Increased production and viscosity can both be determined by comparison with other diutan-producing strains.
Sphingomonas strains, such as the genetically modified strains described herein, can be used to produce sphingans, such as diutan, by fermentation. Generally, a suitable medium for fermentation is an aqueous medium which contains a source of carbon (for example, carbohydrates including glucose, lactose, sucrose, maltose or maltodextrins), a nitrogen source (for example, inorganic ammonium, inorganic nitrate, urea, organic amino acids or proteinaceous materials, such as hydrolyzed yeast, soy flour or casein, distiller's solubles or corn steep liquor), and inorganic salts. A wide variety of fermentation media will support the production of diutan according to the present invention. One of ordinary skill in the art can readily determine an appropriate media formulation.
Carbohydrates can be included in the fermentation broth in varying amounts—usually between about 1 and 10% by weight (preferably 2-8%) of the fermentation medium. The carbohydrates can be added prior to fermentation or, alternatively, during fermentation. The amount of nitrogen can, for example, range from about 0.01% to about 0.4% by weight of the aqueous medium. A single carbon source or nitrogen source can be used, as well as mixtures of these sources. Among the inorganic salts which are useful in fermenting Sphingomonas bacteria are salts which contain sodium, potassium, ammonium, nitrate, calcium, phosphate, sulfate, chloride, carbonate and similar ions. Trace metals, such as magnesium, manganese, cobalt, iron, zinc, copper, molybdenum, iodide and borate, can also be advantageously included in the broth.
In certain embodiments of the present method, Sphingomonas strains undergo fermentation. Fermentation can be carried out, for example, at temperatures between about 25 degrees C. and 40 degrees C., preferably between about 27 degrees C. and 35 degrees C. An inoculum can be prepared by standard methods of volume scale-up, including shake flask cultures and small-scale submerged stirred fermentation. The medium for preparing an inoculum can be the same as the production medium or can be any one of several standard media well-known in the art, such as Luria broth or YM medium. More than one seed stage can be used to obtain the desired volume for inoculation. Typical inoculation volumes range from about 0.5% to about 10% of the total final fermentation volume.
Certain embodiments of the present methods include agitation of the fermentation medium. In some embodiments, an agitator is contained within a fermentation vessel, whereby the contents of the agitation vessel are mixed. The vessel also can have automatic pH and foaming controls. The production medium can be added to the vessel and sterilized in place, e.g., by heating. Alternatively, the media can be sterilized separately before addition. A previously grown seed culture can be added to the cooled medium (typically at the preferred fermentation temperature of about 27 degrees to about 35 degrees C.), and the stirred culture can be fermented for about 48 to about 110 hours, producing a high viscosity broth. The sphingan, such as diutan, can be recovered from the broth by, for example, a standard method of precipitation with an alcohol, generally isopropanol.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows greatly improved diutan productivity of PHB-deficient strains bearing plasmids pX6 and pS8 relative to PHB-deficient strains without the plasmids.
FIG. 2 shows greatly improved diutan yield from PHB-deficient strains bearing plasmids pX6 and pS8 relative to PHB-deficient strains without the plasmids.
FIG. 3A illustrates poor filterability of a PHB-containing diutan preparation (0.04% S657/pS8 diutan in seawater). FIG. 3B illustrates poor filterability of an independent PHB-containing diutan preparation (0.04% S657/pS8 diutan in seawater).
FIG. 4A illustrates improved filterability of a PHB-deficient diutan preparation (0.04% PDD3/pS8 diutan in seawater). FIG. 4B illustrates improved filterability of a PHB-deficient diutan preparation (0.04% PDD3/pS8 diutan in seawater). FIG. 4C illustrates improved filterability of a PHB-deficient diutan preparation (0.04% PDD3/pS8 diutan in seawater).
FIG. 5 presents a map showing the inserts contained in plasmids pS8 and pX6.
FIG. 6 shows the insert sequence contained in plasmid pS8 (SEQ ID NO: 1).
FIG. 7 shows the insert sequence contained in plasmid pX6 (SEQ ID NO: 54).



DETAILED DESCRIPTION
Two PHB-deficient bacterial strains derived from Sphingomonas sp. ATCC 53159 (S657) were previously developed and designated PDD3 and PDD6 (see ref. no. 20). These strains exhibit approximately half of the diutan productivity of the wild-type strain (S657). The plasmid pS8 contains several genes involved in diutan biosynthesis in a multicopy plasmid and has been used to enhance diutan productivity and rheology (ref. no. 18). See also refs. no. 21-23 which describe the use of plasmid mediated gene amplification to increase polysaccharide yield (DNA segments and methods for increasing polysaccharide production).
As is shown in greater detail below, applicants have now shown that introduction of the plasmids pX6 and pS8—which contain multiple genes involved in diutan biosynthesis, but are not known to contain any genes that would offset the metabolic deficiency of a PHB-deficient strain—into PHB-deficient mutants PDD3 and PDD6 results in an unexpected significantly improved productivity (g/L/hr) and dry weight yield (g/L) of the PDD strains (70% to >100% increase) relative to the PHB-deficient strains without the introduced plasmids. The PHB-deficient strains produced fewer cells and no PHB, thus, more of their dry weight yield is diutan polysaccharide. Due to their increased productivity, these strains can be used for more economical production of PHB-deficient diutan than strains lacking these genetic modifications. Moreover, a clarified diutan produced from such strains exhibits improved filterability and clarity due to the absence of PHB particles relative to PHB-containing diutan. Such PHB-deficient diutan can be particularly desirable in a variety of applications, including household and personal care products, cementitious systems, for enhanced oil recovery, fracturing, well bore clean-up and other ‘pay zone’ applications, or any other application involving particle suspension, friction reduction, emulsion and foam stabilization, filter cake deposition and filtration control, or modification of the rheology of aqueous solutions (such as to thicken liquids, suspend solids, stabilize emulsions, or form gels and films, etc.). Additionally, upon acid hydrolysis, the PHB-deficient diutan leaves little to no residue as compared to PHB-containing diutan. The low acid hydrolysis residue renders the PHB-deficient diutan particularly suitable in oil field applications, such as fracturing, in which a viscosifying fluid is degraded after fracturing the formation, so the return flow of oil is maximized. Unlike the PHB-containing diutan, which contains PHB particles that would plug the pores in the rock formation, PHB-deficient diutan would not plug the pores in the formation, leading to improved oil yield.
In one exemplary embodiment of the present strains, a plasmid containing the relevant DNA sequence is inserted into a recipient Sphingomonas bacterium and replicates in the recipient cell, typically giving one or several (at least two and usually 4-10) copies of the DNA segment that result in increased production of high viscosity diutan polysaccharide relative to a strain lacking the DNA sequence. Alternatively or in addition to insertion of a plasmid-borne DNA sequence, DNA sequences that integrate into the bacterial chromosome can also be used. The use of conjugation or mobilization to transfer DNA into recipient bacteria is generally effective. Electroporation or chemical transformation of competent cells with purified DNA can also be used. Other vectors or bacteriophages can be used to transfer DNA into the host cell. Maintaining the DNA segments on plasmids (or other well known delivery vectors) in the recipient diutan-producing Sphingomonas is not necessary. It is routine to introduce additional copies of a DNA segment into the bacterial chromosome so that the segments are replicated each generation by the same mechanism that replicates the bacterial DNA. Alternative to or in conjunction with methods that increase the copy number of a DNA sequence, increased gene expression can be achieved by using stronger promoter elements.
The following terms shall be used throughout the specification in connection with the present invention and have the meaning indicated:
The term “Sphingomonas” is used throughout the specification to refer to strains of gram-negative bacteria from the genus Sphingomonas. 
The term “inserted” is used throughout the specification to describe the process and outcome of transferring DNA into a Sphingomonas strain. Such isolated DNA can be introduced first into, as one non-limiting possibility, a desired plasmid (such as pLAFR3), by well-known techniques in the art, and then transferred, for example, by conjugation or mobilization into a recipient Sphingomonas bacterium.
The term “gene amplification” is used to refer to either increased copies of genes, for example, by cloning the target genes on a multicopy plasmid (such as from 4 to 10 copies) or by insertion of multiple copies (such as from 4 to 10) of the genes into the bacterial genome, or alternatively, increased expression of genes by modification of promoter elements to increase gene expression. Both of these methods and others can result in increased amounts of the encoded proteins.
The term “biosynthesis” is used throughout the specification to describe the biological production or synthesis of a sphingan by Sphingomonas bacteria.
Cloning of DNA in the present invention relies on general techniques and methods which have become standard in the art. It is noted that any number of methods can be used to clone DNA segments according to the present invention, and the present invention is not limited, for example, to the use of plasmid cloning vectors. For example, DNA fragments can be cloned by insertion into a bacteriophage vector. In certain embodiments of the present methods, cloned DNA sequences are introduced to a Sphingomonas strain via a plasmid or other delivery vector.
The term “ectopic promoter” is used to refer to a non-native promoter, i.e., a promoter with some sequence difference(s) relative to the native promoter. Such a promoter can be, for example, a strong promoter which drives a measurably increased level of transcription relative to the native promoter. An ectopic promoter can also be a regulated promoter, whereby gene expression is increased or decreased in response to some factor, such as a small molecule, temperature, presence of a gene product, etc. Suitable promoters for a particular use are well known in the art.
The term “genetic modification” is used throughout the specification to refer to a genetic change. Generally, a genetically modified organism, such as a Sphingomonas strain, is described with reference to a “parent” strain which does not contain the genetic modification. Exemplary genetic modifications include those that increase, decrease, or abolish the expression of a gene. Such changes include modification of chromosomal and extrachromosomal genetic material. Exemplary genetic modifications include introduction of a plasmid, deletion or substitution of a chromosomal sequence. For example, a chromosomal gene can be inactivated by a targeted deletion of part or all of the coding sequence and/or regulatory element (e.g., as described in ref. no. 20), or genetic screen, optionally including mutagenesis (e.g., as described in ref. no. 26). Chromosomal genetic modification can also involve a targeted replacement, e.g., to replace a native gene promoter with an inducible promoter, regulated promoter, strong promoter, etc. Chromosomal gene modification can also involve gene amplification, i.e., introduction of at least one additional copy of at least one gene. Extrachromosomal genetic material can be introduced, for example, on a plasmid, which can be single-copy, multi-copy, or high-copy, as is well known in the art. Genetic modification can be coupled to a selectable marker, such as an antibiotic resistance gene, which helps ensure that the genetic modification is retained.
The term “essentially free of PHB” is used throughout the specification to refer to a composition, such as a sphingan (e.g., diutan), having a greatly reduced PHB content when compared to a similar composition prepared from a wild-type or PHB-containing strain. Great reduction can be at least a 90% reduction, 95% reduction, 99% reduction, 99.5% reduction, etc. in PHB content (where PHB content is expressed as a fraction of the dry weight of the sphingan composition). Suitable assays for measuring PHB content include the 15% HCl solubility and residue test, HPLC, gas chromatography, and gas chromatography coupled to mass spectrometry (GC-MS). In certain embodiments of the present compositions, a clarified (e.g., cellulase clarified) diutan preparation that is essentially free of PHB can yield less than approximately 1%, such as less than approximately 0.5%, such as less than approximately 0.1%, residue in a 15% HCl solubility and residue test.
The term “PHB-deficient diutan” is used throughout the specification to refer to a diutan produced from a PHB-deficient strain, such as strain bearing a genetic modification inactivates the phaA gene, phaB gene, phaC gene, or any combination thereof.
The term “phaC gene” is used throughout the specification to refer to a phaC gene of a Sphingomonas strain. Examples of phaC gene sequences are provided in (ref. no. 20); however, other phaC gene orthologs are also encompassed except where the context indicates otherwise.
When an amount, concentration, or other value or parameter is given as a list of upper preferable values and lower preferable values, this is to be understood as specifically disclosing all ranges formed from any pair of an upper preferred value and a lower preferred value, regardless of whether ranges are separately disclosed.
The term “a” or “an” as used herein means “one” or “one or more”.
The term “about” or “approximately” as used herein means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviations, per practice in the art. Where particular values are described in the application and claims, unless otherwise stated, the term “about” means within an acceptable error range for the particular value.
Unless otherwise indicated, all numbers expressing quantities of ingredients, properties such as molecular weight, reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about” Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.
Except wherein indicated otherwise, all measurements and protocols are conducted at standard temperature and pressure, i.e., approximately 20° C. and approximately 1 atmosphere. Except where indicated otherwise, “sea water 3 rpm viscosity,” “sea water 0.3 rpm viscosity,” and “low shear rate viscosity in the presence of polyethylene glycol” are measured as described in Example 2 below.
The invention will now be described in more detail with respect to the following, specific, non-limiting examples.
EXAMPLES
Example 1
Production of Diutan
This example described an increased yield of PHB-deficient diutan produced from several genetically modified Sphingomonas strains.
Methods
The plasmids pS8 and pX6 were transferred into PHB-deficient Sphingomonas strains PDD3 and PDD6 by triparental conjugal mating as described previously (ref. no. 3) and which is well known in the art. Strains PDD3, PDD6, S657, and S657/pS8 are as described previously (ref. nos. 17, 18, and 20). Strains PDD3/pS8, PDD6/pS8, PDD3/pX6, PDD6/pX6, PDD3, PDD6, S657, and S657/pS8 were grown in 15 L volumes in 20 L Applikon fermentors with agitation and aeration. For the plasmid containing strains, the antibiotic tetracycline at 5 mg/L was added throughout the fermentation to ensure retention of the plasmid. KOH was added as needed to control pH. Two seed stages were used with 1% to 6% inoculum transfers. The fermentation media contained corn syrup as carbohydrate source, an assimilable nitrogen source, and salts.
At the end of the fermentation, each broth was treated by introduction of glucoamylase enzyme to hydrolyze any remaining oligosaccharides from the corn syrup. The viscosities of the fermentation broths were measured via a Brookfield® viscometer run at 60 rpm with a spindle #4. The diutan gums produced were then precipitated from an aliquot of broth with two volumes of isopropyl alcohol. The diutan fibers were collected on a filter and dried. For some strains, multiple replicates were prepared, and the results presented below are the average values across these replicates.
Results
The presence of a plasmid containing genes involved in diutan synthesis (pX6 or pS8, see FIG. 5) greatly improved the diutan production by PHB-deficient strains compared to the parent PHB-deficient strains PDD3 and PDD6. Diutan productivity of PHB-deficient strains was greatly improved by between 70% and 142% (FIG. 1 and Table 1B) relative to the parental strains. This increased productivity was much greater than for the wild-type (S657) strain with the introduced pS8 plasmid, which demonstrated increased productivity by only 33%. Three of the four PHB-deficient, plasmid-containing strains had higher productivity than the wild-type (S657) strain, and strain PDD3/pX6 had productivity essentially equal to S657/pS8. Diutan yield of PHB-deficient strains bearing these plasmids was also greatly improved by between 53% and 90% (FIG. 2 and Table 1B) relative to the parental strains. This increase was much greater than for the wild-type (S657) strain with the introduced pS8 plasmid, which only increased diutan yield by 18%.
Consistent with these results, the PHB-deficient strains also exhibited increases in final broth viscosity due to introduction of the plasmids, indicating greater diutan content. The PHB-deficient, plasmid-containing strains also had lower cell density (measured by OD600) than the wild-type strain with or without plasmid pS8 (Table 1B), indicating that the unclarified products from these strains are expected to contain a higher proportion of diutan (due to the presence of fewer bacterial cells). Due to the higher purity of the diutan produced from PHB-deficient, plasmid containing strains (both due to lower cell content and absence of PHB), the extent of productivity and yield improvement in these strains compared to wild-type strains is likely to be even greater than these measurements indicate.







TABLE 1A







Final culture conditions.














Final Cell
Final Broth




Replicates
Density
Viscosity


Strain
PHB
(n)
(OD600)
(cP)





S657 (wild-type)
+
2
8.22
3000


S657/pS8
+
2
5.84
3775


PDD3
−
1
3.80
3000


PDD3/pX6
−
1
4.14
3650


PDD3/pS8
−
3
3.50
4158


PDD6
−
1
4.15
2500


PDD6/pX6
−
2
3.73
3125


PDD6/pS8
−
3
3.74
3783
















TABLE 1B







Diutan productivity and yield.

















Percent
Percent

Percent
Percent





Change
Change

Change
Change





Over S657
over PHB-

Over S657
over PHB-




Productivity
(wild-
deficient
Yield*
(wild-
deficient


Strain
PHB
(g/L/hr)
type)
parent
(g/L)
type)
parent

















S657 (wild-
+
0.153


17.5




type)


S657/pS8
+
0.203
+33%

20.7
+18%


PDD3
−
0.082
−46%

11.4
−35%


PDD3/pX6
−
0.197

+140%
20.9

+83%


PDD3/pS8
−
0.177

+116%
21.7

+90%


PDD6
−
0.067
−56%

9.4
−46%


PDD6/pX6
−
0.114

 +70%
14.4

+53%


PDD6/pS8
−
0.162

+142%
17.3

+84%





*Total dry weight of unclarified precipitate (dry weight yield).






Example 2
Diutan Analysis
The diutan samples produced in the method of Example 1 were analyzed for uses as oilfield additives for oil recovery and for uses requiring good suspension and stabilization (such as for cement additives for water retention and quick set-up).
Methods
The oilfield industry relies on a “sea water viscosity” (SWV) test as an indicator of acceptable performance for rheology modifiers in oil recovery. This test indicates whether a rheology modifier can sufficiently increase viscosity in briny conditions of sea water, such as those encountered in seabed oil recovery. Typically, a sea water viscosity test employs synthetic seawater produced by mixing 419.53 grams of sea salt (ASTM D-1141-52) per 9800 grams of deionized water. For a seawater viscosity test, a rheology modifier is dispersed in synthetic seawater by vigorous mixing (e.g., 35 minutes at approximately 11,500 rpm in a Fann Multimixer (Model 9B5, part number N5020)). The sample is cooled to approximately 25° C. before the viscosity is measured. For a 3-rpm viscosity test, the sample is placed on the Fann sample platform (Fann model 35 A; Torsion spring MOC 34/35 F0.2b; Bob B1; Rotor R1) and the speed is adjusted to 3 rpm by turning the motor to low speed and setting the gearshift in the middle position. The reading is then allowed to stabilize, and the shear stress value is read from the dial and recorded as the SWV 3 rpm dial reading (DR). For the 0.3-rpm reading, a Brookfield viscometer is used (Brookfield LV DV-II or DV-III viscometer, with LV-2C spindle) to measure the viscosity. The speed of the spindle is set to 0.3 rpm, and the spindle is allowed to rotate at least 6 minutes before the viscosity is recorded as the SWV-0.3 rpm reading and expressed in centipoises (cP).
The LSRV test (a low shear rate viscosity using polyethylene glycol as dispersant as described below) is a general test for viscosity at a low shear rate. Typically, the higher the viscosity the better a sample is at stabilization and suspension. For example, in a cementitious application, a higher viscosity in the LSRV test indicates that a diutan should help suspend particulates in the cement more effectively, giving a more homogeneous cement/concrete, thus, providing better strength and durability. The LSRV test measures the viscosity of a 0.25% solution of biogum in Synthetic Tap Water (STW). STW is prepared by adding 10.0 grams NaCl and 1.47 grams CaCl2.2H2O to 10 liters of deionized water. For the viscosity measurement, 0.75 grams of biogum is added to 4.5 grams Polyethylene Glycol 200 (CAS 25322-68-3) in a 400-mL beaker and thoroughly dispersed. Then, 299 grams of STW are added to the beaker and mixed for approximately 4 hours using a low-pitched, propeller-style stirrer at 800±20 rpm. After the 4-hr mixing time, the beaker is placed in a 25° C. water bath and allowed to sit undisturbed for approximately 30 minutes. The viscosity is then measured using a Brookfield LV viscometer equipped with a 2.5+ torque spring (or equivalent instrument, such as Model DVE 2.5+) at 3 rpm using the LV 1 spindle after allowing the spindle to rotate for 3 minutes and expressed in centipoises (cP).
Results
The diutan samples produced in Example 1 above were analyzed to determine suitability for use in cement and oilfield applications (Table 2). Utility for stabilization and suspension, such as for cement additives for water retention and quick set-up, was evaluated by low shear rate viscosity (LSRV) testing. Suitability for oil recovery was evaluated using sea water viscosity (SWV) tests at 0.3 rpm and 3 rpm as an indicator of the effectiveness of a gum to increase viscosity in brines.
In the LSRV test, diutan produced from PHB-deficient strain PDD3 containing either plasmid performed better than or about equal to the wild-type strain bearing pS8, with greater improvement observed for PDD3/pX6 than for PDD3/pS8 (Table 2). In the SWV test at 0.3 rpm, diutan produced from plasmid-containing PHB-deficient strains derived from PDD3 performed better than wild-type strains bearing pS8. In the SWV test at 3 rpm, either PHB-deficient strain bearing pS8 performed essentially equally to the wild-type strains bearing pS8. Together, these results indicate that a PDD3/pS8 diutan is particularly suitable for oilfield applications and cement applications.







TABLE 2







Rheology of unclarified PHB-deficient diutan.





















SWV

SWV




Diutan

LSRV

0.3 rpm

3 rpm


Strain
PHB
Productivity
n
(centipoise)
n
(centipoise)
n
(dial reading)





S657
+
++
1
5110
2
37,400
2
40.0


S657/pS8
+
+++
1
6610
2
48,600
2
56.5


PDD3
−
+
1
3160
—
nt.
—
nt.


PDD3/pX6
−
+++
1
6910
1
54,400
1
45.5


PDD3/pS8
−
+++
2
6198
3
51,867
2
57.0


PDD6
−
+
1
3020
—
nt.
—
nt.


PDD6/pX6
−
+++
2
5188
2
41,600
1
43.0


PDD6/pS8
−
+++
—
nt.
1
38,400
1
57.0





nt.: Not tested.






Example 3
Low Acid Residue of PHB-Deficient Diutan
Methods
The indicated strains were grown in 1000 gallon fermentors and in multiple Applikon® fermentors to prepare larger samples for testing and analysis. After the fermentations had finaled, the broths were either left untreated or enzyme clarified using one of two methods.
The first method, clarification with a cellulase, CELLUCLASTTM (“Clarified”) was as follows: First, the broth temperature was adjusted to 50° C. Next, the pH was adjusted to between 5.0 and 5.4. CELLUCLASTTM enzyme (1 g/L) was then added, and the broth was incubated for two hours. Stock solutions of EDTA and Lysozyme in distilled water were then sequentially added to the broth to a final concentration of 0.25 g/L EDTA and 0.05 g/L Lysozyme, and the broth incubated for one hour. The pH was then adjusted to 8.0 to 8.5. Protex 6 L protease was then added to the broth at a final concentration of 0.5 g/L and the broth was incubated for two hours. Finally, the diutan gum was precipitated by addition of three volumes of isopropyl alcohol, dried, and milled.
The second enzyme clarification (“Treated”) was similar to the first method, except the initial pH adjustment and the addition of CELLUCLASTTM enzyme were omitted.
Dried diutan samples were analyzed using the 15% HCl Solubility and Residue Test, as follows: 1.6 grams of a sample is rehydrated in 253 ml Synthetic Tap Water (typically 1 hr mixing at 1000 rpm). The mixing speed was then decreased to 500 RPM, and 147 mL of concentrated HCl (37%) is added to the rehydrated sample and mixed for 10 minutes. The sample container was then sealed and incubated at 150 degrees F. for twenty-four hours. The sample was again mixed, then a 100 gram aliquot was removed. The aliquot was quantitatively transferred to a Gelman filter apparatus containing a 0.5 micron filter. The filter was dried, cooled, and weighed prior to filtration and again after filtration. The weight of residue was reported as a percentage of the dry weight of polymer in the 100 gram aliquot (dry weight is determined by drying a sample of the same starting material).
Results
The acid residue test measures the amount of insoluble material that remains in a sample after acid hydrolysis. Low acid residue is preferred for certain uses, for example, an oilfield use in which the diutan is removed by acid hydrolysis and any insoluble residue has the potential to clog pores in the formation. This residue test also provides an indirect indication of the amount of PHB in a diutan preparation because the acid residue of a wild-type diutan is predominantly PHB. For a PHB-deficient diutan, the acid residue indicates an upper bound for the PHB content.
Results of the acid residue test are provided in Table 3, with residue indicated as a percentage of the starting sample material. Unlike the PHB-containing strains, which contained between 1.8 wt % and 6.8% wt % acid residue, the clarified PHB-deficient strain produced only 0.05 wt % acid residue. These results confirmed that the PHB-deficient strain produced diutan that would not damage an oilfield formation and, moreover, that the PHB-deficient diutan contains less than 0.05% PHB by weight.







TABLE 3







Low acid residue of clarified PHB-deficient diutan.











Strain
PHB
Weight Percentage Residue







S657/pS8
+
1.80%



(Treated)



S657
+
6.78%



(untreated)



S657/pS8
+
2.98%



(untreated)



PDD3/pS8
−
0.05%



(Clarified)










Example 4
Confirmation that PHB is Absent from PHB-Deficient Diutan
Methods
The analytical method measured the PHB content of diutan preparations and can also be used to measure the PHB content of other polysaccharides. In this method, the diutan is digested with an aqueous hypochlorite solution leaving the PHB intact; the PHB polymer is then hydrolyzed, then esterified to the propyl ester; and finally, the resulting ester is measured by gas chromatography with flame ionization detection. The instrument used was the Hewlett Packard Model 6890 Gas Chromatograph System equipped with a HP model 7673 auto injector, flame ionization detector, and Hewlett Packard HP 5MS column (30 m×250 μm×0.25 μm nominal id).
The detailed protocol is as follows. Approximately 35-40 mg of each diutan sample was weighed into a glass centrifuge tube, in duplicate and the weight recorded to the nearest 0.1 mg. Approximately 5 mL of approximately 5% sodium hypochlorite (JT Baker Cat #4616 or equivalent) was then added to each tube and the tubes vortexed. Samples were then incubated at approximately 37° C. for 12-18 hours, resulting in hypochlorite digestion. Tubes were then centrifuged at approximately 8000 rpm for approximately 40 minutes, and the hypochlorite supernatants were removed with a disposable pipette and discarded. Samples were then washed twice by addition of 5 mL deionized water with centrifugation and supernatant removal as in the previous step. Samples were then evaporated to dryness under reduced pressure using a vacuum oven, optionally with heating to accelerate the drying process. 2.0 mL of internal standard solution (0.513 mg/mL propyl benzoate, Aldrich Cat #30,700-9 or equivalent, in 1,2-dichloroethane, Aldrich Cat #15,478-4 or equivalent) was then added to each dry sample, followed by 1.0 mL of 20% (vol/vol) HCl (EM Science Cat #HX0603P-1 or equivalent) in n-propanol (Aldrich Cat #29,328-8 or equivalent). Samples were then sealed with polytetrafluoroethylene film (Teflon tape or equivalent), capped tightly, and incubated at approximately 100° C. for 3 hours with vortexing approximately every 30 minutes. Samples were then cooled to room temperature. An aqueous extraction was then performed by addition of 2 mL deionized water to each tube, vortexing for 10-20 seconds, allowing the phases to separate, and removal of the aqueous (top) phase. The aqueous extraction was repeated a second time, then the organic (lower) phase was transferred to a GC vial. Calibration standards containing between 0.2 and 10.0 mg/ml sodium 3-hydroxybutyrate (ICN Biomedical Cat #100964 or equivalent) were also prepared by the same method starting with the step of evaporation to dryness, i.e., the sodium hypochlorite digestion was omitted. Each sample and calibration standard was then analyzed using the Hewlett Packard Model 6890 Gas Chromatograph System.
The Hewlett Packard Model 6890 Gas Chromatograph System was operated with the following parameters: Sample Inlet: GC; Injection Source: GC ALS; Mass Spectrometer: Disabled; OVEN: Initial temp.: 50 C (On); Maximum temp.: 325 C; Initial time: 2.00 min; Equilibration time: 0.50 min; Ramp #1 Rate 7.00, Final temp. 120 C, Final time 0.00; Ramp #2 Rate 18.00, Final temp., 280 C, Final time 2.00; Ramp #3 Rate 0.0 (Off); Post temp: 0 C; Post time: 0.00 min; Run time: 22.89 min; BACK INLET: Mode: Split; Initial temp: 275 C (On); Pressure: 12.96 psi (On); Split ratio: 10:1; Split flow: 11.0 mL/min; Total flow: 13.1 mL/min; Gas saver: On; Saver flow: 20.0 mL/min; Saver time: 2.00 min; Gas type: Helium; COLUMN 2; Capillary Column; Model Number: HP 19091S-433; HP-5MS 5% Phenyl Methyl Siloxane; Max temperature: 325 C; Nominal length: 30.0 m; Nominal diameter: 250.00 um; Nominal film thickness: 0.25 um; Mode: constant flow; Initial flow: 1.1 mL/min; Nominal init pressure: 12.97 psi; Average velocity: 27 cm/sec; Inlet: Back Inlet; Outlet: Back Detector; Outlet pressure: ambient; BACK DETECTOR (FID); Temperature: 280 C (On); Hydrogen flow: 40.0 mL/min (On); Air flow: 450.0 mL/min (On); Mode: Constant makeup flow; Makeup flow: 15.0 mL/min (On); Makeup Gas Type: Helium; Flame: On; Electrometer: On; Lit offset: 2.0; SIGNAL 1; Data rate: 20 Hz; Type: back detector; Save Data: On; Start Save Time: 4.00 min; Stop Save Time: 22.00 min; Zero: 0.0 (Off); Range: 0; Fast Peaks: Off; Attenuation: 0; POST RUN: Post Time: 0.00 min; Front Injector: No parameters specified; BACK INJECTOR: Sample Washes: 0; Sample Pumps: 2; Injection Volume: 1.0 microliters; Syringe Size: 10.0 microliters; Nanoliter Adapter: Off; PostInj Solvent A Washes: 5; PostInj Solvent B Washes: 5; Viscosity Delay: 0 seconds; Plunger Speed: Fast; PreInjection Dwell: 0.00 minutes; Postinjection Dwell: 0.00 minutes.
A standard curve was fitted to the calibration standards by linear regression analysis using multilevel calibration with internal standard, resulting in the equation:

y=mx+b 

Where:



  
    y
    =
    
      
        
          Area
          ⁢
          
            
          
          ⁢
          PHB
        
        
          Area
          ⁢
          
            
          
          ⁢
          Istd
        
      
      =
      
        Area
        ⁢
        
          
        
        ⁢
        ratio
      
    
  




  
    x
    =
    
      
        
          Amount
          ⁢
          
            
          
          ⁢
          PHB
        
        
          Amount
          ⁢
          
            
          
          ⁢
          Istd
        
      
      =
      
        Amount
        ⁢
        
          
        
        ⁢
        ratio
      
    
  



    
    
        Istd. is the internal standard
        m=slope
        b=y-intercept
    
    


PHB content of the samples was then calculated using the following equation:




  
    Amount
    ⁢
    
      
    
    ⁢
    PHB
  
  =
  
    
      
        
          (
          
            Area
            ⁢
            
              
            
            ⁢
            
              PHB
              /
              Area
            
            ⁢
            
              
            
            ⁢
            Istd
          
          )
        
        -
        b
      
      m
    
    ×
    Amount
    ⁢
    
      
    
    ⁢
    Istd
  




Results

The presence or absence of PHB was confirmed using gas chromatography (GC). Diutan samples from strain S657/pS8 contained an average of 4.0% PHB by weight (Table 4). In contrast, PHB was undetectable in four samples from each of two independent diutan preparations from strain PDD3/pS8 (Table 4). These results indicated that strain PDD3/pS8 produced diutan containing less than approximately 0.05% PHB by weight (the estimated detection limit of the method).
As discussed above, abolition of PHB production by deletion of the phaC gene resulted in severe metabolic deficiency, poor growth, and greatly impaired diutan productivity. These results provide further confirmation of the unexpected finding that the diutan productivity and yield of a phaC deletion strain can be greatly enhanced by introduction of a plasmid containing genes involved in diutan synthesis, even though PHB production has not been detectably restored.







TABLE 4







Confirmation of absence of PHB by Gas Chromatography.













Sample Weight
Calculated
Wt %



Strain
(mg)
PHB (mg)
PHB







S657/pS8
39.8
1.68
4.22




39.8
1.65
4.16




36.0
1.39
3.86




36.0
1.36
3.79



PDD3/pS8
33.1
n.d.
n.d.



(Preparation #1)
33.1
n.d.
n.d.




38.0
n.d.
n.d.




38.0
n.d.
n.d.



PDD3/pS8
38.5
n.d.
n.d.



(Preparation #2)
38.5
n.d.
n.d.




38.0
n.d.
n.d.




38.0
n.d.
n.d.







n.d.: Not detected.



The limit of detection was 0.05% by weight.






Example 5
Diutan Filterability for Enhanced Oil Recovery Applications
Methods
Diutan fermentation broths were clarified with cellulase and recovered as described in Example 3.
Filterability studies were performed on 0.04% diutan rehydrated in seawater. The diutan solution was passed through a 47 mm diameter NUCLEPORETM filter (track-etched polycarbonate membranes having stringently controlled pore size, available from Whatman, Inc., Piscataway, N.J.) of the indicated pore size using a flow pressure of 20 psi. The time for each 200 ml of the diutan solution (1 or 2 liters total) to flow through the filter was measured with a graduated cylinder and a stop watch.
Results
In this example, the filterability of enzyme-clarified, rehydrated products from the PDD3/pS8 strain were compared to enzyme-clarified, rehydrated products from the S657/pS8 strain. Enzyme-clarified diutan preparations were filtered through NUCLEPORETM filters of the indicated sizes, and the volume filtered is shown as a function of time (FIGS. 3A-3B and 4A-4C). Clogging of filters is indicated by lines tending towards vertical on the graphs, showing that little additional volume was passing through the filter as time passed. Two preparations containing PHB made from strain S657/pS8 were poorly filterable, clogging filters of 5 microns (FIG. 3A) and 3 microns (FIG. 3B) before one liter could be filtered. In contrast, PHB-deficient diutan preparations made from strain PDD3/pS8 showed improved filterability. Two out of three preparations were filterable at 3 microns (FIG. 4A and FIG. 4C), while the third was filterable at 5 microns (FIG. 4B). Together, these results indicated that the PHB-deficient strains produced diutan with improved filterability.
Example 6
Description of Plasmids pS8 and pX6
The plasmids pS8 and pX6 are as previously described in U.S. Publication No. 2008/0319186. In brief, these plasmids were obtained by screening an ATCC 53159 genomic sequence library (in cosmid cloning vector pLAFR3) for clones able to restore polysaccharide production in the nonmucoid mutant (GPS2) of S. elodea ATCC 31461 or a nonmucoid mutant of Xanthomonas campestris. Plasmid inserts were end-sequenced and/or shotgun sequenced. A map showing the genes contained in complementing plasmids is shown in FIG. 5. The pS8 insert DNA sequence is provided as SEQ ID NO: 1 (FIG. 6), and the pX6 insert DNA sequence is provided as SEQ ID NO: 54 (FIG. 7). Predicted gene functions were designated based on homology to other genes in public databases. Genes contained in plasmid pS8 and pX6 and their predicted functions are listed in Tables 5 and 6, respectively. Pursuant to the Budapest Treaty for the International Recognition of the Deposit of Microorganisms, strains of E. coli containing plasmids pS8 and pX6 have been deposited with the Patent Depository at the American Type Culture Collection at 10801 University Boulevard, Manassas, Va. 20110, and are available as deposit numbers PTA-10102 (deposit date Jun. 2, 2009) and PTA-10103 (deposit date Jun. 2, 2009), respectively.
Plasmid pS8 contains the genes dpsS, dpsG, dpsR, dpsQ, dpsI, dpsK, dpsL, dpsJ, dpsF, dpsD, dpsC, dpsE, dpsM, dpsN, atrD, atrB, dpsB, rmlA, rmlC, rmlB, rmlD, and orf7. Plasmid pX6 contains the genes dpsJ, dpsF, dpsD, dpsC, dpsE, dpsM, dpsN, atrD, atrB, dpsB, rmlA, rmlC, rmlB, rmlD, orf7, orf6, and orf5. Based on their homology to known genes, many of the genes contained in these plasmids are predicted to be involved in diutan production. The genes in the genomic region from which plasmids pS8 and pX6 were derived (FIG. 5) include genes that encode the transferases for the four sugars of the diutan backbone and the four genes for dTDP-rhamnose synthesis. Genes for secretion of the polysaccharide, dpsD, dpsC, and dpsE, were identified based on homology to genes for biosynthesis of other polysaccharides. Two genes, atrB and atrD, encode proteins homologous to proteins involved in protein secretion. Two genes, dpsG and dpsR, putatively encode a polymerase and a lyase, respectively. Two genes, dpsM, and dpsN, encode polysaccharide attachment proteins. The insert in plasmid pX6 contained 17 genes including gene dpsB encoding transferase I (which initiates the first step in diutan synthesis), genes for secretion and four genes for dTDP-rhamnose synthesis, but lacks the genes for transferases II, III and IV and the putative genes for polymerase and lyase. Plasmid pS8 contains 20 genes of the dps gene cluster, including genes for all four backbone sugar transferases, the four genes for dTDP-rhamnose synthesis, and genes for secretion of the polysaccharide, including the putative genes for polymerase and lyase, but lacks the genes of unknown function, orf5, orf6, and orf7.







TABLE 5







Genes contained in plasmid pS8. Start and end coordinates are relative


to the pS8 insert sequence contained in SEQ ID NO: 1.









SEQ ID NO














Gene


Amino


Start
End
Name
Description
DNA
Acid















  2*
1054
dpsS
(partial) homologous to gelS
2
3


 2738
1113
dpsG
putative polymerase
4
5


 4895
2898
dpsR
putative lyase
6
7


 5093
6031
dpsQ
putative rhamnosyl
8
9





transferase IV


 7082
6111
dpsI
unknown
10
11


 7121
8167
dpsK
beta-1,4-glucuronosyl
12
13





transferase II


 8164
9030
dpsL
glucosyl transferase III
14
15


10467
9079
dpsJ
unknown
16
17


11076
12374
dpsF
unknown
18
19


12389
13306
dpsD
polysaccharide export protein
20
21


13341
14687
dpsC
polysaccharide export protein
22
23


14687
15394
dpsE
polysaccharide export protein
24
25


15405
16286
dpsM
polysaccharide attachment
26
27


16270
16968
dpsN
polysaccharide attachment
28
29


18454
17060
atrD
secretion protein
30
31


20637
18451
atrB
secretion protein
32
33


21229
22641
dpsB
glucosyl-isoprenylphosphate
34
35





transferase I


22757
23635
rmlA
glucose-1-phosphate
36
37





thymidylyltransferase


23632
24198
rmlC
dTDP-6-deoxy-D-glucose-3-
38
39





5-epimerase


24202
25263
rmlB
dTDP-D-glucose-4,6-
40
41





dehydratase


25263
26129
rmlD
dTDP-6-deoxy-L-mannose-
42
43





dehydrogenase


26277
26146
orf7
(partial) unknown function
44
45





*First in-frame codon; the start codon is not present.













TABLE 6







Genes contained in plasmid pX6. Start and end coordinates are


relative to the pX6 insert sequence contained in SEQ ID NO: 54.









SEQ ID NO














Gene


Amino


Start
End
Name
Description
DNA
Acid















1
336
dpsL
(partial) glucosyl
46
47





transferase III


1773
385
dpsJ
unknown
16
17


2382
3680
dpsF
unknown
18
19


3695
4612
dpsD
polysaccharide export protein
20
21


4647
5993
dpsC
polysaccharide export protein
22
23


5993
6700
dpsE
polysaccharide export protein
24
25


6711
7592
dpsM
polysaccharide attachment
26
27


7576
8274
dpsN
polysaccharide attachment
28
29


9760
8366
atrD
secretion protein
30
31


11943
9757
atrB
secretion protein
32
33


12535
13947
dpsB
glucosyl-isoprenylphosphate
34
35





transferase I


14063
14941
rmlA
glucose-1-phosphate
36
37





thymidylyltransferase


14938
15504
rmlC
dTDP-6-deoxy-D-glucose-3-
38
39





5-epimerase


15508
16569
rmlB
dTDP-D-glucose-4,6-
40
41





dehydratase


16569
17435
rmlD
dTDP-6-deoxy-L-mannose-
42
43





dehydrogenase


18288
17452
orf7
unknown function
48
49


19433
18618
orf6
unknown function
50
51


19751
20683
orf5
unknown function
52
53









REFERENCES
The entire disclosure of each patent, publication or other reference cited anywhere herein is hereby incorporated by reference in its entirety to the extent that they are not inconsistent with the disclosure herein.
Numbered citations in the text above refer to the list below.
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    13. Thorne, L., M. J. Mikolajczak, R. W. Armentrout, and T. J. Pollock. 2000. Increasing the yield and viscosity of exopolysaccharides secreted by Sphingomonas by augmentation of chromosomal genes with multiple copies of cloned biosynthetic genes. J. Ind. Microbiol. Biotechnol. 25: 49-57.
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While the invention has been described by way of examples and preferred embodiments, it is understood that the words which have been used herein are words of description, rather than words of limitation. Changes may be made, within the purview of the appended claims, without departing from the scope and spirit of the invention in its broader aspects. Although the invention has been described herein with reference to particular means, materials, and embodiments, it is understood that the invention is not limited to the particulars disclosed. The invention extends to all equivalent structures, means, and uses which are within the scope of the appended claims.

## Claims

1. A mutant strain of a genus Sphingomonas, comprising: at least one genetic modification that substantially or entirely eliminates a production of polyhydroxybutyrate (PHB); at least one genetic modification that results in increased production of a sphingan, wherein said genetic modification resulting in increased production of a sphingan comprises a genetic modification that increases the expression of at least one gene involved in sphingan synthesis, wherein said at least one gene involved in sphingan synthesis is selected from the group consisting of the genes-contained in the plasmid contained in strain ATCC PTA-10102 and the plasmid contained in strain ATCC PTA-10103; whereby the mutant strain of the genus Sphingomonas produces an increased production of a sphingan that is essentially free of PHB relative to a congenic strain containing the at least one genetic modification that substantially or entirely eliminates the production of PHB and lacking the at least one genetic modification that results in increased production of a sphingan, wherein the sphingan is diutan, and wherein the mutant strain of the genus Sphingomonas is able to produce diutan at a rate of at least about 0.15 g/L/hr or a yield of diutan of at least about 12 g/L.

2. The mutant strain of the genus Sphingomonas of claim 1, wherein the at least one genetic modification that results in increased production of a sphingan is selected from the group consisting of: (i) an operable linkage of at least one gene involved in sphingan synthesis to an ectopic promoter; (ii) an increased number of copies per bacterial chromosome of at least one gene involved in sphingan synthesis; and (iii) any combination thereof, wherein each of said at least one gene involved in sphingan synthesis are contained in a bacterial chromosome or extrachromosomal element.

3. The mutant strain of the genus Sphingomonas of claim 1, wherein the at least one genetic modification that substantially or entirely eliminates the production of PHB is a mutation that constitutively or conditionally inactivates or deletes a gene selected from the group consisting the phaA gene, the phaB gene, and the phaC gene or a combination thereof.

4. The mutant strain of the genus Sphingomonas of claim 1, wherein the at least one genetic modification that substantially or entirely eliminates the production of PHB is an insertion or deletion that inactivates the phaC gene.

5. The mutant strain of the genus Sphingomonas of claim 1, wherein the mutant strain of the genus Sphingomonas is able to produce diutan at a rate of at least about 0.2 g/L/hr or a yield of diutan of at least about 15 g/L.

6. The mutant strain of the genus Sphingomonas of claim 1, wherein the mutant strain of the genus Sphingomonas increases the rate of production or yield of diutan by at least about 50% relative to a congenic strain containing the at least one genetic modification that substantially or entirely eliminates the production of PHB and lacking the at least one genetic modification that results in increased production of a sphingan.

7. The mutant strain of the genus Sphingomonas of claim 1, wherein the diutan produced from the mutant strain of the genus Sphingomonas is clarified to yield less than 0.5% residue in a 15% HCl solubility and residue test, or less than 0.1 wt % PHB when measured using gas chromatography.

8. The mutant strain of the genus Sphingomonas of claim 1, wherein the diutan produced from the mutant strain of the genus Sphingomonas is clarified, and wherein the clarified diutan is rehydrated as one liter of 0.04% diutan in seawater can pass through a polycarbonate membrane filter in less than five minutes at a flow pressure of approximately 20 psi; wherein the polycarbonate membrane filter is approximately 47 mm in diameter and has a pore size of approximately 3 microns.

9. The mutant strain of the genus Sphingomonas of claim 1, wherein the diutan produced from the mutant strain of the genus Sphingomonas is essentially free from PHB, and wherein the diutan is clarified to exhibit a sea water 3 rpm viscosity of at least about 40 dial reading, a sea water 0.3 rpm viscosity of at least about 37,000 cp, or a low shear rate viscosity in the presence of polyethylene glycol dispersant of at least about 3,500 cp.

10. A mutant strain of a genus Sphingomonas, comprising: at least one genetic modification that substantially or entirely eliminates a production of polyhydroxybutyrate (PHB); at least one genetic modification that results in increased production of a sphingan, wherein said genetic modification resulting in increased production of a sphingan comprises a genetic modification that increases the expression of at least one gene involved in sphingan synthesis, wherein said at least one gene involved in sphingan synthesis is selected from the group consisting of the genes contained in the insert in the plasmid contained in strain ATCC PTA-10102, and the plasmid contained in strain ATCC PTA-10103; whereby the mutant strain of the genus Sphingomonas produces at least 50% increased production of diutan that is essentially free of PHB relative to a congenic strain containing the at least one genetic modification that substantially or entirely eliminates the production of PHB and lacking the at least one genetic modification that results in increased production of a sphingan.

11. The mutant strain of the genus Sphingomonas of claim 10, wherein said at least one gene involved in sphingan synthesis is selected from the group consisting of the genes-contained in the insert in plasmids pS8 (SEQ ID NO: 1) and pX6 (SEQ ID NO: 54).

12. A mutant strain of a genus Sphingomonas, comprising: at least one genetic modification that substantially or entirely eliminates a production of polyhydroxybutyrate (PHB); at least one genetic modification that results in increased production of a sphingan, wherein said genetic modification resulting in increased production of a sphingan comprises a genetic modification that increases the expression of at least one gene involved in sphingan synthesis, whereby the mutant strain of the genus Sphingomonas produces an increased production of a sphingan that is essentially free of PHB relative to a congenic strain containing the at least one genetic modification that substantially or entirely eliminates the production of PHB and lacking the at least one genetic modification that results in increased production of a sphingan, wherein said at least one gene involved in sphingan synthesis is selected from the group consisting of the genes-contained in the insert in plasmids pS8 (SEQ ID NO: 1) and pX6 (SEQ ID NO: 54), wherein the sphingan is diutan, and the mutant strain of the genus Sphingomonas increases the rate of production or yield of diutan by at least about 50% relative to a congenic strain containing the at least one genetic modification that substantially or entirely eliminates the production of PHB and lacking the at least one genetic modification that results in increased production of a sphingan.