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Table 2 Differentially-regulated genes for scFvD.13 cells over the Skp/scFvD1.3 or FkpA/scFvD1.3 cells

From: Co-expression of Skp and FkpA chaperones improves cell viability and alters the global expression of stress response genes during scFvD1.3 production

  scFvD1.3 vs Skp/scFvD1.3 scFvD1.3 vs FkpA/scFvD1.3
Functions Up-regulated Down-regulated Up-regulated Down-regulated
Heat shock stress response, protein folding and related clpS dnaJ grpE hslR lon ybbN asr skp clpS clpP clpX dsbC dnaJ fkpB grpE hslO hslR hslU hslV hspQ htpX ibpA lon ppiC prc secA secY tatB ybbN dps fkpA sodC uspB uspE
Energy metabolism cydA cydB frdB frdC nuoA nuoC nuoE nuoF nuoG nuoH nuoI nuoJ nuoK nuoL nuoM ldhA frdB
TCA cycle and other carbon metabolic pathways gcd acs aldA araD arnT astD fucI fucU gcvP glcC glgX maeB mazG mtlD nagE rffH sdhA sdhB sdhD sucA sucB sucC sucD aceE araB araD gcd aceB aceK acnA acs aldA astD fbaB fucI fumA fumC gatY gatZ glcB gluD glcF glk gltA maeB manX mdh mtlD pckA poxB rbsD sdhB sdhD sucD tktB yiaG yjgB
Transport proP tauA artQ dppB dppC cycA fadL fucK galP glnH glnP glnQ gltJ gltK gltL gntP gntT gntU hcaT hisQ hisM hisP mglA mglB mglC mgtA mtlR nanT nhaA pstA pstS rbsA rbsC rbsK rbsR sdaC sstT tsx uxuB yjcG araE aqpZ arsB dusB potA sotB nepI proP tauA tolA tolR ybeX ygeD argT chbB cycA fadL gabP galP galS glcA glcG glpT glnH glnP glnQ gltI gltJ gltK gltL gntP lamB manY manZ mglA mglB mglC oppA oppB putP rbsA rbsC rbsK srlA srlB tsx ugpA yjcG yjdN yhiP yphF
Amino acids cysW ilvC sdaA astB astC astE beta carA dadX gabT hisA leuB leuD sdaB tnaA ubiH alr argH aroF aroK cysM cysW emrD iaaA ilvC sdaA thrA thrB ygeA aceA aphA astB astC astE dadA dadX gabT katG melA pepE putA tnaA tnaC
Nucleic acids, nucleotides and cofactors menB ribH rrmJ topA fadA polB ppx purB purL ndk rrmA ubiB cmk cobS cyaA der dnaG gpp gsk guaB gyrB hflX holC infB menB menC mfd obgE proW priB prlC queA rdgB recF ribH rimM rluA rnb rnc rng rnhB rplI rplY rpmB rpsK rpsP rrmJ srmB thrC topA truB xerD yjgP allA elaB fadA rsd tnaB yaaF ybaE ybeK yjbJ
Lipid and cell wall-related miaA mltD mutM ddlB fadD fadE fadH fadI fadJ ftsI mepA mraY mrdA murC murD murG yeiU yqeF yrfF cutE fabD glmM lolC lpxP miaA mltD mrcA mrdA msbA mutM prfB rlpB yfgB anmK blc csiE ecnB erfK fadD fadE fadH fadI fadJ hdfR ybaW yqeF
Transcription and translation related rplR rpmC rpmD rpmI rpsN rpsQ   deaD fusA hisS leuS glnS ileS lspA nusA pheS pheT prfC rbfA rluB rplB rplC rplD rplE rplF rplJ rplK rplL rplM rplO rplP rplR rplS rplT rplU rplV rplW rplX rpmA rpmC rpmD rpmI rpmJ rpoA rpoB rpoC rpoD rpsA rpsB rpsC rpsD rpsE rpsG rpsH rpsI rpsJ rpsM rpsN rpsQ rpsR rpsS trmD valS sra
Expression regulators and cell division cbl Spf yceP ycfR zntR araC csiD flhC ftsL
ftsQ galS glnG hcaR malT metH mraW pstB soxS sraH
arsR csdA cspA cysK emrR flgM fis glpE hflB hflC hflK narP rnxG rplA rplQ rpmE spf yceP ycfR zntR bolA csiD cspE cyaR feaR fruR fucR glcC hcaR hexR hokB ldrD melR minD minE mokB omrA sokB yidF yeiL
Signalling and motility   cspD cstA envZ flgD flgG flgH flgI flgJ flgK
flgL purD purH
flgC flgG hepA htpG typA atoD cspD cstA ddpX ompW yjdI yjjM
Unknown or other miscellaneous functions cysD yceD yciS ycjF ycjX ydhQ ydjN yeeD yeeE yhdN yoaE yohJ glgS rffA rffC spr ubiA visC ybhQ ycdN ydhC yeeI yehU yhdP yhhN yjcH yphF ytfS araJ cysD cysH cysJ ecfK folD gntY mdtD mdtH mscS psiE yaeL yafD ybeA ybeD ybeY ybeZ ybjX yceD yciM yciS ycjF ycjX ydhQ ydjN yebC yeeD yeeE yfcJ yfgM ygiQ yhcN yhdN yhhS yncJ yohJ yrbD abgA aldB bfr ddpA dkgA ecfJ gabD glgS msrB nanE osmC osmY psiF ribB rof ryeA sraH ssnA ubiA xdhB yahK yahN yaiY yaiZ ybaY ybhQ ybjP ycaC yccJ ycgB ycgK yciI ydcL ydcS ydcU ydcW yddP ydeN yeaQ yeaT yebV yebW yedX yeeI yeiT ygaM ygcO ygdI ygfJ yggE yghZ ygjR yhaH yifE yihW yncB yniA yodB yohF yphA yphG yqjD yqjK ygeV
  1. Comparison expression analysis of the wildtype scFvD1.3 over the chaperone co-expressing Skp/scFvD1.3 or FkpA/scFvD1.3 cells with Affymetrix GCOS version 1.4. Commonly up- or down-regulated genes (change p-value ≤ 0.0025 or ≥ 0.9975) from two biological replicates are categorized according to their metabolic functions (genes with fold changes of between: (1) 1.5-3 fold are in italics only, (2) 3-4 fold are bold, and (3) above 4 fold are bold and underlined).