Stress Responses of Shewanella

Table 1

Genes predicted to be under the direct control of σ ³² in S. oneidensis.

Locus	Gene	Product	Start	End	Sequence	Weight
SO2016	htpG	heat shock protein HtpG	−84	−55	CTTGAAAAGTGGATTTGCAGCCCCATTTTA	20.3
SO4162	hslV	ATP-dependent protease HslV	−83	−54	CTTGAATTCTGGCTATCCATCCCCATATTT	20.1
SO1126	dnaK	chaperone protein DnaK	−78	−48	CTTGAAAAAAAATGCGTCCGGCCCCATATCT	18.6
SO0406	trxA	thioredoxin 1	−80	−51	CTTGAAAAGCTATTTTTCAGCCCCAATATA	18.4
SO1524	grpE	heat shock protein GrpE	−74	−45	CTTGAAACGTCAAAATTGATCCCCATAATA	18.2
SO2593		conserved hypothetical protein	−262	−232	CTTGAAATGGGGAGTTTAACTCCCCATTTTT	17.9
SO3577	clpB	clpB protein	−77	−48	CTTGAATTTGGTTAAATAGCCCCCATCTTT	16.8
SO0452	trxC	thioredoxin 2	−60	−31	CTTTAAATTCGCCGCAGCGCCCCCATATCT	15.7
SO2017		conserved hypothetical protein	−106	−76	CTTGAGTTGAGACGCAAGTGCCCCGATTTAC	14.4
SO1796	lon	ATP-dependent protease La	−68	−39	ATTGAAAGGGCATAAACCGCCCCAATATAC	14
SO2277	ibpA	16 kDa heat shock protein A	−167	−138	CTTGAAATCCGTTTTCCTATCCTTATATCT	13.5
SO0703	groES	chaperonin GroES	−123	−93	CTTGGATCTGGCGGGGGTGAACCCCATATCA	13.3
SO4492		conserved hypothetical protein	−76	−48	GTTGAAAAGAATTGATTTGCCCCAAGATA	12.8
SO1794	clpP	ATP-dependent Clp protease, proteolytic subunit	−83	−55	CTTGACTTGATTAGCAGTTCGCCATTTAT	12.8
SO1163		conserved hypothetical protein	−60	−31	CTTGAATCGGGTATAATCGCCACCATATAG	12.7
SO3863	modA	molybdenum ABC transporter, periplasmic molybdenum-binding protein	−206	−177	CTTGAGTAAATGTTATTGTCCCCGATCAAT	12.3
SO1196	rrmJ	ribosomal RNA large subunit methyltransferase J	−65	−36	GTTGAAAAACCGCTATTCTACCCTTATATA	12.2
SO2723		HIT family protein	−47	−17	ATTGAATTGCTAGTATACTATCCCAATTAAC	11.8
SO1213		hydrolase, TatD family	−240	−211	GTTTAAAGGCGGTGATTCACCGCCTTTTTT	11.8
SO2705	topA	DNA topoisomerase I	−77	−49	CTTGAAACTCTCAGTGCAACCCTCTATAT	11.1
SO3501		conserved hypothetical protein	−297	−268	CATGAATTTGGCAACGGCACCGCCATTTTC	11
SO2728	htpX	peptidase HtpX	−101	−71	GTAGAAAAACTCTTATCTTTACCCCTTGAAT	10.6
SO1473	smpB	SsrA-binding protein	−69	−39	GTTGAAATAGCTCAAATAAACCCTTATATCC	10.3
SO0698	fsxA	fxsA protein	−64	−34	CTTGAATTAAGACCGGATTGCCCCCATTTAG	10.3
SO3402		hypothetical protein	−396	−367	ATTGAAAAGGGCCTTTATGGCCCTTTTTCG	10.2
SO1937	fur	ferric uptake regulation protein	−164	−135	CTTGAATTGCCGCAATTTATTGCAATTTCA	10.2
SO2706	astB	succinylarginine dihydrolase	−40	−11	TTTGAATAAATAATAACCTTCCCTATCACA	9.7
SO0868		hypothetical protein	−93	−63	GTTTAAATGGGGAGAAAACAACTCCATTTTA	9.4
SO3961	rpoN	RNA polymerase sigma-54 factor	−83	−53	CTTGAATTTGGCAGCGCAAAGCGCCATCAGT	9.4
SO0930	tkt	Transketolase	−161	−133	CTTGAATAGTTCATCCTTAAGCCATTTTT	9.3
SO3528		hypothetical protein	−195	−167	AATGAAAAGAGGCTTTTAGCCTCTTTTTT	9.3
SO1580		TonB-dependent heme receptor	−57	−28	CTTTGATGCCTATAATGCCGCCCTATTTTT	9.3
SO2314		ISSo1, transposase OrfA	−227	−197	GTTAAAATGACAAGCATGGAGCGCAATATCT	9.2
SO1903		hypothetical protein	−71	−42	TTTGGGATTATTTAATTCCCCCCCATTTAT	9.2
SO1097		conserved hypothetical protein	−63	−33	CATGAAATCTGCGATAATCAGCGCCTTATTT	9.2
SO0595		hypothetical protein	−327	−298	CTTGATTAGAGCCACGTCGCTCCAATTTTT	9.2
SO4719		conserved hypothetical protein	−44	−16	CTAGGCATTTGAGTTGGAACCCTATTTTT	9.1
SO4287	motA	chemotaxis motA protein	−127	−99	CTTGAATTTAGTAGATTTTCCTTATAATG	9.1
SO3113	tgt	queuine tRNA-ribosyltransferase	−96	−67	GTTGAACCTTTTAGATCTGTCCCTATCTCT	9

Genome screening with σ ³² weight matrix is performed using RSAT at http://rsat.ulb.ac.be/rsat/RSAT_home.cgi [23]. Genes with a weight score over 9 are shown.