Table 2.
Proteins of T. kodakarensis that were up- or downregulated at least twofolda between the start of stationary phase and twelve hours later, grouped by broad functional categories.
| Genome accession | Annotated name | Average fold change | Broad level protein function prediction | Notes |
|---|---|---|---|---|
| YP_182835 | tRNA (guanine-N2)-dimethyltransferase | 4.20 ± 0.63 | Posttranscriptional modification | Catalyses the SAM-dependent formation of N(1)-methyladenine or N(1)-methylguanine at position 9 in tRNA, which may contribute to thermostability of archaeal tRNAs [9] |
| YP_183167 | tRNA(Met) cytidine acetyltransferase | 4.84 ± 2.20 | Posttranscriptional modification | Catalyses acetyl-CoA-dependent N4-acetylation of tRNAMet important for recognition of the AUG codon and translational fidelity [10] |
| YP_184653 | Lysyl-tRNA synthetase | 4.31 ± 0.30 | tRNA formation | Catalyses formation of lysyl-tRNA |
| YP_183321 | Glutamyl-tRNA(Gln) amidotransferase subunit D | 3.57 ± 0.30 | tRNA editing | Part of a complex that catalyses transamidation to form Gln-tRNAGln from misacylated Glu-tRNAGln [11] |
| YP_183397 | Alanyl-tRNA editing protein AlaX | 1.81 ± 0.39 | tRNA editing | Catalyses hydrolysis of misacylated tRNAAla [12] |
| YP_183917 | 30S ribosomal protein S11 | 3.41 ± 0.63 | Translation | Part of the 30S subunit of the ribosome, the molecular machinery for protein biosynthesis [13] |
| YP_183938 | 50S ribosomal protein L6 | 4.88 ± 2.30 | Translation | Part of the 50S subunit of the ribosome, the molecular machinery for protein biosynthesis [13] |
| YP_183954 | 50S ribosomal protein L4P | 2.03 ± 0.51 | Translation | Part of the 50S subunit of the ribosome, the molecular machinery for protein biosynthesis [13] |
| YP_182519 | Diphthine synthase | 4.75 ± 0.27 | Translation | Catalyses the SAM-dependent trimethylation of an intermediate in diphthamide formation from histidine [14]; diphthamide is required for archaeal translation elongation factor 2 [15] |
| YP_184539 | Protein kinase | 5.12 ± 0.38 | Posttranslational modification | Component of the KEOPS complex responsible for formation of N6-threonylcarbamoyladenosine, important for translational fidelity [16, 17] |
| YP_182619 | Hypothetical protein TK0206 | 3.69 ± 0.48 | RNA/DNA replication and repair | A predicted RAD55 domain comprises half the protein; RAD55 has been implicated in DNA repair and signal transduction [18] |
| YP_182979 | RNA helicase | 4.59 ± 0.34 | RNA/DNA replication and repair | Belongs to DEAD-like helicase superfamily, involved in ATP-dependent RNA or DNA unwinding [19] |
| YP_183694 | Endonuclease | 3.69 ± 0.31 | RNA/DNA replication and repair | 5′-flap endonuclease and 5′-3′-exonuclease activity, characterised in Pyrococcus horikoshii [20] |
| YP_183841 |
Hypothetical protein TK1428 | 2.54 ± 0.39 | RNA/DNA replication and repair | Cleavage and polyadenylation specificity factor subunit-like protein; these are predicted in Archaea to be RNases [21] |
| YP_184316 | DNA polymerase II large subunit | 4.84 ± 2.20 | DNA replication and repair | Catalytic subunit of DNA polymerase, genome replication [22] |
| YP_184182 | Transcriptional regulator | 3.63 ± 0.32 | Transcription regulation | TrmB is a transcriptional regulator first characterized as a repressor of transcription of genes encoding sugar ABC transporters [23] and later shown in Halobacterium salinarum to act on up to 113 archaeal promoters in response to nutritional stress [24] |
| YP_183072 | Ribose ABC transporter permease | 4.59 ± 0.34 | Amino acid cycling and energy generation | ABC transport domain suggests involvement in amino acid/sugar uptake, although ABC transporters may be channels or exporters or serve a regulatory function [25] |
| YP_184170 | Peptide ABC transporter ATPase | 4.31 ± 0.30 | Amino acid cycling and energy generation | ABC transport domain suggests involvement in amino acid/sugar uptake, although ABC transporters may be channels or exporters or serve a regulatory function [25] |
| YP_183697 | Peptidase | 4.21 ± 0.34 | Amino acid cycling and energy generation | Intracellular protease with a type 1 glutamine amidotransferase domain, homologous to proteins thought to hydrolyze small peptides for nutrition [26] and upregulated under peptide-limiting conditions [27] in other Thermococcales |
| YP_184506 | NADH-quinone oxidoreductase | 4.01 ± 0.64 | Energy generation | Subunit of the membrane bound hydrogenase (mbh) complex, involved in disposal of excess reducing equivalents, essential in fermentative growth of T. kodakarensis [28, 29] |
| YP_183806 | Glycerol 3-phosphate dehydrogenase | 4.90 ± 0.42 | Energy generation | Involved in glycerol catabolism in heterotrophic Archaea [30]; it belongs to protein superfamily L-2-hydroxyglutarate oxidase; gene encoding homologous enzyme in Escherichia coli (ygaF) is induced by carbon starvation and stationary phase [31] |
| YP_183284 | Ornithine carbamoyltransferase | 3.36 ± 0.38 | Amino acid biosynthesis (?) | Predicted to play a role in arginine biosynthesis via ornithine; however, T. kodakarensis is an arginine auxotroph [32]; therefore, the role of this enzyme is unclear, potentially functioning in reverse to convert citrulline to ornithine [33]; it may be a stress response factor [34] |
| YP_184227 | L-Tyrosine decarboxylase | 4.19 ± 1.85 | Coenzyme production | Catalyses formation of beta-alanine for coenzyme A production [35] |
| YP_183265 | Hypothetical protein TK0853 | 2.59 ± 0.46 | Coenzyme production | Shows strong homology to nicotinate-nucleotide-dimethylbenzimidazole (NaMN:DMB) phosphoribosyl transferase, involved in formation of alpha-ribazole-5′-phosphate, a precursor of adenosylcobalamin (vitamin B12) [36, 37] |
| YP_183327 | 3-Hydroxy-3-methylglutaryl-CoA reductase | 4.59 ± 0.34 | Lipid synthesis | Catalyses the rate-limiting step in isoprenoid biosynthesis (formation of mevalonate from 3-hydroxy-3-methylglutaryl-CoA) [38] |
| YP_182969 | Methylthioribose-1-phosphate isomerase | 2.91 ± 0.57 | Function unknown | Predicted to play a role in the methionine salvage pathway [39, 40]; however, T. kodakarensis lacks a function methionine salvage pathway [41]; therefore, the role of this enzyme is unknown |
| YP_184329 | Apolipoprotein N-acyltransferase | 4.31 ± 0.30 | Function unknown | Shows strong identity to protein Ph0642 (accession 1J31) within class 13 of the nitrilase superfamily, therefore potentially a carbon-nitrogen hydrolase [42, 43] |
| YP_182427 | Oxetanocin | 8.93 ± 4.22 | Function unknown | Belongs to superfamily of metal-dependent phosphohydrolases whose function is unknown [44]; it may be a stress response protein [34] |
| YP_182912 | Zinc-dependent protease | 3.64 ± 0.58 | Function unknown | Identity to a TldE homologue (Sso0661) that does not display protease activity [45]; TldE homologues may play a role in modulation of DNA gyrase [46] or antibiotic secretion [47] |
| YP_183662 | Hypothetical protein TK1249 | 2.13 ± 0.53 | Function unknown | Shows identity to proteins classified as hypothetical proteins within either aconitase or DUF521 superfamilies |
| YP_183924 | Hypothetical protein TK1511 | 3.25 ± 0.52 | Function unknown | Belongs to uncharacterized protein family UPF0150 |
| YP_184398 | Hypothetical membrane protein | 5.66 ± 0.49 | Function unknown | Thermococcales-specific hypothetical protein with no conserved domains, potentially membrane associated |
| YP_184630 | 2-Amino-3-ketobutyrate coenzyme A ligase | −2.11 ± 0.32 | Amino acid cycling | Involved in conversion of threonine to glycine [48] |
| YP_184213 | Oligopeptide ABC transporter ATP-binding protein | −2.50 ± 0.21 | Amino acid cycling | ABC transport domain suggests involvement in amino acid/sugar uptake, although ABC transporters may be channels or exporters or serve a regulatory function [25] |
| YP_183708 | Predicted thiol protease | −48.88 ± 1.13 | Protein turnover | Belongs to C1 peptidase family of endo- and exopeptidases |
| YP_183338 | Phenylalanyl-tRNA ligase subunit beta | −2.32 ± 0.08 | Translation | Catalyses attachment of phenylalanine to its cognate tRNA [49] |
| YP_183718 | Probable translation initiation factor IF-2 | −8.65 ± 1.04 | Translation | Archaeal/eukaryotic translation initiation factor 5B, homologous to prokaryotic initiation factor 2 which promotes binding of the initiator tRNA to the ribosome during translation; the predicted protein sequence contains an intein that is posttranslationally excised |
| YP_183212 | DNA topoisomerase VI subunit B | −2.31 ± 0.08 | DNA replication and repair | Part of a type IIB DNA topoisomerase, involved in manipulating the topological state of DNA [50] |
| YP_182643 | ABC-type multidrug transport system, ATPase component | −2.29 ± 0.08 | Transport or DNA replication and repair | May be the ATPase component of a system involved in transport of molecules across the membrane or may be an ABC ATPase, involved in DNA repair, translation, or gene regulation [51] |
| YP_184173 | CGP-CTERM sorting domain-containing protein | −4.31 ± 0.36 | Transport (?) | Contains the Cys-Gly-Pro motif and C-terminus transmembrane domain found in various Thermococcales proteins, but of unknown function (potentially related to lipid modification); it shows similarity to ABC transporter substrate-binding proteins and thus may be involved in transport of compounds across the membrane |
| YP_182982 | CGP-CTERM sorting domain-containing protein | −2.46 ± 0.24 | Function unknown | Hypothetical protein with a putative ABC transport domain and a Cys-Gly-Pro motif followed by a transmembrane domain at the C-terminus; such CGP-CTERM domains have so far only been found in members of the Thermococcales and their function is speculative though they may be related to lipid modification |
| YP_183717 | Hypothetical protein TK1304 | −3.92 ± 0.34 | Function unknown | Hypothetical protein with no conserved domains detected; it appears to be Thermococcales specific |
| YP_184217 | Peptide ABC transporter substrate-binding protein | −4.88 ± 0.37 | Function unknown | ABC transport domain suggests involvement in amino acid/sugar uptake, although ABC transporters may be channels or exporters or serve a regulatory function [25] |
| YP_183593 | Hypothetical protein TK1180 | −14.25 ± 0.63 | Function unknown | Thermococcalesspecific protein of unknown function |
aProtein expression ratios were compared for the relevant ICPL labels (ICPL4 : ICPL0, ICPL4 : ICPL6, ICPL10 : ICPL0, and ICPL10 : IPL6) and proteins that were at least twofold upregulated or twofold downregulated as indicated by at least two of the ratios were considered to be of interest. The average of the four ratios and standard error of the mean are presented in the table.