# Patent

## Title
Recombinant host cells having an increase in buoyant density

## Abstract

Methods are provided to obtain recombinant microbial cells having at least one genetic modification that increase the buoyant density of a recombinant microbial cell or the buoyant density of inclusion bodies produced within a recombinant microbial cell. Exemplified are genetic modifications that increase the buoyant density of a recombinant microbial cell expressing heterologous peptides and polypeptides. Increasing expression of the genes ysaB, glyQ, glyS or a combination thereof within the recombinant microbial cell produces cells or inclusion bodies having higher buoyant density. A similar effect was achieved by decreasing or disrupting expression of the endogenous gltA gene. Increases in buoyant density render peptide production more efficient with respect to time and costs.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application claims priority to Indian Provisional Patent Application No. 441/DEL/2011 filed Feb. 21, 2011, currently pending.
FIELD OF THE INVENTION
The invention relates to the field of molecular biology, microbiology, industrial biotechnology and more particularly to recombinant peptide production.
BACKGROUND OF THE INVENTION
Efficient production of bioactive polypeptides and peptides is an important goal of the biomedical and biotechnology industries. Bioactive peptides and proteins are used as therapeutic and diagnostic agents in a variety of diseases such as diabetes (insulin), viral infections and leukemia (interferon), diseases of the immune system (interleukins), and red blood cell deficiencies (erythropoietin), to name a few. Additionally, large quantities of proteins and peptides are needed for various industrial applications including, but not limited to, pulp and paper industries, textiles, food industries, personal care and cosmetics industries, sugar refining, wastewater treatment, production of alcoholic beverages, and as catalysts for the generation of new pharmaceuticals.
In biomedical-related fields small peptides are sometimes used as linkers for the attachment of diagnostic and pharmaceutical agents to surfaces (see U.S. Pat. App. Pub. No. 2003/0185870 to Grinstaff et al. and U.S. Pat. No. 6,620,419 to Lintner, K.). In the field of personal care, small peptides have been used to couple benefit agents to body surfaces such as hair, skin, nail, and teeth (U.S. Pat. Nos. 7,220,405; 7,309,482; 7,129,326; 7,585,495 and 7,285,264; U.S. Pat. App. Pub. Nos. 2002/0098524; 2005/0112692; 2005/0226839; 2007/0196305; 2006/0199206; 2007/0065387; 2008/0107614; 2007/0110686; 2008/0280810; 2006/0171885; and 2008/0175798).
Peptides may be prepared by chemical synthesis or isolated from natural sources. However, these methods are often expensive, time consuming, and characterized by limited production capacity. The preferred method of producing large quantities of peptides or proteins is through the fermentation of recombinant microorganisms engineered to express a genetic construct encoding the peptide or protein of interest. However, recombinant microbial peptide production has a number of obstacles to overcome in order to be cost-effective. For example, peptides produced within a recombinant microbial host cell are often degraded by endogenous proteases, which decrease the yield and increase the cost of production. Additionally, microbial production of smaller peptides in high yield may be adversely affected by size and the amino acid composition of the peptide. This is especially evident when the peptide of interest is soluble under typical physiological conditions found within the production host.
One way to mitigate the difficulties associated with recombinantly producing a soluble peptide of interest (POI) is to produce it in an insoluble form that may accumulate within the host cell as an inclusion body. Soluble POIs may be produced as insoluble fusion proteins by coupling at least one peptidic tag that promotes insolubility (i.e., an inclusion body tag or “IBT”) to the peptide of interest. Producing the peptide of interest in the form of inclusion bodies provides a convenient means to isolate the protein from other cellular components.
One of the difficulties associated with recombinant protein production is controlling the costs associated with processing the recombinant biomass to obtain the desired peptide or protein of interest. Processing steps may include harvesting cells by centrifugation (to “spin down”) to recover the cells from the fermentation medium, lysis or homogenization to disrupt the cells to release the peptide, and the application of various separation methods to isolate the fusion polypeptide. Host cell modifications that aid in distinguishing polypeptides comprising POIs would further decrease the cost of POI recovery. Thus, cellular modifications that render any of these steps more rapid and/or easy to perform would be expected to reduce the cost and/or time associated with processing the recombinant host cells.
Altered expression of endogenous genes and/or the introduction of additional expressible genetic constructs may enhance recombinant peptide/protein production. Chen et al. (Biotech Bioengin (2004) 85 (5):463-474) disclose mutations affecting endogenous periplasmic proteases reported to increase recombinant antibody fragment accumulation in the E. coli periplasmic space. Further, although single gene knockout libraries are available for E. coli (Baba, T., et al., (2006) Mol. Syst. Biol. 2: article 2006.0008), down-regulating or disrupting specific genes or combinations of genes in Escherichia species that significantly effect heterologous peptide production and/or downstream processing are not as well known.
U.S. Pat. No. 7,662,587 to Cheng et al. discloses Escherichia host cells comprising a combination of knockout mutations to gcvA (encoding the glycine cleavage enzyme) and spr (encoding a suppressor of prc) that increased the amount of heterologous peptide produced within the modified host cell. U.S. Pat. Appl. Pub. No. 2010/0227361 to Chen et al. discloses a recombinant Escherichia host cell having a knockout mutation to gcvA, a knockout mutation to spr, and at least one mutation to a portion of the endogenous yejM gene.
Centrifugation is often included as at least one step when recovering the peptide of interest from the recombinant biomass. Rendering cells and/or inclusion bodies denser, larger or heavier than typical inclusion bodies could provide for easier and more rapid isolation. Faster flow rate could be used in continuous centrifugation to harvest cells producing denser inclusion bodies and subsequent washes of the inclusion bodies, which would lead to higher throughput in downstream processing.
One way of achieving this is to provide recombinant host cells having at least one modification that increases the buoyant density of the cell or inclusion bodies within the cell when synthesizing heterologous polypeptides and/or a relative increase in the buoyant density of the inclusion bodies formed within the modified host cell. Increases in buoyant density provides a relatively simple means to identify and obtain cells capable of producing increased amounts of insoluble heterologous protein and/or denser inclusion bodies comprising the heterologous protein.
However, the genetic modifications that one can introduce to a recombinant microbial host cell to increase the buoyant density of the cell or the buoyant density of an inclusion body formed within such a cell are not well understood. The problem to be solved is to provide a method to obtain recombinant host cells having at least one modification that enables more efficient isolation of recombinant polypeptides, including fusion polypeptides comprising the polypeptide of interest.
Increasing the buoyant density of the recombinant host cells or the density of the inclusion bodies produced by recombinant host cells should reduce the cost of isolating the polypeptide of interest. As such, an additional problem to be solved is to provide recombinant microbial host cells having one or more genetic modifications that increase the buoyant density of the cell or inclusion bodies produced within recombinant host cell and methods of using such modified microbial host cells to produce a polypeptide of interest.
SUMMARY OF THE INVENTION
A method to obtain recombinant microbial host cells having an increase in buoyant density is provided. Recombinant microbial host cells having at least one genetic modification increasing the buoyant density of the cell or inclusion bodies provided within the microbial host cell are provided as well as method of using such cells for the production of a polypeptide of interest.
In one embodiment, a method to obtain recombinant microbial cells having at least one genetic modification that increases the buoyant density of the recombinant microbial cell is provided comprising:

    
    
        a) providing a population of recombinant microbial cells, the recombinant microbial cells in the population comprising;
        
            i) at least one introduced genetic modification; and
            ii) a chimeric genetic construct encoding a polypeptide of interest;
        
        
        b) growing the recombinant microbial cells under suitable conditions whereby the polypeptide of interest is produced and accumulates within the recombinant microbial cells;
        c) fractionating the population of recombinant microbial cells grown in (b) by a density gradient centrifugation;
        d) isolating a subpopulation of the recombinant microbial cells from a fraction having a higher buoyant density; and
        e) optionally repeating steps (a) through (d).
    
    


Several genetic modifications were identified that increased the buoyant density of recombinant microbial cells. The identified genetic modifications increasing buoyant density may be introduced into other recombinant microbial host cells to increase buoyant density. In another embodiment, a method is provided comprising:

    
    
        a) providing a recombinant microbial cell comprising a chimeric genetic construct encoding a polypeptide of interest; and
        b) introducing a genetic modification comprising:
        
            i) increasing expression of a gene encoding a polypeptide selected form the group consisting of GlyS, GlyQ, YsaB or a combination thereof;
            ii) decreasing or eliminating expression of gltA encoding citrate synthase; or
            iii) a combination of (i) and (ii); and
        
        
        c) growing the recombinant microbial cell of (a) under conditions whereby the polypeptide of interest is produced in the form inclusion bodies; wherein the presence of the genetic modification introduced in step (b) increases the buoyant density of the recombinant microbial cell.
    
    


In another embodiment, a recombinant Escherichia host cell is provided, comprising:

    
    
        a) a chimeric gene encoding a polypeptide of interest; wherein the peptide of interest is not GlyS, GlyQ, or YsaB; and
        b) a genetic modification that increases expression of at least one endogenous gene selected from the group consisting of the g/yS, glyQ, ysaB, or a combination thereof.
    
    


In another embodiment, a recombinant Escherichia host cell is provided, comprising:

    
    
        a) a chimeric genetic construct encoding a polypeptide of interest; and
        b) a knockout mutation in gene gltA (encoding citrate synthase).
    
    


In another embodiment, a method of producing a polypeptide of interest in a recombinant Escherichia host cell is provided comprising:

    
    
        a) providing a recombinant Escherichia host cell comprising
        
            i) at least one chimeric genetic construct encoding a polypeptide of interest; and
            ii) a knockout mutation in the endogenous gltA gene encoding citrate synthase;
        
        
        b) growing the Escherichia host cell of (a) to produce the polypeptide of interest; and
        c) recovering the polypeptide of interest produced in step (b).
    
    


In another embodiment, the polypeptide of interest in the above compositions and methods is produced in the form of an insoluble fusion protein comprising at least one inclusion body tag, wherein the fusion protein optionally comprises a peptide spacer separating said at least one inclusion body tag from the peptide/polypeptide of interest.



DESCRIPTION OF THE FIGURES
FIGS. 1(a-d). Separation of uninduced QC1525 cells (FIG. 1a) from induced QC1525 cells producing HC415 peptide tagged to inclusion body tag (IBT139) in small scale PercollTM density gradient 3.5 hours after induction (FIG. 1b), 21.5 hours after induction (FIG. 1c), and approximately 24 hours after induction (FIG. 1d). Note appearance of 2 bands in induced cells (FIGS. 1b, 1c, and 1d), one upper band corresponding to the uninduced population (top arrows) and a lower band corresponding to the induced cells with greater buoyant density (lower arrows).
FIGS. 2(a-d). Images of centrifuge tubes showing separation of uninduced QC1525 cells (FIG. 2a; arrow 1) and induced QC1525 E. coli cells producing HC415 peptide tagged to inclusion body tag (IBT139) in large scale density gradient centrifugation 3.5 hours after induction (FIG. 2b; arrow 2), 21.5 hours after induction (FIG. 2c; arrows 3, 4, and 5), and 24 hours after induction (FIG. 2d; arrows 6, 7, and 8).
FIG. 3. Image of SDS-PAGE of the bands extracted from density gradient as shown by numbered arrows pointing to different bands in FIGS. 2a, 2b, 2c, and 2d. The lowermost band corresponding to higher buoyant density from each tube produced the  ̃28 kDa peptide of interest.
FIGS. 4(a-d). Images of centrifuge tubes showing separation of uninduced cells (FIG. 4a; arrow to band 1), and induced cells producing different fusion peptides. Induced QC1101 I (FIG. 4b; arrows to bands 2 and 3), induced QC1525 I (FIG. 4c; arrows 4 and 5), and a mixture of induce cells QC1101 I+DC1525 I (FIG. 4d; arrows 6, 7, and 8).
FIG. 5. Genetic arrangement of the approximate 2 kb region in E. coli BL21 genome that was identified in colony 181 which showed increased buoyant density from sorting of plasmid expression library. This region contains the full length ysaB and glyQ genes and a polynucleotide sequence encoding the N terminal portion of the glyS gene.
FIGS. 6(a-f). Images of centrifuge tubes showing confirmation of isolate of interest by density gradient centrifugation. Uninduced cells QC1101-U (FIG. 6a; arrow to band 1), induced QC1101-I (FIG. 6b; arrows to bands 2 and 3), induced Col-127_I (FIG. 6c, arrows to bands 4 and 5), induced Col-145_I (FIG. 6d, arrows to bands 6 and 7), induced Col-181—1 (FIG. 6e, arrow to band 8), and a tube containing density gradient beads (FIG. 6f). Note the increased buoyant density in induced colony 181 (FIG. 6e; band 8) in comparison to QC1101-I lower band (FIG. 6b; band 3).
FIG. 7. Image of SDS-PAGE of the cell lysate extracted from the bands shown in the PERCOLLTM density gradient of FIGS. 6a, 6b, 6c, 6d, and 6e. The number at the top of each lane corresponds to the numbered bands in the PERCOLLTM gradients shown in FIGS. 6a through 6e. Lane 3 (from band 3; FIG. 6b) is circled and corresponds to the peptide of interest from the control. Lane 8 is the peptide of interest (circled) from band 8 in colony 181 (FIG. 6e; band 8). Note the increase in the approximately 28 kDa peptide of interest in lane 8 compared to lane 3. A SeeBlue Plus 2 molecular weight ladder is shown in the far left lane.
FIG. 8. Image of micro-density gradient centrifugation of selected isolates (F1, B3, C6, F1, A12, B11, D2, and E4) from density gradient sorting of the Keio collection strains. Top panel is the whole cells (WC) and bottom panel is the inclusion bodies (IB). The control is labeled BW. Note the increased buoyant density in isolates F1 and A12.
FIGS. 9(a-f). Images of various centrifuge tubes after density gradient centrifugation. FIGS. 9a and 9d are images of density gradient separated beads of various buoyant densities. FIG. 9b shows a band (approximately 1.082 g/mL) formed after density gradient centrifugation of whole cells of control strain BW25113. FIG. 9c shows a band (approximately 1.115 g/mL) formed after density gradient separation of whole cells from a ΔgltA strain. FIG. 9e shows a band (approximately 1.121 g/mL) formed from the density gradient separation of inclusion bodies from control strain BW25113. FIG. 9f shows a band (approximately 1.142 g/mL) formed from the density gradient separation of inclusion bodies from a strain having a ΔgltA modification.



BRIEF DESCRIPTION OF THE BIOLOGICAL SEQUENCES
The following sequences conform with 37 C.F.R. 1.821-1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and are consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the EPO and PCT (Rules 5.2 and 49.5(a-bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.
Sequences 1 to 125 are peptides having various target-binding functions. The targets include a variety of body surfaces (e.g., hair, skin, tooth, finger and toe nail, and the like), polymers and pigments. These peptides are provided as an illustrative but non-exhaustive list of examples of polypeptides of interests for incorporating into various heterologous fusion polypeptides that can accumulate in inclusion bodies.
SEQ ID NOs: 1-11 are the amino acid sequences of several hair-binding peptides.
SEQ ID NOs: 12-22 are the amino acid sequences of several skin-binding peptides.
SEQ ID NOs: 23-24 are the amino acid sequences of several nail-binding peptides.
SEQ ID NOs: 25-33 are the amino acid sequences of several tooth pellicle-binding peptides.
SEQ ID NOs: 34-44 are the amino acid sequences of several tooth enamel-binding peptides.
SEQ ID NOs: 45-51 are the amino acid sequences of several anti-microbial peptides.
SEQ ID NOs: 52-62 are the amino acid sequences of several clay-binding peptides.
SEQ ID NOs: 63-75 are the amino acid sequences of several calcium carbonate-binding peptides.
SEQ ID NOs: 76-82 are the amino acid sequences of several polypropylene-binding peptides.
SEQ ID NOs: 83-91 are the amino acid sequences of several polytetrafluoroethylene-binding peptides.
SEQ ID NOs: 92-98 are the amino acid sequences of several polyethylene-binding peptides.
SEQ ID NOs: 99-104 are the amino acid sequences of several nylon-binding peptides.
SEQ ID NOs: 105-107 are the amino acid sequences of several polystyrene-binding peptides.
SEQ ID NOs: 108-111 are the amino acid sequences of several cellulose acetate-binding peptides.
SEQ ID NOs: 112-115 are the amino acid sequences of several carbon black-binding peptides.
SEQ ID NOs: 116-120 are the amino acid sequences of CROMOPHTAL® yellow-binding peptides.
SEQ ID NOs: 121-125 are the amino acid sequences of several SUNFAST® magenta-binding peptides.
SEQ ID NOs: 126-139 are the amino acid sequences of several inclusion-body tags.
SEQ ID NO: 140 is the amino acid sequence of a tetracysteine peptide tag.
SEQ ID NO: 141 is the nucleic acid sequence of plasmid pLR199.
SEQ ID NO: 142 is the nucleic acid sequence of the polynucleotide encoding for fusion peptide IBT139-CCPGCC-HC124.
SEQ ID NO: 143 is the amino acid sequence encoding fusion peptide IBT139-CCPGCC-HC124.
SEQ ID NO: 144 is the nucleic acid sequence of plasmid pDCQ523.
SEQ ID NO: 145 is the nucleic acid sequence of a polynucleotide encoding fusion peptide IBT139(5C)-CCPGCC-HC415.
SEQ ID NO: 146 is the amino acid sequence of fusion peptide IBT139(5C)-CCPGCC-HC415.
SEQ ID NO: 147 is the amino acid sequence of a peptide linker.
SEQ ID NO: 148 is the nucleic acid sequence of araBAD promoter.
SEQ ID NO: 149 is the nucleic acid sequence encoding the SlyD protein.
SEQ ID NO: 150 is the amino acid sequence of the SlyD protein.
SEQ ID NO: 151 is the amino acid sequence of a caspase 3 cleavage site.
SEQ ID NO: 152 is the nucleic acid sequence of the approximately 2 Kb polynucleotide fragment comprising the ysaB, glyQ and partial glyS genes.
SEQ ID NO: 153 is the nucleic acid sequence encoding the YsaB protein.
SEQ ID NO: 154 is the amino acid sequence of the YsaB protein.
SEQ ID NO: 155 is the nucleic acid sequence encoding the GlyQ polypeptide.
SEQ ID NO: 156 is the amino acid sequence of the GlyQ polypeptide.
SEQ ID NO: 157 is the nucleic acid sequence encoding the complete GlyS polypeptide.
SEQ ID NO: 158 is the amino acid sequence of the GlyS polypeptide.
SEQ ID NO: 159 is the nucleic acid sequence of plasmid pDCQ601.
SEQ ID NO: 160 is the nucleic acid sequence encoding the partial GlyS protein.
SEQ ID NO: 161 is the amino acid sequence of the partial GlyS protein.
SEQ ID NO: 162 is the nucleic acid sequence of primer pBHR1F.
SEQ ID NO: 163 is the nucleic acid sequence of primer pBHR1R.
SEQ ID NO: 164 is the nucleic acid sequence encoding the E. coli GltA citrate synthase.
SEQ ID NO: 165 is the amino acid sequence of the E. coli GltA citrate synthase, which is deleted in Keio library knockout clone JWO710.
DETAILED DESCRIPTION OF THE INVENTION 
The downstream processing of recombinant microbial biomass accounts for a substantial portion of the total cost to produce a peptide/polypeptide/protein of interest. Centrifugation is often included during the downstream purification process. Genetic modifications to the recombinant microbial cell (not including chimeric genetic construct encoding the peptide/protein of interest) that increase the buoyant density of the recombinant microbial cells or the inclusion bodies comprising the desired peptide/protein should reduce the cost to obtain the desired product.
A method to identify recombinant microbial cells having a genetic modification that increases the buoyant density of the cell or the buoyant density of inclusion bodies produced within the cell is provided herein. Recombinant microbial cells having at least one genetic modification that increases the buoyant density of the cell and/or inclusion bodies produced within the cell are provided as well as methods of using such cells for recombinant peptide/protein production.
The following definitions are used herein and should be referred to for interpretation of the claims and the specification. Unless otherwise noted, all U.S. Patents and U.S. Patent Applications referenced herein are incorporated by reference in their entirety.
As used herein, the indefinite articles “a” and “an” preceding an element or component of the invention are intended to be nonrestrictive regarding the number of instances (i.e., occurrences) of the element or component. Therefore “a” or “an” should be read to include one or at least one, and the singular word form of the element or component also includes the plural unless the number is obviously meant to be singular.
As used herein, the term “comprising” means the presence of the stated features, integers, steps, or components as referred to in the claims, but that it does not preclude the presence or addition of one or more other features, integers, steps, components or groups thereof. The term “comprising” is intended to include embodiments encompassed by the terms “consisting essentially of” and “consisting of”. Similarly, the term “consisting essentially of” is intended to include embodiments encompassed by the term “consisting of”.
As used herein, the term “about” refers to modifying the quantity of an ingredient or reactant of the invention or employed refers to variation in the numerical quantity that can occur, for example, through typical measuring and liquid handling procedures used for making concentrates or use solutions in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of the ingredients employed to make the compositions or carry out the methods; and the like. The term “about” also encompasses amounts that differ due to different equilibrium conditions for a composition resulting from a particular initial mixture. Whether or not modified by the term “about”, the claims include equivalents to the quantities.
Where present, all ranges are inclusive and combinable. For example, when a range of “1 to 5” is recited, the recited range should be construed as including ranges “1 to 4”, “1 to 3”, “1-2”, “1-2 & 4-5”, “1-3 & 5”, and the like.
As used herein, the term “invention” or “present invention” is a non-limiting term and is intended to encompass all possible variations as described in the specification and recited in the claims.
As used herein, the terms “peptide”, “polypeptide”, and “protein” will be used interchangeably to refer to a chain of amino acids each of which is joined to the next amino acid by a peptide bond. In one aspect, this term also includes post translational modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like. Included within the definition are, for example, peptides containing one or more analogues of an amino acid or labeled amino acids and peptidomimetics. The peptides may comprise L-amino acids.
A heterologous polypeptide or peptide is one that the host cell would not normally be expected to synthesize absent some recombinant engineering manipulation that enables the host cell to do so.
As used herein, the terms “peptide of interest”, “polypeptide of interest”, “protein of interest” or “POI,” refer to the desired heterologous peptide/polypeptide/protein product encoded by a recombinantly expressed gene. The peptide of interest may include any peptide/polypeptide product including, but not limited to proteins, fusion polypeptides/peptides, enzymes, peptides, polypeptides, and oligopeptides. In one embodiment, the peptide of interest ranges in size from 14 to 600 amino acids in length. The peptide of interest may be a bioactive peptide. The peptide of interest may have strong affinity for a target surface, such as a body surface. In one embodiment, the peptide of interest may have strong affinity for a surface. In another embodiment, the peptide of interest may have strong affinity for at least one body surface selected from the group consisting of hair, skin, nails, tooth, and tooth pellicle. In one embodiment, the peptide of interest is a single chain peptide from 14 to 600 amino acids in length and lacks any immunoglobulin folds or immunoglobulin subunits or fragments thereof.
As used herein, the terms “bioactive” or “peptide of interest activity” refer to the activity or characteristic associated with a peptide/polypeptide/protein of interest. The bioactive peptides may be used as, for example, curative agents for diseases (e.g., insulin, interferon, interleukins, anti-angiogenic peptides (U.S. Pat. No. 6,815,426); enzymes; polypeptides that bind to defined cellular targets such as receptors, channels, lipids, cytosolic proteins, and membrane proteins; peptides having antimicrobial activity; peptides having an affinity for a particular material (e.g., hair-binding polypeptides, skin-binding polypeptides, nail-binding polypeptides, tooth-binding peptides (include both tooth enamel and tooth pellicle-binding peptides), print media-binding peptides, cellulose-binding polypeptides, polymer-binding polypeptides, clay-binding polypeptides, calcium carbonate-binding peptides, cellulose acetate-binding peptides, carbon nanotube-binding polypeptides and peptides that have an affinity for particular animal or plant tissues) for targeted delivery of benefit agents.
As used herein, the “benefit agent” refers to a molecule that imparts a desired functionality or benefit when applied or coupled to a target surface. The benefit agent may be the polypeptide of interest or a peptide-based reagent coupled to benefit agent. The peptide-based reagent may be used to couple (covalently or non-covalently) a benefit agent to a target surface. The peptide reagent may couple a benefit agent to a body surface by forming a complex between the peptide reagent, the benefit agent, and the body surface. The benefit agent may be a particulate benefit agent (e.g., pigment, particles comprising an active agent) or may be a bioactive peptide, such as an enzyme.
As used herein, an “antimicrobial peptide” is a bioactive peptide having the ability to kill microbial cell populations (U.S. Pat. No. 7,427,656). Examples of antimicrobial peptides are provided as SEQ ID NOs: 45-51.
As used herein, the term “body surface-binding peptide” refers to a peptide having strong affinity for a body surface. Examples of body surfaces include, but are not limited to hair, skin, nail, and tooth. The body surface-binding peptides are typically used to couple a personal or health care benefit agent to the body surface. These agents include colorants, conditioners, antimicrobials, and enzymes, to name a few. Means to identify suitable body-surface binding peptides are well known in the art and may include biopanning techniques such as phage display, bacterial display, yeast display, ribosome display, and mRNA-display. The body surface-binding peptide may also be empirically-generated.
As used herein, “HBP” means hair-binding peptide. As used herein, the term “hair-binding peptide” refers to a peptide that binds with high affinity to hair. Examples of hair-binding peptides have been reported (U.S. Pat. App. Publication No. 2005-0226839 to Huang et al.; International Pub. No. WO 0179479; U.S. Pat. App. Pub. No. 2002-0098524 to Murray et al.; U.S. Pat. No. 7,129,326 to Janssen et al.; U.S. Pat. App. Pub. No 2006-0171885; U.S. Pat. Nos. 7,736,633; and 7,749,957). Examples of hair-binding peptides are provided as SEQ ID NOs: 1-11. The hair-binding peptides may be from about 7 amino acids to about 60 amino acids, more preferably, from about 7 amino acids to about 25 amino acids, most preferably from about 7 to about 20 amino acids in length.
As used herein, “SBP” means skin-binding peptide. As used herein, the term “skin-binding peptide” refers to a peptide sequence that binds with high affinity to skin. Examples of skin-binding peptides have also been reported (U.S. Pat. No. 7,309,482 to Buseman-Williams; U.S. Pat. Nos. 7,341,604; and 7,749,957). Skin as used herein as a body surface will generally comprise a layer of epithelial cells and may additionally comprise a layer of endothelial cells. Examples of skin-binding peptides are provided as SEQ ID NOs: 12-22. The skin-binding peptides may be from about 7 amino acids to about 60 amino acids, more preferably, from about 7 amino acids to about 25 amino acids, most preferably from about 7 to about 20 amino acids in length.
As used herein, “NBP” means nail-binding peptide. As used herein, the term “nail-binding peptide” refers to a peptide that binds with high affinity to nail. Examples of nail-binding peptides have been reported (U.S. Pat. No. 7,749,957). Examples of nail-binding peptides are provided as SEQ ID NOs: 23-24. The nail-binding peptides may be from about 7 amino acids to about 60 amino acids, more preferably, from about 7 amino acids to about 25 amino acids, most preferably from about 7 to about 20 amino acids in length.
As used herein, “TBP” means tooth-binding peptide. A tooth-binding peptide is a peptide that binds with high affinity to a mammalian or human tooth surface. As used herein, the term “tooth-binding peptide” will refer to a peptide that binds to tooth enamel or tooth pellicle. The tooth-binding peptides may be from about 7 amino acids to about 60 amino acids in length, more preferably, from about 7 amino acids to about 25 amino acids in length, most preferably from about 7 to about 20 amino acids in length. The tooth-binding peptides may be combinatorially-generated peptides. Examples of tooth-binding peptides having been disclosed in co-pending and co-owned U.S. Pat. App. Pub. 2008-0280810. Several examples of tooth-binding peptides and are provided as SEQ ID NOs: 25-44.
As used herein, the term “tooth surface” refers to a surface comprised of tooth enamel (typically exposed after professional cleaning or polishing) or tooth pellicle (a surface comprising salivary glycoproteins). Hydroxyapatite can be coated with salivary glycoproteins to mimic a natural tooth pellicle surface (tooth enamel is predominantly comprised of hydroxyapatite).
As used herein, the terms “pellicle” and “tooth pellicle” will refer to the thin film (typically ranging from about 20 nm to about 200 μm thick) derived from salivary glycoproteins which forms over the surface of the tooth crown. Daily tooth brushing tends to only remove a portion of the pellicle surface while abrasive tooth cleaning and/or polishing (typically by a dental professional) will expose more of the tooth enamel surface.
As used herein, the terms “enamel” and “tooth enamel” will refer to the highly mineralized tissue which forms the outer layer of the tooth. The enamel layer is composed primarily of crystalline calcium phosphate (i.e., hydroxyapatite) along with water and some organic material. In one embodiment, the tooth surface is selected from the group consisting of tooth enamel and tooth pellicle.
As used herein, the terms “peptide linker”, “linker”, and “peptide spacer” refer to a peptide used to link together two or more peptides. Peptide linkers/spacers may be comprised of any naturally occurring amino acids and may range from 1 to 100 amino acids in length, 1 to 50 amino acids in length, 1 to 30 amino acids in length, and most preferably 3 to 30 amino acids in length. An example of a peptide linker is provided as SEQ ID NO: 147.
As used herein, the terms “cleavable linker element” and “cleavable peptide linker” are used interchangeably and refer to cleavable peptide segments typically incorporated between an inclusion body tag and the peptide of interest. After the inclusion bodies are separated and/or partially-purified or purified from the cell lysate, the cleavable linker element can be cleaved chemically and/or enzymatically to separate the inclusion body tag from the peptide of interest. The fusion peptide may also include a plurality of regions encoding one or more peptides of interest separated by one or more cleavable peptide linkers. The peptide of interest can then be isolated from the inclusion body tag, if necessary. An example of an enzymatically cleavable peptide linker is provided by SEQ ID NO: 151 (Caspase-3 cleavage sequence). The cleavable linker may be an acid cleavable aspartic acid-proline dipeptide (D-P) moiety. The cleavable peptide linkers may be incorporated into the fusion proteins using any number of techniques well known in the art.
As used herein, a polymer-binding peptide is a peptide that binds with high affinity to a specified polymer (see, for example, U.S. Pat. No. 7,427,656). Examples of polymer-binding peptides may include, but are not limited to, polypropylene-binding peptide (SEQ ID NOs: 76-82), polytetrafluoroethylene-binding peptides (SEQ ID NOs: 83-91), polyethylene-binding peptides (SEQ ID NOs: 92-98), nylon-binding peptides (SEQ ID NOs: 99-104), and polystyrene-binding peptides (SEQ ID NOs: 105-107).
As used herein, a clay-binding peptide is a peptide that binding with high affinity for a clay. Examples of clay-binding peptides include SEQ ID NOs: 52-62.
As used herein, a calcium carbonate-binding peptide is a peptide that binding with high affinity to calcium carbonate. Examples of calcium carbonate-binding peptides include SEQ ID NOs: 63-75.
As used herein, a cellulose acetate-binding peptide is a peptide that binds with high affinity to cellulose acetate. Examples of cellulose acetate-binding peptide are provided as SEQ ID NOs: 108-111.
As used herein, a pigment-binding peptide is a peptide that binds with high affinity for a specified pigment. Examples may include, but are not limited to, carbon black-binding peptides (SEQ ID NOs: 112-115), CROMOPHTAL® yellow-binding peptides (SEQ ID NOs: 116-120), and SUNFAST® magenta-binding peptides (SEQ ID NOs: 121-125).
As used herein, the terms “coupling” and “coupled” refer to any chemical association and may include both covalent and non-covalent interactions in one coupling event. Coupling may also refer to separate, individual covalent interaction or separate, individual non-covalent interaction.
As used herein, a “tetracysteine tag” is a peptide tag having an effective number cysteine residues (typically 4) which are capable of binding a biarsenical labeling agent (U.S. Pat. No. 7,794,963; incorporated herein by reference). An example of a tetracysteine tag is provided as SEQ ID NO: 140.
As used herein, the terms “solubility tag” and “inclusion body tag” and the abbreviation “IBT” refer to a polypeptide that promotes or enhances the formation of inclusion bodies when fused to a peptide/polypeptide of interest. The polypeptide of interest, i.e. POI, may be soluble within the host cell and/or host cell lysate when not fused to an inclusion body tag. Fusion of the polypeptide of interest to the inclusion body tag produces a fusion protein that agglomerates into intracellular bodies, also called inclusion bodies, within the host cell. The fusion protein comprises a portion having an inclusion body tag and a peptide/protein of interest. The polypeptide/protein of interest may be separated from the inclusion body tags using cleavable peptide linker elements (See U.S. Pat. Nos. 7,732,569, 7,662,913, and 7,678,883; each incorporated herein by reference). Examples of inclusion body tags include, but are not limited to, SEQ ID NOs: 126-139.
The inclusion body tag(s) and the peptide of interest may exhibit a different solubility in a defined medium, typically aqueous, thereby facilitating separation of the inclusion body tag from the peptide of interest. Preferably, the inclusion body tag is insoluble in an aqueous solution while the protein/peptide of interest is appreciably soluble in an aqueous solution. The pH, temperature, and/or ionic strength of the aqueous solution can be adjusted to facilitate recovery of the peptide of interest. The differential solubility between the inclusion body tag and the polypeptide of interest may occur in an aqueous solution having a pH of 5 to 10 and a temperature range of 15° C. to 50° C.
As used herein, the term “genetic construct” refers to a series of contiguous nucleic acids useful for modulating the genotype or phenotype of an organism. Non-limiting examples of genetic constructs include but are not limited to a nucleic acid molecule, and open reading frame, a gene, an expression cassette, a vector, a plasmid and the like.
As used herein, the term “endogenous gene” refers to a native gene in its natural form and location in the genome of an organism.
As used herein, a “foreign gene” refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes.
As used herein, the term “recombinant” refers to an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques. “Recombinant” also includes reference to a cell or vector, that has been modified by the introduction of a heterologous nucleic acid or a cell derived from a cell so modified, but does not encompass the alteration of the cell or vector by naturally occurring events (e.g., spontaneous mutation, natural transformation, natural transduction, natural transposition) such as those occurring without deliberate human intervention.
As used herein, the term “Escherichia” refers to a genus of Gram-negative, non-spore forming, facultatively anaerobic, rod-shaped bacteria from the family Enterobacteriaceae. The genus Escherichia include various species, such as Escherichia coli. The Escherichia host cell is an Escherichia coli cell. The Escherichia coli cell may be derived from an Escherichia coli K-12 strain.
As used herein, the terms “fusion protein” and “fusion peptide” are interchangeable and refer to a polymer of amino acids (peptide, oligopeptide, polypeptide, or protein) comprising at least two portions, each portion comprising a distinct function. A first portion of the fusion peptide may comprise at least one inclusion body tag and a second portion of the fusion peptide may comprise at least one peptide of interest. The fusion protein may additionally include at least one cleavable peptide linker that facilitates chemical and/or enzymatic cleavage and separation of the inclusion body tag(s) and the peptide(s) of interest.
As used herein, the term “immunoglobulin fold” refers to a common all-β protein fold that consists of a 2-layer sandwich of  ̃7 antiparallel β-strands arranged in two β-sheets. The backbone switches repeatedly between the two β-sheets. Typically, the pattern is (N-terminal β-hairpin in sheet 1)-(β-hairpin in sheet 2)-(β-strand in sheet 1)-(C-terminal β-hairpin in sheet 2). The cross-overs between sheets form an “X”, so that the N- and C-terminal hairpins are facing each other.
The term “amino acid” refers to the basic chemical structural unit of a protein or polypeptide. The following abbreviations are used herein to identify specific amino acids:
















Three-Letter
One-Letter



Amino Acid
Abbreviation
Abbreviation









Alanine
Ala
A



Arginine
Arg
R



Asparagine
Asn
N



Aspartic acid
Asp
D



Cysteine
Cys
C



Glutamine
Gln
Q



Glutamic acid
Glu
E



Glycine
Gly
G



Histidine
His
H



Isoleucine
Ile
I



Leucine
Leu
L



Lysine
Lys
K



Methionine
Met
M



Phenylalanine
Phe
F



Proline
Pro
P



Serine
Ser
S



Threonine
Thr
T



Tryptophan
Trp
W



Tyrosine
Tyr
Y



Valine
Val
V



Miscellaneous (or as
Xaa
X



defined herein)










As used herein, the term “operably-linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). The definition of “operably linked” may also be extended to describe the products of chimeric genes. As such, “operably-linked” may also refer to the linking of two or more peptides/polypeptides by at least one peptide linker.
Polynucleotides encoding heterologous polypeptides may be operably linked to various known promoters, specifically encompassing non-inducible and inducible promoters. Suitable promoters exist for virtually all cell types, including mammalian and microbial cell types. Thus, it is well known in the art that both types of promoters that are suitable for heterologous polypeptide expression in bacteria, yeast, fungi, and mammalian cells are commonly used to provide suitably high levels of synthesis of a polypeptide of interest.
Examples of inducible promoters suitable for inducing the expression of the polynucleotide encoding the heterologous polypeptide may include the β-lactamase and lactose promoter systems (Chang et al., Nature, (1978) 275: 615; Goeddel et al., Nature, (1979) 281: 544), the arabinose promoter system (Guzman et al., J. Bacteriol., (1992) 174: 7716-7728), alkaline phosphatase, a tryptophan (trp) promoter system (Goeddel, Nucleic Acids Res., (1990)8: 4057 and EP 36,776) and hybrid promoters such as the tac promoter (deBoer et al., Proc. Natl. Acad. Sci. USA, (1983) 80: 21-25). However, persons of ordinary skill in the art are clearly aware of the numerous non-inducible and inducible promoters are available and have the means to construct the corresponding gene expression cassettes tailored for their systems. For example, the nucleotide sequences of non-inducible and inducible promoters for numerous microbial and mammalian species have been published, thereby enabling a skilled worker to ligate them operably to any DNA encoding a polypeptide of interest, using restriction enzymes or, if necessary, linkers or adaptors or polymerase chain reaction (i.e., PCR) to supply any required restriction sites.
Density Gradient Centrifugation
As used herein, the terms “density gradient centrifugation” and “equilibrium density gradient centrifugation” will be used to describe a technique to separate cellular components on the basis of their buoyant density. A mixture of components is centrifuged through a steep density gradient. The density gradient medium often contains a high concentration of sucrose, or more often, cesium chloride (CsCl). In these gradients, the molecules being studied have a density somewhere in between the highest and lowest densities generated in the gradient. The components of the sample begin to move down this gradient until a point is reached where the density of the solution is equal to the individual components density. The component then stops moving further and forms a distinct band. The position of the band in the tube is characteristic of the buoyancy of that component. Buoyancy, or buoyant density of a substance is its tendency to float in a medium, which in this case is the density gradient.
The isolation of either the cells containing the inclusion bodies or the inclusion bodies that formed therein may be conveniently performed by density gradient centrifugation using a gradient medium selected from the group consisting of PERCOLLTM, FICOLLTM, metrizamide, sucrose or cesium chloride. PERCOLLTM is a preferred medium but others can be adapted for the relevant purposes encompassed by the methods disclosed herein. As described in the Examples, removal from the density gradient after centrifugation of either cells or inclusion bodies can be achieved with the use of conventional pipetting devices.
The components with a mixture are separated/fractionated within the density gradient based on their respective buoyant density, forming distinct bands within the centrifuge tube. As used herein, the term “fractionating” will be used to describe the step of performing equilibrium density gradient centrifugation whereby a population of cells or inclusion bodies having different buoyant densities is separated into subpopulations based on differences in buoyant density. Recombinant microbial cells and/or inclusion bodies produced by such cells can be fractionated based on their respective buoyant density. Bands corresponding to relative higher buoyant density can be collected and the process can be repeated to obtain cells and/or inclusion bodies produce by such cells having higher buoyant density.
The genetic modification associated with the increase in buoyant density identified by the present methods can be introduced into other microbial production hosts. Through repeated genetic modification and selection, one can obtain 1) modified microbial host cells having even higher buoyant density or 2) modified microbial host cells capable producing inclusion bodies having increased buoyant density.
Introducing Genetic Modifications to Increase Buoyant Density
Provided herein is a method to identify a genetic modification that increases the buoyant density of a recombinant microbial cell and/or an inclusion body produced by a recombinant microbial cell. In one embodiment, the introduced genetic modification increases the buoyant density of the recombinant microbial cell. In another embodiment, the introduced genetic modification increases the buoyant density of the inclusion body. In one aspect, the buoyant density of the inclusion body increases without increasing the amount of POI in the inclusion body (i.e., denser inclusion bodies formed). In a further embodiment, the introduced genetic modification increases the buoyant density of the recombinant microbial cell comprising at least one inclusion body (comprising the polypeptide of interest).
The present genetic modifications are modifications in addition to the chimeric genetic construct designed to recombinantly express a polypeptide of interest. As such, the introduced genetic modification does not include chimeric genetic construct producing the desired polypeptide of interest. Conversely, the desired polypeptide of interest (POI) will not include, by proviso, the protein encoded by ysaB, glyQ, glyS, a truncated glyS or any combination thereof.
The introduced genetic modification may include recombinant expression of an introduced polynucleotide, decreased or disrupted expression of an endogenous gene or a combination there.
Recombinant Expression of a Polynucleotide to Increase Buoyant Density
Described herein are compositions and methods for increasing the buoyant density of a microbial cell or inclusion body produced by a microbial cell by expressing or over-expressing a polynucleotide encoding ysaB, glyQ, glyS, a truncated glyS or any combination thereof. In one embodiment, the source of the polynucleotide comprising ysaB, glyQ, glyS or a truncated glyS is Escherichia. In a further embodiment, the source of polynucleotide is Escherichia coli. In a preferred embodiment, the source of the polynucleotide is Escherichia coli BL21.
In one embodiment, the recombinantly expressed polynucleotide used to increase buoyant density encodes the YsaB protein having the amino acid sequence SEQ ID NO: 154. In one aspect, the polynucleotide comprises the nucleic acid sequence SEQ ID NO: 153.
In one embodiment, the recombinantly expressed polynucleotide used to increase buoyant density encodes the GlyQ protein having the amino acid sequence SEQ ID NO: 156. In one aspect, the polynucleotide comprises the nucleic acid sequence SEQ ID NO: 155.
In one embodiment, the recombinantly expressed polynucleotide used to increase buoyant density encodes the complete GlyS protein having the amino acid sequence SEQ ID NO: 158. In one aspect, the polynucleotide comprises the nucleic acid sequence SEQ ID NO: 157.
In one embodiment, the recombinantly expressed polynucleotide used to increase buoyant density encodes a truncated GlyS protein having the amino acid sequence SEQ ID NO: 161. In one aspect, the polynucleotide comprises the nucleic acid sequence SEQ ID NO: 160.
In one embodiment, the recombinantly expressed polynucleotide used to increase the buoyant density encodes the combination of proteins comprising amino acid sequences SEQ ID NOs: 154, 156, and 161. In yet a further aspect, the polynucleotide used to increase the buoyant density comprises nucleic acid sequence SEQ ID NO: 152.
Screening a Genomic Library
As exemplified herein, a genomic library having DNA fragments ranging from about 2 kb to about 3 kb was prepared. The present method may use larger or smaller DNA fragments, however, an average size of 1 kb to 4 kb is preferred. The random fragments were inserted into an expression vector. The vector was introduced into recombinant microbial host cells comprising a chimeric genetic construct encoding a polypeptide of interest. The recombinant microbial cells were grown under conditions whereby the introduced polynucleotide from the genomic library and the chimeric gene encoding the polypeptide of interest were expressed. The polypeptide of interest accumulated within the cells in the form of inclusion bodies. The inserted DNA fragment may be expressed by operably linking the fragment to suitable regulatory sequence or may have its own regulatory sequence capable of expression within the recombinant microbial host cell.
The population of cells comprising the genomic inserts and the polypeptide of interest were then fractioned using density gradient centrifugation. Subpopulations of cells exhibiting higher buoyant density were selected. The subpopulation exhibiting an increase in buoyant density can be obtained after the first fractionation. In one embodiment, the process may be repeated to obtain recombinant microbial cells and/or inclusion bodies having even higher buoyant densities.
The genomic DNA used to prepare the genomic library may be obtained for any source organism. In one embodiment, the genomic DNA library is prepared from a microbial cell is selected from the group consisting of Aspergillus, Trichoderma, Saccharomyces, Pichia, Phaffia, Kluyveromyces, Candida, Hansenula, Yarrowia, Salmonella, Bacillus, Acinetobacter, Zymomonas, Agrobacterium, Erythrobacter, Chlorobium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Synechococcus, Anabaena, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus. In one embodiment, the source of the genomic DNA used to prepare the library is Escherichia. Preferably the source is Escherichia coli. In another embodiment, the source may be derived from Escherichia coli BL21.
Method to Obtain Recombinant Microbial Cells Having Genetic Modifications which Increase Buoyant Density
The process exemplified herein may be repeated to obtain cells having further increases buoyant density. The process may be used to screen libraries of mutants to identify further genetic modifications that may increase the buoyant density of the cells and/or inclusion bodies produced by the modified cells.
As such, a method to obtain recombinant microbial cells having at least one genetic modification that increases the buoyant density of the recombinant microbial cell is provided herein comprising:

    
    
        a) providing a population of recombinant microbial cells, the recombinant microbial cells in the population comprising;
        
            i) at least one introduced genetic modification; and
            ii) a chimeric genetic construct encoding a polypeptide of interest;
        
        
        b) growing the recombinant microbial cells under suitable conditions whereby the polypeptide of interest is produced and accumulates within the recombinant microbial cells;
        c) fractionating the population of recombinant microbial cells grown in (b) by a density gradient centrifugation;
        d) isolating a subpopulation of the recombinant microbial cells from a fraction having a higher buoyant density; and
        e) optionally repeating steps (a) through (d).

Decreased or Disrupted Expression of Endogenous Genes to Increase Buoyant Density

    
    


As used herein, the terms “disrupted functional expression”, “disrupted expression”, and “disrupted gene” refer to a genetic modification to a specified gene that stops functional expression of the gene's product, such as an active enzyme, functional RNA, and/or functional regulatory protein. Generally, disruption in the production a gene product can be accomplished by, for example, an insertion, deletion, or substitution to a portion of the gene, which results in no formation or reduced formation of the active gene product. The disruption may preferably be a partial or complete deletion of the gene. A genetic modification that complete abolishes production of the gene product may be referred to as a “knockout” and may be denoted by the symbol “A”. For example, “ΔgltA” would refer to a knockout of the gltA gene that complete disrupted production of a functional GltA protein.
When the sequence of the gene to be disrupted is known, down regulating gene expression may be accomplished by targeted gene disruption and involves creating genetic cassettes that includes DNA to be inserted into the to-be-disrupted gene. This DNA is often a genetic marker and is flanked by sequence(s) having a high degree of homology to a portion of the targeted gene. Introduction of the cassette into the host cell results in insertion of the foreign DNA into the targeted gene via native DNA replication mechanisms of the cell (Hamilton et al., J. Bacteriol., 171:4617-4622 (1989); Balbas et al., Gene, 136:211-213 (1993); Gueldener et al., Nucleic Acids Res., 24:2519-2524 (1996); and Smith et al., Methods Mol. Cell. Biol., 5:270-277 (1996)) and interferes with transcription of the targeted gene, which produces no mRNA transcripts from which to translate a gene product.
Down regulation of expression does not require completely eliminating all expression of the gene and its corresponding gene product. Targeted genes may be down-regulated using several other techniques known in the art. For example, target genes can be modified to be under the control of non-native promoters. When desired that a pathway and/or functional gene product operate at a particular point in a cell cycle or during a fermentation run, regulated or inducible promoters can replace the native promoter of the target gene. Similarly, the native or endogenous promoter can be modified to decrease gene expression. For example, endogenous promoters can be altered in vivo by mutation, deletion, and/or substitution (see, U.S. Pat. No. 5,565,350 to Kmiec, Eric B.).
Down regulating can involve antisense technology when the sequence of the target gene is known. Here, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the anti-sense strand of RNA will be transcribed. This construct is then introduced into the host cell and the antisense strand of RNA is produced, which inhibits gene expression by preventing the accumulation of mRNA. Antisense technology is within the skill of the art. That is, a skilled artisan understands that achieving a down-regulated expression through antisense genes involves the use of chimeric genes having various regulatory elements.
Besides targeted gene disruption and antisense technology, other down regulation methods exist that do not require knowing the sequence of the to-be-disrupted gene. For example, cells may be exposed to UV radiation and then screened for the desired phenotype. Mutagenesis with chemical agents is also effective for generating mutants and commonly used substances include chemicals that affect non-replicating DNA such as HNO2 and NH2OH, as well as agents that affect replicating DNA such as acridine dyes, notable for causing frameshift mutations. Specific methods for creating mutants using radiation or chemical agents are well documented in the art. See for example Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass., (hereinafter “Brock”) or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36:227 (1992) (hereinafter “Deshpande”).
Transposon mutagenesis represents another non-specific method of gene disruption and is exemplified herein. Transposons are genetic elements that insert randomly in DNA but can be later retrieved on the basis of sequence to determine where the insertion has occurred. Both in vivo and in vitro transposition methods are known. Both methods involve the use of a transposable element in combination with a transposase enzyme. When the transposable element or transposon, is contacted with a nucleic acid molecule in the presence of the transposase, the transposable element will randomly insert into the nucleic acid molecule. The technique is useful for random mutagenesis and for gene isolation, since the disrupted gene may be identified on the basis of the sequence of the transposable element. Kits for in vitro transposition are commercially available (see for example The Primer Island Transposition Kit, available from Perkin Elmer Applied Biosystems, Branchburg, N.J., based upon the yeast Ty1 element; The Genome Priming System, available from New England Biolabs, Beverly, Mass.; based upon the bacterial transposon Tn7; and the EZ::TN Transposon Insertion Systems, available from Epicentre Technologies, Madison, Wis., based upon the Tn5 bacterial transposable element.
Exemplified herein is a method of increasing the buoyant density of a recombinant microbial cell and/or inclusion body produced by a recombinant microbial cell by decreasing or disrupting expression the gene gltA (encoding citrate synthase).
In one aspect, the endogenous copy of gltA is a knockout mutation. In a preferred aspect, the recombinant microbial host cell comprising the decreased or disrupted expression of gltA is a genetically engineered Escherichia cell expressing a chimeric gene encoding a polypeptide of interest (POI).
Methods to Identify Substantially Similar Nucleic Acid Sequences Associated with Increasing Buoyant Density
Nucleic acid hybridization may also be used to identify substantially similar nucleic acid molecules to those reported herein to increase buoyant density. The present nucleic acid molecules described herein may be used to identify genes encoding substantially similar polypeptides/proteins expected to have similar function (increased buoyant density). Nucleic acid hybridization may be conducted under stringent conditions. Substantially similar sequences are defined by their ability to hybridize, under the following stringent conditions (0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS, 65° C.).
Each of the proposed modifications is well within the routine skill in the art (see Sambrook, J. and Russell, D., Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2001)). Moreover, the skilled artisan recognizes that substantially similar sequences are also encompassed by the present invention. Furthermore, the genetic modifications illustrated herein in Escherichia coli should apply to other members of the genus Escherichia. 
As illustrated herein, the Escherichia host cell may also have a knockout to the endogenous chromosomal araBAD operon (a pBAD expression vector and arabinose induction was used to drive expression of the chimeric gene encoding the fusion peptide) and a knockout to the slyD gene (to remove possible binding between the LUMIOTM biarsenical labeling reagent and cysteine rich sequences in slyD). The recombinant Escherichia production host may comprise decreased expression and/or a disruption (such as a knockout) in the endogenous araBAD operon, the slyD gene, or a combination thereof (in addition to the genetic modification increasing buoyant density).
Peptide/Polypeptide of Interest
The function of the peptide of interest is not limited by the present method and may include, but is not limited to bioactive molecules that act as curative agents for diseases, such as insulin, interferon, interleukins, peptide hormones, immunoglobulins, antibodies, anti-angiogenic peptides, active enzymes, and peptides that bind to and affect defined cellular targets such as receptors, channels, lipids, cytosolic proteins, and membrane proteins (see U.S. Pat. No. 6,696,089); peptides having an affinity for a particular material, such as biological tissues, biological molecules, hair-binding peptides (see U.S. patent application Ser. No. 11/074,473; Intl Pat. App. No. WO 0179479; U.S. Pat. App. Pub. No. 2002/0098524; U.S. Pat. App. Pub. No. 2003/0152976; Intl Pat. App. No. WO 04048399; U.S. Pat. App. Pub. No 2007/0067924; and U.S. Pat. App. Pub. No. 2007/0249805), skin-binding peptides (see U.S. Pat. No. 7,309,482; Intl. Pat. App. No. WO 2004/000257; and U.S. Pat. App. Pub. No. 2007/0249805), nail-binding peptides (see U.S. Pat. App. Pub. No. 2007/0249805), cellulose-binding peptides, polymer-binding peptides (see U.S. Pat. App. Pub. Nos. 2007/0141629, 2007/0264720, 2008/0207872, 2007/0141628, and 2007/0261775), clay-binding peptides for targeted delivery of at least one benefit agent (see U.S. patent application Ser. No. 10/935,642; U.S. patent application Ser. No. 11/074,473; and U.S. Pat. App. Pub. No. 2007/0249805).
The peptide of interest may be a single chain peptide ranging in size from about 14 to about 600 amino acids in length and lacks an immunoglobulin fold. The peptide of interest may range in size from 14 to 400 amino acids in length, 14 to 300 amino acids in length, or 14 to about 200 amino acids in length.
The heterologous polypeptide of interest can be a polypeptide that may accumulate in inclusion bodies upon culturing a recombinant cell comprising a heterologous polypeptide-encoding polynucleotide operably linked to a promoter, to synthesize the heterologous polypeptide. The heterologous polypeptide of interest may be integrated into chromosome of production host and synthesized from chromosome, or it could be synthesized from expression plasmids present in production host. The polypeptide of interest may be produced in the form of an insoluble fusion protein. The fusion protein may include at least one peptidic solubility tag (inclusion body tag; “IBT”) to enhance accumulation of the fusion protein as inclusion bodies. Inclusion body tags are exemplified herein and in other patent applications and issued patents that are incorporated by reference. Example of inclusion body tags are provided by SEQ ID NOs: 126-139.
In general, the polypeptide can be composed of two or preferably three, segments; the IBT, the POI and optionally but preferably a peptide linker that joins the IBT and POI to each other. It is irrelevant which of the IBT or POI is positioned at the amino-terminal portion and carboxyl-terminal portion of the heterologous fusion polypeptide and vice versa.
In one embodiment, the fusion peptide may be comprised of at least one solubility tag, such as an inclusion body tag. The fusion peptide/polypeptide/protein may have the general form of:
IBT-CL-POI
or
POI-CL-IBT
wherein;
IBT=at least one inclusion body tag;
CL=at least one cleavable peptide linker; and
POI=the polypeptide of interest.
When using a cleavage peptide linker, it is preferable that the peptide linker have an enzymatic and/or chemically cleavable site. With this in mind, a linker may be designed to have any recognition and cleavage site that corresponds to the many known proteases that have been purified; such as trypsin, proteinase K, a Caspase such as Caspase 3, and the like. An example of a Caspace-3 cleavage sequence is provided as SEQ ID NO: 151.
It is similarly desirable to have one or more chemically sensitive cleavage sites on the linker that, preferably, does not also cleave the IBT and POI. A convenient chemical sensitivity is pH cleavage of the linker, more specifically, low pH. Such acid-cleavable sites may be comprised of one or more aspartic acid-proline, i.e., DP, pairs. In such embodiments of the inventive method, the pH range at which cleavage of the linker occurs is between about pH 1 to about pH 6, preferably from about pH 2 to about pH 5 and most preferably between about pH 2 to about pH 4.
The applicability of the method is broad with respect to cell type. Therefore, virtually any recombinant host cell capable of synthesizing suitable amounts of a heterologous polypeptide such that the synthesized heterologous polypeptide accumulates in inclusion bodies may be used. In a preferred embodiment, the recombinant host cell is a recombinant microbial host cell, such as yeast, fungi and bacteria. In one embodiment, the recombinant microbial cell is selected from the group consisting of Aspergillus, Trichoderma, Saccharomyces, Pichia, Phaffia, Kluyveromyces, Candida, Hansenula, Yarrowia, Salmonella, Bacillus, Acinetobacter, Zymomonas, Agrobacterium, Erythrobacter, Chlorobium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Synechococcus, Anabaena, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus. The more preferred cell types for use in the method are Saccharomyces sp., Salmonella sp., Bacillus sp. and Escherichia sp. Even more preferred is Escherichia coli. 
Single Chain Peptides Having Affinity for a Target Surface
Proteinaceous materials having strong affinity for a body surface can target delivery of one or more personal care benefit agents. Some of these materials comprise or derive from immunoglobulins or immunoglobulin fragments (antibodies, antibody fragments, Fab, single-chain variable fragments (scFv), and Camelidae VHH) having affinity for the target surface. Other such proteinaceous materials comprise non-immunoglobulin derived scaffold proteins. Further, these materials for delivery of a personal care benefit agent can include a single chain, linear peptide.
The peptide of interest used in the fusion proteins described herein may be proteinaceous material that has at least one domain having strong affinity for a target surface but does not comprise an immunoglobulin fold or underlying scaffold support. Thus, the POI preferably comprises at least one single chain peptide. Moreover, the peptide of interest described herein is heterologous to the recombinant microbial host cell and may be produced in the cytoplasm and not targeted for secretion and/or accumulation in the periplasm.
Single-chain peptides that target surfaces can be identified and isolated from peptide libraries using any number of biopanning techniques well known to those skilled in the art including, but not limited to bacterial display, yeast display, combinatorial solid phase peptide synthesis, phage display, ribosome display, and mRNA display. Techniques to generate random peptide libraries are described in Dani, M., J. of Receptor & Signal Transduction Res., 21(4):447-468 (2001). Phage display libraries are available commercially from companies such as New England BioLabs (Beverly, Mass.).
The peptide of interest may be a peptide-based reagent comprising a plurality of biopanned target surface-binding peptides coupled together (optionally through one or more spacers) to form at least one target surface binding domain. The peptide of interest may comprise multiple target surface-binding domains, wherein each domain may have affinity for the same or a different target surface. The individual biopanned target surface-binding peptides are typically about 7 to about 60 amino acids in length and often have a binding affinity (as measured or reported as an MB50 or KD value) of 10−5 M or less for the surface of the target material. The individual biopanned target surface-binding peptides may be from about 7 amino acids to about 60 amino acids in length, more preferably, from about 7 amino acids to about 25 amino acids in length, most preferably from about 7 to about 20 amino acids in length. The peptide of interest may also be a an individual target surface-binding peptide.
Examples of single chain peptide-based reagents having affinity for at least one target surface include, but are not limited to body surfaces such as hair, skin, nail, and teeth (U.S. Pat. Nos. 7,220,405; 7,309,482; and 7,285,264; U.S. Pat. App. Pub. Nos. 2005/0226839; 2007/0196305; 2006/0199206; 2007/0065387; 2008/0107614; 2007/0110686; and 2006/0073111; and Intl Pat. App. Pub. Nos. WO2008/054746; WO2004/048399, and WO2008/073368) as well as other surfaces such as pigments and miscellaneous print media (U.S. Pat. App. Pub. No. 2005/0054752), and various polymers such as polymethyl methacrylate (U.S. Pat. App. Pub. No. 2007/0265431), polypropylene (U.S. Pat. App. Pub. No. 2007/0264720), nylon (U.S. Pat. App. Pub. Nos. 2007/0141629 and 2003/0185870), polytetrafluoroethylene (U.S. patent application Ser. No. 11/607,734), polyethylene (U.S. Pat. App. Pub. No. 2007/0141628), and polystyrene (U.S. Pat. App. Pub. No. 2007/0261775). Examples of various target surface-binding peptides are provided in the present sequence listing.
The target surface-binding peptide may have strong affinity for a particulate benefit agent surface (such as a pigment, a sunscreen agent, a whitening agent, etc.), a polymeric coating applied to a particulate benefit agent (such as a coated pigment), a clay, calcium carbonate or a body surface.
Binding Affinity
The term “MB50” refers to the concentration of the binding peptide that gives a signal that is 50% of the maximum signal obtained in an ELISA-based binding assay (see present Example 11 and U.S. Published Patent Application No. 2005-0226839). The MB50 value provides an indication of the strength of the binding interaction or affinity of the components of the complex. The lower the MB50 value, the stronger the interaction of the peptide with its corresponding substrate. The term “binding affinity” refers to the strength of the interaction of a binding peptide with a given substrate. The binding affinity is defined herein in terms of the MB50 value, determined in an ELISA-based binding assay.
Peptides having an affinity for a target surface (i.e., target surface-binding peptides) may be selected using combinatorial methods that are well known in the art or may be empirically generated. It is preferred that the polypeptide of interest having affinity for a target surface has a binding affinity as measured by MB50 values, of less than or equal to about 10−5 M, more preferably less than or equal to about 10−6 M, even more preferably less than or equal to about 10−7 M, and even more preferably less than or equal to about 10−8 M.
In one embodiment, the term “high affinity” or “strong affinity” will be used to describe a binding affinity, as measured by an MB50 value, less than or equal to about 10−5 M, preferably less than or equal to about 10−6 M, more preferably less than or equal to about 10−7 M, and even more preferably less than or equal to about 10−8 M.
Microbial Host Cells
Transcription, translation, and the protein biosynthetic apparatus are universal genetic processes. Examples of microbial production hosts may include, but are not limited to bacterial species such as Salmonella, Bacillus, Acinetobacter, Zymomonas, Agrobacterium, Erythrobacter, Chlorobium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Synechococcus, Anabaena, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus. Preferably, the microbial host strain is a member of the genus Escherichia. The host strain may be Escherichia coli. The Escherichia coli host strain used to produce the polypeptide of interest is preferably derived from a K-12 strain, such as E. coli K-12 substrain MG1655 (ATCC® 47076TM).
Inclusion Body Isolation
Because of the insolubility of the inclusion body, a convenient method for isolating it would start with lysing the cells, with or without mechanical disruption. These methods generally involve suspending cells in an isotonic or hypotonic solution containing a non-denaturing surfactant (e.g., octylglucoside, TRITON® x-100, NP-40 and the like) and, optionally, disrupting the cells, such as by (ultra)sonication, pressure cycling or other homogenization method. In some methods, the suspended bacteria are treated with commercially available enzymes that lyse the cell wall, e.g., lysozyme. The relevant end point is that the contents of the bacterial cytoplasm, i.e., the polypeptide of interest, preferably in the form of inclusion bodies, are released into the lysing media.
Once lysed or disrupted, the cell lysate is usually subjected to one or more kinds of centrifugation in order to obtain a preparation of the inclusion bodies. For example, the density of the medium may be increased to an empirically determined value that is suitable for allowing the inclusion bodies to form a pellet after centrifugation. The increase in density range of the gradient may be achieved by adding sucrose, glycerol, FICOLLTM and the like, to the desired concentration. The relative buoyant density of the inclusion bodies may be determined by density gradient centrifugation, as illustrated herein.
Cleavable Peptide Linkers
The use of cleavable peptide linkers is well known in the art. Fusion peptides comprising at least one inclusion body tag will typically include at least one cleavable sequence separating the inclusion body tag from the peptide of interest. The cleavable sequence facilitates separation of the inclusion body tag(s) from the peptide(s) of interest. The cleavable sequence may be provided by a portion of the inclusion body tag and/or the peptide of interest (e.g., inclusion of an acid cleavable aspartic acid-proline moiety). The cleavable sequence preferably includes in the fusion peptide at least one cleavable peptide linker between the inclusion body tag and the peptide of interest.
Means to cleave the peptide linkers are well known in the art and may include chemical hydrolysis, enzymatic cleavage agents, and combinations thereof. One or more chemically cleavable peptide linkers are included in the fusion construct to facilitate recovery of the peptide of interest from the inclusion body fusion protein. Examples of chemical cleavage reagents include cyanogen bromide, which cleaves methionine residues; N-chloro succinimide, iodobenzoic acid or BNPS-skatole [2-(2-nitrophenylsulfenyl)-3-methylindole], which cleaves tryptophan residues; dilute acids, which cleave at aspartyl-prolyl bonds, one or more aspartic acid-proline acid cleavable recognition sites (i.e., a cleavable peptide linker comprising one or more D-P dipeptide moieties) may preferably be included in the fusion protein construct to facilitate separation of the inclusion body tag(s) form the peptide of interest. The fusion peptide may include multiple regions encoding peptides of interest separated by one or more cleavable peptide linkers.
Moreover, one or more enzymatic cleavage sequences may be included in the fusion protein construct to facilitate recovery of the peptide of interest. Proteolytic enzymes and their respective cleavage site specificities are well known in the art. Preferably, the proteolytic enzyme is selected to specifically cleave only the peptide linker separating the inclusion body tag and the peptide of interest. Examples of enzymes useful for cleaving the peptide linker include, but are not limited, to Arg-C proteinase, Asp-N endopeptidase, chymotrypsin, clostripain, enterokinase, Factor Xa, glutamyl endopeptidase, Granzyme B, Achromobacter proteinase I, pepsin, proline endopeptidase, proteinase K, Staphylococcal peptidase I, thermolysin, thrombin, trypsin, and members of the Caspase family of proteolytic enzymes (e.g. Caspases 1-10) (Talanian et al., J. Biol. Chem. (1997) 272(15): 9677-9682).
Typically, cleavage occurs after the insoluble inclusion bodies and/or insoluble fusion peptides are isolated from the cell lysate. Methods of lysing cells and isolation peptide from the cell lysate are well known in the art. Once isolated, the insoluble inclusion bodies and/or fusion peptides can be treated with a chemical cleavage agent or enzymatic cleavage agent to cleave the inclusion body tag from the peptide of interest. After cleavage step, preferably, the peptide of interest can be separated and/or isolated from the fusion protein and the inclusion body tags based on a differential solubility of the components. Parameters such as pH, salt concentration, and temperature may be adjusted to facilitate separation of the inclusion body tag from the peptide of interest. The peptide of interest may be soluble or insoluble while the inclusion body tag and/or fusion protein is insoluble or soluble in the defined process matrix, typically aqueous. Optionally, the peptide of interest may be further purified using any number of well known purification techniques in the art such as ion exchange, gel purification techniques, and column chromatography (see U.S. Pat. No. 5,648,244).
Fermentation Media
Fermentation media must contain suitable carbon substrates. Suitable substrates may include, but are not limited to, monosaccharides such as glucose and fructose, oligosaccharides such as lactose or sucrose, polysaccharides such as starch or cellulose or mixtures thereof and unpurified mixtures from renewable feedstocks such as cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt. L-arabinose is used to induce the present arabinose inducible expression system. As such, L-arabinose is typically not included in the fermentation media until expression of the desired chimeric gene (encoding the peptide or protein of interest) is desired. L-arabinose can be added at any time during the fermentation, although it is often preferable to induce expression only after a desired cell density/mass is achieved in the fermentor. It is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of organism. Preferred carbon substrates include glucose, fructose, and sucrose.
In addition to a carbon source, fermentation media may or must contain other components suitable and/or necessary for the growth of the cultures and promotion of the expression of the present fusion peptides. These are known to those skilled in the art and include minerals, salts, cofactors, buffers, etc.
Culture Conditions
Suitable growth conditions can vary and depend on the chosen production host and are generally known in the art. Typically, cells are grown at a temperature in the range of about 25° C. to about 40° C. in an appropriate medium. Suitable growth media in the present invention are common commercially prepared media such as Luria Bertani (LB) broth, Sabouraud Dextrose (SD) broth or Yeast medium (YM) broth. Other defined or synthetic growth media may also be used and the appropriate medium for growth of the particular microorganism will be known by one skilled in the art of microbiology or fermentation science. The use of agents known to modulate catabolite repression directly or indirectly, e.g., cyclic adenosine 2′:3′-monophosphate, may also be incorporated into the fermentation medium.
Suitable pH ranges for the fermentation are typically between pH 5.0 to pH 9.0, where pH 6.0 to pH 8.0 is preferred. Fermentation may be performed under either aerobic or anaerobic conditions whereas aerobic conditions are generally preferred.
Industrial Batch and Continuous Fermentations
Classical batch fermentation is a closed system where the composition of the medium is set at the beginning of the fermentation and not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation the medium is inoculated with the desired organism or organisms, and fermentation is permitted to occur without adding anything to the system. Typically, a “batch” fermentation is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems the metabolite and biomass compositions of the system change constantly up to the time the fermentation is stopped. Within batch cultures cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase generally are responsible for the bulk of production of end product or intermediate.
A variation on the standard batch system is the Fed-Batch system. Fed-Batch fermentation processes are also suitable in the present invention and comprise a typical batch system with the exception that the substrate is added in increments as the fermentation progresses. Fed-Batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO2. Batch and Fed-Batch fermentations are common and well known in the art and examples may be found in Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass. (hereinafter “Brock”), or Deshpande, Mukund V., Appl. Biochem. Biotechnol., (1992) 36:227-234.
Although typically performed in batch mode, it is contemplated that the methods described herein would be adaptable to continuous fermentation methods. Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth.
Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to the medium being drawn off must be balanced against the cell growth rate in the fermentation. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, supra.
The methods described herein may be practiced using either batch, fed-batch or continuous processes and that any known mode of fermentation would be suitable.
General Methods
Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described by Sambrook, J. and Russell, D., Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2001); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory Cold Press Spring Harbor, N.Y. (1984); and by Ausubel, F. M. et. al., Short Protocols in Molecular Biology, 5th Ed. Current Protocols and John Wiley and Sons, Inc., N.Y., 2002.
All reagents and materials were obtained from DIFCO Laboratories (Detroit, Mich.), GIBCO/BRL (Gaithersburg, Md.), TCI America (Portland, Oreg.), Roche Diagnostics Corporation (Indianapolis, Ind.) or Sigma/Aldrich Chemical Company (St. Louis, Mo.), unless otherwise specified.
The following abbreviations in the specification correspond to units of measure, techniques, properties, or compounds as follows: “sec” or “s” means second(s), “min” means minute(s), “h” or “hr” means hour(s), “μL” means microliter(s), “mL” means milliliter(s), “L” means liter(s), “mM” means millimolar, “M” means molar, “mmol” means millimole(s), “ppm” means part(s) per million, “wt” means weight, “wt %” means weight percent, “g” means gram(s), “mg” means milligram(s), “μg” means microgram(s), “ng” means nanogram(s), “g” means gravity, “gf” means maximum grams force, “HPLC” means high performance liquid chromatography, “dd H2O” means distilled and deionized water, “dcw” means dry cell weight, “ATCC” or “ATCC®” means the American Type Culture Collection (Manassas, Va.), “rpm” means revolution(s) per minute, and “EDTA” means ethylenediaminetetraacetic acid.
Compositions of Growth Media and Buffers







TABLE 1







Media and Buffers











Media/Buffer
Ingredient
Amount
















Miller LB
Casein protein
10
g/L




NaCl
10
g/L




Yeast extract
5
g/L



Dubelco's1X PBS
KCl
0.2
g/L




KH2PO4
0.2
g/L




NaCl
8
g/L




Na2HPO4•7H2O
2.16
g/L



DEK Media
KH2PO4
9
g/L




(NH4)2HPO4
4
g/L




Citric acid•H2O
1.86
g/L




Yeast extract
5
g/L




Biospumex 153K
0.1
mL/L




(Post sterilization)




MgSO4•7H2O
1.2
g/L




Thiamine HCl
4.5
mg/L




Trace elements
10
mL/L




(batch - see below)




Uracil
50
mg/L



Trace elements
EDTA
840
mg/L




CoCl2•6H2O
250
mg/L




MnCl2•4H2O
1500
mg/L




CuCl2•2H2O
150
mg/L




H3BO3
300
mg/L




Na2MoO4•2H2O
250
mg/L




Zn(CH3COO)2•2H2O
1300
mg/L




Fe(III) Citrate
10000
mg/L










EXAMPLE 1
Density Gradient Separation of Uninduced E. coli Cells from Induced E. coli Cells Expressing the POI as Inclusion Bodies
This example describes a method for separating E. coli cells producing a peptide of interest (POI) that accumulates as inclusion bodies from those cells lacking inclusion bodies. The method of separating these populations of cells is based on their differences in buoyant density. PERCOLLTM (Sigma-Aldrich) was chosen as the density gradient medium because of its non-toxic nature, low viscosity at high concentrations, and its self-forming gradient properties.
In order to reach high production yield and reduce separation costs, peptides of interest were produced to accumulate in the form of insoluble inclusion bodies (i.e., “IB”) in E. coli production hosts. Inclusion body promoting sequences referred to as inclusion body tags (“IBT”) were usually fused to the N-terminus of the POI to direct peptide accumulation into inclusion bodies. An acid cleavable site consisting of an aspartic acid-proline pair (i.e., DP) was introduced between the inclusion body promoting sequence and the POI in order to facilitate the release of the POI from the IB. Following are the strains used in this study; 1) QC1100: KK2000 ΔslyD, 2) QC1525: KK2000 ΔslyD containing plasmid pDCQ523 (SEQ ID NO:144), which expresses the genetic construct encoding IBT139(5C)-CCPGCC-HC415 (SEQ ID NO:146) peptide ( ̃28 kDa) under araBAD promoter (SEQ ID NO:148), 3) QC1101: KK2000 ΔslyD containing plasmid pLR199 (SEQ ID NO:141), which expresses IBT139-CCPGCC-HC124 peptide (SEQ ID NO: 143) ( ̃28 kDa) under araBAD promoter (SEQ ID NO: 148). KK2000 is a derivative of E. coli MG1655 (ATCC® 47076) that contained the deletion of the endogenous araBAD genes. IBT139(5C) is in an inclusion body tag derived from IBT139 where an effective number of cross-linkable cysteine residues (5 resides) was inserted into inclusion body tag IBT139 (see co-owned U.S. Patent Application Publication 2009-0043075A to Alsop et al.; hereby incorporated by reference in its entirety).
QC1525 cells were grown overnight in LB medium containing ampicillin (100 μg/mL). QC1525 cells from fresh overnight cultures were grown until they reached an optical density (OD600) of approximately 0.5-0.7, and were then inoculated into four flasks, one flask of cells that were grown but not induced and another 3 flasks of cells that were induced with 0.02% L-arabinose (Sigma-Aldrich). Induced cells were incubated for 3.5 h, 21.5 h or 24 h at 37° C. with 250 rpm shaking speed. Following induction and incubation as described, the OD600 of all four flasks of cells were measured and cells corresponding to 9 OD600 (45×108 cells total) were added to a mix of 30 mL comprising of 21 mL (70%) PERCOLLTM (a density gradient-forming composition comprising non colloidal silica (15-30 nm diameter coated with a non-dialyzable polyvinylpyrrolidone coating), and LB medium was added to a final volume of 30 mL and mixed well. One mL of each mix was centrifuged in 2-mL centrifuge tubes in a table top centrifuge (Eppendorf, model 5417R) at 14000 rpm for 90 minutes. The distribution of the cells in the 2-mL centrifuge tubes was then photographed.
The uninduced cells showed a single band (FIG. 1a), while cells induced for 3.5 h, 21.5 h or 24 h showed 2 major bands including a band lower than that observed in the uninduced cells (FIGS. 1b, 1c, and 1d, respectively). The remaining 29 mL of each mixed sample was centrifuged in a polycarbonate tube at 15000 rpm in a SS-34 rotor ( ̃27000×g) at 20° C. for one hour in a Sorvall RC-5B centrifuge. Polycarbonate tubes with the density gradient profile of uninduced and induced cells (3.5 h, 21.5 h or 24 h) were photographed (FIGS. 2a, 2b, 2c, and 2d). Different density gradient profiles were observed for uninduced and induced cells. The uninduced cells (FIG. 2a) had a major band of cells more towards the meniscus at the top of the gradient while cells induced for 3.5 h (FIG. 2b) had one faint upper band and one major band (arrow 2) significantly lower than the band observed in the uninduced cells. Cells induced for 21.5 h (FIG. 2c) or 24 h (FIG. 2d) showed multiple bands all lower than the band seen in uninduced cells (FIG. 2a). The bands as indicated in FIGS. 2a, 2b, 2c, and 2d were extracted by inserting a sterile syringe from the top of the centrifuge tubes. To prevent contamination of cells from one layer to another, a new syringe was used for every layer. The extracted cells were washed with 1×PBS, cells were pelleted down at 6500 rpm for 15 minutes, resuspended in 1 mL of 1×PBS, and then the OD600 was measured. Cell samples were normalized to 0.4 OD, to which was added 15 μL of deionized water and 15 μL of 2×SDS loading dye. The cells within the resultant mix of each sample were lysed by heating to 100° C. for 15 min in a heated dry block and centrifuged briefly. The samples were run on a NUPAGE® 4-12% Bis-Tris gel with the SEEBLUE® Plus2 pre-stained standard (Invitrogen). At the end of the run the gel was rinsed with water, stained with SIMPLYBLUETM (Invitrogen) and destained with deionized water. A band corresponding to a  ̃28 kDa protein was observed in cells extracted from lower band of the induced cells (FIG. 3, bands 2, 5, and 8). The  ̃28 kDa band was absent in uninduced cells and the upper layers from induced cells (FIG. 3, bands 1, 3, 4, 6, and 7). Therefore, this density gradient centrifugation method can be utilized for the separation of uninduced cells from induced cells expressing a polypeptide of interest (POI).
EXAMPLE 2
Density Gradient Separation of Induced E. coli Cells Producing Different Inclusion Bodies
This example illustrates that cells producing different inclusion bodies can have sufficiently distinct buoyant densities to permit separation on density gradients.
The density gradient band profile of QC1101 cells (Strain QC1101: KK2000 ΔslyD containing plasmid pLR199 (SEQ ID NO: 141), which expresses IBT139-CCPGCC-HC124 (SEQ ID NO: 143) under control of an araBAD promoter (SEQ ID NO:148) were compared with the QC1525 cells described above, which express IBT139(5C)-CCPGCC-HC415 (SEQ ID NO: 146) peptide. Both E. coli strains were grown overnight in LB medium containing ampicillin (100 μg/mL). The following morning, QC1101 and QC1525 cells were respectively sub-cultured into LB flasks containing carbenicillin (100 μg/mL). One batch each of QC1101 and QC1525 cells was induced with 0.02% L-arabinose (Sigma-Aldrich) at OD600 ̃0.5-0.7, while a batch of QC1101 cells was not induced (control). All three flasks of cells were grown for 22 hours following the time of induction and the OD600 was monitored.
As previously described a total of 9 OD600 (approximately 45×108 cells total) cells of each of the above described samples were individually added to their respective tubes containing 21 mL (70%) PERCOLLTM in 0.9% NaCl followed by LB media to a total volume of 30 mL. In addition to QC1101 uninduced (QC1101 U), QC1101 induced (QC1101 I), and QC1525 (QC1525 I) induced samples, another sample was prepared by mixing QC1101 induced cells and QC1525 induced cells (QC1101 I+QC1525 I) and added to a tube containing 21 mL (70%) PERCOLLTM, 0.9% NaCl in a total volume of 30 mL. All samples were mixed well and transferred to polycarbonate centrifuge tubes and centrifuged as described above. The tubes after centrifugation were digitally photographed and bands corresponding to the cells were compared (FIGS. 4a, 4b, 4c, and 4d).
QC1101 uninduced cells showed a major band towards the top of the gradient (FIG. 4a; arrow 1) while QC1101 induced cells showed 2 prominent bands, upper and lower (FIG. 4b; arrows 2 and 3). QC1525 induced cells also showed 2 bands, an upper band (arrow 4) that is much fainter than the QC1101 induced sample and a lower band (arrow 5) that is lower than lower band seen in QC1101 induced cells (FIG. 4c). The sample which had both QC1101 induced and QC1525 induced cells mixed together had an intermediate profile matching QC1101 induced and QC1525 induced cells (FIG. 4d). The three bands (FIG. 4d; arrows 6, 7, and 8) characteristic of QC1101 and QC1525 induced cells were all clearly distinguishable indicating that the separation of the three bands was based on the respective buoyant densities of the cell samples.
Bands as indicated in FIGS. 4a, 4b, 4c, and 4d were extracted by inserting a sterile syringe from top and processed as described earlier in Example 1. A band corresponding to the  ̃28 kDa POI was observed in cells extracted from lower band of the QC1101 induced cells, while no bands were seen in upper band of QC1101 induced or QC1101 uninduced cells. A band corresponding to the  ̃28 kDa POI was seen in cells extracted from the lower band of induced QC1525 cells, while no protein specific band was visualized from upper band of QC1525 induced cells. QC1525 induced cells had higher buoyant density compared to QC1101 induced cells and could be separated on density gradient as seen in density gradient pattern of the mixed sample containing both QC1101 induced and QC1525 induced cells (FIG. 4d). This was confirmed by the SDS-PAGE pattern of the same. In order to quantify the difference in buoyant density, the experiment was repeated with custom synthesized density marker beads (American density Material Inc., VA, USA) for approximating the densities of specific points of buoyant density that correspond to those of QC1101 and QC1525.
The buoyant density of QC1101 uninduced cells was  ̃1.082 g/mL, while the upper band of QC1101 induced cells had buoyant density of  ̃1.103 g/mL and lower band had a buoyant density of  ̃1.118 g/mL. QC1525 induced cells had buoyant density of  ̃1.126 g/mL for the major lower band. One milliliter of each of the above 4 samples, (i.e., QC1101 uninduced, QC1101 induced, QC1525 induced, and mixed samples of QC1101 induced and QC1525 induced) were mixed with 70% PERCOLLTM, LB media, and 0.9% NaCl and centrifuged in microcentrifuge tubes as described in Example 1. It was demonstrated that cells with different inclusion bodies (i.e., induced QC1101 cells) could be distinguished from induced QC1525 cells, thus allowing the method to be applied for larger scale density gradient screening.
EXAMPLE 3
Generation of BL21 Genomic DNA Library to Identify Genes that May Increase Buoyant Density of E. coli Cells Producing HC124
To identify genes that can increase the buoyant density of E. coli cells, genomic DNA library from E. coli BL21 strain was constructed. Genomic DNA fragments of approximately 2 to 3 kb in size were obtained from E. coli BL21 strain by partial digestion of the BL21 genomic DNA with Tas I restriction enzyme at a non-ideal temperature (to prevent complete digestion) of 55° C. for 50 minutes. The digested fragments were subjected to agarose gel electrophoresis alongside a DNA molecular weight ladder. Agarose slices containing genomic DNA fragments corresponding in size to approximately 2 to 3 kb were excised from gel and the DNA therein eluted.
Vector pDCQ601 (SEQ ID NO: 159) was digested with 5 units of EcoRI (NEB, USA) at 37° overnight. The 5.3 kb fragment corresponding to EcoRI digested plasmid was eluted from an agarose gel. The eluted EcoRI digested plasmid was treated with Antarctic phophatase (New Engand Biolabs, USA) for 1 hour at 37° C., followed by heat inactivation of the Antarctic phophatase by incubating the reaction mix at 65° C. for 5 minutes. The reaction mix was cleaned by using DNA Cleanup Kit (Zymo Research, USA). Aliquots of the eluates of both EcoRI digested and phosphatase treated vector and the Tas I digested genomic DNA (2-3 Kb fragments) were combined for ligation using Roche Rapid DNA Ligation Kit (Roche, USA). The ligation reaction used vector ends and insert ends ratio of 1:3 at 24° C. for 15 min in a total volume of 21 μL.
An aliquot of 10 μL of the ligation mix was used to transform CB5 alpha competent cells (Chromous Biotech, Bangalore, India; Catalog #PCR 16-NP) which were then plated on 4 different LB Kan plates. An average of 2000 colonies per plate was obtained. Additional ligations were done in four batches and four plasmid pools of approximately 15000 colonies each were prepared and transformed into QC1101 electrocompetent cells to have  ̃10-fold coverage of the E. coli BL21 genome. Thirty colonies from transformed QC1101 cells were randomly picked and tested for  ̃2-3 Kb inserts by colony PCR using PBHR1F (SEQ ID NO: 162) and PBHR1R (SEQ ID NO: 163) primers in the following manner. Random colonies were picked from LBAmp+Kan+ plates and were lysed by heating at 95° C. for 5 min. Standard PCR was performed with annealing temperature of 55° C. for 30 sec and extension temperature of 72° C. for 3.5 min. All colonies were found to have  ̃2-3 kb inserts. Sequencing of greater than 30 plasmids isolated from these colonies revealed that all of them had unique DNA inserts. The BL21 genomic DNA library with 2-3 kb insert size (designated as RK1) was used to screen for genes that can increase the buoyant density of E. coli cells that are synthesizing polypeptides that accumulate in the form of inclusion bodies.
EXAMPLE 4
Density Gradient Sorting of Inclusion Bodies is Influenced by Genes Obtained from a BL21 Genomic DNA Library and Introduced into Inclusion Body-Expressing E. coli Cells
To screen and identify genes that can increase the buoyant density of E. coli that contain inclusion bodies, QC1101 cells that harbor plasmid pLR199 (SEQ ID NO: 141), which expresses the genetic construct encoding IBT139-CCPGCC-HC124 (SEQ ID NO: 142) under the araBAD (SEQ ID NO: 148) promoter and transformed with pDCQ601 plasmid library pools of 2-3 Kb BL21 genomic DNA fragments (RK1 library) were grown overnight in LB medium containing 100 μg/mL ampicillin, 50 μg/mL kanamycin. The following morning, the RK1-transformed cells were freshly inoculated into 2 flasks of LB medium containing 100 μg/mL carbenicillin, 50 μg/mL kanamycin and grown to an OD600 of  ̃0.6. One flask of cells was induced with 0.02% L-arabinose while the other flask was used as an uninduced control. Cells were grown for 5 hours following induction and OD600 of both the flasks of cells was measured. Cells corresponding to 9 OD600 (45×108 cells total) were added to a mix of 30 mL volume comprising of 21 mL (70%) PERCOLLTM, 0.9% NaCl and rest of the volume was made up with LB medium. A density marker sample with varying density marker beads (American Density Materials Inc.) was prepared similarly. All the samples were mixed well and spun at 15000 rpm (approximately 27000×g) in a SS-34 rotor at 20° C. for one hour in Sorvall centrifuge in polycarbonate tubes. Following centrifugation the tubes were digitally photographed.
In comparison with control (i.e., uninduced cells) which had a single band upwards towards the meniscus with buoyant density of  ̃1.094, induced cells had 2 bands, an upper band with buoyant density of  ̃1.106 and a lower band which was significantly lower than the band seen in uninduced cells with a buoyant density of  ̃1.120. All bands were aspirated out with sterile 10-mL syringes and washed with 1×PBS by centrifuging at 6500 rpm at 4° C. for 15 min and OD600 was taken. OD600 of the extracted cells was normalized. Cell lysates from the uninduced and induced samples were electrophoresed on 4-12% bis-tris gel as described in Example 1.
The lower band corresponded to cells having intracellular inclusion body was confirmed by SDS-PAGE. Cells extracted from the lower band of RK1 induced cells from the density gradient were used as the inoculum for the next round of growth and sorting. Four more sorting cycles for a total of 5 rounds of sorting were performed. Cells from each sorting cycle were plated onto LBAmp+Kan+ plate and 20 random colonies were picked for DNA sequencing and for micro density gradient centrifugation. One of the colonies in the fifth sort, colony 181, demonstrated increased buoyant density in the micro density gradient. The sequence of the insert (SEQ ID NO: 152) identified the region to be an approximately 2 Kb genomic DNA insert containing ysaB, glyQ, and partial glyS genes (FIG. 5). The vector housing the BL21 library, pDCQ601, did not provide a heterologous promoter in an orientation that would account for the expression of the insert containing ysaB, glyQ, and partial glyS genes. Accordingly, it is believed that the insert contains one or more endogenous promoters in addition to the nucleotide sequences encoding the YsaB (a conserved hypothetical protein), GlyQ (glycyl-tRNA synthetase; subunit alpha) and partial GlyS (glycyl-tRNA synthetase; beta subunit) polypeptides.
A density gradient was set up with control strain QC1101, two other candidates from sort 3 (colony 127 and colony 145) and colony 181 (sort 5) were grown and induced along with uninduced QC1101 cells as control as described earlier in the Example 3. All samples, i.e., QC1101 uninduced cells (FIG. 6a; QC1101-U), QC1101 induced cells (FIG. 6b; QC1101-I), colony 127 induced cells (FIG. 6c; Col-127—1), colony 145 induced cells (FIG. 6d; Coli-145_I), and colony 181 induced cells (FIG. 6e; Col-181—1) were subjected to a density gradient separation as described earlier. Density gradient beads were also subjected to a density gradient (FIG. 6f). QC1101 induced cells had two bands of cells with buoyant density of  ̃1.098 g/mL and  ̃1.118 g/mL) (FIG. 6b; arrows 2 and 3), while colony 181 induced cells had a single band with buoyant density of  ̃1.125 g/mL) (FIG. 6e; arrow 8) confirming the increase in the buoyant density of E. coli cells with the DNA insert comprising ysaB, glyQ, and partial glyS genes. Cells from each of the cultures of QC1101 uninduced cells, QC1101 induced cells, colony 127 induced cells, colony 145 induced cells, and colony 181 induced cells were normalized by OD600 and following lysis and electrophoresis were examined for band intensity corresponding to  ̃28 kDa band of interest by densitometry in Bio-Rad densitometer. An increase of  ̃34% in  ̃28 kDa POI was noted in colony 181 induced cells in comparison to induced QC1101 cells (FIG. 7, lane 3 and lane 8).
It was then determined whether or not this increased buoyant density was a result of having the DNA insert (comprising ysaB, glyQ, and partial glyS gene (SEQ ID NO: 152)). Vector pDCQ601 (SEQ ID NO: 159) carrying a  ̃2 Kb DNA insert (ysaB, glyQ, partial glyS gene as explained above) and pLR199 (SEQ ID NO: 141) were extracted from colony 181 induced cells by standard plasmid extraction methods. The vector and plasmid were transformed into new QC1100 host cells that lack both of the above described plasmids. The transformed QC1100 strain, along with QC1101 induced and uninduced controls were checked for changes in buoyant density and peptide expression. QC1101 was grown and induced exactly as described earlier as a control. Uninduced and induced QC1101 cells along with transformed QC1100 induced cells were subjected to a density gradient. The increase in buoyant density was evident in transformed QC1100 cells in comparison to induced QC1101 and uninduced QC1101. SDS-PAGE of cell lysates from these samples revealed an increase of  ̃34% in  ̃28 kDa POI in QC1100 transformed with the plasmids validating that the BL21 genomic region comprising ysaB, glyQ and partial glyS (SEQ ID NO: 152) was responsible for conferring the phenotype of heavier buoyant density to E. coli cells.
EXAMPLE 5
Density Gradient Sorting of a Knock-Out Library to Identify Genes Altering the Buoyant Density of Inclusion Body-Expressing E. coli Cells
To screen for gene knockouts that may increase buoyant density of inclusion body producing cells, a gene knockout library was made by pooling the individual gene deletions of E. coli in the Keio collection (Baba, T., et al., supra). The Keio collection is essentially a library of non-lethal in-frame single gene knockouts.
The plasmid which expresses the genetic construct encoding IBT139(5C)-CCPGCC-HC415 (SEQ ID NO: 145) under araBAD promoter (SEQ ID NO: 148) was transformed into the pooled Keio deletion strains. The transformed cells were plated on LB plates with carbenicillin 100 μg/mL. All the colonies grown on carbenicillin selection plates were scraped off and resuspended in DEK medium with carbenicillin 100 μg/mL. This suspension was diluted to an OD600  ̃4 and used to inoculate 10 mL of fresh DEK medium with carbenicillin 100 μg/mL. The cultures were grown at 37° C. with shaking for 2 hours until an OD600  ̃1.5 was reached. The cells were induced with 0.2% L-arabinose for 3 hours. Six milliliters of the induced cultures were diluted with 3 mL of fresh DEK medium and mixed with 21 mL of PERCOLLTM to make the final volume of 30 mL. The mixture was centrifuged at 27,000×g for 1 hour at 18° C. The cells from the bottom one-third of the band on density gradient were recovered using a 1-mL pipette. The cells were washed twice with 35 mL of phosphate buffered saline (PBS) and resuspended in fresh DEK medium with 100 μg/mL carbenicillin and were used as the seed culture for the next round of enrichment. A total of three rounds of enrichment of denser inclusion body-producing cells were performed. At the end of the third round, the recovered cells were diluted and plated on LB medium with 100 μg/mL carbenicillin plates. Colonies were randomly picked for sequencing to identify the gene mutation. Eight clones with multiple hits were selected to be tested by density gradient centrifugation. The eight individual isolates (F1, B3, C6, F1, A12, B11, D2, and E4) were grown in LB medium with carbenicillin (100 μg/mL) and kanamycin (25 μg/mL) together with the control; wild type strain BW25113 (FIG. 8; “BW”) containing the same inclusion body producing plasmid) in LB medium with carbenicillin (100 μg/mL) till OD600  ̃0.6 and induced with 0.2% L-arabinose for approximately 17 hours. Normalized concentrations of whole cells were loaded in 70% PERCOLLTM in microfuge tubes.
In addition, whole cells were frozen at −80° C. and subsequently lysed using Celytic Express (Sigma-Aldrich, St Louis, Mo.) for 1 hour at 37° C. The crude inclusion body preparations obtained from the lysed cells were also loaded in 70% PERCOLLTM in microfuge tubes. The microfuge density gradient samples were centrifuged at 15,000×g for 90 min. After centrifugation, the samples were taken out and photographed as shown in FIG. 8. The top panel (WC) shows the whole cell samples which had wider density gradient bands than were previously observed. The lower panel (IB) shows the banding of the crude inclusion body samples obtained from the corresponding whole cell samples shown directly above (panel WC). The IB bands clearly demonstrate more discrete density gradient bands than the whole cells in FIG. 8. As shown for both the cell bands and the IB bands, isolates F1 and A12 showed increased density when compared to the respective controls (FIG. 8, BW).
The two positive hits were repeated as described above. Additional IB samples were prepared from 3.5 mL of induced cultures by freeze-thawing and lysing with Celytic for 1 hour at 37° C. The crude IB preparation was loaded onto 70% PERCOLLTM in the 30-mL large centrifuge tubes and centrifuged at 27,000×g for 60 min. Both isolates exhibited denser inclusion bodies than the control. Sequencing of the two isolates showed that they contained the gltA deletion (ΔgltA). GRA is encoded by the polynucleotide SEQ ID NO: 164 encoding citrate synthase (SEQ ID NO: 165).
It was also determined whether or not additional deletions, especially deletions neighboring the gltA deletion, would also confer increased buoyant density to induced cells and their corresponding inclusion bodies. The JW0710 strain (Baba et al., supra) containing the gltA deletion and the JW0709 strain containing the adjacent ybgD deletion from the Keio collection were transformed with the peptide production plasmid. Duplicates of these two cultures and the control were grown and induced as describe above. The whole cells (FIGS. 9b and 9c) and the crude inclusion bodies (FIGS. 9e and 9f) from these cultures were analyzed by density gradient centrifugation. A set of beads were used as density standards to determine the buoyant density values (FIGS. 9a and 9d). The buoyant density of the control cells had a wider distribution of about 1.08-1.09 (FIG. 9b). The buoyant density of the ΔgltA cells was estimated to be about 1.115 (FIG. 9c). The buoyant density of the inclusion body from the control was approximately 1.121 (FIG. 9e) and the buoyant density of the inclusion body from the ΔgltA cells was approximately 1.142. Results confirmed that the cells and the inclusion bodies from the ΔgltA strain showed increased buoyant density than the control strain, whereas the cells and the inclusion bodies from the ΔybgD strain showed similar buoyant densities as the control strain and the corresponding IBs.
The induced cultures were also loaded on SDS-PAGE gel and analyzed. Similar amounts of peptide were produced from all these strains. The results show that more dense inclusion bodies (not more inclusion body) were produced in the ΔgltA strain and that this was indeed due to the deletion of the gltA gene.

## Claims

1. A method comprising:
a) providing a population of recombinant microbial cells, the recombinant microbial cells in the population comprising;
i) at least one introduced genetic modification that increases expression of GlyS, GlyQ, YsaB, or a combination thereof; and
ii) a chimeric genetic construct encoding a polypeptide of interest, which polypeptide is not GlyS, GlyQ, or YsaB;

b) growing the recombinant microbial cells under suitable conditions whereby the polypeptide of interest is produced and accumulates within the recombinant microbial cells ;
c) fractionating the population of recombinant microbial cells grown in (b) by a density gradient centrifugation;
d) isolating a subpopulation of the recombinant microbial cells from a fraction having a higher buoyant density; and
e) optionally repeating steps (a) through (d).

2. The method of claim 1 wherein the polypeptide of interest accumulates within the recombinant microbial cells in the form of at least one inclusion body.

3. The method of claim 1 wherein polypeptide of interest is 14 to 600 amino acids in length.

4. The method of claim 3 wherein the polypeptide of interest is expressed as a fusion protein.

5. The method of claim 4 wherein the fusion protein comprises the general structure:
IBT-CL-POI
or
POI-CL-IBT
wherein;
IBT =at least one inclusion body tag;
CL =at least one cleavable peptide linker; and POI=the polypeptide of interest.

6. The method of claim 1 wherein the recombinant microbial cells are bacterial cells, yeast cells or fungal cells.

7. The method of claim 6 wherein the recombinant microbial cells are selected from the group consisting of Aspergillus, Trichoderma, Saccharomyces, Pichia, Phaffia, Kluyveromyces, Candida, Hansenula, Yarrowia, Salmonella, Bacillus, Acinetobacter, Zymomonas, Agrobacterium, Erythrobacter, Chlorobium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Synechococcus, Anabaena, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus.

8. The method of claim 7 wherein the recombinant microbial cells are Escherichia coli.

9. The method of claim l further comprising introducing at least one genetic modification that decreases or disrupts expression of GltA.

10. The method of claim 1 wherein the isolated subpopulation of cells of step (d) has a buoyant density of at least 1.1 g/mL.

11. A method comprising:
a) providing a population of recombinant microbial cells, the recombinant microbial cells in the population comprising;
i) at least one introduced genetic modification that decreases or disrupts expression of GltA; and
ii) a chimeric genetic construct encoding a polypeptide of interest;

b) growing the recombinant microbial cells under suitable conditions whereby the polypeptide of interest is produced and accumulates within the recombinant microbial cells ;
c) fractionating the population of recombinant microbial cells grown in (b) by a density gradient centrifugation;
d) isolating a subpopulation of the recombinant microbial cells from a fraction having a higher buoyant density; and
e) optionally repeating steps (a) through (d).

12. The method of claim 11 wherein the polypeptide of interest accumulates within the recombinant microbial cells in the form of at least one inclusion body.

13. The method of claim 11 wherein the at least one introduced genetic modification is a knockout mutation.

14. The method of claim 11 wherein polypeptide of interest is 14 to 600 amino acids in length.

15. The method of claim 11 wherein the polypeptide of interest is expressed as a fusion protein.

16. The method of claim 15 wherein the fusion protein comprises the general structure:
IBT-CL-POI
or
POI-CL-IBT
wherein;
IBT=at least one inclusion body tag;
CL=at least one cleavable peptide linker; and POI=the polypeptide of interest.

17. The method of claim 11 wherein the recombinant microbial cells are bacterial cells, yeast cells or fungal cells.

18. The method of claim 17 wherein the recombinant microbial cells are selected from the group consisting of Aspergillus, Trichoderma, Saccharomyces, Pichia, Phaffia, Kluyveromyces, Candida, Hansenula, Yarrowia, Salmonella, Bacillus, Acinetobacter, Zymomonas, Agrobacterium, Erythrobacter, Chlorobium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Synechococcus, Anabaena, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus.

19. The method of claim 18 wherein the recombinant microbial cells are Escherichia coli.

20. The method of claim 11 further comprising introducing at least one genetic modification that increases expression of GlyS, GlyQ, YsaB, or a combination thereof.

21. The method of claim 11 wherein the isolated subpopulation of cells of step (d) has a buoyant density of at least 1.1 g/mL.