Mining a database of single amplified genomes from red sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA)

Frontiers in Microbiology

Volumn 5, Issue APR, 2014, Pages

  Grötzinger, Stefan W ^a   Alam, Intikhab ^a   Alawi, Wail Ba ^a   Bajic, Vladimir B ^a   Stingl, Ulrich ^a   Eppinger, Jörg ^a  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

Author keywords

Bioinformatics; Extermophile; Functional genomics; Go terms; Halophiles; Prosite ids; Protein sequence consensus patterns; Single amplified genomes

Indexed keywords

ALGORITHM; ARTICLE; BACTERIUM ISOLATION; DATA MINING; FUNCTIONAL GENOMICS; GENE AMPLIFICATION; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; GENOME ANALYSIS; HALOPHILE; METHODOLOGY; MICROBIAL GENETICS; MICROBIAL GENOME; NONHUMAN; PROFILE AND PATTREN MATCHING ALGORITHM; QUANTITATIVE ANALYSIS; SAMPLING;

EID: 84899675189     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00134     Document Type: Article

References (58)

1. Alain, K., and Querellou, J. (2009). Cultivating the uncultured: limits, advances and future challenges. Extremophiles 13, 583-594. doi:10.1007/s00792-009-0261-3
2. Alam, I., Antunes, A., Kamau, A. A., Kalkatawi, M., Stingl, U., and Bajic, V. B. (2013). INDIGO-INtegrated Data Warehouse of MIcrobial GenOmes with examples from the red sea extremophiles. PLoS ONE 8:e82210. doi:10.1371/journal.pone.0082210
3. Amann, R. I., Ludwig, W., and Schleifer, K.-H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169.
4. Anschutz, P., and Blanc, G. (1995). Geochemical dynamics of the Atlantis II Deep (Red Sea): silica behavior. Mar. Geol. 128, 25-36. doi:10.1016/0025-3227(95)00085-D
5. Antunes, A., Ngugi, D. K., and Stingl, U. (2011). Microbiology of the Red Sea (and other) deep-sea anoxic brine lakes. Environ. Microbiol. Rep. 3, 416-433. doi:10.1111/j.1758-2229.2011.00264.x
6. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29. doi:10.1038/75556
7. Backer, H., and Schoell, M. (1972). New deeps with brines and metalliferous sediments in the Red Sea. Nat. Phys. Sci. 240, 153-158. doi:10.1038/physci240153a0
8. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi:10.1089/cmb.2012.0021
9. Bruneau, L., Jerlov, N. G., and Koczy, F. F. (1953). "Physical and chemical methods," in Reports of the Swedish Deep Sea Expedition, Vol. 3. (Elanders: Göteborg), 99-112.
10. Chistoserdova, L. (2010). Recent progress and new challenges in metagenomics for biotechnology. Biotechnol. Lett. 32, 1351-1359. doi:10.1007/s10529-010-0306-9
11. Chitsaz, H., Yee-Greenbaum, J. L., Tesler, G., Lombardo, M.-J., Dupont, C. L., Badger, J. H., et al. (2011). Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat. Biotechnol. 29, 915-921. doi:10.1038/nbt.1966
12. Cita, M. B. (2006). Exhumation of Messinian evaporites in the deep-sea and creation of deep anoxic brine-filled collapsed basins. Sediment. Geol. 188, 357-378. doi:10.1016/j.sedgeo.2006.03.013
13. DasSarma, S., and Arora, P. (2001). "Halophiles," in Encyclopedia of Life Sciences, (London: John Wiley & Sons, Ltd), 1-9. doi:10.1038/npg.els.0000394
14. De Castro, E., Sigrist, C. J., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., et al. (2006). ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 34, W362-W365. doi:10.1093/nar/gkl124
15. Dolled-Filhart, M. P., Lee, M. Jr., Ou-Yang, C.-W., Haraksingh, R. R., and Lin, J. C.-H. (2013). Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing. Sci. World J. 2013:730210. doi:10.1155/2013/730210
16. Eder, W., Jahnke, L. L., Schmidt, M., and Huber, R. (2001). Microbial diversity of the brine-seawater interface of the Kebrit Deep, Red Sea, studied via 16S rRNA gene sequences and cultivation methods. Appl. Environ. Microbiol. 67, 3077-3085. doi:10.1128/AEM.67.7.3077-3085.2001
17. Emery, K., Hunt, J., and Hays, E. (1969). "Summary of hot brines and heavy metal deposits in the Red Sea," in Hot Brines and Heavy Metal Deposits in the Red Sea, eds E. T. Degens, and D. A. Ross (Berlin: Springer Verlag), 557-571. doi:10.1007/978-3-662-28603-6_50
18. Faber, E., Botz, R., Poggenburg, J., Schmidt, M., Stoffers, P., and Hartmann, M. (1998). Methane in Red Sea brines. Org. Geochem. 29, 363-379. doi:10.1016/S0146-6380(98)00155-7
19. Garber, M., Grabherr, M. G., Guttman, M., and Trapnell, C. (2011). Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods 8, 469-477. doi:10.1038/nmeth.1613
20. Gurvich, E. (2006). Metalliferous sediments of the world ocean: fundamental theory of deep-sea hydrothermal sedimentation. Heidelberg: Springer Berlin Heidelberg.
21. Hartmann, M., Scholten, J. C., Stoffers, P., and Wehner, F. (1998). Hydrographic structure of brine-filled deeps in the Red Sea-new results from the Shaban, Kebrit, Atlantis II, and Discovery Deep. Mar. Geol. 144, 311-330. doi:10.1016/S0025-3227(97)00055-8
22. Horner, D. S., Pavesi, G., Castrignanò, T., De Meo, P. D. O., Liuni, S., Sammeth, M., et al. (2010). Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief. Bioinformatics 11, 181-197. doi:10.1093/bib/bbp046
23. Hovland, M., Kuznetsova, T., Rueslåtten, H., Kvamme, B., Johnsen, H. K., Fladmark, G. E., et al. (2006). Sub-surface precipitation of salts in supercritical seawater. Basin Res. 18, 221-230. doi:10.1111/j.1365-2117.2006.00290.x
24. Hugenholtz, P., and Tyson, G. W. (2008). Microbiology: metagenomics. Nature 455, 481-483. doi:10.1038/455481a
25. Jeyakanthan, J., Rangarajan, S., Mridula, P., Kanaujia, S. P., Shiro, Y., Kuramitsu, S., et al. (2008). Observation of a calcium-binding site in the-class carbonic anhydrase from Pyrococcus horikoshii. Acta Crystallogr. D Biol. Crystallogr. 64, 1012-1019. doi:10.1107/S0907444908024323
26. Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., and Madden, T. L. (2008). NCBI BLAST: a better web interface. Nucleic Acids Res. 36, W5-W9. doi:10.1093/nar/gkn201
27. Kanehisa, M., and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30. doi:10.1093/nar/28.1.27
28. Karan, R., Kumar, S., Sinha, R., and Khare, S. (2012). "Halophilic microorganisms as sources of novel enzymes," in Microorganisms in Sustainable Agriculture and Biotechnology, eds T. Satyanarayana, B. Narain Johri, and A. Prakash (New Delhi: Springer), 555-579.
29. Karbe, L. (1987). "Hot brines and the deep sea environment," in Red Sea. Key Environments Series, eds A. J. Edwards, and S. M. Head (Oxford: Pergamon Press), 70-89.
30. Kisker, C., Schindelin, H., Alber, B. E., Ferry, J. G., and Rees, D. C. (1996). A left-hand beta-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila. EMBO J. 15, 2323.
31. Könneke, M., Bernhard, A. E., José, R., Walker, C. B., Waterbury, J. B., and Stahl, D. A. (2005). Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543-546. doi:10.1038/nature03911
32. Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K., and Hugenholtz, P. (2008). A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev. 72, 557-578. doi:10.1128/MMBR.00009-08
33. Lasken, R. S. (2007). Single-cell genomic sequencing using multiple displacement amplification. Curr. Opin. Microbiol. 10, 510-516. doi:10.1016/j.mib.2007.08.005
34. Liszka, M. J., Clark, M. E., Schneider, E., and Clark, D. S. (2012). Nature versus nurture: developing enzymes that function under extreme conditions. Annu. Rev. Chem. Biomol. Eng. 3, 77-102. doi:10.1146/annurev-chembioeng-061010-114239
35. Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M., et al. (2012). RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 40, W622-W627. doi:10.1093/nar/gks540
36. Madigan, M., Martinko, J. M., and Parker, J. (2003). Brock Biology of Microorganisms. New Jersey: Pearson Education International.
37. Ollivier, B., Caumette, P., Garcia, J.-L., and Mah, R. A. (1994). Anaerobic bacteria from hypersaline environments. Microbiol. Rev. 58, 27-38.
38. Pabinger, S., Dander, A., Fischer, M., Snajder, R., Sperk, M., Efremova, M., et al. (2014). A survey of tools for variant analysis of next-generation genome sequencing data. Brief. Bioinform. 15, 256-278. doi:10.1093/bib/bbs086
39. Peng, Y., Leung, H. C., Yiu, S. M., and Chin, F. Y. (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428. doi:10.1093/bioinformatics/bts174
40. Prakash, T., and Taylor, T. D. (2012). Functional assignment of metagenomic data: challenges and applications. Brief. Bioinformatics 13, 711-727. doi:10.1093/bib/bbs033
41. Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., et al. (2005). InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116-W120. doi:10.1093/nar/gki442
42. Radivojac, P., Clark, W.T., Oron, T.R., Schnoes, A.M., Wittkop, T., Sokolov, A., et al. (2013). A large-scale evaluation of computational protein function prediction. Nat. Methods 10, 221-227. doi:10.1038/nmeth.2340
43. Rohde, H., Qin, J., Cui, Y., Li, D., Loman, N. J., Hentschke, M., et al. (2011). Open-source genomic analysis of Shiga-toxin-producing E. coli O104: H4. N. Engl. J. Med. 365, 718-724. doi:10.1056/NEJMoa1107643
44. Ross, D. A. (1972). Red Sea hot brine area: revisited. Science 175, 1455-1457. doi:10.1126/science.175.4029.1455
45. Saitou, N., and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
46. Schnoes, A. M., Ream, D. C., Thorman, A. W., Babbitt, P. C., and Friedberg, I. (2013). Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Comput. Biol. 9:e1003063. doi:10.1371/journal.pcbi.1003063
47. Schomburg, I., Chang, A., Placzek, S., Söhngen, C., Rother, M., Lang, M., et al. (2013). BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res. 41, D764-D772. doi:10.1093/nar/gks1049
48. Searle, R. C., and Ross, D. A. (1975). A geophysical study of the Red Sea axial trough between 20· 5° and 22° N. Geophys. J. Int. 43, 555-572. doi:10.1111/j.1365-246X.1975.tb00647.x
49. Sigrist, C. J., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., et al. (2002). PROSITE: a documented database using patterns and profiles as motif descriptors. Brief. Bioinformatics 3, 265-274. doi:10.1093/bib/3.3.265
50. Sigrist, C. J. A., De Castro, E., Cerutti, L., Cuche, B. A., Hulo, N., Bridge, A., et al. (2013). New and continuing developments at PROSITE. Nucleic Acids Res. 41, D344-D347. doi:10.1093/nar/gks1067
51. Ŝkunca, N., Altenhoff, A., and Dessimoz, C. (2012). Quality of computationally inferred gene ontology annotations. PLoS Comput. Biol. 8:e1002533. doi:10.1371/journal.pcbi.1002533
52. Smith, K. S., and Ferry, J. G. (2000). Prokaryotic carbonic anhydrases. FEMS Microbiol. Rev. 24, 335-366. doi:10.1111/j.1574-6976.2000.tb00546.x
53. Smith, R. N., Aleksic, J., Butano, D., Carr, A., Contrino, S., Hu, F., et al. (2012). InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics 28, 3163-3165. doi:10.1093/bioinformatics/bts577
54. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725-2729. doi:10.1093/molbev/mst197
55. Triplet, T., and Butler, G. (2013). A review of genomic data warehousing systems. Brief. Bioinform. doi:10.1093/bib/bbt031. [Epub ahead of print].
56. Watson, S. W., and Waterbury, J. B. (1969). "The sterile hot brines of the Red Sea," in Hot Brines and Recent Heavy Metal Deposits in the Red Sea, eds E. T. Degens, and D. A. Ross (New York, NY: Springer Berlin Heidelberg), 272-281. doi:10.1007/978-3-662-28603-6_27
57. Yooseph, S., Sutton, G., Rusch, D. B., Halpern, A. L., Williamson, S. J., Remington, K., et al. (2007). The sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biol. 5:e16. doi:10.1371/journal.pbio.0050016
58. Zuckerkandl, E., and Pauling, L. (1965). Evolutionary divergence and convergence in proteins. Evolving Genes Proteins 97, 97-166.