Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Kochiwa, Hiromi ^a   Tomita, Masaru ^a   Kanai, Akio ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; DOUBLE STRANDED RNA; RIBONUCLEASE H; BACTERIAL PROTEIN; RIBONUCLEASE; RIBONUCLEASE HI; RIBONUCLEASE HII; RIBONUCLEASE HIII; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; DNA RNA HYBRIDIZATION; EUKARYOTE EVOLUTION; GENE FUNCTION; GENE SEQUENCE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PROKARYOTE; BACTERIAL GENE; BACTERIAL GENOME; BAYES THEOREM; BIOLOGICAL MODEL; ENZYMOLOGY; GENE; GENETIC DATABASE; GENETICS; GENOME; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; PROKARYOTIC CELL; SEQUENCE HOMOLOGY;

EUKARYOTA; PROKARYOTA;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BAYES THEOREM; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENES, ARCHAEAL; GENES, BACTERIAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROKARYOTIC CELLS; RIBONUCLEASE H, CALF THYMUS; RIBONUCLEASES; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 34548089729     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-128     Document Type: Article

References (66)

1. Gene duplication and biased functional retention of paralogs in bacterial genomes. D Gevers K Vandepoele C Simillon Y Van de Peer, Trends Microbiol 2004 12 4 148 154 10.1016/j.tim.2004.02.007 15116722
2. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. T Baba T Ara M Hasegawa Y Takai Y Okumura M Baba KA Datsenko M Tomita BL Wanner H Mori, Mol Syst Biol 2006 2 2006 0008 16738554 10.1038/msb4100050
3. Essential Bacillus subtilis genes. K Kobayashi SD Ehrlich A Albertini G Amati KK Andersen M Arnaud K Asai S Ashikaga S Aymerich P Bessieres F Boland SC Brignell S Bron K Bunai J Chapuis LC Christiansen A Danchin M Debarbouille E Dervyn E Deuerling K Devine SK Devine O Dreesen J Errington S Fillinger SJ Foster Y Fujita A Galizzi R Gardan C Eschevins T Fukushima K Haga CR Harwood M Hecker D Hosoya MF Hullo H Kakeshita D Karamata Y Kasahara F Kawamura K Koga P Koski R Kuwana D Imamura M Ishimaru S Ishikawa I Ishio D Le Coq A Masson C Mauel R Meima RP Mellado A Moir S Moriya E Nagakawa H Nanamiya S Nakai P Nygaard M Ogura T Ohanan M O'Reilly M O'Rourke Z Pragai HM Pooley G Rapoport JP Rawlins LA Rivas C Rivolta A Sadaie Y Sadaie M Sarvas T Sato HH Saxild E Scanlan W Schumann JF Seegers J Sekiguchi A Sekowska SJ Seror M Simon P Stragier R Studer H Takamatsu T Tanaka M Takeuchi HB Thomaides V Vagner JM van Dijl K Watabe A Wipat H Yamamoto M Yamamoto Y Yamamoto K Yamane K Yata K Yoshida H Yoshikawa U Zuber N Ogasawara, Proc Natl Acad Sci U S A 2003 100 8 4678 4683 12682299 10.1073/pnas.0730515100
4. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. A Wagner, Mol Biol Evol 2001 18 7 1283 1292 11420367
5. Evolution of genetic redundancy. MA Nowak MC Boerlijst J Cooke JM Smith, Nature 1997 388 6638 167 171 10.1038/40618 9217155
6. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. J Zhang YP Zhang HF Rosenberg, Nat Genet 2002 30 4 411 415 10.1038/ng852 11925567
7. Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys. J Zhang, Nat Genet 2006 38 7 819 823 10.1038/ng1812 16767103
8. Positive Darwinian selection after gene duplication in primate ribonuclease genes. J Zhang HF Rosenberg M Nei, Proc Natl Acad Sci U S A 1998 95 7 3708 3713 9520431 10.1073/pnas.95.7.3708
9. Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. HS Malik TH Eickbush, Genome Res 2001 11 7 1187 1197 10.1101/gr.185101 11435400
10. Enzyme from calf thymus degrading the RNA moiety of DNA-RNA Hybrids: effect on DNA-dependent RNA polymerase. H Stein P Hausen, Science 1969 166 903 393 395 10.1126/science.166.3903.393 5812039
11. Molecular diversities of RNases H. N Ohtani M Haruki M Morikawa S Kanaya, J Biosci Bioeng 1999 88 1 12 19 10.1016/S1389-1723(99)80168-6 16232566
12. Function of RNase H in DNA replication revealed by RNase H defective mutants of Escherichia coli. T Ogawa T Okazaki, Mol Gen Genet 1984 193 2 231 237 10.1007/BF00330673 6319961
13. Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice. SM Cerritelli EG Frolova C Feng A Grinberg PE Love RJ Crouch, Mol Cell 2003 11 3 807 815 10.1016/S1097-2765(03)00088-1 12667461
14. Cooperative regulation for Okazaki fragment processing by RNase HII and FEN-1 purified from a hyperthermophilic archaeon, Pyrococcus furiosus. A Sato A Kanai M Itaya M Tomita, Biochem Biophys Res Commun 2003 309 1 247 252 10.1016/j.bbrc.2003.08.003 12943689
15. Excision of misincorporated ribonucleotides in DNA by RNase H (type 2) and FEN-1 in cell-free extracts. B Rydberg J Game, Proc Natl Acad Sci U S A 2002 99 26 16654 16659 12475934 10.1073/pnas.262591699
16. Cleavage of a DNA-RNA-DNA/DNA chimeric substrate containing a single ribonucleotide at the DNA-RNA junction with prokaryotic RNases HII. M Haruki Y Tsunaka M Morikawa S Kanaya, FEBS Lett 2002 531 2 204 208 10.1016/S0014-5793(02) 03503-2 12417313
17. Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I. M Drolet P Phoenix R Menzel E Masse LF Liu RJ Crouch, Proc Natl Acad Sci U S A 1995 92 8 3526 3530 7536935 10.1073/pnas.92.8.3526
18. RNase H overproduction allows the expression of stress-induced genes in the absence of topoisomerase I. B Cheng S Rui C Ji VW Gong TK Van Dyk M Drolet YC Tse-Dinh, FEMS Microbiol Lett 2003 221 2 237 242 10.1016/S0378-1097(03)00209- X 12725933
19. Drug targeting of HIV-1 RNA.DNA hybrid structures: thermodynamics of recognition and impact on reverse transcriptase-mediated ribonuclease H activity and viral replication. TK Li CM Barbieri HC Lin AB Rabson G Yang Y Fan BL Gaffney RA Jones DS Pilch, Biochemistry 2004 43 30 9732 9742 10.1021/bi0497345 15274628
20. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutieres syndrome and mimic congenital viral brain infection. YJ Crow A Leitch BE Hayward A Garner R Parmar E Griffith M Ali C Semple J Aicardi R Babul-Hirji C Baumann P Baxter E Bertini KE Chandler D Chitayat D Cau C Dery E Fazzi C Goizet MD King J Klepper D Lacombe G Lanzi H Lyall ML Martinez-Frias M Mathieu C McKeown A Monier Y Oade OW Quarrell CD Rittey RC Rogers A Sanchis JB Stephenson U Tacke M Till JL Tolmie P Tomlin T Voit B Weschke CG Woods P Lebon DT Bonthron CP Ponting AP Jackson, Nat Genet 2006 38 8 910 916 10.1038/ng1842 16845400
21. RNase H1 of Saccharomyces cerevisiae: methods and nomenclature. RJ Crouch A Arudchandran SM Cerritelli, Methods Enzymol 2001 341 395 413 11582793
22. Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction. N Ohtani H Yanagawa M Tomita M Itaya, Biochem J 2004 381 Pt 3 795 802 15115438
23. Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. N Ohtani H Yanagawa M Tomita M Itaya, Nucleic Acids Res 2004 32 19 5809 5819 15520465 10.1093/nar/gkh917
24. Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products. S Yamamoto S Harayama, Int J Syst Bacteriol 1996 46 2 506 511 8934907
25. Eukaryotic RNAse H shares a conserved domain with caulimovirus proteins that facilitate translation of polycistronic RNA. AR Mushegian HK Edskes EV Koonin, Nucleic Acids Res 1994 22 20 4163 4166 7937142 10.1093/nar/22.20.4163
26. Eukaryotic RNases H1 act processively by interactions through the duplex RNA-binding domain. SA Gaidamakov Gorshkova P Schuck PJ Steinbach H Yamada RJ Crouch SM Cerritelli, Nucleic Acids Res 2005 33 7 2166 2175 15831789 10.1093/nar/gki510
27. A common 40 amino acid motif in eukaryotic RNases H1 and caulimovirus ORF VI proteins binds to duplex RNAs. SM Cerritelli OY Fedoroff BR Reid RJ Crouch, Nucleic Acids Res 1998 26 7 1834 1840 9512560 10.1093/nar/26.7.1834
28. The non-RNase H domain of Saccharomyces cerevisiae RNase H1 binds double-stranded RNA: magnesium modulates the switch between double-stranded RNA binding and RNase H activity. SM Cerritelli RJ Crouch, Rna 1995 1 3 246 259 7489497
29. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. M Nowotny SA Gaidamakov RJ Crouch W Yang, Cell 2005 121 7 1005 1016 10.1016/j.cell.2005.04.024 15989951
30. Identification of RNase HII from psychrotrophic bacterium, Shewanella sp. SIB1 as a high-activity type RNase H. H Chon T Tadokoro N Ohtani Y Koga K Takano S Kanaya, Febs J 2006 273 10 2264 2275 10.1111/j.1742-4658.2006.05241.x 16650002
31. Isolation of RNase H genes that are essential for growth of Bacillus subtilis 168. M Itaya A Omori S Kanaya RJ Crouch T Tanaka K Kondo, J Bacteriol 1999 181 7 2118 2123 10094689
32. DNA sequence of the gene coding for Escherichia coli ribonuclease H. S Kanaya RJ Crouch, J Biol Chem 1983 258 2 1276 1281 6296074
33. Three-dimensional structure of ribonuclease H from E. coli. K Katayanagi M Miyagawa M Matsushima M Ishikawa S Kanaya M Ikehara T Matsuzaki K Morikawa, Nature 1990 347 6290 306 309 10.1038/347306a0 1698262
34. Kinetic and stoichiometric analysis for the binding of Escherichia coli ribonuclease HI to RNA-DNA hybrids using surface plasmon resonance. M Haruki E Noguchi S Kanaya RJ Crouch, J Biol Chem 1997 272 35 22015 22022 10.1074/jbc.272.35.22015 9268340
35. NMR structure of the N-terminal domain of Saccharomyces cerevisiae RNase HI reveals a fold with a strong resemblance to the N-terminal domain of ribosomal protein L9. SP Evans M Bycroft, J Mol Biol 1999 291 3 661 669 10.1006/jmbi.1999.2971 10448044
36. Comparative genomics of the lactic acid bacteria. K Makarova A Slesarev Y Wolf A Sorokin B Mirkin E Koonin A Pavlov N Pavlova V Karamychev N Polouchine V Shakhova I Grigoriev Y Lou D Rohksar S Lucas K Huang DM Goodstein T Hawkins V Plengvidhya D Welker J Hughes Y Goh A Benson K Baldwin JH Lee I Diaz-Muniz B Dosti V Smeianov W Wechter R Barabote G Lorca E Altermann R Barrangou B Ganesan Y Xie H Rawsthorne D Tamir C Parker F Breidt J Broadbent R Hutkins D O'Sullivan J Steele G Unlu M Saier T Klaenhammer P Richardson S Kozyavkin B Weimer D Mills, Proc Natl Acad Sci U S A 2006 103 42 15611 15616 17030793 10.1073/pnas. 0607117103
37. Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. AC Berglund-Sonnhammer P Steffansson MJ Betts DA Liberles, J Mol Evol 2006 63 2 240 250 10.1007/s00239-005-0096-1 16830091
38. Identification of the genes encoding Mn2+-dependent RNase HII and Mg2+-dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families. N Ohtani M Haruki M Morikawa RJ Crouch M Itaya S Kanaya, Biochemistry 1999 38 2 605 618 10.1021/bi982207z 9888800
39. Lateral gene transfer and the nature of bacterial innovation. H Ochman JG Lawrence EA Groisman, Nature 2000 405 6784 299 304 10.1038/35012500 10830951
40. Ribonuclease H1 maps to chromosome 2 and has at least three pseudogene loci in the human genome. AL ten Asbroek M van Groenigen ME Jakobs C Koevoets B Janssen F Baas, Genomics 2002 79 6 818 823 10.1006/geno.2002.6776 12036296
41. Stage-specific expression of Caenorhabditis elegans ribonuclease H1 enzymes with different substrate specificities and bivalent cation requirements. H Kochiwa M Itaya M Tomita A Kanai, Febs J 2006 273 2 420 429 10.1111/j.1742-4658.2005.05082.x 16403028
42. Drosophila RNase H1 is essential for development but not for proliferation. V Filippov M Filippov SS Gill, Mol Genet Genomics 2001 265 5 771 777 10.1007/s004380100483 11523794
43. Yeast RNase H(35) is the counterpart of the mammalian RNase HI, and is evolutionarily related to prokaryotic RNase HII. P Frank C Braunshofer-Reiter U Wintersberger, FEBS Lett 1998 421 1 23 26 10.1016/S0014-5793(97)01528-7 9462832
44. Disruption of the Crithidia fasciculata RNH1 gene results in the loss of two active forms of ribonuclease H. DS Ray JC Hines, Nucleic Acids Res 1995 23 13 2526 2530 7630731 10.1093/nar/23.13.2526
45. The evolutionary fate and consequences of duplicate genes. M Lynch JS Conery, Science 2000 290 5494 1151 1155 10.1126/science.290.5494.1151 11073452
46. Retention of enzyme gene duplicates by subfunctionalization. FN Braun DA Liberles, Int J Biol Macromol 2003 33 1-3 19 22 10.1016/S0141-8130(03)00059-X 14599579
47. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. S Rastogi DA Liberles, BMC Evol Biol 2005 5 1 28 15831095 10.1186/1471-2148-5-28
48. The SCO2299 gene from Streptomyces coelicolor A3(2) encodes a bifunctional enzyme consisting of an RNase H domain and an acid phosphatase domain. N Ohtani N Saito M Tomita M Itaya A Itoh, Febs J 2005 272 11 2828 2837 10.1111/j.1742-4658.2005.04704.x 15943815
49. Pseudogene evolution and natural selection for a compact genome. DA Petrov DL Hartl, J Hered 2000 91 3 221 227 10.1093/jhered/91.3.221 10833048
50. Energy constraints on the evolution of gene expression. A Wagner, Mol Biol Evol 2005 22 6 1365 1374 10.1093/molbev/msi126 15758206
51. GenBank. ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
52. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 9254694 10.1093/nar/25.17.3389
53. Profile hidden Markov models. SR Eddy, Bioinformatics 1998 14 9 755 763 10.1093/bioinformatics/14.9.755 9918945
54. BLAST. ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
55. Taxonomy. ftp://ftp.ncbi.nih.gov/pub/taxonomy/
56. Pfam. http://www.sanger.ac.uk/Software/Pfam/
57. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. K Arakawa K Mori K Ikeda T Matsuzaki Y Kobayashi M Tomita, Bioinformatics 2003 19 2 305 306 10.1093/bioinformatics/19.2.305 12538262
58. CDD: a Conserved Domain Database for protein classification. A Marchler-Bauer JB Anderson PF Cherukuri C DeWeese-Scott LY Geer M Gwadz S He DI Hurwitz JD Jackson Z Ke CJ Lanczycki CA Liebert C Liu F Lu GH Marchler M Mullokandov BA Shoemaker V Simonyan JS Song PA Thiessen RA Yamashita JJ Yin D Zhang SH Bryant, Nucleic Acids Res 2005 33 Database issue D192 6 15608175 10.1093/nar/gki069
59. CDD. ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/
60. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 22 4673 4680 7984417 10.1093/nar/22.22.4673
61. MODELTEST: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 9 817 818 10.1093/bioinformatics/14.9.817 9918953
62. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. DL Swofford, Sinauer Associates Sunderland, Massachusetts 2003
63. A new look at the statistical model identification. H Akaike, IEEE Transactions on Automatic Control 1974 19 6 716 723 10.1109/TAC.1974.1100705
64. MRBAYES: Bayesian inference of phylogenetic trees. JP Huelsenbeck F Ronquist, Bioinformatics 2001 17 8 754 755 10.1093/bioinformatics/17.8.754 11524383
65. The general stochastic model of nucleotide substitution. F Rodriguez JL Oliver A Marin JR Medina, J Theor Biol 1990 142 4 485 501 2338834
66. TreeView: an application to display phylogenetic trees on personal computers. RD Page, Comput Appl Biosci 1996 12 4 357 358 8902363