Home LiteratureArticle Details
PMID: 12490701 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

The phylogenetic distribution of bacterial ribonucleases.

Nucleic acids research ·Vol. 30 ·No. 24 ·2002-12-15 ·Pages 5339-46

Condon C, Putzer H

Abstract

Ribonucleases play key, often essential, roles in cellular metabolism. Nineteen ribonuclease activities, from 22 different proteins, have so far been described in bacteria, the majority of them from either Escherichia coli or Bacillus subtilis. Here we examine the phylogenetic distribution of all of these ribonucleases in 50 eubacterial and archaeal species whose genomes have been completely sequenced, with particular emphasis on the endoribonucleases. Although some enzymes are very highly conserved throughout evolution, there appears to be no truly universal ribonuclease. While some organisms, like E.coli, have a large selection of ribonucleases, many with overlapping functions, others seem to have relatively few or have many that remain to be discovered.

MeSH Terms
Bacillus subtilis/enzymology,genetics Bacteria/enzymology,genetics Escherichia coli/enzymology,genetics Genome, Bacterial Phylogeny Ribonucleases/genetics
Chemicals
Ribonucleases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Condon Ciarán
Institut de Biologie Physico-Chimique, UPR 9073, 13 rue Pierre et Marie Curie, 75005 Paris, France. condon@ibpc.fr
Putzer Harald
References (65)
65 references, click to expand
  1. The first step in the functional inactivation of the Escherichia coli polynucleotide phosphorylase messenger is a ribonuclease III processing at the 5' end.
    EMBO J. 1987 Jul;6(7):2165-70 PMID: 3308454
  2. RNase G (CafA protein) and RNase E are both required for the 5' maturation of 16S ribosomal RNA.
    EMBO J. 1999 May 17;18(10):2878-85 PMID: 10329633
  3. Endoribonuclease RNase III is essential in Bacillus subtilis.
    Mol Microbiol. 2000 Dec;38(5):1027-33 PMID: 11123676
  4. Role for a bidentate ribonuclease in the initiation step of RNA interference.
    Nature. 2001 Jan 18;409(6818):363-6 PMID: 11201747
  5. Exoribonuclease superfamilies: structural analysis and phylogenetic distribution.
    Nucleic Acids Res. 2001 Mar 1;29(5):1017-26 PMID: 11222749
  6. Identification of the gene encoding the 5S ribosomal RNA maturase in Bacillus subtilis: mature 5S rRNA is dispensable for ribosome function.
    RNA. 2001 Feb;7(2):242-53 PMID: 11233981
  7. The plant tRNA 3' processing enzyme has a broad substrate spectrum.
    Biochemistry. 2001 Jul 27;40(28):8264-72 PMID: 11444972
  8. Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon.
    Mol Microbiol. 2001 Jul;41(2):409-22 PMID: 11489127
  9. A natural classification of ribonucleases.
    Methods Enzymol. 2001;341:3-28 PMID: 11582786
  10. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans.
    Genes Dev. 2001 Oct 15;15(20):2654-9 PMID: 11641272
  11. Escherichia coli RNase M is a multiply altered form of RNase I.
    RNA. 2001 Dec;7(12):1702-7 PMID: 11780627
  12. RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors.
    RNA. 2002 Jan;8(1):97-109 PMID: 11871663
  13. Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme.
    Science. 1988 Jan 8;239(4836):178-81 PMID: 3122322
  14. Transfer RNA is a substrate for RNase D in vivo.
    J Biol Chem. 1988 Dec 5;263(34):17909-12 PMID: 3056931
  15. Autoregulation of RNase III operon by mRNA processing.
    EMBO J. 1989 Nov;8(11):3401-7 PMID: 2583104
  16. Cleavage by RNase III in the transcripts of the met Y-nus-A-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA.
    J Mol Biol. 1989 Nov 20;210(2):293-302 PMID: 2481042
  17. Ribonuclease H: from discovery to 3D structure.
    New Biol. 1990 Sep;2(9):771-7 PMID: 2177653
  18. RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression.
    Biochimie. 1990 Nov;72(11):825-34 PMID: 2085545
  19. Gene cloning and characterization of a novel extracellular ribonuclease of Bacillus subtilis.
    Eur J Biochem. 1992 Oct 1;209(1):121-7 PMID: 1396690
  20. Escherichia coli topoisomerase III-catalyzed cleavage of RNA.
    J Biol Chem. 1992 Oct 15;267(29):20532-5 PMID: 1383203
  21. Mutational analysis of a ribonuclease III processing signal.
    Biochemistry. 1993 Jul 27;32(29):7549-58 PMID: 8338852
  22. The winds of (evolutionary) change: breathing new life into microbiology.
    J Bacteriol. 1994 Jan;176(1):1-6 PMID: 8282683
  23. Structural characterization of a ribonuclease III processing signal.
    Nucleic Acids Res. 1994 Feb 25;22(4):604-12 PMID: 8127710
  24. There must be a prokaryote somewhere: microbiology's search for itself.
    Microbiol Rev. 1994 Mar;58(1):1-9 PMID: 8177167
  25. The tRNA processing enzyme RNase T is essential for maturation of 5S RNA.
    Proc Natl Acad Sci U S A. 1995 Jul 18;92(15):6883-6 PMID: 7542780
  26. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome.
    Nature. 1996 May 9;381(6578):169-72 PMID: 8610017
  27. Proteins associated with RNase E in a multicomponent ribonucleolytic complex.
    Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):3865-9 PMID: 8632981
  28. Maturation pathways for E. coli tRNA precursors: a random multienzyme process in vivo.
    Cell. 1996 Aug 9;86(3):503-12 PMID: 8756732
  29. Expression and regulation of the rnc and pdxJ operons of Escherichia coli.
    Mol Microbiol. 1996 Dec;22(5):977-89 PMID: 8971718
  30. Processing of the Bacillus subtilis thrS leader mRNA is RNase E-dependent in Escherichia coli.
    J Mol Biol. 1997 May 2;268(2):235-42 PMID: 9159466
  31. An lrp-like gene of Bacillus subtilis involved in branched-chain amino acid transport.
    J Bacteriol. 1997 Sep;179(17):5448-57 PMID: 9287000
  32. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
    Nucleic Acids Res. 1997 Dec 15;25(24):4876-82 PMID: 9396791
  33. Site-specific ribonuclease activity of eukaryotic DNA topoisomerase I.
    Mol Cell. 1997 Dec;1(1):89-97 PMID: 9659906
  34. Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
    Nucleic Acids Res. 1998 Sep 15;26(18):4205-13 PMID: 9722641
  35. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome.
    Genes Dev. 1998 Sep 1;12(17):2770-81 PMID: 9732274
  36. The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly.
    Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11637-42 PMID: 9751718
  37. The Ribonuclease P Database.
    Nucleic Acids Res. 1999 Jan 1;27(1):314 PMID: 9847214
  38. The CafA protein required for the 5'-maturation of 16 S rRNA is a 5'-end-dependent ribonuclease that has context-dependent broad sequence specificity.
    J Biol Chem. 2000 Mar 24;275(12):8726-32 PMID: 10722715
  39. Temperature sensitive mutants of Escherichia coli for tRNA synthesis.
    Nucleic Acids Res. 1974 Mar;1(3):355-71 PMID: 10793671
  40. A novel secreted ribonuclease from Bacillus intermedius: gene structure and regulatory control.
    Mol Gen Genet. 2000 May;263(4):571-80 PMID: 10852477
  41. Identification of the genes encoding Mn2+-dependent RNase HII and Mg2+-dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families.
    Biochemistry. 1999 Jan 12;38(2):605-18 PMID: 9888800
  42. Maturation of 23S ribosomal RNA requires the exoribonuclease RNase T.
    RNA. 1999 Jan;5(1):139-46 PMID: 9917073
  43. Translational control of mRNA processing in the F1845 fimbrial operon of Escherichia coli.
    Mol Microbiol. 1998 Nov;30(4):843-53 PMID: 10094632
  44. Isolation of RNase H genes that are essential for growth of Bacillus subtilis 168.
    J Bacteriol. 1999 Apr;181(7):2118-23 PMID: 10094689
  45. Endonuclease cleavage of messenger RNA in Bacillus subtilis.
    Mol Microbiol. 2002 Mar;43(5):1319-29 PMID: 11918816
  46. Ribonuclease M5 has few, if any, mRNA substrates in Bacillus subtilis.
    J Bacteriol. 2002 May;184(10):2845-9 PMID: 11976317
  47. Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli.
    Genes Dev. 2002 May 1;16(9):1102-15 PMID: 12000793
  48. Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins.
    RNA. 2002 Mar;8(3):296-306 PMID: 12003490
  49. Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes.
    EMBO J. 2002 Jun 3;21(11):2769-77 PMID: 12032089
  50. Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II.
    J Biol Chem. 2002 Jun 14;277(24):21624-9 PMID: 11948193
  51. mRNA decay in Escherichia coli comes of age.
    J Bacteriol. 2002 Sep;184(17):4658-65; discussion 4657 PMID: 12169588
  52. Bacillus subtilis YhaM, a member of a new family of 3'-to-5' exonucleases in gram-positive bacteria.
    J Bacteriol. 2002 Nov;184(22):6250-9 PMID: 12399495
  53. tRNA maturation in Aquifex aeolicus.
    Biochimie. 2002 Aug;84(8):713-22 PMID: 12457559
  54. Mutants of Escherichia coli thermosensitive for the synthesis of transfer RNA.
    Proc Natl Acad Sci U S A. 1973 Jul;70(7):2091-5 PMID: 4579013
  55. 30 S pre-ribosomal RNA of Escherichia coli and products of cleavage by ribonuclease III: length and molecular weight.
    J Mol Biol. 1974 Jul 15;86(4):741-7 PMID: 4610145
  56. In vitro maturation of precursors of 5S ribosomal RNA from Bacillus subtilis.
    Nature. 1974 Dec 13;252(5484):598-600 PMID: 4215038
  57. Purification of potential 3' processing nucleases using synthetic tRNA precursors.
    Nucleic Acids Res. 1978 Oct;5(10):3831-42 PMID: 364419
  58. Structural analysis and in vitro processing to p5 rRNA of a 9S RNA molecule isolated from an rne mutant of E. coli.
    Cell. 1978 Nov;15(3):1055-66 PMID: 365352
  59. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme.
    Cell. 1983 Dec;35(3 Pt 2):849-57 PMID: 6197186
  60. RNase H confers specificity in the dnaA-dependent initiation of replication at the unique origin of the Escherichia coli chromosome in vivo and in vitro.
    Proc Natl Acad Sci U S A. 1984 Feb;81(4):1040-4 PMID: 6322184
  61. The ribonucleoprotein substrate for a ribosomal RNA-processing nuclease.
    J Biol Chem. 1984 Sep 25;259(18):11448-53 PMID: 6432797
  62. Function of ribonuclease H in initiation of DNA replication in Escherichia coli K-12.
    Mol Gen Genet. 1985;200(1):103-9 PMID: 2993805
  63. RNase T is responsible for the end-turnover of tRNA in Escherichia coli.
    Proc Natl Acad Sci U S A. 1985 Oct;82(19):6427-30 PMID: 2413440
  64. Ribosomal RNA phylogeny and the primary lines of evolutionary descent.
    Cell. 1986 May 9;45(3):325-6 PMID: 3084106
  65. cmp, a cis-acting plasmid locus that increases interaction between replication origin and initiator protein.
    J Bacteriol. 1986 Oct;168(1):160-6 PMID: 3759903
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkf691
Email
condon@ibpc.fr
Published
2002-12-15
Pages
5339-46
Language
English
Region
England
NLM ID
0411011
PMCID
PMC140075
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkf691 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2