The transcriptome response of the ruminal methanogen Methanobrevibacter ruminantium strain M1 to the inhibitor lauric acid

Zhou, Xuan; Stevens, Marc J. A.; Neuenschwander, Stefan; Schwarm, Angela; Kreuzer, Michael; Bratus-Neuenschwander, Anna; Zeitz, Johanna O.

doi:10.1186/s13104-018-3242-8

Table 2 Significant changes of gene expression in M. ruminantium M1 cultures exposed to C₁₂

From: The transcriptome response of the ruminal methanogen Methanobrevibacter ruminantium strain M1 to the inhibitor lauric acid

Category and subcategory	ORF	Gene name	Annotated function	log2-fold change	log2 counts per 106 reads
Amino acid metabolism
Lysine	mru_0152	lysA	Diaminopimelate decarboxylase LysA	− 1.02	7.66
	mru_0153	dapF	Diaminopimelate epimerase DapF	− 1.00	7.01
Histidine	mru_0182	hisH	Imidazole glycerol phosphate synthase glutamine amidotransferase subunit HisH	− 1.07	6.27
Serine	mru_0678	serA	Phosphoglycerate dehydrogenase SerA	1.03	9.59
Tryptophan	mru_2159	trpB2	Tryptophan synthase beta subunit TrpB2	1.00	11.31
Cell cycle
Cell division	mru_2160	minD	Cell division ATPase MinD	1.08	5.46
Cell envelope
Cell surface proteins	mru_1500	mru_1500	Adhesin-like protein	1.00	8.58
	mru_0160	mru_0160	Adhesin-like protein	1.02	6.70
	mru_0963	mru_0963	Adhesin-like protein	1.08	12.13
	mru_1263	mru_1263	Adhesin-like protein	1.15	9.15
	mru_0331	mru_0331	Adhesin-like protein	1.15	10.34
	mru_0338	mru_0338	Adhesin-like protein	1.17	8.55
	mru_1124	mru_1124	Adhesin-like protein	1.20	12.55
	mru_0031	mru_0031	Adhesin-like protein	1.27	11.29
	mru_0687	mru_0687	Adhesin-like protein	1.28	10.46
	mru_0245	mru_0245	Adhesin-like protein	1.32	8.78
	mru_1417	mru_1417	Adhesin-like protein	1.43	9.49
	mru_1650	mru_1650	Adhesin-like protein	1.44	4.24
	mru_1465	mru_1465	Adhesin-like protein	1.61	6.82
	mru_1506	mru_1506	Adhesin-like protein	1.61	7.76
	mru_0417	mru_0417	Adhesin-like protein	1.70	5.86
	mru_0327	mru_0327	Adhesin-like protein	1.73	10.86
	mru_0019	mru_0019	Adhesin-like protein	2.04	7.42
	mru_0084	mru_0084	Adhesin-like protein	2.07	6.71
	mru_2049	mru_2049	Adhesin-like protein	2.25	11.23
	mru_2043	mru_2043	Adhesin-like protein	2.27	8.58
	mru_1726	mru_1726	Adhesin-like protein	2.32	8.37
	mru_2090	mru_2090	Adhesin-like protein	2.51	13.88
	mru_2147	mru_2147	Adhesin-like protein	2.73	13.13
	mru_0326	mru_0326	Adhesin-like protein	5.04	12.58
	mru_0015	mru_0015	Adhesin-like protein with cysteine protease domain	1.49	9.07
	mru_0020	mru_0020	Adhesin-like protein with cysteine protease domain	2.78	7.86
Teichoic acid biosynthesis	mru_1079	mru_1079	CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase	1.27	6.32
Pseudomurein biosynthesis	mru_1118	mru_1118	Cell wall biosynthesis protein Mur ligase family	1.07	9.37
Cellular processes
Oxidative stress response	mru_1507	fprA1	F420H2 oxidase FprA1	1.37	10.47
	mru_0131	fprA2	F420H2 oxidase FprA2	3.58	12.42
	mru_1367	rbr2	Rubrerythrin Rbr2	1.27	13.19
Stress response	mru_0183	mru_0183	Protein disulfide-isomerase thioredoxin-related protein	− 1.19	7.79
Central carbon metabolism
Gluconeogenesis	mru_0628	pgk2A	2-Phosphoglycerate kinase Pgk2A	1.85	7.69
Other	mru_1685	deoC	Deoxyribose-phosphate aldolase DeoC	5.12	11.11
Acetate	mru_1786	mru_1786	Transporter SSS family	− 1.18	8.66
Energy metabolism
Electron transfer	mru_0915	mru_0915	4Fe–4S binding domain-containing protein	− 1.06	7.64
	mru_2036	mru_2036	4Fe–4S binding domain-containing protein	1.25	5.60
	mru_1345	mru_1345	4Fe–4S binding domain-containing protein	1.30	7.63
Methanogenesis pathway	mru_0569	mer	5,10-methylenetetrahydro-methanopterin reductase Mer	− 1.36	12.71
	mru_0526	hmd	Coenzyme F420-dependent N(5), N(10)-methenyltetrahydromethanopterin reductase Hmd	1.41	10.96
	mru_1850	atwA2	Methyl-coenzyme M reductase component A2 AtwA2	1.05	10.86
	mru_1927	mcrD	Methyl-coenzyme M reductase D subunit McrD	− 1.43	11.33
	mru_0441	mtrA2	Tetrahydromethanopterin S-methyltransferase subunit A MtrA2	− 2.14	11.99
	mru_1918	mtrF	Tetrahydromethanopterin S-methyltransferase subunit F MtrF	− 1.24	9.71
Electron transfer	mru_0184	dsbD	Cytochrome C-type biogenesis protein DsbD	− 1.16	6.17
	mru_0830	mru_0830	Ferredoxin	2.56	9.31
H2 metabolism	mru_1410	ehaC	Energy-converting hydrogenase A subunit C EhaC	− 1.63	6.30
	mru_1408	ehaE	Energy-converting hydrogenase A subunit E EhaE	− 1.74	7.34
	mru_1632	hypB	Hydrogenase accessory protein HypB	2.25	7.90
	mru_1633	hypA	Hydrogenase nickel insertion protein HypA	2.19	7.47
Formate metabolism	mru_0332	fdhC	Formate/nitrite transporter FdhC	− 1.11	11.98
Alcohol metabolism	mru_1445	adh3	NADP-dependent alcohol dehydrogenase Adh3	6.42	7.81
	mru_1444	npdG2	NADPH-dependent F420 reductase NpdG2	3.84	5.32
Mobile elements
Prophage	mru_0269	mru_0269	ATPase involved in DNA replication control MCM family	2.51	4.60
	mru_0323	mru_0323	dnd system-associated protein 2	1.11	6.63
	mru_0280	mru_0280	ParB-like nuclease domain-containing protein	2.52	1.87
	mru_0256	mru_0256	Phage integrase	1.69	6.95
	mru_0287	mru_0287	Phage portal protein	2.73	1.86
	mru_0315	mru_0315	Phage tail tape measure protein	2.47	3.39
	mru_0270	mru_0270	Phage-related protein	1.91	4.54
	mru_0288	mru_0288	Phage-related protein	2.21	2.32
	mru_0058	mru_0058	Phage-related protein	2.53	− 0.04
	mru_0282	mru_0282	Phage-related protein	2.64	1.93
	mru_0316	mru_0316	Phage-related protein	2.66	3.40
	mru_0317	mru_0317	Phage-related protein	2.89	3.42
	mru_0311	mru_0311	Phage-related protein	3.14	2.55
	mru_0310	mru_0310	Phage-related protein	3.18	1.56
	mru_0284	mru_0284	Phage-related protein	3.35	1.93
	mru_0307	mru_0307	Phage-related protein	3.38	2.86
	mru_0313	mru_0313	Phage-related protein	3.40	2.83
	mru_0308	mru_0308	Phage-related protein	3.48	3.46
	mru_0324	mru_0324	Type II restriction enzyme, methylase subunit	1.88	5.99
CRISPR-associated genes	mru_0798	mru_0798	CRISPR-associated protein Cas1-1	1.93	4.09
	mru_1181	mru_1181	CRISPR-associated RAMP protein Csm3 family	1.03	7.23
Nitrogen metabolism
Other	mru_2121	hcp	Hydroxylamine reductase Hcp	− 1.46	12.26
Nucleic acid metabolism
Helicase	mru_0981	mru_0981	Rad3-related DNA helicase	1.09	7.97
Recombination and repair	mru_2097	recJ1	ssDNA exonuclease RecJ1	1.39	11.06
	mru_1383	mru_1383	Staphylococcal nuclease domain-containing protein	− 1.30	7.06
Protein fate
Protein folding	mru_1511	mru_1511	Nascent polypeptide-associated complex protein	− 1.00	6.61
Protein secretion	mru_1581	mru_1581	Signal peptidase I	− 1.21	7.34
Protein synthesis
RNA processing	mru_0589	mru_0589	NMD3 family protein	1.50	7.52
Translation factors	mru_0728	mru_0728	Peptide chain release factor aRF1	1.46	7.74
Ribosomal proteins	mru_0865	rpl5p	Ribosomal protein L5P Rpl5p	1.03	8.24
	mru_0868	rpl6p	Ribosomal protein L6P Rpl6p	1.05	7.92
	mru_2098	mru_2098	Ribosomal protein S15P Rps15p	1.19	9.21
Other	mru_0519	mru_0519	RNA-binding protein	− 1.68	8.08
	mru_1978	mru_1978	RNA-metabolising metallo-beta-lactamase	1.58	8.74
RNA processing	mru_1846	dusA2	tRNA-dihydrouridine synthase DusA2	1.06	6.58
Purines and pyrimidines
Interconversion	mru_2104	surE1	5′-Nucleotidase SurE1	1.02	7.02
	mru_0241	nrdD	Anaerobic ribonucleoside-triphosphate reductase NrdD	1.47	11.08
Regulation
Protein interaction	mru_1186	mru_1186	TPR repeat-containing protein	− 1.05	8.81
Transcriptional regulator	mru_2122	mru_2122	Transcriptional regulator	− 1.62	8.68
	mru_1447	mru_1447	Transcriptional regulator	− 1.55	8.56
	mru_1446	mru_1446	Transcriptional regulator ArsR family	− 1.21	7.78
	mru_0442	mru_0442	Transcriptional regulator MarR family	− 1.68	4.74
Secondary metabolites
Other	mru_0514	mru_0514	4′-Phosphopantetheinyl transferase family protein	1.26	6.32
	mru_0069	mru_0069	MatE efflux family protein	1.20	7.17
	mru_0352	mru_0352	MatE efflux family protein	1.64	6.73
NRPS	mru_0351	mru_0351	Non-ribosomal peptide synthetase	1.06	10.17
Transcription
RNA polymerase	mru_0161	rpoF	DNA-directed RNA polymerase subunit F RpoF	1.05	9.66
Transporters
Amino acids	mru_1775	mru_1775	Amino acid ABC transporter ATP-binding protein	1.03	5.46
	mru_1776	mru_1776	Amino acid ABC transporter permease protein	1.25	4.94
Cations	mru_1861	mru_1861	Heavy metal translocating P-type ATPase	− 6.61	10.24
	mru_1706	nikD2	Nickel ABC transporter ATP-binding protein NikD2	1.15	6.54
	mru_1617	nikB1	Nickel ABC transporter permease protein NikB1	1.10	7.35
	mru_1709	nikB2	Nickel ABC transporter permease protein NikB2	1.43	7.34
	mru_1708	nikC2	Nickel ABC transporter permease protein NikC2	1.31	7.03
	mru_1710	nikA2	Nickel ABC transporter substrate-binding protein NikA2	1.14	11.86
Other	mru_0253	mru_0253	ABC transporter ATP-binding protein	1.97	7.23
	mru_0252	mru_0252	ABC transporter permease protein	1.71	7.40
	mru_0251	mru_0251	ABC transporter substrate-binding protein	2.06	9.13
	mru_0329	mru_0329	MotA/TolQ/ExbB proton channel family protein	1.56	6.00
Vitamins and cofactors
Biotin	mru_0527	bioB2	Biotin synthase BioB2	1.24	7.09
Cobalamin	mru_0539	cbiM1	Cobalamin biosynthesis protein CbiM1	1.21	9.82
	mru_0540	cbiN1	Cobalt transport protein CbiN1	1.18	8.30
	mru_0360	cbiA1	Cobyrinic acid a,c-diamide synthase CbiA1	− 1.60	8.09
	mru_1852	cysG	Siroheme synthase CysG	1.20	7.47
Coenzyme B	mru_0385	aksA	Homocitrate synthase AksA	− 1.15	10.22
Metal-binding pterin	mru_0200	modB	Molybdate ABC transporter permease protein ModB	2.04	9.37
	mru_0201	modA	Molybdate ABC transporter substrate-binding protein ModA	2.83	10.54
Thiamine	mru_0247	thiC1	Thiamine biosynthesis protein ThiC1	− 1.18	9.24
	mru_0532	mru_0532	ThiF family protein	1.38	4.67
Others	mru_1769	nifB	Nitrogenase cofactor biosynthesis protein NifB	2.58	8.89
Unknown function
Enzyme	mru_0455	mru_0455	Acetyltransferase	− 1.16	9.80
	mru_1758	mru_1758	Acetyltransferase	− 1.10	6.05
	mru_2170	mru_2170	Acetyltransferase	1.32	6.12
	mru_0574	mru_0574	Acetyltransferase GNAT family	− 1.92	1.81
	mru_1707	mru_1707	Acetyltransferase GNAT family	1.48	5.54
	mru_0560	mru_0560	ATPase	1.11	8.14
	mru_1613	mru_1613	SAM-dependent methyltransferase	1.58	4.18
Other	mru_0231	mru_0231	CAAX amino terminal protease family protein	− 1.09	8.53
	mru_1993	mru_1993	CBS domain-containing protein	− 1.65	10.72
	mru_1994	mru_1994	CBS domain-containing protein	− 1.31	11.57
	mru_0474	mru_0474	HD domain-containing protein	1.33	7.47
	mru_1034	mru_1034	HEAT repeat-containing protein	2.35	8.75
	mru_2109	mru_2109	Methanogenesis marker protein 12	− 1.01	7.90
	mru_0562	mru_0562	PP-loop family protein	1.59	7.50
	mru_1678	mru_1678	Redox-active disulfide protein	1.51	7.12
	mru_0561	mru_0561	Von Willebrand factor type A domain-containing protein	1.33	8.52
	mru_1510	mru_1510	YhgE/Pip-like protein	− 1.31	8.45
	mru_0627	mru_0627	ZPR1 zinc-finger domain-containing protein	2.04	6.70

C₁₂-treated cultures were compared to DSMO-exposed control cultures (significant change with log₂fold changes < 1 and > 1 and a false discovery rate < 0.05). The list does not include the 71 regulated hypothetical proteins. The M. ruminantium (mru) open reading frame (ORF) codes are adopted from the Kyoto Encyclopedia of Genes and Genomes

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