UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M (2013)
Proceedings of the National Academy of Sciences of the United States of America 110(14): 5540-5545.

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Abstract
The composition of the human microbiota is recognized as an important factor in human health and disease. Many of our cohabitating microbes belong to phylum-level divisions for which there are no cultivated representatives and are only represented by small subunit rRNA sequences. For one such taxon (SR1), which includes bacteria with elevated abundance in periodontitis, we provide a single-cell genome sequence from a healthy oral sample. SR1 bacteria use a unique genetic code. In-frame TGA (opal) codons are found in most genes (85%), often at loci normally encoding conserved glycine residues. UGA appears not to function as a stop codon and is in equilibrium with the canonical GGN glycine codons, displaying strain-specific variation across the human population. SR1 encodes a divergent tRNA(Gly)UCA with an opal-decoding anticodon. SR1 glycyl-tRNA synthetase acylates tRNA(Gly)UCA with glycine in vitro with similar activity compared with normal tRNA(Gly)UCC. Coexpression of SR1 glycyl-tRNA synthetase and tRNA(Gly)UCA in Escherichia coli yields significant β-galactosidase activity in vivo from a lacZ gene containing an in-frame TGA codon. Comparative genomic analysis with Human Microbiome Project data revealed that the human body harbors a striking diversity of SR1 bacteria. This is a surprising finding because SR1 is most closely related to bacteria that live in anoxic and thermal environments. Some of these bacteria share common genetic and metabolic features with SR1, including UGA to glycine reassignment and an archaeal-type ribulose-1,5-bisphosphate carboxylase (RubisCO) involved in AMP recycling. UGA codon reassignment renders SR1 genes untranslatable by other bacteria, which impacts horizontal gene transfer within the human microbiota.
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Campbell JH, O'Donoghue P, Campbell AG, et al. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(14):5540-5545.
Campbell, J. H., O'Donoghue, P., Campbell, A. G., Schwientek, P., Sczyrba, A., Woyke, T., Söll, D., et al. (2013). UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings of the National Academy of Sciences of the United States of America, 110(14), 5540-5545.
Campbell, J. H., O'Donoghue, P., Campbell, A. G., Schwientek, P., Sczyrba, A., Woyke, T., Söll, D., and Podar, M. (2013). UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings of the National Academy of Sciences of the United States of America 110, 5540-5545.
Campbell, J.H., et al., 2013. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings of the National Academy of Sciences of the United States of America, 110(14), p 5540-5545.
J.H. Campbell, et al., “UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota”, Proceedings of the National Academy of Sciences of the United States of America, vol. 110, 2013, pp. 5540-5545.
Campbell, J.H., O'Donoghue, P., Campbell, A.G., Schwientek, P., Sczyrba, A., Woyke, T., Söll, D., Podar, M.: UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings of the National Academy of Sciences of the United States of America. 110, 5540-5545 (2013).
Campbell, James H., O'Donoghue, Patrick, Campbell, Alisha G., Schwientek, Patrick, Sczyrba, Alexander, Woyke, Tanja, Söll, Dieter, and Podar, Mircea. “UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota”. Proceedings of the National Academy of Sciences of the United States of America 110.14 (2013): 5540-5545.
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PMID: 27153586
The mysterious orphans of Mycoplasmataceae.
Tatarinova TV, Lysnyansky I, Nikolsky YV, Bolshoy A., Biol. Direct 11(1), 2016
PMID: 26747447
Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities.
Hanke A, Berg J, Hargesheimer T, Tegetmeyer HE, Sharp CE, Strous M., Front Microbiol 6(), 2015
PMID: 26779132
Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads.
Nolla-Ardevol V, Peces M, Strous M, Tegetmeyer HE., BMC Microbiol. 15(), 2015
PMID: 26680455
Protein Mis-Termination Initiates Genetic Diseases, Cancers, and Restricts Bacterial Genome Expansion.
Wong TY, Schwartzbach SD., J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 33(3), 2015
PMID: 26087060
Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1.
Dueholm MS, Albertsen M, Stokholm-Bjerregaard M, McIlroy SJ, Karst SM, Nielsen PH., Genome Announc 3(3), 2015
PMID: 26067967
In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3).
Youssef NH, Farag IF, Rinke C, Hallam SJ, Woyke T, Elshahed MS., PLoS ONE 10(6), 2015
PMID: 26039074

39 References

Data provided by Europe PubMed Central.

Worlds within worlds: evolution of the vertebrate gut microbiota.
Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI., Nat. Rev. Microbiol. 6(10), 2008
PMID: 18794915
Recognition of tRNA(Gly) by three widely diverged glycyl-tRNA synthetases: evolution of tRNA recognition.
Nameki N, Tamura K, Asahara H, Hasegawa T., Nucleic Acids Symp. Ser. (37), 1997
PMID: 9586030
Translational suppression: When two wrongs DO make a right
Murgola EJ., 1994
An extreme codon preference strategy: codon reassignment.
Andersson GE, Kurland CG., Mol. Biol. Evol. 8(4), 1991
PMID: 1921708
Evolution of the genetic code as affected by anticodon content.
Osawa S, Jukes TH., Trends Genet. 4(7), 1988
PMID: 3070867
Transfer RNA mutation and the malleability of the genetic code.
Schultz DW, Yarus M., J. Mol. Biol. 235(5), 1994
PMID: 8107079
Selective advantages created by codon ambiguity allowed for the evolution of an alternative genetic code in Candida spp.
Santos MA, Cheesman C, Costa V, Moradas-Ferreira P, Tuite MF., Mol. Microbiol. 31(3), 1999
PMID: 10048036
Lack of peptide-release activity responding to codon UGA in Mycoplasma capricolum.
Inagaki Y, Bessho Y, Osawa S., Nucleic Acids Res. 21(6), 1993
PMID: 8464722
Population genomics of early events in the ecological differentiation of bacteria.
Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabo G, Polz MF, Alm EJ., Science 336(6077), 2012
PMID: 22491847
Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome.
Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA 3rd, Loomer P, Armitage GC, Relman DA., ISME J 6(5), 2012
PMID: 22158393
Ecology drives a global network of gene exchange connecting the human microbiome.
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ., Nature 480(7376), 2011
PMID: 22037308
Whole genome amplification and de novo assembly of single bacterial cells.
Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW., PLoS ONE 4(9), 2009
PMID: 19724646

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