C/D box sRNA, CRISPR RNA and tRNA processing in an archaeon with a minimal fragmented genome

Biochemical Society Transactions

Volumn 41, Issue 1, 2013, Pages 411-415

  Richter, Hagen ^a   Mohr, Sabine ^a   Randau, Lennart ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

Author keywords

C D box small non coding RNA (C D box sRNA); Clustered regularly interspaced short palindromic repeats (CRISPR); Genomic fragmentation; Nanoarchaeum; Split gene; TRNA

Indexed keywords

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT RNA; RNA; RNA PRECURSOR; SMALL UNTRANSLATED RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

ARCHAEON; CONFERENCE PAPER; DNA REPAIR; GENE CLUSTER; GENE FUNCTION; GENE LOSS; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; NANOARCHAEUM EQUITANS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA PROCESSING; RNA SYNTHESIS; SEQUENCE ANALYSIS;

ARCHAEA; GENOME, ARCHAEAL; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, ARCHAEAL; RNA, TRANSFER;

EID: 84873129485     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20120276     Document Type: Conference Paper

References (47)

1. Jäger, D., Sharma, C. M., Thomsen, J., Ehlers, C., Vogel, J. and Schmitz, R. A. (2009) Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability. Proc. Natl. Acad. Sci. U. S. A. 106, 21878-21882
2. Wurtzel, O., Sapra, R., Chen, F., Zhu, Y., Simmons, B. A. and Sorek, R. (2010) A single-base resolution map of an archaeal transcriptome. Genome Res. 20, 133-141
3. Bernick, D. L., Dennis, P. P., Lui, L. M. and Lowe, T. M. (2012) Diversity of antisense and other non-coding RNAs in archaea revealed by comparative small RNA sequencing in four Pyrobaculum species. Front. Microbiol. 3, 231
4. Omer, A. D., Lowe, T. M., Russell, A. G., Ebhardt, H., Eddy, S. R. and Dennis, P. P. (2000) Homologs of small nucleolar RNAs in archaea. Science 288, 517-522 (Pubitemid 30236034)
5. Fischer, S., Benz, J., Spath, B., Jellen-Ritter, A., Heyer, R., Dorr, M., Maier, L. K., Menzel-Hobeck, C., Lehr, M., Jantzer, K. et al. (2011) Regulatory RNAs in Haloferax volcanii. Biochem. Soc. Trans. 39, 159-162
6. Tang, T. H., Polacek, N., Zywicki, M., Huber, H., Brügger, K., Garrett, R., Bachellerie, J. P. and Hüttenhofer, A. (2005) Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol. Microbiol. 55, 469-481 (Pubitemid 40179381)
7. Phok, K., Moisan, A., Rinaldi, D., Brucato, N., Carpousis, A. J., Gaspin, C. and Clouet-d'Orval, B. (2011) Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi. BMC Genomics 12, 312
8. Tang, T. H., Bachellerie, J. P., Rozhdestvensky, T., Bortolin, M. L., Huber, H., Drungowski, M., Elge, T., Brosius, J. and Hüttenhofer, A. (2002) Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc. Natl. Acad. Sci. U. S. A. 99, 7536-7541 (Pubitemid 34568726)
9. Huber, H., Hohn, M. J., Rachel, R., Fuchs, T., Wimmer, V. C. and Stetter, K. O. (2002) A new phylum of archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63-67 (Pubitemid 34498815)
10. Waters, E., Hohn, M. J., Ahel, I., Graham, D. E., Adams, M. D., Barnstead, M., Beeson, K. Y., Bibbs, L., Bolanos, R., Keller, M. et al. (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. U. S. A. 100, 12984-12988 (Pubitemid 37340012)
11. Randau, L., Münch, R., Hohn, M. J., Jahn, D. and Söll, D. (2005) Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'-and 3'-halves. Nature 433, 537-541 (Pubitemid 40204312)
12. Raabe, C. A., Hoe, C. H., Randau, G., Brosius, J., Tang, T. H. and Rozhdestvensky, T. S. (2011) The rocks and shallows of deep RNA sequencing: examples in the Vibrio cholerae RNome. RNA 17, 1357-1366
13. Randau, L. (2012) RNA processing in the minimal organism Nanoarchaeum equitans. Genome Biol. 13, R63
14. Das, S., Paul, S., Bag, S. K. and Dutta, C. (2006) Analysis of Nanoarchaeum equitans genome and proteome composition: indications for hyperthermophilic and parasitic adaptation. BMC Genomics 7, 186
15. Klein, R. J., Misulovin, Z. and Eddy, S. R. (2002) Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc. Natl. Acad. Sci. U. S. A. 99, 7542-7547 (Pubitemid 34568727)
16. Randau, L., Schröder, I. and Söll, D. (2008) Life without RNase P. Nature 453, 120-123 (Pubitemid 351630325)
17. Schaefer, K. P., Altman, S. and Söll, D. (1973) Nucleotide modification in vitro of the precursor of transfer RNA of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A 70, 3626-3630
18. Randau, L., Calvin, K., Hall, M., Yuan, J., Podar, M., Li, H. and Söll, D. (2005) The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves. Proc. Natl. Acad. Sci. U. S. A. 102, 17934-17939 (Pubitemid 41798480)
19. Randau, L., Pearson, M. and Söll, D. (2005) The complete set of tRNA species in Nanoarchaeum equitans. FEBS Lett. 579, 2945-2947 (Pubitemid 40725271)
20. Heinemann, I. U., Söll, D. and Randau, L. (2010) Transfer RNA processing in archaea: unusual pathways and enzymes. FEBS Lett. 584, 303-309
21. Mitchell, M., Xue, S., Erdman, R., Randau, L., Söll, D. and Li, H. (2009) Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease. Nucleic Acids Res. 37, 5793-5802
22. Tocchini-Valentini, G. D., Fruscoloni, P. and Tocchini-Valentini, G. P. (2005) Coevolution of tRNA intron motifs and tRNA endonuclease architecture in archaea. Proc. Natl. Acad. Sci. U. S. A. 102, 15418-15422 (Pubitemid 41528072)
23. Santangelo, T. J., Cubonova, L., Skinner, K. M. and Reeve, J. N. (2009) Archaeal intrinsic transcription termination in vivo. J. Bacteriol. 191, 7102-7108
24. Dennis, P. P. and Omer, A. (2005) Small non-coding RNAs in archaea. Curr. Opin. Microbiol. 8, 685-694 (Pubitemid 41643037)
25. Barbezier, N., Canino, G., Rodor, J., Jobet, E., Saez-Vasquez, J., Marchfelder, A. and Echeverria, M. (2009) Processing of a dicistronic tRNA-snoRNA precursor: combined analysis in vitro and in vivo reveals alternate pathways and coupling to assembly of snoRNP. Plant Physiol. 150, 1598-1610
26. Danan, M., Schwartz, S., Edelheit, S. and Sorek, R. (2012) Transcriptome-wide discovery of circular RNAs in archaea. Nucleic Acids Res. 40, 3131-3142
27. Starostina, N. G., Marshburn, S., Johnson, L. S., Eddy, S. R., Terns, R. M. and Terns, M. P. (2004) Circular box C/D RNAs in Pyrococcus furiosus. Proc. Natl. Acad. Sci. U. S. A. 101, 14097-14101 (Pubitemid 39305036)
28. Trp. Nucleic Acids Res. 29, 4518-4529 (Pubitemid 33095012)
29. Singh, S. K., Gurha, P., Tran, E. J., Maxwell, E. S. and Gupta, R. (2004) Sequential 2'-O-methylation of archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J. Biol. Chem. 279, 47661-47671 (Pubitemid 39540912)
30. Weber, M. J. (2006) Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet. 2, e205
31. Luo, Y. and Li, S. (2007) Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs. Nucleic Acids Res. 35, 559-571 (Pubitemid 46232072)
32. Lillestol, R. K., Redder, P., Garrett, R. A. and Brügger, K. (2006) A putative viral defence mechanism in archaeal cells. Archaea 2, 59-72 (Pubitemid 44377988)
33. Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A. and Horvath, P. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712 (Pubitemid 46515624)
34. Bolotin, A., Quinquis, B., Sorokin, A. and Ehrlich, S. D. (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551-2561 (Pubitemid 41149778)
35. Sorek, R., Kunin, V. and Hugenholtz, P. (2008) CRISPR: a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6, 181-186 (Pubitemid 351256313)
36. van der Oost, J., Jore, M. M., Westra, E. R., Lundgren, M. and Brouns, S. J. (2009) CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem. Sci. 34, 401-407
37. Richter, H., Zoephel, J., Schermuly, J., Maticzka, D., Backofen, R. and Randau, L. (2012) Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis. Nucleic Acids Res. 40, 9887-9896
38. Carte, J., Wang, R., Li, H., Terns, R. M. and Terns, M. P. (2008) Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 22, 3489-3496
39. Gesner, E. M., Schellenberg, M. J., Garside, E. L., George, M. M. and Macmillan, A. M. (2011) Recognition and maturation of effector RNAs in a CRISPR interference pathway. Nat. Struct. Mol. Biol. 18, 688-692
40. Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K. and Doudna, J. A. (2010) Sequence-and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355-1358
41. Sashital, D. G., Jinek, M. and Doudna, J. A. (2011) An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat. Struct. Mol. Biol. 18, 680-687
42. Westra, E. R., Pul, U., Heidrich, N., Jore, M. M., Lundgren, M., Stratmann, T., Wurm, R., Raine, A., Mescher, M., Van Heereveld, L. et al. (2010) H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol. Microbiol. 77, 1380-1393
43. Plagens, A., Tjaden, B., Hagemann, A., Randau, L. and Hensel, R. (2012) Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax. J. Bacteriol. 194, 2491-2500
44. Orcutt, B. N., Sylvan, J. B., Knab, N. J. and Edwards, K. J. (2011) Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol. Mol. Biol. Rev. 75, 361-422
45. Williamson, S. J., Cary, S. C., Williamson, K. E., Helton, R. R., Bench, S. R., Winget, D. and Wommack, K. E. (2008) Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents. ISME J. 2, 1112-1121
46. Babu, M., Beloglazova, N., Flick, R., Graham, C., Skarina, T., Nocek, B., Gagarinova, A., Pogoutse, O., Brown, G., Binkowski, A. et al. (2011) A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol. Microbiol. 79, 484-502
47. Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I. and Koonin, E. V. (2006) A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1, 7