The morphology and metabolic changes of Actinobacillus pleuropneumoniae during its growth as a biofilm

Zhang, Qiuhong; Peng, Lu; Han, Weiyao; Chen, Hongyu; Tang, Hao; Chen, Xiabing; Langford, Paul R.; Huang, Qi; Zhou, Rui; Li, Lu

doi:10.1186/s13567-023-01173-x

Veterinary Research

Table 1 Identification of Fnr binding sites^a in the promoter regions of differentially expressed genes (BF compared with PK)

From: The morphology and metabolic changes of Actinobacillus pleuropneumoniae during its growth as a biofilm

Functional class	Target genes^b	Transcription change^c
Transcription, Translation	*rplKA, rplJL, rpsJ- rplCDWB- rpsS- rplV-rpsC-rplP- rpmC-rpsQ, rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ*, rpsMKD-rpoA-rplQ, *rplU-rpmA, raiA, rraA*	Down
Transcription, Translation	*argS*, folE-truA, ttcA, *rpoE*	Up
Energy metabolism	*cydAB, ppc, pta-ackA*, atpEFHAGDC, fbaA, *glpX*, gpmA, *torY*, torA, *dmsABCD, nrfABCD, ppa, pfkA, napFDA, nqrABCDEF, hypBDE, hypF, eno, nudE-cysQ*	Down
Energy metabolism	*glpE-ybbN, can, cysJL*	Up
Carbohydrate metabolism	*pgk, pyk, tkt, frdABCD, tpiA, pckA, ilvB, mdh,* gloA, *hxpB, tal,* fumC, focA-pflB, *lpd-aceF*	Down
Carbohydrate metabolism	*fbp, APPSER1_RS05435, indK, lldD, gntR, APPSER1_RS09580-nanEKA-nagB*	Up
Amino acids	metE, asnA, pepA, *adhE, ilvE, cysK, proB, dapA, gdhA, argG, aspC, mmsB*	Down
Amino acids	*gshAB, tyrA, hisC, hisIE,* hisG, metJ	Up
Membrane transport	APPSER1_RS06785, *scrA, afuA, fruBKA, ptsH, ptsI-crr*	Down
Membrane transport	*sbp-cysUWA, fhuCD, znuC,* malK-lamB-malM, *sitCD*	Up
Signal transduction	*hybOAB, sodA, cydAB, ducB, eno, pfkA, frdA, hfq*	Down
Signal transduction	*fnr, fbp,* APPSER1_RS05435, *htpG*	Up
Cofactors and Vitamins	fabB, *pdxST, pntAB*	Down
Cofactors and Vitamins	*folB, ribF, ribDEBA, hemA, folE-truA, folC, lipA, cysGHDN*	Up
Lipid metabolism	fabB, *adhE*	Down
Lipid metabolism	*adhP, glpQ, psd*	Up
Folding, sorting and degradation	*hfq, eno, pfkA*	Down
Folding, sorting and degradation	moaCDE, *rppH, pcnB-folK, tusE, htpG, tusBCD*	Up
Cellular community	*hfq*, cyaA	Down
Cellular community	*fis*, pgaABCD, *ribDEBA, APPSER1_RS00145*	Up
Replication and repair	*dnaE*	Down
Replication and repair	*rnhA, nfo,* ung	Up
Nucleotide metabolism	*ushA, cpdB,* pyrE, cyaA	Down
Nucleotide metabolism	dtd, *rsml*	Up
Virulence factor	apxICA, *apxIICA*	Down

Genes in bold indicate those also with Fis binding sites in the promoter regions.
^aThe Fnr motif used for searching was TTGATNWNDMKCAH.
^bTarget genes were predicted from the MEME-FIMO online tool, p-value < 0.001.
^cTranscriptional changes of target genes were derived from differentially expressed genes in RNA-Seq data, Down, down-regulated, log₂FC ≤ -1, FDR < 0.05; Up, up-regulated, log₂FC ≥ 1, FDR < 0.05.

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ISSN: 1297-9716

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