Selenoproteins and the Metabolic Features of the Archaeal Ancestor of Eukaryotes
http://www.100md.com
《分子生物学进展》
Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore
Correspondence: E-mail: cfoster@jhmi.edu.
Abstract
In all three branches of life, some organisms incorporate the rare amino acid selenocysteine. Selenoproteins are relevant to the controversy over the metabolic features of the archaeal ancestor of eukaryotes because among archaea, several known selenoproteins are involved in methanogenesis and autotrophic growth. Although the eukaryotic selenocysteine-specific translation apparatus and at least one selenoprotein appear to be of archaeal origin, selenoproteins have not been identified among sulfur-metabolizing crenarchaeotes. In this regard, both the phylogeny and function of archaeal selenoproteins are consistent with the argument that the archaeal ancestor was a methanogen. Selenium, however, is abundant in sulfur-rich environments, and some anaerobic bacteria reduce sulfur and have selenoproteins similar to those in archaea. As additional archaeal sequence data becomes available, it will be important to determine whether selenoproteins are present in nonmethanogenic archaea, especially the sulfur-metabolizing crenarchaeotes.
Key Words: archaea ? origin of life ? methanogen ? sulfur ? hydrogen hypothesis ? crenarchaeote
Introduction
Selenoproteins are relevant to the controversy over the metabolic features of the archaeal ancestor of eukaryotes because, among archaea, they facilitate autotrophic growth and methanogenesis (Rother et al. 2001). Selenium, as selenocysteine, is incorporated into the primary structure of a small group of enzymes known as selenoproteins (Hatfield and Gladyshev 2002; Kryukov et al. 2003; Kryukov and Gladyshev 2004). Archaeal selenoproteins include two necessary for reduction of CO2 to methane (formyl-methanofuran dehydrogenase and heterodisulfide reductase) and three [NiFe]-hydrogenase subunits (the F420 reducing and nonreducing hydrogenases and vhuU, a small subunit) (Halboth and Klein 1992; Sorgenfrei et al. 1993; Vorholt, Vaupel, and Thauer 1997; Wilting et al. 1997). Hydrogenases catalyze the conversion of H2 into protons and electrons, providing a source of electrons necessary for anaerobic archaea to maintain redox balance (Vignais, Billoud, and Meyer 2001). Additional archaeal selenoproteins include a formate dehydrogenase, selenophosphate synthetase (SelD), and a HesB-like protein (Guimaraes et al. 1996; Wilting et al. 1997; Kryukov and Gladyshev 2004). To determine whether the phylogeny and distribution of archaeal selenoproteins might provide insight into the metabolic features of the archaeal ancestor of eukaryotes, I have created up to date phylogenetic trees for known archaeal selenoproteins and the factors necessary for selenoprotein synthesis.
Methods
For each archaeal selenoprotein and SelB, the NCBI PHI-Blast program with a blosum 45 matrix was used to search the nonredundant protein sequence database. Protein sequences were aligned using ClustalW, and minimum-evolution phylogenetic trees were constructed in MEGA version 2.1 based on the gamma-corrected amino acid distance, the complete deletion model, and 1,000 bootstrap replications. Identified tRNA-sec sequences were found through literature review (Rao et al. 2003) and NCBI and Genomic tRNA databases (http://rna.wustl.edu/GtRDB/) (Lowe and Eddy 1997). Nucleotide sequences were aligned using ClustalW, and phylogenetic trees were constructed as outlined above.
Results and Discussion
Although selenoproteins are present in all three branches of life, important similarities exist between selenoprotein synthesis in archaea and eukaryotes. In contrast to the 20 standard amino acids, selenocysteine does not have its own codon (Hatfield and Gladyshev 2002). Rather, the UGA stop codon is recoded to allow translational read through. The insertion of selenocysteine requires an RNA stem loop known as a SECIS element (selenocysteine insertion sequence), tRNA-selenocysteine (tRNA-sec), and a selenocysteine-specific elongation factor (SelB). An important difference between bacteria and both archaea and eukaryotes is the location of SECIS elements. In bacteria, SECIS elements are located adjacent to the UGA codon (Zinoni, Heider, and Bock 1990); in both archaea and eukaryotes SECIS elements are in the 3' UTR (Berry et al. 1991; Wilting et al. 1997). The movement of the SECIS may have had evolutionary consequences, such as allowing incorporation of more than one selenocysteine, relaxing constraint on coding sequence, or altering the dynamic between the UGA-codon and bacterial releasing factor–2 (RF-2) (Wilting et al. 1997; Mansell et al. 2001).
The phylogenies of SelB, tRNA-sec, and SelD are each consistent with an archaeal origin of the eukaryotic selenocysteine-specific translation apparatus. The close relationship between the archaeal and eukaryotic SelB correlates with known structural differences with the bacterial SelB (fig. 1) (Fagegaltier et al. 2000; Rother et al. 2000; Tujebajeva et al. 2000; Fagegaltier, Carbon, and Krol 2001). The N-terminal portion of the bacterial SelB is homologous to the bacterial elongation factor EF-Tu, whereas the C-terminal portion of the protein binds to SECIS elements. Both the archaeal and the eukaryotic SelB proteins have shorter C-terminal extensions, which lack the ability to interact with SECIS elements (Rother et al. 2000; Tujebajeva et al. 2000). The loss of SelB SECIS binding activity parallels the movement of the SECIS to the 3' UTR. In eukaryotes, the SECIS binding domain is located in a different protein, SECIS binding protein 2 (Copeland and Driscoll 1999). Known structural differences also exist between the bacterial tRNA-sec, which folds to form an 8/5 secondary structure, and the archaeal and eukaryal tRNA-sec, which form a 9/4 structure, supporting a bacterial root for the tRNA-sec tree (fig. 2) (Hubert et al. 1998; Rao et al. 2003). Most archaeal selenoproteins lack eukaryal homologs and are, therefore, not helpful with regard to the study of the origin of eukaryotes (see Supplementary Material online). The one archaeal selenoprotein with a close homolog to a eukaryotic selenoprotein is SelD, a protein involved in tRNA modification and necessary to catalyze the formation of a reactive selenium donor for selenocysteine synthesis from ATP and selenide. Like SelB and tRNA-sec, the SelD tree is entirely compatible with a close relationship between the archaeal and eukaryal sequences, although because this tree is unrooted, alternative topologies are possible (fig. 3) (Guimaraes et al. 1996).
FIG. 1.— Minimum-evolution tree of the selenocysteine-specific elongation factor (SelB), the elongation initiation factor 2-gamma (EIF-2), elongation factor 1-alpha (EF-1a), and the elongation factor Tu (EF-Tu). The tree is rooted on EF-Tu and is based on the gamma-corrected amino acid distance. Numbers on the branches are confidence levels for the significance test of the interior branch. Prefixes are as follows: a (archaeal), e (eukaryotic), b (bacterial), and m (mitochondrial).
FIG. 2.— Minimum-evolution tree (unrooted) of tRNA-sec based on the number of nucleotide differences. Numbers on the branches are confidence levels for the significance test of the interior branch.
FIG. 3.— Minimum-evolution tree (unrooted) of selenophosphate synthetase (SelD) based on the gamma-corrected amino acid distance. Numbers on the branches are confidence levels for the significance test of the interior branch. Selenoproteins are indicated by U.
Several additional observations support the archaeal origin of selenocysteine-specific translation. Foremost are similarities between the standard protein translation apparatus of archaea and eukaryotes. Both archaea and eukaryotes use a single orthologous principle releasing factor (RF-1), which recognizes all three termination codons (Bell and Jackson 1998; Inagaki and Doolittle 2000). In bacteria, however, termination is catalyzed by one of two releasing factors, RF-1 (which recognizes UAA and UAG) and RF-2 (which recognizes UGA and UAA). Neither the archaeal nor the eukaryal RF1 has close homology to either RF-1 or RF-2. In addition, the bacterial initiation factor 2 (IF2) consists of a single subunit, whereas in archaea and eukaryotes, IF2 is a complex of three subunits (Kyrpides and Woese 1998). Interestingly, the gamma-subunit of IF2 is most closely related to the SelB required for selenoprotein synthesis (fig. 1) (Keeling, Fast, and McFadden 1998).
An observation with possible relevance to the identity of the archaeal mother cell is that selenoproteins, SelB, and tRNA-sec have only been identified among certain methanogenic euryarchaeotes (Rother et al. 2000, 2001; Kryukov and Gladyshev 2004). Not only do known sulfur metabolizing crenarchaotes not incorporate selenocysteine but also the distribution of selenoproteins among euryarchaeotes appears to be further restricted to Methanococci and Methanopyri (table 1 and Supplementary Material online). The finding that selenoproteins and the machinery for selenoprotein synthesis are present in eukaryotes and archaeal methanogens, but not crenarchaeotes, I would argue, lends both phylogenetic and functional support to two recent hypotheses suggesting a methanogenic origin for the eukaryotic cell. The hydrogen hypothesis of the first eukaryote, proposed by Martin and Muller (1998), argues that the eukaryotic cell arose from a symbiotic association between a bacteria that produced H2, CO2, and acetate as waste products and a strictly anaerobic methanogenic archaea that used each of these products to satisfy nutritional needs (Martin and Muller 1998). Moreira and Lopez-Garci a's syntrophic hypothesis also predicts similarities between eukaryotes and methanogens, although it addresses the origin of mitochondria differently (Moreira and Lopez-Garcia 1998). Under either hypothesis, archaeal selenoproteins involved in methanogenesis and autotrophic growth could have played a central role. Because neither autotrophy nor methanogenesis are known to be necessary for eukaryotes, it is likely that any archaeal selenoprotein genes involved in these processes were subsequently either lost or rapidly evolved new functions in eukaryotes.
Table 1 Archaea That Have and do not Have Selenoproteins
Despite the absence of selenoproteins among known sulfur-metabolizing crenarchaeotes, there is considerable support for a prevailing hypothesis that eukaryotes and crenarchaeotes share a common origin (Rivera and Lake 1992; Baldauf, Palmer, and Doolittle 1996). Indeed, selenium is abundant in sulfur-rich environments, and some anaerobic bacteria both reduce sulfur and have selenoproteins similar to those found in archaea (Rother et al. 2001). It is, therefore, possible that some crenarchaeotes (whether now extant or not) possessed selenoproteins other than those involved in methanogenesis. In addition, a lack of selenoproteins among known sulfur-metabolizing archaea would not exclude the possibility that eukaryotes are descended from an as yet uncultivated archaea with features common to both crenarchaeotes and methanogens. It is worth noting that a close relationship between euryarchaeotes and eukaryotes has also been described for deoxyhypusine synthase, another gene involved in protein translation (Brochier, Lopez-Garcia, and Moreira 2004).
Conclusion
Whether multiple molecular markers and exhaustive tree reconstruction techniques will resolve the controversy over the origin of the eukaryotic cell remains to be determined. It is, therefore, important that the evolutionary implications of key biochemical features linking eukaryotes with particular branches of archaea be considered fully. The data presented here suggests that both the function and phylogeny of archaeal selenoproteins are in agreement with recent hypotheses proposing a methanogenic origin of the "archaeal-like" part of the eukaryotic genome. As additional archaeal species are sequenced, it will be important to determine whether the ability to incorporate selenocysteine is truly restricted to methanogens. In this regard, the phylogeny and function of selenoproteins may provide insight into the metabolic features of early archaea and perhaps as to whether the archaeal ancestor of eukaryotes was an H2-dependent methanogen or a sulfur-metabolizing crenarchaeote.
Acknowledgements
Grant support was provided through a Child Health Research Center (CHRC) Scholar Award and a K-22 career transition award from the National Cancer Institute, National Institutes of Health. Austin Hughes, Stephen Chanock, Kashama Aswath, and Jonathan Pevsner are thanked for helpful discussions.
References
Baldauf, S. L., J. D. Palmer, and W. F. Doolittle. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. USA 93:7749–7754.
Bell, S. D., and S. P. Jackson. 1998. Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6:222–228.
Berry, M. J., L. Banu, Y. Y. Chen, S. J. Mandel, J. D. Kieffer, J. W. Harney, and P. R. Larsen. 1991. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3' untranslated region. Nature 353:273–276.
Brochier, C., P. Lopez-Garcia, and D. Moreira. 2004. Horizontal gene transfer and archaeal origin of deoxyhypusine synthase homologous genes in bacteria. Gene 330:169–176.
Copeland, P. R., and D. M. Driscoll. 1999. Purification, redox sensitivity, and RNA binding properties of SECIS-binding protein 2, a protein involved in selenoprotein biosynthesis. J. Biol. Chem. 274:25447–25454.
Fagegaltier, D., P. Carbon, and A. Krol. 2001. Distinctive features in the SelB family of elongation factors for selenoprotein synthesis. A glimpse of an evolutionary complexified translation apparatus. Biofactors 14:5–10.
Fagegaltier, D., N. Hubert, K. Yamada, T. Mizutani, P. Carbon, and A. Krol. 2000. Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation. EMBO J. 19:4796–4805.
Guimaraes, M. J., D. Peterson, A. Vicari et al. (11 co-authors). 1996. Identification of a novel selD homolog from eukaryotes, bacteria, and archaea: is there an autoregulatory mechanism in selenocysteine metabolism?. Proc. Natl. Acad. Sci. USA 93:15086–15091.
Halboth, S., and A. Klein. 1992. Methanococcus voltae harbors four gene clusters potentially encoding two and two hydrogenases, each of the cofactor F420-reducing or F420-non-reducing types. Mol. Gen. Genet. 233:217–224.
Hatfield, D. L., and V. N. Gladyshev. 2002. How selenium has altered our understanding of the genetic code. Mol. Cell. Biol. 22:3565–3576.
Hubert, N., C. Sturchler, E. Westhof, P. Carbon, and A. Krol. 1998. The 9/4 secondary structure of eukaryotic selenocysteine tRNA: more pieces of evidence. RNA 4:1029–1033.
Inagaki, Y., and W. F. Doolittle. 2000. Evolution of the eukaryotic translation termination system: origins of release factors. Mol. Biol. Evol. 17:882–889.
Keeling, P. J., N. M. Fast, and G. I. McFadden. 1998. Evolutionary relationship between translation initiation factor eIF-2gamma and selenocysteine-specific elongation factor SELB: change of function in translation factors. J. Mol. Evol. 47:649–655.
Kryukov, G. V., S. Castellano, S. V. Novoselov, A. V. Lobanov, O. Zehtab, R. Guigo, and V. N. Gladyshev. 2003. Characterization of mammalian selenoproteomes. Science 300:1439–1443.
Kryukov, G. V., and V. N. Gladyshev. 2004. The prokaryotic selenoproteome. EMBO Rep 5:538–543.
Kyrpides, N. C., and C. R. Woese. 1998. Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families. Proc. Natl. Acad. Sci. USA 95:3726–3730.
Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964.
Mansell, J. B., D. Guevremont, E. S. Poole, and W. P. Tate. 2001. A dynamic competition between release factor 2 and the tRNA(Sec) decoding UGA at the recoding site of Escherichia coli formate dehydrogenase H. Embo. J. 20:7284–7293.
Martin, W., and M. Muller. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392:37–41.
Moreira, D., and P. Lopez-Garcia. 1998. Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J. Mol. Evol. 47:517–530.
Rao, M., B. A. Carlson, S. V. Novoselov, D. P. Weeks, V. N. Gladyshev, and D. L. Hatfield. 2003. Chlamydomonas reinhardtii selenocysteine tRNASec. RNA 9:923–930.
Rivera, M. C., and J. A. Lake. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:74–76.
Rother, M., A. Resch, R. Wilting, and A. Bock. 2001. Selenoprotein synthesis in archaea. Biofactors 14:75–83.
Rother, M., R. Wilting, S. Commans, and A. Bock. 2000. Identification and characterisation of the selenocysteine-specific translation factor SelB from the archaeon Methanococcus jannaschii. J. Mol. Biol. 299:351–358.
Sorgenfrei, O., D. Linder, M. Karas, and A. Klein. 1993. A novel very small subunit of a selenium containing hydrogenase of Methanococcus voltae is postranslationally processed by cleavage at a defined position. Eur. J. Biochem. 213:1355–1358.
Tujebajeva, R. M., P. R. Copeland, X. M. Xu, B. A. Carlson, J. W. Harney, D. M. Driscoll, D. L. Hatfield, and M. J. Berry. 2000. Decoding apparatus for eukaryotic selenocysteine insertion. EMBO Rep. 1:158–163.
Vignais, P. M., B. Billoud, and J. Meyer. 2001. Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25:455–501.
Vorholt, J. A., M. Vaupel, and R. K. Thauer. 1997. A selenium-dependent and a selenium-independent formylmethanofuran dehydrogenase and their transcriptional regulation in the hyperthermophilic Methanopyrus kandleri. Mol. Microbiol. 23:1033–1042.
Wilting, R., S. Schorling, B. C. Persson, and A. Bock. 1997. Selenoprotein synthesis in archaea: identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion. J. Mol. Biol. 266:637–641.
Zinoni, F., J. Heider, and A. Bock. 1990. Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. Proc. Natl. Acad. Sci. USA 87:4660–4664.(Charles B. Foster1)
Correspondence: E-mail: cfoster@jhmi.edu.
Abstract
In all three branches of life, some organisms incorporate the rare amino acid selenocysteine. Selenoproteins are relevant to the controversy over the metabolic features of the archaeal ancestor of eukaryotes because among archaea, several known selenoproteins are involved in methanogenesis and autotrophic growth. Although the eukaryotic selenocysteine-specific translation apparatus and at least one selenoprotein appear to be of archaeal origin, selenoproteins have not been identified among sulfur-metabolizing crenarchaeotes. In this regard, both the phylogeny and function of archaeal selenoproteins are consistent with the argument that the archaeal ancestor was a methanogen. Selenium, however, is abundant in sulfur-rich environments, and some anaerobic bacteria reduce sulfur and have selenoproteins similar to those in archaea. As additional archaeal sequence data becomes available, it will be important to determine whether selenoproteins are present in nonmethanogenic archaea, especially the sulfur-metabolizing crenarchaeotes.
Key Words: archaea ? origin of life ? methanogen ? sulfur ? hydrogen hypothesis ? crenarchaeote
Introduction
Selenoproteins are relevant to the controversy over the metabolic features of the archaeal ancestor of eukaryotes because, among archaea, they facilitate autotrophic growth and methanogenesis (Rother et al. 2001). Selenium, as selenocysteine, is incorporated into the primary structure of a small group of enzymes known as selenoproteins (Hatfield and Gladyshev 2002; Kryukov et al. 2003; Kryukov and Gladyshev 2004). Archaeal selenoproteins include two necessary for reduction of CO2 to methane (formyl-methanofuran dehydrogenase and heterodisulfide reductase) and three [NiFe]-hydrogenase subunits (the F420 reducing and nonreducing hydrogenases and vhuU, a small subunit) (Halboth and Klein 1992; Sorgenfrei et al. 1993; Vorholt, Vaupel, and Thauer 1997; Wilting et al. 1997). Hydrogenases catalyze the conversion of H2 into protons and electrons, providing a source of electrons necessary for anaerobic archaea to maintain redox balance (Vignais, Billoud, and Meyer 2001). Additional archaeal selenoproteins include a formate dehydrogenase, selenophosphate synthetase (SelD), and a HesB-like protein (Guimaraes et al. 1996; Wilting et al. 1997; Kryukov and Gladyshev 2004). To determine whether the phylogeny and distribution of archaeal selenoproteins might provide insight into the metabolic features of the archaeal ancestor of eukaryotes, I have created up to date phylogenetic trees for known archaeal selenoproteins and the factors necessary for selenoprotein synthesis.
Methods
For each archaeal selenoprotein and SelB, the NCBI PHI-Blast program with a blosum 45 matrix was used to search the nonredundant protein sequence database. Protein sequences were aligned using ClustalW, and minimum-evolution phylogenetic trees were constructed in MEGA version 2.1 based on the gamma-corrected amino acid distance, the complete deletion model, and 1,000 bootstrap replications. Identified tRNA-sec sequences were found through literature review (Rao et al. 2003) and NCBI and Genomic tRNA databases (http://rna.wustl.edu/GtRDB/) (Lowe and Eddy 1997). Nucleotide sequences were aligned using ClustalW, and phylogenetic trees were constructed as outlined above.
Results and Discussion
Although selenoproteins are present in all three branches of life, important similarities exist between selenoprotein synthesis in archaea and eukaryotes. In contrast to the 20 standard amino acids, selenocysteine does not have its own codon (Hatfield and Gladyshev 2002). Rather, the UGA stop codon is recoded to allow translational read through. The insertion of selenocysteine requires an RNA stem loop known as a SECIS element (selenocysteine insertion sequence), tRNA-selenocysteine (tRNA-sec), and a selenocysteine-specific elongation factor (SelB). An important difference between bacteria and both archaea and eukaryotes is the location of SECIS elements. In bacteria, SECIS elements are located adjacent to the UGA codon (Zinoni, Heider, and Bock 1990); in both archaea and eukaryotes SECIS elements are in the 3' UTR (Berry et al. 1991; Wilting et al. 1997). The movement of the SECIS may have had evolutionary consequences, such as allowing incorporation of more than one selenocysteine, relaxing constraint on coding sequence, or altering the dynamic between the UGA-codon and bacterial releasing factor–2 (RF-2) (Wilting et al. 1997; Mansell et al. 2001).
The phylogenies of SelB, tRNA-sec, and SelD are each consistent with an archaeal origin of the eukaryotic selenocysteine-specific translation apparatus. The close relationship between the archaeal and eukaryotic SelB correlates with known structural differences with the bacterial SelB (fig. 1) (Fagegaltier et al. 2000; Rother et al. 2000; Tujebajeva et al. 2000; Fagegaltier, Carbon, and Krol 2001). The N-terminal portion of the bacterial SelB is homologous to the bacterial elongation factor EF-Tu, whereas the C-terminal portion of the protein binds to SECIS elements. Both the archaeal and the eukaryotic SelB proteins have shorter C-terminal extensions, which lack the ability to interact with SECIS elements (Rother et al. 2000; Tujebajeva et al. 2000). The loss of SelB SECIS binding activity parallels the movement of the SECIS to the 3' UTR. In eukaryotes, the SECIS binding domain is located in a different protein, SECIS binding protein 2 (Copeland and Driscoll 1999). Known structural differences also exist between the bacterial tRNA-sec, which folds to form an 8/5 secondary structure, and the archaeal and eukaryal tRNA-sec, which form a 9/4 structure, supporting a bacterial root for the tRNA-sec tree (fig. 2) (Hubert et al. 1998; Rao et al. 2003). Most archaeal selenoproteins lack eukaryal homologs and are, therefore, not helpful with regard to the study of the origin of eukaryotes (see Supplementary Material online). The one archaeal selenoprotein with a close homolog to a eukaryotic selenoprotein is SelD, a protein involved in tRNA modification and necessary to catalyze the formation of a reactive selenium donor for selenocysteine synthesis from ATP and selenide. Like SelB and tRNA-sec, the SelD tree is entirely compatible with a close relationship between the archaeal and eukaryal sequences, although because this tree is unrooted, alternative topologies are possible (fig. 3) (Guimaraes et al. 1996).
FIG. 1.— Minimum-evolution tree of the selenocysteine-specific elongation factor (SelB), the elongation initiation factor 2-gamma (EIF-2), elongation factor 1-alpha (EF-1a), and the elongation factor Tu (EF-Tu). The tree is rooted on EF-Tu and is based on the gamma-corrected amino acid distance. Numbers on the branches are confidence levels for the significance test of the interior branch. Prefixes are as follows: a (archaeal), e (eukaryotic), b (bacterial), and m (mitochondrial).
FIG. 2.— Minimum-evolution tree (unrooted) of tRNA-sec based on the number of nucleotide differences. Numbers on the branches are confidence levels for the significance test of the interior branch.
FIG. 3.— Minimum-evolution tree (unrooted) of selenophosphate synthetase (SelD) based on the gamma-corrected amino acid distance. Numbers on the branches are confidence levels for the significance test of the interior branch. Selenoproteins are indicated by U.
Several additional observations support the archaeal origin of selenocysteine-specific translation. Foremost are similarities between the standard protein translation apparatus of archaea and eukaryotes. Both archaea and eukaryotes use a single orthologous principle releasing factor (RF-1), which recognizes all three termination codons (Bell and Jackson 1998; Inagaki and Doolittle 2000). In bacteria, however, termination is catalyzed by one of two releasing factors, RF-1 (which recognizes UAA and UAG) and RF-2 (which recognizes UGA and UAA). Neither the archaeal nor the eukaryal RF1 has close homology to either RF-1 or RF-2. In addition, the bacterial initiation factor 2 (IF2) consists of a single subunit, whereas in archaea and eukaryotes, IF2 is a complex of three subunits (Kyrpides and Woese 1998). Interestingly, the gamma-subunit of IF2 is most closely related to the SelB required for selenoprotein synthesis (fig. 1) (Keeling, Fast, and McFadden 1998).
An observation with possible relevance to the identity of the archaeal mother cell is that selenoproteins, SelB, and tRNA-sec have only been identified among certain methanogenic euryarchaeotes (Rother et al. 2000, 2001; Kryukov and Gladyshev 2004). Not only do known sulfur metabolizing crenarchaotes not incorporate selenocysteine but also the distribution of selenoproteins among euryarchaeotes appears to be further restricted to Methanococci and Methanopyri (table 1 and Supplementary Material online). The finding that selenoproteins and the machinery for selenoprotein synthesis are present in eukaryotes and archaeal methanogens, but not crenarchaeotes, I would argue, lends both phylogenetic and functional support to two recent hypotheses suggesting a methanogenic origin for the eukaryotic cell. The hydrogen hypothesis of the first eukaryote, proposed by Martin and Muller (1998), argues that the eukaryotic cell arose from a symbiotic association between a bacteria that produced H2, CO2, and acetate as waste products and a strictly anaerobic methanogenic archaea that used each of these products to satisfy nutritional needs (Martin and Muller 1998). Moreira and Lopez-Garci a's syntrophic hypothesis also predicts similarities between eukaryotes and methanogens, although it addresses the origin of mitochondria differently (Moreira and Lopez-Garcia 1998). Under either hypothesis, archaeal selenoproteins involved in methanogenesis and autotrophic growth could have played a central role. Because neither autotrophy nor methanogenesis are known to be necessary for eukaryotes, it is likely that any archaeal selenoprotein genes involved in these processes were subsequently either lost or rapidly evolved new functions in eukaryotes.
Table 1 Archaea That Have and do not Have Selenoproteins
Despite the absence of selenoproteins among known sulfur-metabolizing crenarchaeotes, there is considerable support for a prevailing hypothesis that eukaryotes and crenarchaeotes share a common origin (Rivera and Lake 1992; Baldauf, Palmer, and Doolittle 1996). Indeed, selenium is abundant in sulfur-rich environments, and some anaerobic bacteria both reduce sulfur and have selenoproteins similar to those found in archaea (Rother et al. 2001). It is, therefore, possible that some crenarchaeotes (whether now extant or not) possessed selenoproteins other than those involved in methanogenesis. In addition, a lack of selenoproteins among known sulfur-metabolizing archaea would not exclude the possibility that eukaryotes are descended from an as yet uncultivated archaea with features common to both crenarchaeotes and methanogens. It is worth noting that a close relationship between euryarchaeotes and eukaryotes has also been described for deoxyhypusine synthase, another gene involved in protein translation (Brochier, Lopez-Garcia, and Moreira 2004).
Conclusion
Whether multiple molecular markers and exhaustive tree reconstruction techniques will resolve the controversy over the origin of the eukaryotic cell remains to be determined. It is, therefore, important that the evolutionary implications of key biochemical features linking eukaryotes with particular branches of archaea be considered fully. The data presented here suggests that both the function and phylogeny of archaeal selenoproteins are in agreement with recent hypotheses proposing a methanogenic origin of the "archaeal-like" part of the eukaryotic genome. As additional archaeal species are sequenced, it will be important to determine whether the ability to incorporate selenocysteine is truly restricted to methanogens. In this regard, the phylogeny and function of selenoproteins may provide insight into the metabolic features of early archaea and perhaps as to whether the archaeal ancestor of eukaryotes was an H2-dependent methanogen or a sulfur-metabolizing crenarchaeote.
Acknowledgements
Grant support was provided through a Child Health Research Center (CHRC) Scholar Award and a K-22 career transition award from the National Cancer Institute, National Institutes of Health. Austin Hughes, Stephen Chanock, Kashama Aswath, and Jonathan Pevsner are thanked for helpful discussions.
References
Baldauf, S. L., J. D. Palmer, and W. F. Doolittle. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. USA 93:7749–7754.
Bell, S. D., and S. P. Jackson. 1998. Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6:222–228.
Berry, M. J., L. Banu, Y. Y. Chen, S. J. Mandel, J. D. Kieffer, J. W. Harney, and P. R. Larsen. 1991. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3' untranslated region. Nature 353:273–276.
Brochier, C., P. Lopez-Garcia, and D. Moreira. 2004. Horizontal gene transfer and archaeal origin of deoxyhypusine synthase homologous genes in bacteria. Gene 330:169–176.
Copeland, P. R., and D. M. Driscoll. 1999. Purification, redox sensitivity, and RNA binding properties of SECIS-binding protein 2, a protein involved in selenoprotein biosynthesis. J. Biol. Chem. 274:25447–25454.
Fagegaltier, D., P. Carbon, and A. Krol. 2001. Distinctive features in the SelB family of elongation factors for selenoprotein synthesis. A glimpse of an evolutionary complexified translation apparatus. Biofactors 14:5–10.
Fagegaltier, D., N. Hubert, K. Yamada, T. Mizutani, P. Carbon, and A. Krol. 2000. Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation. EMBO J. 19:4796–4805.
Guimaraes, M. J., D. Peterson, A. Vicari et al. (11 co-authors). 1996. Identification of a novel selD homolog from eukaryotes, bacteria, and archaea: is there an autoregulatory mechanism in selenocysteine metabolism?. Proc. Natl. Acad. Sci. USA 93:15086–15091.
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