Regulatory RNAs in archaea: First target identification in methanoarchaea

Biochemical Society Transactions

Volumn 41, Issue 1, 2013, Pages 344-349

  Prasse, Daniela ^a   Ehlers, Claudia ^a   Backofen, Rolf ^b   Schmitz, Ruth A ^a  

^a UNIVERSITY OF KIEL   (Germany)

^b UNIVERSITY OF FREIBURG   (Germany)

Author keywords

Archaea; Methanosarcina mazei; Post transcriptional regulation; Small non coding RNA (sRNA); Target gene

Indexed keywords

CIS ACTING ELEMENT; SMALL UNTRANSLATED RNA; TRANS ACTING FACTOR;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARCHAEON; COMPUTER MODEL; CONFERENCE PAPER; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENOME ANALYSIS; HALOBACTERIALES; HIGH THROUGHPUT SEQUENCING; METHANOARCHAEA; METHANOSARCINA MAZEI; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PYROBACULUM; RIBOSWITCH; TRANSCRIPTION REGULATION;

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

EID: 84873184455     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20120280     Document Type: Conference Paper

References (60)

1. Gottesman, S. (2004) The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol. 58, 303-328 (Pubitemid 39551989)
2. Romby, P., Vandenesch, F. and Wagner, E. G. (2006) The role of RNAs in the regulation of virulence-gene expression. Curr. Opin. Microbiol. 9, 229-236
3. Waters, L. S. and Storz, G. (2009) Regulatory RNAs in bacteria. Cell 136, 615-628
4. Guleria, P., Mahajan, M., Bhardwaj, J. and Yadav, S. K. (2011) Plant small RNAs: biogenesis, mode of action and their roles in abiotic stresses. Genomics, Proteomics Bioinformatics 9, 183-199
5. Krol, J., Loedige, I. and Filipowicz, W. (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat. Rev. 11, 597-610
6. Brantl, S. (2012) Acting antisense: plasmid-and chromosome-encoded sRNAs from Gram-positive bacteria. Future Microbiol. 7, 853-871
7. Mallory, A. C. and Vaucheret, H. (2006) Functions of microRNAs and related small RNAs in plants. Nat. Genet. 38(Suppl.), S31-S36
8. Carthew, R. W. and Sontheimer, E. J. (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642-655
9. Repoila, F. and Darfeuille, F. (2009) Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects. Biol. Cell 101, 117-131
10. Brantl, S. (2009) Bacterial chromosome-encoded small regulatory RNAs. Future Microbiol. 4, 85-103
11. Storz, G., Vogel, J. and Wassarman, Karen M. (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol. Cell 43, 880-891
12. Brennan, R. G. and Link, T. M. (2007) Hfq structure, function and ligand binding. Curr. Opin. Microbiol. 10, 125-133 (Pubitemid 46590055)
13. Dennis, P. P., Omer, A. and Lowe, T. (2001) A guided tour: small RNA function in archaea. Mol. Microbiol. 40, 509-519 (Pubitemid 32453106)
14. Schattner, P. (2002) Searching for RNA genes using base-composition statistics. Nucleic Acids Res. 30, 2076-2082 (Pubitemid 34537606)
15. Rozhdestvensky, T. S., Tang, T. H., Tchirkova, I. V., Brosius, J., Bachellerie, J. P. and Hüttenhofer, A. (2003) Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in archaea. Nucleic Acids Res. 31, 869-877 (Pubitemid 36240424)
16. Omer, A. D., Ziesche, S., Decatur, W. A., Fournier, M. J. and Dennis, P. P. (2003) RNA-modifying machines in archaea. Mol. Microbiol. 48, 617-629 (Pubitemid 36819050)
17. Dennis, P. P. and Omer, A. (2005) Small non-coding RNAs in archaea. Curr. Opin. Microbiol. 8, 685-694 (Pubitemid 41643037)
18. 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)
19. Tang, T. H., Rozhdestvensky, T. S., d'Orval, B. C., Bortolin, M. L., Huber, H., Charpentier, B., Branlant, C., Bachellerie, J. P., Brosius, J. and Huttenhofer, A. (2002) RNomics in archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res. 30, 921-930 (Pubitemid 34679660)
20. Tang, T. H., Polacek, N., Zywicki, M., Huber, H., Brugger, 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)
21. Zago, M. A., Dennis, P. P. and Omer, A. D. (2005) The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Microbiol. 55, 1812-1828 (Pubitemid 40445215)
22. 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
23. Jochl, C., Rederstorff, M., Hertel, J., Stadler, P. F., Hofacker, I. L., Schrettl, M., Haas, H. and Hüttenhofer, A. (2008) Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res. 36, 2677-2689 (Pubitemid 351659581)
24. Sittka, A., Lucchini, S., Papenfort, K., Sharma, C. M., Rolle, K., Binnewies, T. T., Hinton, J. C. and Vogel, J. (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet. 4, e1000163
25. Yoder-Himes, D. R., Chain, P. S., Zhu, Y., Wurtzel, O., Rubin, E. M., Tiedje, J. M. and Sorek, R. (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc. Natl. Acad. Sci. U. S. A. 106, 3976-3981
26. Sharma, C. M. and Vogel, J. (2009) Experimental approaches for the discovery and characterization of regulatory small RNA. Curr. Opin. Microbiol. 12, 536-546
27. Jager, D., Sharma, C. M., Thomsen, J., Ehlers, C., Vogel, J. and Schmitz, R. A. (2009) Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability. Proc. Natl. Acad. Sci. U. S. A. 106, 21878-21882
28. 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
29. Xu, N., Li, Y., Zhao, Y. T., Guo, L., Fang, Y. Y., Zhao, J. H., Wang, X. J., Huang, L. and Guo, H. S. (2012) Identification and characterization of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. PloS ONE 7, e35306
30. Straub, J., Brenneis, M., Jellen-Ritter, A., Heyer, R., Soppa, J. and Marchfelder, A. (2009) Small RNAs in haloarchaea: identification, differential expression and biological function. RNA Biol. 6, 281-292
31. 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
32. Heyer, R., Dorr, M., Jellen-Ritter, A., Spath, B., Babski, J., Jaschinski, K., Soppa, J. and Marchfelder, A. (2012) High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments in Haloferax volcanii. RNA Biol. 9, 1011-1018
33. 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
34. Randau, L. (2012) RNA processing in the minimal organism Nanoarchaeum equitans. Genome Biol. 13, R63
35. Marchfelder, A., Fischer, S., Brendel, J., Stoll, B., Maier, L. K., Jager, D., Prasse, D., Plagens, A., Schmitz, R. A. and Randau, L. (2012) Small RNAs for defence and regulation in archaea. Extremophiles 16, 685-696
36. Lim, J., Thomas, T. and Cavicchioli, R. (2000) Low temperature regulated DEAD-box RNA helicase from the Antarctic archaeon, Methanococcoides burtonii. J. Mol. Biol. 297, 553-567
37. Opulencia, R. B., Bose, A. and Metcalf, W. W. (2009) Physiology and posttranscriptional regulation of methanol: coenzyme M methyltransferase isozymes in Methanosarcina acetivorans C2A. J. Bacteriol. 191, 6928-6935
38. Anderson, K. L., Apolinario, E. E., MacAuley, S. R. and Sowers, K. R. (2009) A 5' leader sequence regulates expression of methanosarcinal CO dehydrogenase/acetyl coenzyme A synthase. J. Bacteriol. 191, 7123-7128
39. Lange, C., Zaigler, A., Hammelmann, M., Twellmeyer, J., Raddatz, G., Schuster, S. C., Oesterhelt, D. and Soppa, J. (2007) Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea. BMC Genomics 8, 415
40. Xia, Q., Hendrickson, E. L., Zhang, Y., Wang, T., Taub, F., Moore, B. C., Porat, I., Whitman, W. B., Hackett, M. and Leigh, J. A. (2006) Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol. Cell. Proteomics 5, 868-881 (Pubitemid 43792796)
41. Brenneis, M., Hering, O., Lange, C. and Soppa, J. (2007) Experimental characterization of cis-acting elements important for translation and transcription in halophilic archaea. PLoS Genet. 3, e229
42. Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H. and Breaker, R. R. (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol. 11, R31
43. Brenneis, M. and Soppa, J. (2009) Regulation of translation in haloarchaea: 5'-and 3'-UTRs are essential and have to functionally interact in vivo. PLoS ONE 4, e4484
44. Rother, M. and Metcalf, W. W. (2005) Genetic technologies for archaea. Curr. Opin. Microbiol. 8, 745-751 (Pubitemid 41643044)
45. Ehlers, C., Jäger, D. and Schmitz, R. A. (2011) Establishing a markerless genetic exchange system for Methanosarcina mazei strain Go1 for constructing chromosomal mutants of small RNA genes. Archaea 2011, 439608
46. Said, N., Rieder, R., Hurwitz, R., Deckert, J., Urlaub, H. and Vogel, J. (2009) In vivo expression and purification of aptamer-tagged small RNA regulators. Nucleic Acids Res. 37, e133
47. Corcoran, C. P., Rieder, R., Podkaminski, D., Hofmann, B. and Vogel, J. (2012) Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs. Methods Mol. Biol. 905, 177-200
48. Urban, J. H. and Vogel, J. (2009) A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo. Methods Mol. Biol. 540, 301-319
49. Corcoran, C. P., Podkaminski, D., Papenfort, K., Urban, J. H., Hinton, J. C. and Vogel, J. (2012) Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA. Mol. Microbiol. 84, 428-445
50. Mückstein, U., Tafer, H., Hackermuller, J., Bernhart, S. H., Stadler, P. F. and Hofacker, I. L. (2006) Thermodynamics of RNA-RNA binding. Bioinformatics 22, 1177-1182 (Pubitemid 43779008)
51. Pichon, C. and Felden, B. (2008) Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics 24, 2807-2813
52. Tafer, H. and Hofacker, I. L. (2008) RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics 24, 2657-2663
53. Busch, A., Richter, A. S. and Backofen, R. (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24, 2849-2856
54. Ying, X., Cao, Y., Wu, J., Liu, Q., Cha, L. and Li, W. (2011) sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization. PLoS ONE 6, e22705
55. Chitsaz, H., Salari, R., Sahinalp, S. C. and Backofen, R. (2009) A partition function algorithm for interacting nucleic acid strands. Bioinformatics 25, i365-i373
56. Huang, F. W., Qin, J., Reidys, C. M. and Stadler, P. F. (2009) Partition function and base pairing probabilities for RNA-RNA interaction prediction. Bioinformatics 25, 2646-2654
57. Richter, A. S. and Backofen, R. (2012) Accessibility and conservation: general features of bacterial small RNA-mRNA interactions? RNA Biol. 9, 954-965
58. Seemann, S. E., Richter, A. S., Gesell, T., Backofen, R. and Gorodkin, J. (2011) PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics 27, 211-219
59. Jäger, D., Pernitzsch, S. R., Richter, A. S., Backofen, R., Sharma, C. M. and Schmitz, R. A. (2012) An archaeal sRNA targeting cis-and trans-encoded mRNAs via two distinct domains. Nucleic Acids Res. 40, 10964-10979
60. Garrett, R. A. and Klenk, H.-P. (2007) Archaea: Evolution, Physiology, and Molecular Biology, Blackwell Publishing, Oxford