E. coli Separatome-Based Protein Expression And Purification Platform

Abstract

Provided is a separatome-based peptide, polypeptide, and protein expression and purification platform based on the juxtaposition of the binding properties of host cell genomic peptides, polypeptides, and proteins with the characteristics and location of the corresponding genes on the host cell chromosome of E. coli. The separatome-based protein expression and purification platform quantitatively describes and identifies priority deletions, modifications, or inhibitions of certain gene products to increase chromatographic separation efficiency, defined as an increase in column capacity, column selectivity, or both, with emphasis on the former. Moreover, the separatome-based protein expression and purification platform provides a computerized knowledge tool that, given separatome data and a target recombinant peptide, polypeptide, or protein, intuitively suggests strategies facilitating efficient product purification. The separatome-based protein expression and purification platform is an efficient bioseparation system that intertwines host cell expression systems and chromatography.

What is claimed is: 
     
         1 . An isolated  E. coli  host cell for expression of a target host cell peptide, polypeptide, or protein, or a target recombinant peptide, polypeptide, or protein, wherein the genome of said isolated  E. coli  host cell is:
 i) a reduced genome, and/or   ii) a modified genome, and/or   iii) a genome in which expression of genes is reduced or completely inhibited,   wherein genes that are deleted, modified, or the expression of which is reduced or completely inhibited in said isolated  E. coli  host cell code for peptides, polypeptides, or proteins that interfere with and impair the chromatographic separation efficiency of said target host cell peptide, polypeptide, or protein, or said target recombinant peptide, polypeptide, or protein, expressed in said isolated  E. coli  host cell,   wherein said genes are selected from the group consisting of:
 a) combinations of the genes listed in Table 8; 
 b) combinations of the genes listed in Table 9; 
 c) combinations of any of the genes listed in Tables 8 and 9 taken together; 
 d) combinations of the genes listed in Table 14; and 
 e) combinations of any of the genes listed in Tables 8, 9, and 14 taken together, 
   wherein deletion, modification, or reduction or complete inhibition of expression of said genes improves the chromatographic separation efficiency of said target host cell peptide, polypeptide, or protein, or said target recombinant peptide, polypeptide, or protein, in an amount in the range of from about 5% to about 50% compared to the chromatographic separation efficiency of said target host cell peptide, polypeptide, or protein, or said target recombinant peptide, polypeptide, or protein, in the presence of host cell peptides, polypeptides, or proteins coded for by said genes that are deleted, modified, and/or the expression of which is reduced or completely inhibited in said isolated  E. coli  host cell upon affinity or adsorption, non-affinity column chromatography of said target host cell peptide, polypeptide, or protein, or said target recombinant peptide, polypeptide, or protein.   
     
     
         2 . The isolated  E. coli  host cell of  claim 1 , which is an  E. coli  strain selected from the group consisting of strain K-12, strain B, strain C, and strain W. 
     
     
         3 . The isolated  E. coli  host cell of  claim 2 , wherein:
 said  E. coli  strain K-12 is selected from the group consisting of W3110, DH10B, DH5alpha, DH1, MG1655, and BW2952; and   said  E. coli  strain B is selected from the group consisting of B REL606, BL21, and BL21-DE3.   
     
     
         4 . The isolated  E. coli  host cell of  claim 1 , which is selected from the group consisting of:
 Alpha-Select Bacteriophage T1-Resistant Gold Efficiency (F− deoR endA1 recA1 relA1 gyrA96 hsdR17(rk − , mk + ) supE44 thi-1 phoA Δ(lacZYA-argF)U169 Φ80lacZΔM15λ−),   Alpha-Select Bacteriophage T1-Resistant Silver Efficiency (F− deoR endA1 recA1 relA1 gyrA96 hsdR17(rk − , mk + ) supE44 thi-1 phoA Δ(lacZYA-argF)U169 Φ80lacZΔM15λ−),   Alpha-Select Bronze Efficiency (F− deoR endA1 recA1 relA1 gyrA96 hsdR17(rk−, mk+) supE44 thi-1 phoA Δ(lacZYA-argF)U169 Φ80lacZΔM15λ−),   Alpha-Select (F− deoR endA1 recA1 relA1 gyrA96 hsdR17(rk−, mk+) supE44 thi-1 phoA Δ(lacZYA-argF)U169 Φ80lacZΔM15λ−),   AG1 (endA1 recA1 gyrA96 thi-1 relA1 glnV44 hsdR17(r K   −  m K   + )),   AB1157 (thr-1, araC14, leuB6(Am), Δ(gpt-proA)62, lacY1, tsx-33, qsr′-0, glnV44(AS), galK2(Oc), LAM−, Rac-0, hisG4(Oc), rfbC1, mgl-51, rpoS396(Am), rpsL31(strR), kdgK51, xylA5, mtl-1, argE3(Oc), thi-1),   B2155 (thrB1004 pro thi strA hsdsS lacZD M15 (F′lacZD M15 lacI q  traD36 proA + proB + ) Δ dapA::erm (Erm r ) pir::RP4 [::kan (Km r ) from SM10]),   B834(DE3) (F − ompT hsdS B (r B   −  m B   − ) gal dcm met (DE3)),   BIOBlue (recA1 endA1 gyrA96 thi-1 hsdR17(rk−, mk+) supE44 relA1 lac [F′ proAB lacI q ZΔM15 Tn10(Tet r )]),   BL21 ( E. coli  B F− dcm ompT hsdS(r B   −  m B   − ) gal [malB + ] K-12 (λ S )),   BL21(AI) (F −  ompT gal dcm lon hsdS B (r B   −  m B   − ) araB::T7RNAP-tetA),   BL21(DE3) (F −  ompT gal dcm lon hsdS B (r B   −  m B   − ),(DE3 [lacI lacUV5-T7 gene 1 ind1 sam7 nin5])),   BL21 (DE3) pLysS (F− ompT hsdS B (rB−, mB−) gal dcm (DE3) pLysS (CamR)),   BL21-T1R (F− ompT hsdSB(rB− mB−) gal dcm tonA),   BNN93 (F −  tonA21 thi-1 thr-1 leuB6 lacY1 glnV44 rfbC1 fhuA1 mcrB e14−(mcrA − ) hsdR(r K   − m K   − ) λ − ),   BNN97 (BNN93 (λgt11)),   BW26434 (Δ(araD-araB)567, Δ(lacA-lacZ)514(::kan), lacI P -4000(lacI q ), λ − , rpoS396(Am)?, rph-1, Δ(rhaD-rhaB)568, hsdR514),   C600 (F −  tonA21 thi-1 thr-1 leuB6 lacY1 glnV44 rfbC1 fhuA1λ − ),   CAG597 (F −  lacZ(am) pho(am) tyrT[supC(ts)] trp(am) rpsL(Str R ) rpoH(am)165 zhg::Tn10 mal(am)),   CAG626 (F −  lacZ(am) pho(am) ion trp(am) tyrT[supC(ts)] rpsL(Str R ) mal(am)),   CAG629 (F −  lacZ(am) pho(am) ion supC(ts) trp(am) rpsL rpoH(am)165 zhg::Tn10 mal(am)),   CH3-Blue (F− ΔmcrA Δ(mrr-hsdRMS-mcrBC) T80lacZΔM15 ΔlacX74 recA1 endA1 ara Δ139 Δ(ara, leu)7697 galU galrpsL(Str R ) nupG λ−),   CSH50 (F −  λ −  ara Δ(lac-pro) rpsL thi fimE::IS1),   D1210 (HB101 lac q  lacY + ),   dam-dcm-Bacteriophage T1-Resistant (F− dam-13:Tn9(Cam R )dcm-6 ara-14 hisG4 leuB6 thi-1 lacY1 galK2 galT22 glnV44 hsdR2 xylA5 mtl-1 rpsL136(Str R ) rtbD1 tonA31 tsx78 mcrA mcrB1),   DB3.1 (F− gyrA462 endA1 glnV44 Δ(sr1-recA) mcrB mrr hsdS20(r B   − , m B   − ) ara14 galK2 lacY1 proA2 rpsL20(Sm r ) xyl5 Δleu mtl1),   DH1 (endA1 recA1 gyrA96 thi-1 glnV44 relA1 hsdR17(r K   −  m K   + ) λ − ),   DH5α Turbo (F′ proA + B+ lacI q  Δ lacZ M15/fhuA2 Δ(lac-proAB) glnV gal R(zgb-210::Tn10)Tet S  endA1 thi-1 Δ(hsdS-mcrB)5),   DH12S (mcrA Δ(mrr-hsdRMS-mcrBC) φ80d lacZΔM15 ΔlacX74 recA1 deoR Δ(ara, leu)7697 araD139 galU galK rpsL F′ [proAB +  lacI q ZΔM15]),   DM1 (F− dam-13::Tn9(Cm R ) dcm− mcrB hsdR-M+gal1 gal2 ara− lac− thr− leu− tonR tsxR Su0),   E. CLONI® 5ALPHA (fhuA2Δ(argF-lacZ) U169 phoA glnV44 Φ80 Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17),   E. CLONI® 10G (F− mcrA Δ(mrr-hsdRMS-mcrBC) endA1 recA1 Φ80dlacZΔM15 ΔlacX74 araD139 Δ(ara, leu)7697galU galK rpsL nupG λ− tonA (StrR)),   E. CLONI® 10GF′ ([F′ pro A+B+lacI q ZΔM15::Tn10 (Tet R )]/mcrA Δ(mrr-hsdRMS-mcrBC) endA1 recA1 T80dlacZΔM15 ΔlacX74 araD139 Δ(ara, leu)7697 galU galK rpsL nupG λ− tonA (StrR)),     E. coli  K12 ER2738 (F′proA+B+ lacI q  Δ(lacZ)M15 zzf::Tn10(Tet R )/fhuA2 glnV Δ(lac-proAB) thi-1 Δ(hsdS-mcrB)5),   ElectroMax™ DH10B (FmcrA Δ(mrr-hsdRMS-mcrBC) Φ80lacZΔM15 ΔlacX74 recA1 endA1 araD139Δ(ara,leu)7697 galU galK λ − rpsL nupG),   ELECTROMAX™ DH5ALPHA-E (F− φ80lacZΔM15 Δ(lacZYA-argF) U169 recA1 endA1 hsdR17 (rk−, mk+) galphoA supE44λ-thi-1 gyrA96 relA1),   ElectroSHOX (F− mcrA Δ(mrr-hsdRMS-mcrBC) T80lacZΔM15 ΔlacX74 recA1 endA1 ara Δ139 Δ(ara, leu)7697 galU galKrpsL(Str R ) nupG λ − ),   EP-MAX™10B F′ (mcrA Δ(mrr-hsdRMS-mcrBC) φ80dlacZΔM15 ΔlacX74 deoR recA1 endA1 araD139 Δ(ara, leu)7697 galU galK rpsL nupG λ−/F′[lacI q ZΔM15 Tn10 (Tet R )]),   ER1793 (F −  huA2 Δ(lacZ)r1 glnV44 e14 − (McrA − ) trp-31 his-1 rpsL104 xyl-7 mtl-2 metB1 Δ(mcrC-mrr)114::IS10),   ER1821 (F −  glnV44 e14 − (McrA − ) rfbD1? relA1? endA1 spoT1? thi-1 Δ(mcrC-mrr)114::IS10),   ER2738 (F′proA + B +  lacI q    (lacZ)M5 zzf::Tn10(Tet R )/fhuA2 glnV  (lac-proAB) thi-1  (hsdS-mcrB)5),   ER2267 (F′ proA + B +  lacI q    (lacZ)M15 zzf:mini-Tn10 (Kan R )/ (argF-lacZ) U169 glnV44 e14 − (McrA − ) rfbD1? recA1 relA1? endA1 spoT1? thi-1  (mcrC-mrr)114::IS10),   ER2507 (F −  ara-14 leuB6 fhuA2  (argF-lac) U169 lacY1 glnV44 galK2 rpsL20 xyl-5 mtl-5  (malB) zjc::Tn5(Kan R ) (mcrC-mrr) HB101 ),   ER2508 (F −  ara-14 leuB6 fhuA2  (argF-lac)U169 lacY1 lon::miniTn10(Tet R ) glnV44 galK2 rpsL20(Str R ) xyl-5 mtl-5  (malB) zjc::Tn5(Kan R )  (mcrC-mrr) HB101 ),   ER2738 (F′proA + B +  lacI P  Δ(lacZ)M15 zzf::Tn10(Tet R )/fhuA2 glnV  (lac-proAB) thi-1  (hsdS-mcrB)5),   ER2925 (ara-14 leuB6 fhuA31 lacY1 tsx78 glnV44 galK2 galT22 mcrA dcm-6 hisG4 rfbD1 R(zgb210::Tn10)Tet S  endA1 rpsL136 dam13::Tn9 xylA-5 mtl-1 thi-1 mcrB1 hsdR2),   GC5™ (: F− Φ80lacZ   M15   (lacZYA-argF) U169 endA1 recA1 relA1 gyrA96 hsdR17 (r k   − , m k   + ) phoA supE44 thi-1λ-T1R),   GC10 (F− mcrA Δ(mrr-hsdRMSmcrBC) Φ80dlacZ   M15 Δ lacX74 endA1 recA1   (ara, leu) 7697 araD139 galUgalK nupG rpsL λ-T1R),   GENEHOGS® (FmcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(araleu) 7697 galU galK rpsL (StrR) endA1 nupG fhuA::IS2 (confers phage T1 resistance)),   HB101,   HMS174,   HMS174(DE3),   HI-CONTROL™ BL21(DE3) (F −  ompT gal dcm hsdS B (r B   −  m B   − ) (DE3)/Mini-F lacI q1  (Gent r )),   HI-CONTROL™ 10G (F− mcrA Δ(mrr-hsdRMS-mcrBC) endA1 recA1 Φ80dlacZΔM15 ΔlacX74araD139 Δ(ara,leu)7697 galU galK rpsL nupG λ− tonA/Mini-F lac q1 (Gent r )),   HT96™ NOVABLUE (endA1 hsdR17 (r K12   −  m K2   + ) supE44 thi-1 recA1 gyrA96 relA1 lac F′[proA + B +  lacI q ZΔM15::Tn10] (Tet R )),   IJ1126, IJ1127, INV110, JM83,   JM101 (F′ traD36proA + B +  lacI q  Δ(lacZ)M15/Δ(lac-proAB) glnV thi),   JM103, JM105, JM106, JM107, JM108,   JM109 (F′ traD36proA + B +  lacI q    (lacZ)M15  (lac-proAB) glnV44 e14 −  gyrA96 recA1 relA1 endA1 thi hsdR17),   JM109(DE3), JM110, JS5, KS1000 (F′ lac q  lac + pro + /ara (lac-pro)  (tsp)= (prc)::Kan R  eda51::Tn10(Tet R ) gyrA(Nal R ) rpoB thi-1 argE(am)), LE392,   Lemo21(DE3) (fhuA2 [lon] ompT gal (λ DE3) [dcm] ΔhsdS/pLemo(Cam R ) λ DE3=λ sBamHlo ΔEcoRI-B int::(lacI::PlacUV5::T7 gene1) i21 Δnin5 pLemo=pACYC184-PrhaBAD-lysY),   LIBRARY EFFICIENCY® DH5A™ (F-φ80lacZΔM15 Δ(lacZYA-argF)U169 recA1 endA1 hsdR17(r k   − , m k   + ) phoA supE44 thi-1 gyrA96 relA1λ−),   MACH1™ T1R (F− Φ80lacZΔM15 ΔlacX74 hsdR(rK−, mK+) ΔrecA1398 endA1 tonA),   MAX EFFICIENCY® DH10B™ (F-mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 recA1 endA1 araD139 Δ(ara, leu) 7697 galUgalK λ-rpsL nupG/pMON14272/pMON7124),   MC1061, MC4100, MDS™ 42(MG1655 fhuACDB(del) endA(del)+deletion of 699 additional genes, including all IS elements and cryptic prophages as listed in Posfai et al. (2006)  Science  (312):1044-1046), MFDpir,   NEB Express l q (MiniF lacI q  (Cam R )/fhuA2 [lon] ompT gal sulA11 R(mcr-73::miniTn10—Tet S )2 [dcm] R(zgb-210::Tn10—Tet S ) endA1  (mcrC-mrr) 114::IS10), NEB Express, dam − /dcm − ,   NEB 5-alpha (fhuA2  (argF-lacZ) U169 phoA glnV44 Φ80  (lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17),   NEB 10-beta (Δ(ara-leu) 7697 araD139 fhuA ΔlacX74 galK16 galE15 e14-ϕ80dlacZΔM15 recA1 relA1 endA1 nupG rpsL (Str R ) rph spoT1 Δ(mrr-hsdRMS-mcrBC)),   NiCo21(DE3) (can::CBD fhuA2 [lon] ompT gal (λ DE3) [dcm] arnA::CBD slyD::CBD glmS6Ala ΔhsdS λ DE3=λ sBamHlo ΔEcoRI-B int::(lacI::PlacUV5::T7 gene1) i21 Δnin5),   NM522 (F′ proA + B +  lacI q    (lacZ)M15  (lac-proAB) glnV thi-1  (hsdS-mcrB)5),   NOVABLUE™ (endA1 hsdR17 (r K12   −  m K12   + ) supE44 thi-1 recA gyrA96 relA1 lac F′[proA + B +  lac q ZΔM15::Tn10] (Tet R )),   NovaF− (F − endA1 hsdR17 (r K12   −  m K12   + ) supE44 thi-1 recA1 gyrA96 relA1 lac),   NOVAXGF′ ZAPPERS™ (mcrA Δ(mcrC mrr) endA1recA1 φ80dlacZΔM15 ΔlacX74araD139 Δ(ara-leu)7697 galUgalKrpsLnupGλ − tonA F′[lacI q Tn10] (Tet R )),   OMNIMAX™2T1® (F′ {proAB+ lacIq lacZΔM15 Tn10(Tet R ) Δ(ccdAB)} mcrA Δ(mrr-hsdRMS-mcrBC) Φ80lacZΔM15 Δ(lacZYA-argF) U169 endA1 recA1 supE44 thi-1 gyrA96 relA1 tonA panD),   ONE SHOT® BL21 STAR™ (DE3) (F−ompThsdSB (rB−, mB−) galdcmrne131 (DE3)),   ONESHOT® TOP10 (F− mcrA Δ(mrr-hsdRMS-mcrBC) Φ80lacZΔM15 Δ lacX74 recA1 araD139 Δ(araleu)7697galU galK rpsL (StrR) endA1 nupG), ORIGAMI™ (A (ara-leu) 7697  lacX74  phoA PvuII phoR araD139 ahpC galE galK rpsLF′[lac +  lacI q  pro] (DE3)gor522::Tn10 trxB (Kan R , Str R , Tet R )),   ORAGAMI™ 2 ( (ara-leu) 7697  lacX74  phoA PvuII phoR araD139 ahpC galE galK rpsL F′[lac +  lacI q  pro] gor522::Tn10 trxB (Str R , Tet R )),   OVEREXPRESS™ C41(DE3) (F− ompThsdSB (rB− mB−) gal dcm (DE3)),   OVEREXPRESS™ C41(DE3)PLYSS (F− ompThsdSB (rB− mB−) gal dcm (DE3) pLysS (Cm R )),   OVEREXPRESS™ C43(DE3) (F− ompThsdSB (rB− mB−) gal dcm (DE3)),   OVEREXPRESS™ C43(DE3)PLYSS (F− ompThsdSB (rB− mB−) gal dcm (DE3) pLysS (Cm R )),   POP2136/pFOS1 (F −  glnV44 hsdR17 endA1 thi-1 aroB mal −  c1857 lambdaPR),   PR1031 (F −  thr:Tn10(Tet R ) dnaJ259 leu fhuA2 lacZ90(oc) lacY glnV44 thi),   ROSETTA™ (F − ompT hsdS B (r B   −  m B   − ) gal dcm pRARE (Cam R )),   ROSETTA™(DE3)PLYSS (F − ompT hsdS B (r B   −  m B   − ) gal dcm (DE3) pLysSRARE2 (Cam R )),   ROSETTA-GAMI™ (Δ(ara-leu)7697 ΔlacX74 ΔphoA PvuII phoR araD139 ahpC galE galK rpsL F′[lac +  lacI q  pro] gor522::Tn10 trxB pRARE2 (Cam R , Str R , Tet R )),   ROSETTA-GAMI™(DE3)PLYSS (Δ(ara-leu)7697 ΔlacX74 ΔphoA PvuII phoR araD139 ahpC galE galK rpsL (DE3) F′[lac +  lacI q  pro]gor522::Tn10 trxB pLysSRARE2 (Cam R , Str R , Tet R )),   RR1, RV308, SCARABXPRESS® T7LAC (MDS™42 multiple-deletion strain (1) with a chromosomal copy of the T7 RNA Polymerase gene),   SS320 (F′[proAB+lacIqlacZΔM15 Tn10 (tet r )]hsdR mcrB araD139  (araABC-leu)7679 ΔlacX74 galUgalK rpsL thi),   SHUFFLE® (F′ lac pro lacI q /Δ(ara-leu)7697 araD13 fhuA2 Δ(lac)X74 Δ(phoA)PvuII phoR ahpC* galE (or U) galK Δλatt::pNEB3-r1-cDsbC (SpecR, lacI q ) ΔtrxB rpsL150(StrR) Δgor Δ(malF)3),   SHUFFLE® T7 (F′ lac, pro, lacI q / (ara-leu) 7697 araD139 fhuA2 lacZ::T7 gene1  (phoA)PvuII phoR ahpC* galE (or U) galK λatt::pNEB3-r1-cDsbC (Spec R , lac q )  trxB rpsL150(Str R )  gor  (malF)3),   SHUFFLE® T7 EXPRESS (huA2 lacZ::T7 gene1 [lon] ompT ahpC gal λatt::pNEB3-r1-cDsbC (Spec R , lacI q ) ΔtrxB sulA11 R(mcr-73::miniTn10—Tet S )2 [dcm] R(zgb-210::Tn10—Tet S ) endA1  gor Δ(mcrC-mrr)114::IS10),   SOLR (e14-(McrA − ) Δ(mcrCB-hsdSMR-mrr)171 sbcC recB recJ uvrC umuC::Tn5 (Kan r ) lac gyrA96 relA1 thi-1 endA1λ R  [F′ proAB lac q Z ΔM15] C  Su−),   SCS110, STBL2™ (F− endA1 glnV44 thi-1 recA1 gyrA96 relA1  (lac-proAB) mcrA  (mcrBC-hsdRMS-mrr) λ − ),   STBL3™ (F− glnV44 recA13 mcrB mrr hsdS20(rB−, mB−) ara-14 galK2 lacY1 proA2 rpsL20 xyl-5 leu mtl-1),   STBL4™ (endA1 glnV44 thi-1 recA1 gyrA96 relA1  (lac-proAB) mcrA  (mcrBC-hsdRMS-mrr) λ −  gal F′[proAB +  lacI q  lacZ M15 Tn10]),   STELLAR™ (F−, endA1, supE44, thi-1, recA1, relA1, gyrA96, phoA, Φ80d lacZ  M15,  (lacZYA−argF) U169,  (mrr−hsdRMS−mcrBC),  mcrA, λ−).   SURE (endA1 glnV44 thi-1 gyrA96 relA1 lac recB recJ sbcC umuC::Tn5 uvrC e14−  (mcrCB-hsdSMR-mrr)171 F′[proAB +  lacI q  lacZ M15 Tn10]),   SURE2 (endA1 glnV44 thi-1 gyrA96 relA1 lac recB recJ sbcC umuC::Tn5 uvrC e14- (mcrCB-hsdSMR-mrr) 171 F′[proAB +  lacI q  lacZ M15 Tn10 Amy Cm R ]),   T7 Express Crystal (fhuA2 lacZ::T7 gene1 [lon] ompT gal sulA11 R(mcr-73::miniTn10—Tet S )2 [dcm] R(zgb-210::Tn10—Tet S ) endA1 metB1  (mcrC-mrr)114::IS10),   T7 Express lysY\I q  (MiniF lysY lacI q (Cam R )/fhuA2 lacZ::T7 gene1 [lon] ompT gal sulA11 R(mcr-73::miniTn10—Tet S )2 [dcm] R(zgb-210::Tn10—Tet S ) endA1  (mcrC-mrr) 114::IS10),   T7 Express lysY (MiniF lysY (Cam R )/fhuA2 lacZ::T7 gene1 [lon] ompT gal sulA11 R(mcr-73::miniTn10—Tet S )2 [dcm] R(zgb-210::Tn10—Tet S ) endA1 Δ(mcrC-mrr)114::IS10),   T7 Express I q  (MiniF lacI q (Cam R )/fhuA2 lacZ::T7 gene1 [lon] ompT gal sulA11 R(mcr-73::miniTn10—Tet S )2 [dcm] R(zgb-210::Tn10—Tet S ) endA1  (mcrC-mrr)114::IS10),   T7 Express (fhuA2 lacZ::T7 gene1 [lon] ompT gal sulA11 R(mcr-73::miniTn10—Tet S )2 [dcm] R(zgb-210::Tn10—Tet S ) endA1  (mcrC-mrr) 14::IS10),   TB1 (F −  ara Δ(lac-proAB) [Φ80dlac Δ(lacZ)M15] rpsL(Str R ) thi hsdR),   TG1 (F′ [traD36proAB +  lacI lacZ M15]supE thi-1  (lac-proAB)  (mcrB-hsdSM)5, (r K   − m K   − )),   THUNDERBOLT™ GC10 (F− mcrA   (mrr-hsdRMSmcrBC) Φ80dlacZ Δ M15 DlacX74 endA1recA1  (ara, leu) 7697 araD139 galU galK nupG rpsL1λ-T1R),   UT5600 (F −  ara-14 leuB6 secA6 lacY1 proC14 tsx-67  (ompT-fepC)266 entA403 trpE38 rfbD1 rpsL109 xyl-5 mtl-1 thi-1),   VEGGIE™ BL21(DE3) (F − ompT hsdS B (r B   −  m B   − ) gal dcm(DE3)), W3110 (λ857S7),   WM3064,   XL1-Blue (endA1 gyrA96(nal R ) thi-1 recA1 relA1 lac glnV44 F′[::Tn10 proAB +  lacI q Δ(lacZ)laM15] hsdR17(r K   −  m K   + )),   XL1-Blue MRF′(Δ(mcrA)183 Δ(mcrCB-hsdSMR-mrr)173 endA1 supE44 thi-1 recA1 gyrA96 relA1 lac [F′proAB lacI q Z M15 Tn10 (Tet r )]),   XL2-Blue (endA1 gyrA96(nal R ) thi-1 recA1 relA1 lac glnV44 F′[::Tn10 proAB +  lacI q   (lacZ)M15 Amy Cm R ] hsdR17(r K   −  m K   + )),   XL2-Blue MRF′(endA1 gyrA96(nal R ) thi-1 recA1 relA1 lac glnV44 e14−  (mcrCB-hsdSMR-mrr)171 recB recJ sbcC umuC::Tn5 uvrC F′[::Tn10 proAB +  lacI q   (lacZ)M15 Amy Cm R ]),   XL1-Red (F− endA1 gyrA96(nal R ) thi-1 relA1 lac glnV44 hsdR17(r K   −  m K   + ) mutS mutT mutD5 Tn10),   XL10-Gold (endA1 glnV44 recA1 thi-1 gyrA96 relA1 lac Hte  (mcrA)183  (mcrCB-hsdSMR-mrr)173 tet R  F′[proAB lacI q ZΔM15 Tn10(Tet R  Amy Cm R )]), and   XL10-Gold KanR (endA1 gln V44 recA1 thi-1 gyrA96 relA1 lac Hte Δ(mcrA)183  (mcrCB-hsdSMR-mrr)173 tet R  F′[proAB lac F ZΔM15 Tn10(Tet R  Amy Tn5(Kan R )]).   
     
     
         5 . The isolated  E. coli  host cell of  claim 1 , wherein the number of said combinations of said genes either for Table 8 alone, Table 9 alone, Tables 8 and 9 taken together, Table 14, or for Tables 8, 9, and 14 taken together is determined by combination Equation 6: 
       
         
           
             
               
                 
                   
                     
                       n 
                       ! 
                     
                     
                       
                         r 
                         ! 
                       
                        
                       
                         
                           ( 
                           
                             n 
                             - 
                             r 
                           
                           ) 
                         
                         ! 
                       
                     
                   
                 
                 
                   
                     Equation 
                      
                     
                         
                     
                      
                     6 
                   
                 
               
             
           
         
         wherein n is the set of genes out of which selection occurs, and 
         r is the number of genes selected for deletion, modification, and/or reduction or complete inhibition of expression. 
       
     
     
         6 . The isolated  E. coli  host cell of  claim 1 , wherein said combinations of said genes are selected from the group consisting of:
   hldD usg rraA;     hldD usg rraA cutA;     hldD usg rraA cutA nagD;     hldD usg rraA cutA nagD speA;     hldD usg rraA cutA nagD speA gldA;     hldD usg rraA cutA nagD speA gldA glnA;     hldD usg rraA cutA nagD speA gldA glnA zmetE;     hldD usg rraA cutA nagD speA gldA glnA metE tgt;     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG;     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG typA;     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG typA entF;     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG typA entF ycaO;     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG typA entF ycaO slyD;     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG typA entF ycaO slyD gatZ;     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG typA entF ycaO slyD gatZ ilvB;     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG typA entF ycaO slyD gatZ ilvB glgP;     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG typA entF ycaO slyD gatZ ilvB glgP nusA; and     hldD usg rraA cutA nagD speA gldA glnA metE tgt argG typA entF ycaO slyD gatZ ilvB glgP nusA metH,
 wherein in any of said gene combinations, one or more of these genes can be omitted as long as the resulting isolated  E. coli  host cell exhibits growth rate, viability, or both, and/or capacity for expression of said target host cell peptide, polypeptide, or protein, or said target recombinant peptide, polypeptide, or protein, in the range of from about 60% to about 100%, or more, compared to that of said isolated  E. coli  host cell in which said gene combinations are not deleted, not modified, or in which the expression thereof is not reduced or completely inhibited, and as long as chromatographic separation capacity of said target host cell peptide, polypeptide, or protein, or said target recombinant peptide, polypeptide, or protein, is improved in an amount in the range of from about 5% to about 50%, or more, compared to that of said isolated  E. coli  host cell in which said gene combinations are not deleted, not modified, or in which the expression thereof is not reduced or completely inhibited, depending on the number and particular combination of genes deleted, modified, or inhibited, and/or   wherein any of said gene combinations can also further comprise deletion, modification, and/or reduction or complete inhibition of expression of one or more essential genes selected from among rpoB, rpoC, tufa, ycfD, groL, prs, fusA, hemL, slyD, infB, mukB, and rnt as long as the resulting isolated  E. coli  host cell exhibits growth rate, viability, or both, and/or capacity for expression of said target host cell peptide, polypeptide, or protein, or said target recombinant peptide, polypeptide, or protein, in the range of from about 60% to about 100%, or more, compared to that of said isolated  E. coli  host cell in which said gene combinations are not deleted, not modified, or in which the expression thereof is not reduced or completely inhibited, and as long as chromatographic separation capacity of said target host cell peptide, polypeptide, or protein, or said target recombinant peptide, polypeptide, or protein, is improved in an amount in the range of from about 5% to about 50%, or more, compared to that of said isolated  E. coli  host cell in which said gene combinations are not deleted, not modified, or in which the expression thereof is not reduced or completely inhibited, depending on the number and particular combination of genes deleted, modified, or inhibited.     
     
     
         7 . The isolated  E. coli  host cell of  claim 1 , wherein said target host cell peptide, polypeptide, or protein or said target recombinant peptide, polypeptide, or protein is present in a lysate of said isolated  E. coli  host cell, or is secreted by said isolated  E. coli  host cell. 
     
     
         8 . The isolated  E. coli  host cell of  claim 1 , wherein said target host cell peptide, polypeptide, or protein, or said target recombinant peptide, polypeptide, or protein is an endogenous peptide, polypeptide, or protein, and said target recombinant peptide, polypeptide, or protein is a heterologous peptide, polypeptide, or protein. 
     
     
         9 . The isolated  E. coli  host cell of  claim 8 , wherein said heterologous peptide, polypeptide, or protein is selected from the group consisting of an enzyme and a therapeutic peptide, polypeptide, or protein. 
     
     
         10 . The isolated  E. coli  host cell of  claim 9 , wherein said enzyme is selected from the group consisting of a nuclease, a ligase, a polymerase, an RNA- or DNA-modifying enzyme, a carbohydrate-modifying enzyme, an isomerase, a proteolytic enzyme, and a lipolytic enzyme, and said therapeutic peptide, polypeptide, or protein is selected from the group consisting of antibody, an antibody fragment, a vaccine, an enzyme, a growth factor, a blood clotting factor, a hormone, a nerve factor, an interferon, an interleukin, tissue plasminogen activator, and insulin. 
     
     
         11 . A method of preparing a pharmaceutical or veterinary composition comprising a therapeutic peptide, polypeptide, or protein, comprising the steps of:
 i) expressing said therapeutic peptide, polypeptide, or protein in said isolated  E. coli  host cell of  claim 1 ;   ii) in the case where said therapeutic peptide, polypeptide, or protein is not secreted from said isolated  E. coli  host cell, preparing a lysate of said host cell containing said therapeutic peptide, polypeptide, or protein, producing an initial therapeutic peptide-, polypeptide-, or protein-containing mixture; or   iii) in the case where said therapeutic peptide, polypeptide, or protein is secreted from said isolated  E. coli  host cell, harvesting culture medium in which said isolated  E. coli  host cell is grown, containing said therapeutic peptide, polypeptide, or protein, thereby obtaining an initial therapeutic peptide-, polypeptide-, or protein-containing mixture;   iv) chromatographing said initial therapeutic peptide-, polypeptide-, or protein-containing mixture of step ii) or step iii) via affinity or adsorption-based, non-affinity chromatography and collecting elution fractions, thereby obtaining one or more fractions containing an enriched amount of said therapeutic peptide, polypeptide, or protein relative to other peptides, polypeptides, or proteins in said fraction compared to the amount of said therapeutic peptide, polypeptide, or protein relative to other peptides, polypeptides, or proteins in said initial protein mixture;   v) optionally, further chromatographing an enriched fraction of step iv) to obtain said therapeutic peptide, polypeptide, or protein in a desired degree of purity; and   vi) recovering said therapeutic peptide, polypeptide, or protein.   
     
     
         12 . The method of  claim 11 , further comprising formulating said therapeutic peptide, polypeptide, or protein with a pharmaceutically or veterinarily acceptable carrier, diluent, or excipient to produce a pharmaceutical or veterinary composition, respectively. 
     
     
         13 . The method of  claim 11 , wherein said adsorption-based, non-affinity chromatography is ion exchange chromatography. 
     
     
         14 . The method of  claim 13 , wherein said ion exchange chromatography employs a ligand selected from the group consisting of diethylaminoethyl cellulose (DEAE), monoQ or other Q resin, and S. 
     
     
         15 . The method of  claim 11 , wherein said therapeutic peptide, polypeptide, or protein is selected from among an antibody, an antibody antigen-binding fragment, a vaccine, al-Antitrypsin, deoxyribonuclease, epidermal growth factor, erythropoietin, Factor VIII, Factor IX, fibroblast growth factor, follicle stimulating hormone, granulocyte colony stimulating factor, insulin, insulin-like growth factor 1, interferon-α, interferon-β, interferon-γ, an interleukin, lung surfactant protein, relaxin, serum albumin, somatostatin, somatotrophin, superoxide dismutase, tissue plasminogen activator, and tumor necrosis factor. 
     
     
         16 . A method of purifying an enzyme, comprising the steps of:
 i) expressing said enzyme in said isolated  E. coli  host cell of  claim 1 ;   ii) in the case where said enzyme is not secreted from said isolated  E. coli  host cell, preparing a lysate of said isolated  E. coli  host cell containing said enzyme, producing an initial enzyme-containing mixture; or   iii) in the case where said enzyme is secreted from said isolated  E. coli  host cell, harvesting culture medium in which said host cell is grown, containing said enzyme, thereby obtaining an initial enzyme-containing mixture;   iv) chromatographing said initial enzyme-containing mixture of step ii) or step iii) via affinity or adsorption-based, non-affinity chromatography and collecting elution fractions, thereby obtaining one or more fractions containing an enriched amount of said enzyme relative to other peptides, polypeptides, or proteins in said fraction compared to the amount of said enzyme relative to other peptides, polypeptides, or proteins in said initial protein mixture;   v) optionally, further chromatographing an enriched fraction of step iv) to obtain said enzyme in a desired degree of purity; and   vi) recovering purified enzyme.   
     
     
         17 . The method of  claim 16 , wherein said adsorption-based, non-affinity chromatography is ion exchange chromatography. 
     
     
         18 . The method of  claim 17 , wherein said ion exchange chromatography employs a ligand selected from the group consisting of diethylaminoethyl cellulose (DEAE), monoQ or other Q resin, and S. 
     
     
         19 . The method of  claim 16 , wherein said enzyme is an endogenous  E. coli  enzyme or a heterologous enzyme. 
     
     
         20 . The method of  claim 19 , wherein said endogenous  E. coli  enzyme is selected from the group consisting of a nuclease, a ligase, a polymerase, an RNA- or DNA-modifying enzyme, a carbohydrate-modifying enzyme, an isomerase, a proteolytic enzyme, and a lipolytic enzyme, and said heterologous enzyme is selected from the group consisting of a nuclease, a ligase, a polymerase, an RNA- or DNA-modifying enzyme, a carbohydrate-modifying enzyme, an isomerase, a proteolytic enzyme, and a lipolytic enzyme.