Inteins as indicators of gene flow in the halobacteria

Frontiers in Microbiology

Volumn 5, Issue JUN, 2014, Pages

  Soucy, Shannon M ^a   Fullmer, Matthew S ^a   Thane Papke, R ^a   Gogarten, Johann Peter ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Gene flow; Gene symbiosis; Genome as an ecosystem; Halobacteria; Horizontal gene transfer; Inteins; Mobile genetic elements

Indexed keywords

DEAMINASE; DEOXYCYTIDINE TRIPHOSPHATE; DNA DIRECTED DNA POLYMERASE ALPHA; DNA DIRECTED DNA POLYMERASE BETA; DNA HELICASE; DNA TOPOISOMERASE; ENDONUCLEASE; EXTEIN; INTEIN; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; PROTEIN P21; REPLICATION FACTOR C; RIBONUCLEOSIDE DIPHOSPHATE REDUCTASE; RIBOSOME PROTEIN; RNA POLYMERASE BETA SUBUNIT; SELF SPLICING RIBOSOMAL RNA; URIDINE DIPHOSPHATE GLUCOSE DEHYDROGENASE;

AMINO ACID SEQUENCE; ARTICLE; GENE FLOW; GENE TRANSFER; HALOFERAX; HALOQUADRATUM WALSBYI; HALORUBRUM; HALOTERRIGENA; HORIZONTAL GENE TRANSFER; NATRINEMA; NONHUMAN; PHYLOGENY; POSITION WEIGHT MATRIX; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIVERSITY; SYMBIOSIS;

EID: 84904899378     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00299     Document Type: Article

References (38)

1. Altschul, S. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402. doi: 10.1093/nar/25.17.3389
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410. doi: 10.1016/S0022-2836(05)80360-2
3. Andam, C. P., Williams, D., and Gogarten, J. P. (2010). Biased gene transfer mimics patterns created through shared ancestry. Proc. Natl. Acad. Sci. U.S.A. 107, 10679-10684. doi: 10.1073/pnas.1001418107
4. Atanasova, N. S., Roine, E., Oren, A., Bamford, D. H., and Oksanen, H. M. (2012). Global network of specific virus-host interactions in hypersaline environments. Environ. Microbiol. 14, 426-440. doi: 10.1111/j.1462-2920.2011.02603.x
5. Barzel, A., Obolski, U., Gogarten, J. P., Kupiec, M., and Hadany, L. (2011). Home and away- the evolutionary dynamics of homing endonucleases. BMC Evol. Biol. 11:324. doi: 10.1186/1471-2148-11-324
6. Butler, M. I., Gray, J., Goodwin, T. J., and Poulter, R. T. (2006). The distribution and evolutionary history of the PRP8 intein. BMC Evol. Biol. 6:42. doi: 10.1186/1471-2148-6-42
7. Darriba, D., Taboada, G. L., Doallo, R., and Posada, D. (2011). ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164-1165. doi: 10.1093/bioinformatics/btr088
8. Demaere, M. Z., Williams, T. J., Allen, M. A., Brown, M. V., Gibson, J. A. E., Rich, J., et al. (2013). High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc. Natl. Acad. Sci. U.S.A. 110, 16939-16944. doi: 10.1073/pnas.1307090110
9. Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. doi: 10.1093/nar/gkh340
10. Fullmer, M. S., Soucy, S. M., Swithers, K. S., Makkay, A. M., Wheeler, R., Ventosa, A., et al. (2014). Population and genomic analysis of the genus Halorubrum. Front. Microbiol. 5:140. doi: 10.3389/fmicb.2014.00140
11. Gimble, F. S., and Thorner, J. (1992). Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature 357, 301-306. doi: 10.1038/357301a0
12. Giraldo-Perez, P., and Goddard, M. R. (2013). A parasitic selfish gene that affects host promiscuity. Proc. Biol. Sci. 280:20131875. doi: 10.1098/rspb.2013.1875
13. Goddard, M. R., and Burt, A. (1999). Recurrent invasion and extinction of a selfish gene. Proc. Natl. Acad. Sci. 96, 13880-13885. doi: 10.1073/pnas.96.24.13880
14. Gogarten, J. P., and Hilario, E. (2006). Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements. BMC Evol. Biol. 6:94. doi: 10.1186/1471-2148-6-94
15. Gogarten, J. P., Senejani, A. G., Zhaxybayeva, O., Olendzenski, L., and Hilario, E. (2002). Inteins: structure, function, and evolution. Annu. Rev. Microbiol. 56, 263-287. doi: 10.1146/annurev.micro.56.012302.160741
16. Gouy, M., Guindon, S., and Gascuel, O. (2010). SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27, 221-224. doi: 10.1093/molbev/msp259
17. Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321. doi: 10.1093/sysbio/syq010
18. Hirata, R., Ohsumk, Y., Nakano, A., Kawasaki, H., Suzuki, K., and Anraku, Y. (1990). Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. J. Biol. Chem. 265, 6726-6733.
19. Kane, P. M., Yamashiro, C. T., Wolczyk, D. F., Neff, N., Goebl, M., and Stevens, T. H. (1990). Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase. Science 250, 651-657. doi: 10.1126/science.2146742
20. Katoh, K., and Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780. doi: 10.1093/molbev/mst010
21. Khomyakova, M., Bükmez, Ö., Thomas, L. K., Erb, T. J., and Berg, I. A. (2011). A methylaspartate cycle in haloarchaea. Science 331, 334-337. doi: 10.1126/science.1196544
22. Lang, A. S., Zhaxybayeva, O., and Beatty, J. T. (2012). Gene transfer agents: phage-like elements of genetic exchange. Nat. Rev. Microbiol. 10, 472-482. doi: 10.1038/nrmicro2802
23. Liu, K., Warnow, T. J., Holder, M. T., Nelesen, S. M., Yu, J., Stamatakis, A. P., et al. (2012). SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst. Biol. 61, 90-106. doi: 10.1093/sysbio/syr095
24. Ng, W. V., Kennedy, S. P., Mahairas, G. G., Berquist, B., Pan, M., Shukla, H. D., et al. (2000). Genome sequence of Halobacterium species NRC-1. Proc. Natl. Acad. Sci. U.S.A. 97, 12176-12181. doi: 10.1073/pnas.190337797
25. Papke, R. T., and Gogarten, J. P. (2012). Ecology. How bacterial lineages emerge. Science 336, 45-46. doi: 10.1126/science.1219241
26. Papke, R. T., Koenig, J. E., Rodríguez-Valera, F., and Doolittle, W. F. (2004). Frequent recombination in a saltern population of halorubrum. Science 306, 1928-1929. doi: 10.1126/science.1103289
27. Papke, R. T., Zhaxybayeva, O., Feil, E. J., Sommerfeld, K., Muise, D., and Doolittle, W. F. (2007). Searching for species in haloarchaea. Proc. Natl. Acad. Sci. U.S.A. 104, 14092-14097. doi: 10.1073/pnas.0706358104
28. Perler, F. B. (2002). InBase: the Intein Database. Nucleic Acids Res. 30, 383-384. doi: 10.1093/nar/30.1.383
29. Perler, F. B., Olsen, G. J., and Adam, E. (1997). Compilation and analysis of intein sequences. Nucleic Acids Res. 25, 1087-1093. doi: 10.1093/nar/25.6.1087
30. Pietrokovski, S. (2001). Intein spread and extinction in evolution. Trends Genet. 17, 465-472. doi: 10.1016/S0168-9525(01)02365-4
31. Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., et al. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539-542. doi: 10.1093/sysbio/sys029
32. Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., et al. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539. doi: 10.1038/msb.2011.75
33. Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313. doi: 10.1093/bioinformatics/btu033
34. Swithers, K. S., Senejani, A. G., Fournier, G. P., and Gogarten, J. P. (2009). Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements. BMC Evol. Biol. 9:303. doi: 10.1186/1471-2148-9-303
35. Swithers, K. S., Soucy, S. M., Lasek-Nesselquist, E., Lapierre, P., and Gogarten, J. P. (2013). Distribution and evolution of the mobile vma-1b intein. Mol. Biol. Evol. 30, 2676-2687. doi: 10.1093/molbev/mst164
36. Williams, D., Gogarten, J. P., and Papke, R. T. (2012). Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol. Evol. 4, 1223-1244. doi: 10.1093/gbe/evs098
37. Yahara, K., Fukuyo, M., Sasaki, A., and Kobayashi, I. (2009). Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer. Proc. Natl. Acad. Sci. U.S.A. 106, 18861-18866. doi: 10.1073/pnas.0908404106
38. Zhaxybayeva, O., Gogarten, J. P., Charlebois, R. L., Doolittle, W. F., and Papke, R. T. (2006). Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res. 16, 1099-1108. doi: 10.1101/gr.5322306