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 2 Identification of Fis 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	*rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ*, rpmBG, *rplU-rpmA, rplKA*, rpsP-rimM-trmD-rplS, rpsT, rpsB-tsf, rpsO, rplM-rpsI, *rpsJ-rplCDWB- rpsS- rplV-rpsC-rplP- rpmC-rpsQ*, rpsF-priB-rpsR-rplI, rpsL, *rplJL*, rpoZ, frr, *raiA, rraA*	Down
Transcription, Translation	*argS, rpoE,* rimP-nusA-infB	Up
Energy metabolism	*cydAB, ppc, pta-ackA, dmsABCD, napFDA, nrfABCD, ppa, pfkA, torY, glpX, eno, hypBDE, hypF, nqrABCDEF, nudE-cysQ*	Down
Energy metabolism	*glpE-ybbN, can, cysJL*, fdhE	Up
Carbohydrate metabolism	*pgk, tkt, frdABCD, tpiA, pckA, ilvB, mdh, hxpB, tal,* manXYZ, fucO, *lpd-aceF*	Down
Carbohydrate metabolism	*fbp, APPSER1_RS05435, indK, lldD, APPSER1_RS09580-nanEKA-nagB, gntR*	Up
Amino acids	glmS, *adhE, ilvE, cysK, proB, dapA, gdhA, argG, aspC, mmsB*	Down
Amino acids	*gshAB, tyrA, hisC, hisIE,* hisD, APPSER1_RS10930	Up
Membrane transport	*scrA, afuA, fruBKA, ptsH, ptsI-crr,* xylGH, cbiKLM, ompW	Down
Membrane transport	*sbp-cysUWA, fhuCD, znuC,* fliY, *sitCD*	Up
Signal transduction	*hybOAB, sodA, cydAB, ducB, eno, pfkA, frdA, hfq*	Down
Signal transduction	*fnr, fbp, htpG*	Up
Cofactors and Vitamins	ushA, *pdxST, pntAB*, ilvB, ilvE	Down
Cofactors and Vitamins	*folB, ribF, ribDEBA, hemA, folE-truA, folC, lipA, cysGHDN*	Up
Lipid metabolism	*adhE*	Down
Lipid metabolism	*adhP, glpQ, psd*	Up
Folding, sorting and degradation	*hfq, eno, pfkA,* secG	Down
Folding, sorting and degradation	*rppH, pcnB-folK, tusE, htpG, tusBCD*	Up
Cellular community	*hfq,* secG	Down
Cellular community	*fis, ribDEBA,* dksA, *APPSER1_RS00145*	Up
Replication and repair	*dnaE*	Down
Replication and repair	holD-rimI-srmB-pdxH, dnaG, *rnhA, nfo*	Up
Nucleotide metabolism	*ushA, cpdB*	Down
Nucleotide metabolism	trmA, *rsml*	Up
Virulence factor	*apxIICA*	Down

Genes in bold indicate those also with Fnr binding sites in the promoter regions.
^aThe Fis motif used for searching was GNNBRWWWWWTVNNCRN.
^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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