Phylogenomics of Reichenowia parasitica, an alphaproteobacterial endosymbiont of the freshwater leech Placobdella parasitica

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Kvist, Sebastian ^a   Narechania, Apurva ^a   Oceguera Figueroa, Alejandro ^a,b   Fuks, Bella ^c   Siddall, Mark E ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

^c Long Island University (Brooklyn Campus)   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; AMINO ACID; BACTERIAL DNA; CYANOCOBALAMIN; IRON; NITROGEN; FRESH WATER;

ALPHAPROTEOBACTERIA; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL SURVIVAL; COMPUTER MODEL; CONTROLLED STUDY; DNA SEQUENCE; ENDOSYMBIONT; LEECH; NITROGEN FIXATION; NONHUMAN; PHYLOGENOMICS; PHYLOGENY; PLACOBDELLA PARASITICA; PLASMID; REICHENOWIA PARASITICA; SEPARATION TECHNIQUE; SYMBIONT; ANIMAL; CLUSTER ANALYSIS; GENETICS; GENOME SIZE; GENOMICS; MICROBIOLOGY; NONLINEAR SYSTEM; SYMBIOSIS; ULTRASTRUCTURE;

AGROBACTERIUM; ALPHAPROTEOBACTERIA; ANIMALIA; BACTERIA (MICROORGANISMS); FRESHWATER LEECH; HELOBDELLA ROBUSTA; HIRUDINIDA; PLACOBDELLA; PLACOBDELLA PARASITICA; REICHENOWIA; RHIZOBIACEAE; RHIZOBIUM; TEREBRANTIA;

ALPHAPROTEOBACTERIA; ANIMALS; CLUSTER ANALYSIS; FRESH WATER; GENOME SIZE; GENOME, BACTERIAL; GENOMICS; LEECHES; NONLINEAR DYNAMICS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SYMBIOSIS;

EID: 81755166598     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028192     Document Type: Article

References (58)

1. Graf J, Kikuchi Y, Rio RVM, (2006) Leeches and their microbiota: naturally simple symbiosis models. Trends Microbiol 14: 365-371.
2. Reichenow E, (1921) Über intrazelluläre Symbionten bei Blutsaugern. Arch Schiffs-u Tropen-Hyg 25.
3. Reichenow E, (1922) Intrazelluläre Symbionten bei blutsaugenden Milben und Egeln Arch Protistenk 45.
4. Siddall ME, Perkins SL, Desser SS, (2004) Leech mycetome endosymbionts are a new lineage of alphaproteobacteria related to the Rhizobiaceae. Mol Phylogenet Evol 30: 178-186.
5. Akman L, Yamashita A, Watanabe H, Oshima K, Shiba T, et al. (2002) Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinida. Nat Genet 32: 402-407.
6. Perkins SL, Budinoff RB, Siddall ME, (2005) New Gammaproteobacteria associated with blood-feeding leeches and a broad phylogenetic analysis of leech endosymbionts. Appl Environ Microbiol 71: 5219-5224.
7. Moran NA, McCutcheon JP, Nakabachi A, (2008) Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 42: 165-190.
8. Kikutchi Y, Fukatsu T, (2002) Endosymbiotic bacteria in the esophageal organ of glossiphoniid leeches. Appl Environ Microbiol 68: 4637-4641.
9. Siddall ME, Min G-S, Fontanella FM, Phillips AJ, Watson SC, (2011) Bacterial symbiont and salivary peptide evolution in the context of leech phylogeny. Parasitol 138: 1815-1827.
10. Moran NA, Wernegreen JJ, (2000) Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends Ecol Evol 15: 321-326.
11. Andersson SGE, Kurland CG, (1998) Reductive evolution of resident genomes. Trends Microbiol 6: 263-268.
12. Moreno E, (1998) Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome? FEMS Micribiol Rev 22: 255-275.
13. Fischer HM, (1994) Genetic regulation of nitrogen fixation in rhizobia. Microbiol Mol Biol Rev 58: 352-386.
14. Townsend AR, Howarth RW, Bazzaz FA, Booth MS, Cleveland CC, et al. (2003) Human health effects of a changing global nitrogen cycle. Frontiers Ecol Environ 1: 240-246.
15. Carpenter SR, Caraco NF, Correll DL, Howarth RW, Sharpley AN, et al. (1998) Nonpoint pollution of surface waters with phosphorus and nitrogen. Ecol Appl 8: 559-568.
16. Howarth RW, Marino R, Cole JJ, (1988) Nitrogen fixation in freshwater, estuarine, and marine ecosystems. 2. Biogeochemical controls. Limnol Oceanogr 33: 688-701.
17. Moran NA, Baumann P, (2000) Bacterial endosymbionts in animals. Curr Opin Microbiol 3: 270-275.
18. Tamames J, González-Moreno M, Mingorance J, Valencia A, Vicente M, (2001) Bringing gene order into bacterial shape. Trends Genet 17: 124-126.
19. Lefèvre C, Charles H, Vallier A, Delobel B, Farrell B, et al. (2004) Endosymbiont phylogenesis in the Dryophtoridae weevils: evidence for bacterial replacement. Mol Biol Evol 21: 965-973.
20. van Borm S, Buschinger A, Boomsma JJ, Billen J, (2002) Tetraponera ants have gut symbionts related to nitrogen-fixing root-nodule bacteria. Proc R Soc Lond B 269: 2023-2027.
21. Fontana R, Canepari P, Satta G, (1979) Alterations in peptidoglycan chemical composition associated with rod-to-sphere transition in a conditional mutant of Klebsiella pneumoniae. J Bacteriol 139: 1028-1038.
22. Henning U, Rehn K, Braun V, Hohn B, (1972) Cell envelope and shape of Escherichia coli K12. Properties of a temperature-sensitive rod mutant. Eur J Biochem 26: 570-586.
23. Rogers GB, Carroll MP, Bruce KD, (2009) Studying bacterial infections through culture-independent approaches. J Med Microbiol 58: 1401-1418.
24. Siddall ME, Budinoff RB, Borda E, (2005) Phylogenetic evaluation of systematics and biogeography of the leech family Glossiphoniidae. Invertebr Syst 19: 105-112.
25. Light JE, Siddall ME, (1999) Phylogeny of the leech family Glossiphoniidae based on mitochondrial gene sequences and morphological data. J Parasitol 85: 815-823.
26. Lukashin AV, Borodovsky M, (1998) GeneMark.hmm: new solutions for gene finding. Nucl Acids Res 26: 1107-1115.
27. Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, et al. (2006) OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 22: 699-707.
28. Katoh K, Kuma K-I, Toh H, Miyata T, (2005) MAFFT verison 5: improvement in accuracy of multiple sequence alignment. Nucl Acids Res 33: 511-518.
29. Goloboff PA, Farris JS, Nixon KC, (2008) TNT, a free program for phylogenetic analysis. Cladistics 24: 774-786.
30. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
31. Siddall ME, (2010) Unringing a bell: metazoan phylogenomics and the partition bootstrap. Cladistics 26: 444-452.
32. Swofford D, (2002) PAUP*: Phylogenetic analysis using parsimony (*and other methods), ver. 4.0b10. Sunderland, MA Sinauer Associates.
33. Snel B, Bork P, Huynen MA, (1999) Genome phylogeny based on gene content. Nat Genet 21: 108-110.
34. Ochman H, Moran NA, (2001) Genes lost and found: evolution of bacterial pathogenesis and symbiosis. Science 292: 1096-1099.
35. Casjens S, (1998) The diverse and dynamic structure of bacterial genomes. Annu Rev Genet 32: 339-377.
36. Röther D, Poppe L, Viergutz S, Langer B, Rétey J, (2001) Characterization of the active site of histidine ammonia-lyase from Pseudomonas putida. Eur J Biochem 268: 6011-6019.
37. Weidner S, Pühler A, Küster H, (2003) Genomic insights into symbiotic nitrogen fixation. Curr Opin Biotechnol 14: 200-205.
38. Kahn D, David M, Domergue O, Daveran ML, Ghai J, et al. (1989) Rhizobium meliloti fixGHI sequence predicts involvement of a specific cation pump in symbiotic nitrogen fixation. J Bacteriol 171: 929-939.
39. Batut J, Bostard P, Debelle F, Denarie J, Ghai J, et al. (1985a) Developmental biology of the Rhizobium meliloti-alfalfa symbiosis: a joint genetic and cytological approach. In: Evans HJ, Bottomley PJ, Newton WE, editors. Nitrogen fixation research progress Dordrecht Martinus Nijhoff pp. 109-115.
40. Batut J, Terzaghi B, Ghérardi M, Huguet M, Terzaghi E, et al. (1985b) Localization of a symbioticfix region on Rhizobium meliloti pSym megaplasmid more than 200 kilobases from the nod-nif region. Mol Gen Genet 19: 232-239.
41. Rubinstein B, Stern AI, (1986) Relationship of transplasmalemma redox activity to proton and solute transport by roots of Zea mays. Plant Physiol 80: 805-811.
42. Lechene CP, Luyten Y, McMahon G, Distel DL, (2007) Quantitative imaging of nitrogen fixation by individual bacteria within animal cells. Science 317: 1563-1566.
43. Higgins CF, (2001) ABC transporters: physiology, structure and mechanism- an overview. Res Microbiol 152: 205-210.
44. Borths EL, Locher KP, Lee AT, Rees DC, (2002) The structure of Escherichia coli BtuF and binding to its cognate ATP binding cassette transporter. Proc Natl Acad Sci U S A 99: 16642-16647.
45. Nogge G, (1981) Significance of symbionts for the maintenance of an optimal nutritional state for successful reproduction in hematophagous arthropods. Parasitol 82: 101-104.
46. Nogge G, (1976) Sterility in tsetse flies (Glossina morsitans Westwood) caused by loss of symbionts. Experientia 32: 995-996.
47. Lehnerr H, Yarmolinsky MB, (1995) Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli. Proc Natl Acad Sci U S A 92: 3274-3277.
48. Engelberg-Kulka H, Hazan R, Amitai S, (2005) mazEF: a chromosomal toxin-antitoxin module that triggers programmed cell death in bacteria. J Cell Sci 118: 4327-4332.
49. Nekrasov SV, Agafonova OV, Belogurova NG, Delver EP, Belogurov AA, (2007) Plasmid-encoded antirestriction protein ArdA can descriminate Type I methyltransferase and complete restriction-modification system. J Mol Biol 365: 284-297.
50. Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, et al. (2009) The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucl Acids Res 37: 762-770.
51. Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, et al. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9: 189-197.
52. Spaepen S, Das F, Luyten E, Michiels J, Vanderleyden J, (2009) Indole-3-acetic acid-regulated genes in Rhizobium etli CNPAF512. FEMS Microbiol Lett 291: 195-200.
53. Ausmees N, Jacobsson K, Lindberg M, (2001) A unipolarly located, cell-surface-associated agglutinin, RapA, belongs to a family of Rhizobium-adhering proteins (Rap) in Rhizobium leguminosarum bv. trifolii. Microbiol-SGM 147: 549-559.
54. Bouchon D, Rigaud T, Juchault P, (1998) Evidence for widespread Wolbachia infection in isopod crustaceans: molecular identification and host feminization. Proc R Soc Lond B 265: 1081-1090.
55. Burnett WJ, McKenzie JD, (1997) Subcuticular bacteria from the brittle star Ophiactis balli (Echinodermata: Ophiuroidea) represent a new lineage of extracellular marine symbionts in the a subdivision of the class Proteobacteria. Appl Environ Microbiol 63: 1721-1724.
56. Manz W, Amann R, Ludwig W, Vancanneyt M, Schleifer K-H, (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Micriobiology 142: 1097-1106.
57. van Brussel AAN, Planqué K, Quispel A, (1977) The wall of Rhizobium leguminosarum in bacteroid and free-living forms. J Gen Microbiol 101: 51-56.
58. Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, et al. (2006) EGassembler: online bioinformatics service for large-scale processing, clustering and assembling EST's and genomic DNA fragments. Nucl Acids Res 34 (suppl 2): W459-W462.