The frontier between cell and organelle: Genome analysis of Candidatus Carsonella ruddii

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Tamames, Javier ^a   Gil, Rosario ^a,b   Latorre, Amparo ^a,b   Peretó, Juli ^a,b   Silva, Francisco J ^a,b   Moya, Andrés ^a,b  

^a UNIVERSITY OF VALENCIA   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ESSENTIAL AMINO ACID; BACTERIAL DNA;

AEROBIC BACTERIUM; AMINO ACID SYNTHESIS; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CANDIDATUS CARSONELLA RUDDII; CELL NUCLEUS; CELL ORGANELLE; DEGRADATION; DNA REPLICATION; DNA TRANSCRIPTION; ECOLOGICAL NICHE; ENDOSYMBIONT; GENE SEQUENCE; GENOME ANALYSIS; INSECT; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PSYLLID; SYMBIOSIS; ANIMAL; BACTERIAL GENE; DNA SEQUENCE; GAMMAPROTEOBACTERIA; GENETICS; HEMIPTERA; MICROBIOLOGY; OPEN READING FRAME; POLYMERASE CHAIN REACTION; RNA GENE;

BACTERIA (MICROORGANISMS); CANDIDATUS CARSONELLA RUDDII; HEXAPODA; PSYLLIDAE;

ANIMALS; DNA, BACTERIAL; GAMMAPROTEOBACTERIA; GENES, BACTERIAL; GENES, RRNA; GENOME, BACTERIAL; HEMIPTERA; OPEN READING FRAMES; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SYMBIOSIS;

EID: 37849032376     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-181     Document Type: Article

References (36)

1. Biology bacteriocyte-associated endosymbionts of plant sap-sucking insects. P Baumann, Annu Rev Microbiol 2005 59 155 189 10.1146/annurev.micro.59. 030804.121041 16153167
2. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. S Shigenobu H Watanabe M Hattori Y Sakaki H Ishikawa, Nature 2000 407 6800 81 86 10.1038/35024074 10993077
3. 50 million years of genomic stasis in endosymbiotic bacteria. I Tamas L Klasson B Canback AK Naslund AS Eriksson JJ Wernegreen JP Sandstrom NA Moran SG Andersson, Science 2002 296 5577 2376 2379 10.1126/science.1071278 12089438
4. Reductive genome evolution in Buchnera aphidicola. RC van Ham J Kamerbeek C Palacios C Rausell F Abascal U Bastolla JM Fernandez L Jimenez M Postigo FJ Silva J Tamames E Viguera A Latorre A Valencia F Moran A Moya, Proc Natl Acad Sci U S A 2003 100 2 581 586 12522265 10.1073/pnas.0235981100
5. Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. PH Degnan AB Lazarus JJ Wernegreen, Genome Res 2005 15 8 1023 1033 16077009 10.1101/gr.3771305
6. The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. R Gil FJ Silva E Zientz F Delmotte F Gonzalez-Candelas A Latorre C Rausell J Kamerbeek J Gadau B Holldobler RC van Ham R Gross A Moya, Proc Natl Acad Sci U S A 2003 100 16 9388 9393 12886019 10.1073/pnas.1533499100
7. A small microbial genome: the end of a long symbiotic relationship? V Perez-Brocal R Gil S Ramos A Lamelas M Postigo JM Michelena FJ Silva A Moya A Latorre, Science 2006 314 5797 312 313 10.1126/science.1130441 17038625
8. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. L Akman A Yamashita H Watanabe K Oshima T Shiba M Hattori S Aksoy, Nat Genet 2002 32 3 402 407 10.1038/ng986 12219091
9. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. D Wu SC Daugherty SE Van Aken GH Pai KL Watkins H Khouri LJ Tallon JM Zaborsky HE Dunbar PL Tran NA Moran JA Eisen, PLoS Biol 2006 4 6 e188 16729848 10.1371/journal.pbio.0040188
10. The notion of a DNA minimal cell: a general discourse and some gidelines for an experimental approach. PL Luisi T Oberholzer A Lazcano, Helv Chim Acta 2002 85 1759 1777 10.1002/1522-2675(200206)85:6<1759::AID-HLCA1759>3.0. CO;2-7
11. The 160-kilobase genome of the bacterial endosymbiont Carsonella. A Nakabachi A Yamashita H Toh H Ishikawa HE Dunbar NA Moran M Hattori, Science 2006 314 5797 267 10.1126/science.1134196 17038615
12. Minimal genomes required for life. R Gil V Pérez-Brocal A Latorre A Moya, Prokaryotic diversity Mecanisms and significance Cambridge University Press, Logan NA, Lappin-Scott HM, Oyston CF, 2006 105 121
13. Determination of the core of a minimal bacterial gene set. R Gil FJ Silva J Pereto A Moya, Microbiol Mol Biol Rev 2004 68 3 518 537 15353568 10.1128/MMBR.68.3.518-537.2004
14. Faculty of 1000 Biology. J Glass, http://www.f1000biology.com/article/id/ 1021418/evaluation
15. Activation of stable DNA replication in rapidly growing Escherichia coli at the time of entry to stationary phase. X Hong GW Cadwell T Kogoma, Molecular Microbiology 1996 21 5 953 961 10.1046/j.1365-2958.1996.591419.x 8885266
16. Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana. AM Duchene A Giritch B Hoffmann V Cognat D Lancelin NM Peeters M Zaepfel L Marechal-Drouard ID Small, Proc Natl Acad Sci U S A 2005 102 45 16484 16489 16251277 10.1073/pnas.0504682102
17. Plant organellar protein targeting: a traffic plan still under construction. SA Mackenzie, Trends Cell Biol 2005 15 10 548 554 10.1016/j.tcb.2005.08.007 16143534
18. Cospeciation of psyllids and their primary prokaryotic endosymbionts. ML Thao NA Moran P Abbot EB Brennan DH Burckhardt P Baumann, Appl Environ Microbiol 2000 66 7 2898 2905 10877784 10.1128/AEM.66.7.2898-2905.2000
19. Phloem-sap feeding by animals: problems and solutions. AE Douglas, J Exp Bot 2006 57 4 747 754 10.1093/jxb/erj067 16449374
20. Metabolic Interdependence of Obligate Intracellular Bacteria and Their Insect Hosts. E Zientz T Dandekar R Gross, Microbiol Mol Biol Rev 2004 68 4 745 770 15590782 10.1128/MMBR.68.4.745-770.2004
21. The Calyptogena magnifica chemoautotrophic symbiont genome. IL Newton T Woyke TA Auchtung GF Dilly RJ Dutton MC Fisher KM Fontanez E Lau FJ Stewart PM Richardson KW Barry E Saunders JC Detter D Wu JA Eisen CM Cavanaugh, Science 2007 315 5814 998 1000 10.1126/science.1138438 17303757
22. A novel eukaryotic extracellular symbiont in an aphid, Astegopterys styraci (Homoptera, Aphidinae, Hormaphidinae). T Fukatsu H Ishikawa, J Insect Physiol 1992 38 765 773 10.1016/0022-1910(92)90029-D
23. Strict host-symbiont cospeciation and reductive genome evolution in insect gut bacteria. T Hosokawa Y Kikuchi N Nikoh M Shimada T Fukatsu, PLoS Biol 2006 4 10 e337 17032065 10.1371/journal.pbio.0040337
24. Endosymbiont Phylogenesis in the Dryophthoridae Weevils: Evidence for Bacterial Replacement. C Lefevre H Charles A Vallier B Delobel B Farrell A Heddi, Mol Biol Evol 2004 21 6 965 973 10.1093/molbev/msh063 14739242
25. Improved microbial gene identification with GLIMMER. AL Delcher D Harmon S Kasif O White SL Salzberg, Nucl Acids Res 1999 27 23 4636 4641 10556321 10.1093/nar/27.23.4636
26. 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
27. EcoCyc: Encyclopedia of Escherichia coli K-12 Genes and Metabolism. http://ecocyc.org/
28. EcoGene: The EcoGene Database of Escherichia coli Sequence and Function. http://ecogene.org/
29. Pfam: Protein families database. http://www.sanger.ac.uk/Software/Pfam/
30. Uniprot, the universal protein resource. http://www.ebi.uniprot.org/ index.shtml
31. Profile hidden Markov models. SR Eddy, Bioinformatics 1998 14 9 755 763 10.1093/bioinformatics/14.9.755 9918945
32. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. TM Lowe SR Eddy, Nucleic Acids Res 1997 25 5 955 964 9023104 10.1093/nar/25.5.955
33. TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase. DH Ardell SG Andersson, Nucleic Acids Res 2006 34 3 893 904 16473847 10.1093/nar/gkj449
34. Differential annotation of tRNA genes with anticodon CAT in bacterial genomes. FJ Silva E Belda SE Talens, Nucleic Acids Res 2006 34 20 6015 6022 17071718 10.1093/nar/gkl739
35. KEGG: Kyoto Encyclopedia of Genes and Genomes. M Kanehisa S Goto, Nucl Acids Res 2000 28 1 27 30 10592173 10.1093/nar/28.1.27
36. BRENDA, enzyme data and metabolic information. I Schomburg A Chang D Schomburg, Nucl Acids Res 2002 30 1 47 49 11752250 10.1093/nar/30.1.47