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

The analysis of deep sequencing data allows for a genome-wide overview of all the small RNA molecules (the 'sRNome') that are present in a single organism. In the present paper, we review the processing of CRISPR (clustered regularly interspaced short palindromic repeats) RNA, C/D box sRNA (small non-coding RNA) and tRNA in Nanoarchaeum equitans. The minimal and fragmented genome of this tiny archaeon permits a sequencing depth that enables the identification of processing intermediates in the study of RNA processing pathways. These intermediates include circular C/D box sRNA molecules and tRNA half precursors.

[1]  A. Marchfelder,et al.  Regulatory RNAs in Haloferax volcanii. , 2011, Biochemical Society transactions.

[2]  Dieter Jahn,et al.  Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves , 2005, Nature.

[3]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[4]  Dipali G. Sashital,et al.  An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3 , 2011, Nature Structural &Molecular Biology.

[5]  J. Reeve,et al.  Archaeal Intrinsic Transcription Termination In Vivo , 2009, Journal of bacteriology.

[6]  Sean R Eddy,et al.  Circular box C/D RNAs in Pyrococcus furiosus. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[7]  D. Söll,et al.  The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[8]  B. Simmons,et al.  A single-base resolution map of an archaeal transcriptome. , 2010, Genome research.

[9]  Andrew Emili,et al.  A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair , 2011, Molecular microbiology.

[10]  G. Tocchini-Valentini,et al.  Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  A. Marchfelder,et al.  Processing of a Dicistronic tRNA-snoRNA Precursor: Combined Analysis in Vitro and in Vivo Reveals Alternate Pathways and Coupling to Assembly of snoRNP1 , 2009, Plant Physiology.

[12]  Rolf Backofen,et al.  Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis , 2012, Nucleic acids research.

[13]  Ilka U. Heinemann,et al.  Transfer RNA processing in archaea: Unusual pathways and enzymes , 2010, FEBS letters.

[14]  D. Söll,et al.  Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease , 2009, Nucleic acids research.

[15]  S. Eddy,et al.  Homologs of small nucleolar RNAs in Archaea. , 2000, Science.

[16]  L. Randau,et al.  RNA processing in the minimal organism Nanoarchaeum equitans , 2012, Genome Biology.

[17]  Dieter Söll,et al.  Life without RNase P , 2008, Nature.

[18]  Schraga Schwartz,et al.  Transcriptome-wide discovery of circular RNAs in Archaea , 2011, Nucleic acids research.

[19]  R. Garrett,et al.  A putative viral defence mechanism in archaeal cells. , 2006, Archaea.

[20]  D. Söll,et al.  The complete set of tRNA species in Nanoarchaeum equitans , 2005, FEBS letters.

[21]  Yuping Li,et al.  Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs , 2006, Nucleic acids research.

[22]  B. Tjaden,et al.  Characterization of the CRISPR/Cas Subtype I-A System of the Hyperthermophilic Crenarchaeon Thermoproteus tenax , 2012, Journal of bacteriology.

[23]  Jennifer A. Doudna,et al.  Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease , 2010, Science.

[24]  Danielle M. Winget,et al.  Lysogenic virus–host interactions predominate at deep-sea diffuse-flow hydrothermal vents , 2008, The ISME Journal.

[25]  S. Eddy,et al.  Noncoding RNA genes identified in AT-rich hyperthermophiles , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Stan J. J. Brouns,et al.  CRISPR-based adaptive and heritable immunity in prokaryotes. , 2009, Trends in biochemical sciences.

[27]  R. Garrett,et al.  Identification of novel non‐coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus , 2004, Molecular microbiology.

[28]  Todd M. Lowe,et al.  Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species , 2012, Front. Microbio..

[29]  Elizabeth J. Tran,et al.  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* , 2004, Journal of Biological Chemistry.

[30]  M. Fenner,et al.  CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. , 2007 .

[31]  Katrina J. Edwards,et al.  Microbial Ecology of the Dark Ocean above, at, and below the Seafloor , 2011, Microbiology and Molecular Reviews.

[32]  R. Terns,et al.  Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. , 2008, Genes & development.

[33]  A. Omer,et al.  Small non-coding RNAs in Archaea. , 2005, Current opinion in microbiology.

[34]  D. Söll,et al.  Nucleotide modification in vitro of the precursor of transfer RNA of Escherichia coli. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[35]  A. Hüttenhofer,et al.  Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[36]  N. Grishin,et al.  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 , 2006, Biology Direct.

[37]  A. MacMillan,et al.  Recognition and maturation of effector RNAs in a CRISPR interference pathway , 2011, Nature Structural &Molecular Biology.

[38]  Sandip Paul,et al.  Analysis of Nanoarchaeum equitans genome and proteome composition: indications for hyperthermophilic and parasitic adaptation , 2006, BMC Genomics.

[39]  Dieter Söll,et al.  The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[40]  C Gaspin,et al.  Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. , 2001, Nucleic acids research.

[41]  J. Vogel,et al.  Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability , 2009, Proceedings of the National Academy of Sciences.

[42]  N. Brucato,et al.  Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi , 2011, BMC Genomics.

[43]  S. Ehrlich,et al.  Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. , 2005, Microbiology.

[44]  Harald Huber,et al.  A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont , 2002, Nature.

[45]  Stan J. J. Brouns,et al.  H‐NS‐mediated repression of CRISPR‐based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO , 2010, Molecular microbiology.

[46]  Michel J. Weber,et al.  Mammalian Small Nucleolar RNAs Are Mobile Genetic Elements , 2006, PLoS genetics.

[47]  J. Brosius,et al.  The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome. , 2011, RNA.