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. 2006 Aug;2(1):11-30.
doi: 10.1155/2006/562404.

Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota

Mark K Ashby  1
Affiliations

Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota

Mark K Ashby. Archaea. 2006 Aug.

Abstract

The publicly available annotated archaeal genome sequences (23 complete and three partial annotations, October 2005) were searched for the presence of potential two-component open reading frames (ORFs) using gene category lists and BLASTP. A total of 489 potential two-component genes were identified from the gene category lists and BLASTP. Two-component genes were found in 14 of the 21 Euryarchaeal sequences (October 2005) and in neither the Crenarchaeota nor the Nanoarchaeota. A total of 20 predicted protein domains were identified in the putative two-component ORFs that, in addition to the histidine kinase and receiver domains, also includes sensor and signalling domains. The detailed structure of these putative proteins is shown, as is the distribution of each class of two-component genes in each species. Potential members of orthologous groups have been identified, as have any potential operons containing two or more two-component genes. The number of two-component genes in those Euryarchaeal species which have them seems to be linked more to lifestyle and habitat than to genome complexity, with most examples being found in Methanospirillum hungatei, Haloarcula marismortui, Methanococcoides burtonii and the mesophilic Methanosarcinales group. The large numbers of two-component genes in these species may reflect a greater requirement for internal regulation. Phylogenetic analysis of orthologous groups of five different protein classes, three probably involved in regulating taxis, suggests that most of these ORFs have been inherited vertically from an ancestral Euryarchaeal species and point to a limited number of key horizontal gene transfer events.

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Figures

Figure T2a.
Figure T2a.
Compilation and cartoon diagrams of all putative archaeal open reading frames encoding two-component proteins. Compilation and cartoon diagrams of all putative archaeal open reading frames encoding two-component proteins. Abbreviations; Cach = Cache; ConA = ConA-like glucanase; Gly = Glycos_transf_2; HKA = His_KA (and KA2); HATP = HATPase_c; Hkd = H-kinase_dim; H10 = HTH_10; PC = PAC; and SBPBac3 = SBP_bac_3. See Table 1 for gene name prefixes. Continued in Figure 2.
Figure T2b.
Figure T2b.
Continued from Table 2. Compilation and cartoon diagrams of all putative archaeal open reading frames encoding two-component proteins. Abbreviations; Cach = Cache; ConA = ConA-like glucanase; Gly = Glycos_transf_2; HKA = His_KA (and KA2); HATP = HATPase_c; Hkd = H-kinase_dim; H10 = HTH_10; PC = PAC; and SBPBac3 = SBP_bac_3. See Table 1 for gene name prefixes. Continued in Figure 3.
Figure T2c.
Figure T2c.
Continued from Table 2. Compilation and cartoon diagrams of all putative archaeal open reading frames encoding two-component proteins. Abbreviations; Cach = Cache; ConA = ConA-like glucanase; Gly = Glycos_transf_2; HKA = His_KA (and KA2); HATP = HATPase_c; Hkd = H-kinase_dim; H10 = HTH_10; PC = PAC; and SBPBac3 = SBP_bac_3. See Table 1 for gene name prefixes.
Figure 1.
Figure 1.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from histidine kinase II groups ahk5 and ahk22. Group ahk5 = MaceMA2890, MbarA_ 2935, MmazMM3295, MtheMTH174 and Mhun_401800550; and group ahk22 = MaceMA2294, Mbur_401657970, HaloVNG1374G, Mhun_401803800, AfulAF0450, NphaNP1154A and HmarrnB0156. The bacterial ORFs are Ppropionicus, NpunNpR2903 and Linterrogans. Abbreviations: Ppropionicus = P. propionicus_500413890; NpunNpR2903 = N. punctiforme; and Linterrogans = L. interrogansLA2540
Figure 2.
Figure 2.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from the histidine kinase IV groups ahk40–43. Group ahk40 = MaceMA3066, MmazMM0328, AfulAF1040 and Mbur_401647520; group ahk41 = MaceMA0014, MmazMM1325 and MbarA_0984; group ahk42 = PAB1332, PH0484, Tkod_610170420/30 and MmarMMP0927; and group ahk43 = HaloVNG0971G, HmarrnAC2205, NphaNP2172A and Mhun_401793120. The bacterial ORFs are CtetaniE17170, TmaritimaMSB_824070 and HpyloriHP0392. Abbreviations: CtetaniE17170 = C. tetaniE88_1817170; TmaritimaMSB_824070 = T. maritima; and HpyloriHP0392 = H. pylori.
Figure 3.
Figure 3.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from the response regulator I orphans arr7, arr10, arr12 and arr14. Group arr7 = HaloVNG0974G, AfulAF1042, MmarMMP0933, Mbur_401647540, MaceMA3068, MmazMM0330, PAB1330, PH0482, HmarrnAC2194, Tkod_610170400 , Mhun_401793100 and NphaNP2102A; group arr10 = MaceMA0016, MbarA_0986 and MmazMM1327;group arr12 = MaceMA4376, MbarA_1051, MmazMM1068, AfulAF2419, Mbur_401644620 and Mhun_401789540; and group arr14 = MaceMA2445, MbarA_3109, MMAZMM3007, Mbur_401658280 and Mhun_401776210. The bacterial ORFs are CtetaniE88, Tmaritima and Gmetallired. Abbreviations: CtetaniE88 = C. tetaniE88_1817150; Tmaritima = T. maritimaMSB8_24050; and Gmetallired = G. metallireducens_401349760.
Figure 4.
Figure 4.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from response regulator IV group arr18 and arr19. Group arr18 = MaceMA0015, MbarA_0985 and MmazMM1326; and group arr19 = PAB1331, PH0483, Tkod_ 610170410, HaloVNG0973G, HmarrnAC2204, MaceMA3067, MmazMM0329, Mbur_401647530, AfulAF1041, MmarMMP0926, NphaNP2174A and Mhun_401793110. The bacterial ORFs are Sthermophilum, Tmaritima and Tcrunogena. Abbreviations: Thermoco =T. kodakaraensis; Sthermophilum = S. thermophilum_3768360; Tmaritima = T.maritimaMSB8_21060; and Tcrunogena = T. crunogena Tcr0758
Figure 5.
Figure 5.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from hybrid kinase 1 group ahy2. The bacterial ORFs are Gviolglr3434, RrubRruA1653 and SaverSAV3017. Abbreviations: Gviolglr3434 = G. violaceus; RrubRruA1653 = R. rubrum; and SaverSAV3017 = S. avermitilis.
Figure A1.
Figure A1.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from histidine kinase II groups ahk5 and ahk22. Group ahk5 = MaceMA2890, MbarA_2935, MmazMM3295, MtheMTH174 and Mhun_401800550; and group ahk22 = MaceMA2294, Mbur_401657970, HaloVNG1374G, Mhun_401803800, AfulAF0450, NphaNP1154A and HmarrnB0156. The bacterial ORFs are Ppropionicus, NpunNpR2903 and Linterrogans. Abbreviations: Ppropionicus = P. propionicus_500413890; NpunNpR2903 = N. punctiforme; and Linterrogans = L. interrogansLA2540.
Figure A2.
Figure A2.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from histidine kinase VI groups ahk40–43. Group ahk40 = MaceMA3066, MmazMM0328, AfulAF1040 and Mbur_ 401647520; group ahk41 = MaceMA0014, MmazMM1325 and MbarA_ 0984;group ahk42 = PAB1332, PH0484, Tkod_610170420/30 and MmarMMP0927; and group ahk43 = HaloVNG0971G, HmarrnAC2205, NphaNP2172A and Mhun_ 401793120. The bacterial ORFs are CtetaniE17170, TmaritimaMSB_824070 and HpyloriHP0392.Abbreviations: CtetaniE17170 = C. tetaniE88_1817170; T. maritima = TmaritimaMSB_824070; and H. pylori = HpyloriHP0392.
Figure A3.
Figure A3.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from response regulator I groups arr7, arr10, arr12 and arr14. Group arr7 = HaloVNG0974G, AfulAF1042, MmarMMP0933, Mbur_401647540, MaceMA3068, MmazMM0330, PAB1330, PH0482, HmarrnAC2194, Tkod_610170400, Mhun_401793100 and NphaNP2102A; group arr10 = MaceMA0016, MbarA_0986 and MmazMM1327; group arr12 = MaceMA4376, MbarA_1051, MmazMM1068, AfulAF2419, Mbur_401644620 and Mhun_401789540; and group arr14 = MaceMA2445, MbarA_3109, MMAZMM3007, Mbur_401658280 and Mhun_401776210. The bacterial ORFs are CtetaniE88, Tmaritima and Gmetallired.Abbreviations: CtetaniE88 = C. tetaniE88_1817150; Tmaritima = T. maritimaMSB8_24050; and Gmetallired = G. metallireducens_401349760.
Figure A4.
Figure A4.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from response regulator IV groups arr18 and arr19. Group arr18 = MaceMA0015, MbarA_0985 and MmazMM1326; and group arr19 = PAB1331, PH0483, Tkod_610170410, HaloVNG0973G, HmarrnAC2204, MaceMA3067, MmazMM0329, Mbur_401647530, AfulAF1041, MmarMMP0926, NphaNP2174A and Mhun_401793110. The bacterial ORFs are Sthermophilum and Tmaritima, Tcrunogena. Abbreviations: Thermoco = T. kodakaraensis;Sthermophilum = S. thermophilum_3768360; Tmaritima = T.maritimaMSB8_21060; and Tcrunogena = T. crunogena Tcr0758.
Figure A5.
Figure A5.
Phylogenetic analysis by neighbor-joining of putative two-component open reading frames (ORFs) from hybrid kinase 1 group ahy2. The bacterial ORFs are Gviolglr3434, RrubRruA1653 and SaverSAV3017. Abbreviations: Gviolglr3434 = G. violaceus; RrubRruA1653 = R. rubrum; and SaverSAV3017 = S. avermitilis.
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