Targeted diversity generation by intraterrestrial archaea and archaeal viruses

Nature Communications

Volumn 6, Issue , 2015, Pages

  Paul, Blair G ^a   Bagby, Sarah C ^a   Czornyj, Elizabeth ^b   Arambula, Diego ^b   Handa, Sumit ^c   Sczyrba, Alexander ^d,e   Ghosh, Partho ^c   Miller, Jeff F ^b   Valentine, David L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d BIELEFELD UNIVERSITY   (Germany)

^e DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BINDING; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOME; LIGAND; MUTATION; PATHOGEN; PROTEIN; VIRUS;

ARCHAEAL VIRUS; ARTICLE; DNA SEQUENCE; GENE TARGETING; GENETIC VARIABILITY; NANOARCHAEOTA; NONHUMAN; PHYLOGENY; RETROPOSON; VIRUS GENOME; VIRUS MUTATION; VIRUS PURIFICATION; ARCHAEON; GENETIC VARIATION; GENETICS; METAGENOME; MOLECULAR GENETICS; MUTATION RATE; NUCLEOTIDE SEQUENCE; VIROLOGY;

ARCHAEA; NANOARCHAEOTA;

ARCHAEAL PROTEIN; RETROPOSON;

ARCHAEA; ARCHAEAL PROTEINS; ARCHAEAL VIRUSES; BASE SEQUENCE; GENETIC VARIATION; METAGENOME; MOLECULAR SEQUENCE DATA; MUTATION RATE; NANOARCHAEOTA; RETROELEMENTS;

EID: 84925358666     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7585     Document Type: Article

References (47)

1. Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C. & DHondt, S. Global distribution of microbial abundance and biomass in subseafloor sediment. Proc. Natl Acad. Sci. USA 109, 16213-16216 (2012).
2. Lipp, J., Morono, Y., Inagaki, F. & Hinrichs, K.-U. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature 454, 991-994 (2008).
3. Valentine, D. L. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat. Rev. Microbiol. 5, 316-323 (2007).
4. Hoehler, T. M. & Jørgensen, B. B. Microbial life under extreme energy limitation. Nat. Rev. Microbiol. 11, 83-94 (2013).
5. Lewin, A. et al. The microbial communities in two apparently physically separated deep subsurface oil reservoirs show extensive DNA sequence similarities. Environ. Microbiol. 16, 545-558 (2014).
6. Liu, M. et al. Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science 295, 2091-2094 (2002).
7. Doulatov, S. et al. Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature 431, 476-481 (2004).
8. Medhekar, B. & Miller, J. F. Diversity-generating retroelements. Curr. Opin. Microbiol. 10, 388-395 (2007).
9. McMahon, S. A. et al. The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat. Struct. Mol. Biol. 12, 886-892 (2005).
10. Guo, H. et al. Diversity-generating retroelement homing regenerates target sequences for repeated rounds of codon rewriting and protein diversification. Mol. Cell 31, 813-823 (2008).
11. Le Coq, J. & Ghosh, P. Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement. Proc. Natl Acad. Sci. USA 108, 14649-14653 (2011).
12. Rohwer, F. & Vega Thurber, R. Viruses manipulate the marine environment. Nature 459, 207-212 (2009).
13. Rowlands, T., Baumann, P. & Jackson, S. P. The TATA-binding protein: a general transcription factor in eukaryotes and archaebacteria. Science 264, 1326-1329 (1994).
14. Dwivedi, B., Xue, B., Lundin, D., Edwards, R. A. & Breitbart, M. A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evol. Biol. 13, 33 (2013).
15. Arambula, D. et al. Surface display of a massively variable lipoprotein by a Legionella diversity-generating retroelement. Proc. Natl Acad Sci. USA 110, 8212-8217 (2013).
16. Schillinger, T., Lisfi, M., Chi, J., Cullum, J. & Zingler, N. Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF. BMC Genomics 13, 430 (2012).
17. Goldrath, A. W. & Bevan, M. J. Selecting and maintaining a diverse T-cell repertoire. Nature 402, 255-262 (1999).
18. Alder, M. N. et al. Diversity and function of adaptive immune receptors in a jawless vertebrate. Science 310, 1970-1973 (2005).
19. Stokke, R., Roalkvam, I., Lanzen, A., Haflidason, H. & Steen, I. H. Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. Environ. Microbiol. 14, 1333-1346 (2012).
20. Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437 (2013).
21. Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63-67 (2002).
22. Podar, M. et al. Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol. Direct 8, 9 (2013).
23. Minot, S., Grunberg, S., Wu, G. D., Lewis, J. D. & Bushman, F. D. Hypervariable loci in the human gut virome. Proc. Natl Acad. Sci. USA 109, 3962-3966 (2012).
24. Simon, D. M. & Zimmerly, S. A diversity of uncharacterized reverse transcriptases in bacteria. Nucleic Acids Res. 36, 7219-7229 (2008).
25. Ye, Y. Identification of diversity-generating retroelements in human microbiomes. Int. J. Mol. Sci. 15, 14234-14246 (2014).
26. Louis-Jeune, C., Andrade-Navarro, M. A. & Perez-Iratxeta, C. Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins 80, 374-381 (2012).
27. Paull, C. K., Normark, W. R., Ussler, W., Caress, D. W. & Keaten, R. Association among active seafloor deformation, mound formation, and gas hydrate growth and accumulation within the seafloor of the Santa Monica Basin, offshore California. Mar. Geol. 250, 258-275 (2008).
28. nd edn (eds Balows, A., Trüper, H. G., Dworkin, M., Harder, W. & Schleifer, K.-H.) (Springer, 1992).
29. Thurber, R. V., Haynes, M., Breitbart, M., Wegley, L. & Rohwer, F. Laboratory procedures to generate viral metagenomes. Nat. Protoc. 4, 470-483 (2009).
30. Henn, M. R. et al. Analysis of high-throughput sequencing and annotation strategies for phage genomes. PLoS ONE 5, e9083 (2010).
31. Schmieder, R., Lim, Y., Rohwer, F. & Edwards, R. TagCleaner: identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics 11, 341 (2010).
32. Hurwitz, B., Deng, L., Poulos, B. & Sullivan, M. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ. Microbiol. 15, 1428-1440 (2013).
33. Niu, B., Fu, L., Sun, S. & Li, W. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics. 11, 187 (2010).
34. Sun, S. et al. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res. 39, D546-D551 (2011).
35. Delcher, A. L., Bratke, K. A., Powers, E. C. & Salzberg, S. L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673-679 (2007).
36. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
37. Leplae, R., Hebrant, A., Wodak, S. J. & Toussaint, A. ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Res. 32, D45-D49 (2004).
38. Hurwitz, B. L. & Sullivan, M. B. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS ONE 8, e57355 (2013).
39. Kelley, L. A. & Sternberg, M. J. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 4, 363-371 (2009).
40. Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276-277 (2000).
41. Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948 (2007).
42. Kumar, S., Nei, M., Dudley, J. & Tamura, K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 9, 299-306 (2008).
43. Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321 (2010).
44. Pride, D. T., Meinersmann, R. J., Wassenaar, T. M. & Blaser, M. J. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res. 13, 145-158 (2003).
45. Teeling, H., Meyerdierks, A., Bauer, M., Amann, R. & Glöckner, F. O. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ. Microbiol. 6, 938-947 (2004).
46. Dick, G. J. et al. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 10, R85 (2009).
47. Oksanen, J. et al. Vegan: Community Ecology Package. R package version 1.13-1 http://vegan.r-forge.r-project.org/ (2008).