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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
  1. 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