Table 2.

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

	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	clpSdnaJ 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 nuoGnuoH nuoI nuoJ nuoK nuoL nuoM	ldhA	frdB
TCA cycle and other carbon metabolic pathways	gcd	acs aldAaraD arnT astDfucI fucU gcvP glcC glgX maeB mazG mtlD nagErffH sdhA sdhB sdhD sucA sucB sucC sucD	aceE araBaraD gcd	aceBaceK acnA acs aldA astD fbaBfucI fumA fumC gatY gatZ glcB gluD glcFglk gltA maeB manXmdh mtlD pckA poxB rbsD sdhB sdhD sucD tktB yiaG yjgB
Transport	proPtauA	artQ dppB dppC cycA fadL fucKgalP glnH glnP glnQ gltJgltK gltL gntP gntT gntU hcaT hisQ hisM hisP mglAmglB mglCmgtA mtlR nanT nhaA pstA pstS rbsA rbsC rbsK rbsR sdaC sstT tsx uxuB yjcG	araE aqpZ arsBdusB potA sotBnepI proP tauA tolA tolRybeX ygeD	argTchbB cycA fadLgabP galP galS glcA glcGglpT glnH glnP glnQ gltI gltJ gltKgltL gntP lamBmanY manZ mglAmglB mglC oppA oppBputP rbsA rbsC rbsK srlA srlB tsx ugpA yjcGyjdN yhiP yphF
Amino acids	cysW ilvCsdaA	astBastC astEbeta carA dadX gabT hisA leuB leuD sdaB tnaA ubiH	alr argH aroF aroK cysM cysW emrD iaaA ilvCsdaA thrA thrB ygeA	aceAaphA astB astC astEdadA dadX gabTkatG melA pepE putA tnaA tnaC
Nucleic acids, nucleotides and cofactors	menB ribH rrmJ topA	fadApolB ppx purB purL ndk rrmA ubiB	cmk cobS cyaA der dnaG gpp gsk guaB gyrB hflX holCinfB menB menCmfd obgEproW priB prlC queA rdgBrecF ribHrimM rluA rnb rnc rng rnhBrplI rplY rpmBrpsK rpsP rrmJ srmB thrCtopA truB xerDyjgP	allA elaB fadArsd tnaByaaF ybaE ybeK yjbJ
Lipid and cell wall-related	miaA mltD mutM	ddlB fadD fadE fadH fadI fadJ ftsImepA mraY mrdA murC murDmurG yeiU yqeF yrfF	cutE fabD glmM lolC lpxP miaA mltD mrcA mrdA msbAmutM prfB rlpB yfgB	anmK blc csiE ecnBerfK fadD fadE fadH fadI fadJhdfR ybaWyqeF
Transcription and translation related	rplR rpmC rpmD rpmI rpsN rpsQ		deaD fusA hisSleuS glnS ileSlspA nusA pheS pheT prfCrbfA rluB rplBrplC rplD rplErplF rplJ rplK rplL rplMrplO rplP rplR rplS rplT rplUrplV rplW rplX rpmA rpmC rpmD rpmI rpmJ rpoA rpoBrpoC rpoDrpsA rpsB rpsCrpsD rpsE rpsGrpsH rpsIrpsJ rpsMrpsN rpsQ rpsRrpsS trmD valS	sra
Expression regulators and cell division	cbl Spf yceP ycfR zntR	araC csiDflhC ftsL ftsQ galS glnG hcaR malT metHmraW pstB soxSsraH	arsR csdA cspA cysKemrR flgMfis glpEhflB hflC hflK narP rnxG rplArplQ rpmE spf yceP ycfR zntR	bolA csiDcspE cyaRfeaR fruR fucR glcC hcaRhexR hokB ldrD melR minD minE mokB omrA sokB yidF yeiL
Signalling and motility		cspD cstA envZ flgD flgGflgH flgI flgJ flgK flgL purD purH	flgC flgGhepA htpGtypA	atoD cspDcstA ddpX ompW yjdI yjjM
Unknown or other miscellaneous functions	cysDyceD yciS ycjF ycjX ydhQ ydjN yeeD yeeE yhdNyoaE yohJ	glgS rffA rffC spr ubiA visC ybhQ ycdN ydhC yeeI yehU yhdP yhhN yjcHyphF ytfS	araJcysD cysH cysJ ecfK folD gntY mdtD mdtH mscS psiEyaeL yafD ybeAybeD ybeY ybeZ ybjXyceD yciM yciS ycjF ycjXydhQ ydjN yebC yeeD yeeE yfcJ yfgM ygiQ yhcN yhdNyhhS yncJ yohJ yrbD	abgA aldB bfrddpA dkgA ecfJ gabD glgSmsrB nanE osmCosmY psiF ribB rof ryeA sraH ssnAubiA xdhB yahK yahNyaiY yaiZ ybaY ybhQ ybjP ycaC yccJ ycgBycgK yciI ydcL ydcS ydcU ydcW yddP ydeN yeaQ yeaT yebVyebW yedX yeeI yeiTygaM ygcO ygdIygfJ yggE yghZ ygjR yhaH yifE yihW yncByniA yodB yohF yphA yphGyqjD yqjK ygeV

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).