The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase

Table 2

Proteins of T. kodakarensis that were up- or downregulated at least twofold 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 tRNA 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-tRNA from misacylated Glu-tRNA [11]
YP_183397	Alanyl-tRNA editing protein AlaX	1.81 ± 0.39	tRNA editing	Catalyses hydrolysis of misacylated tRNA [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

Protein 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.