Alphaproteobacteria

Alphaproteobacteria
Transmission electron micrograph of Wolbachia within an insect cell.
Credit:Public Library of Science / Scott O'Neill
Scientific classification
Domain: Bacteria
Phylum: Proteobacteria
Class: Alphaproteobacteria
Garrity et al. 2006
subclasses

Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria (See also bacterial taxonomy).[3] Its members are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all Proteobacteria, its members are Gram-negative and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.[3][4]

Characteristics

The Alphaproteobacteria is a diverse taxon and comprises several phototrophic genera, several genera metabolising C1-compounds (e.g., Methylobacterium spp.), symbionts of plants (e.g., Rhizobium spp.), endosymbionts of arthropods (Wolbachia) and intracellular pathogens (e.g. Rickettsia). Moreover, the class includes (as an extinct member) the protomitochondrion, the bacterium that was engulfed by the eukaryotic ancestor and gave rise to the mitochondria, which are organelles in eukaryotic cells (See endosymbiotic theory).[2] A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes.[5] Aerobic anoxygenic phototrophic bacteria, such as Pelagibacter ubique, are alphaproteobacteria that are a widely distributed marine plankton that may constitute over 10% of the open ocean microbial community.

Evolution and genomics

There is some disagreement on the phylogeny of the orders, especially for the location of the Pelagibacterales, but overall there is some consensus. This issue stems form the large difference in gene content (e.g. genome streamlining in Pelagibacter ubique) and the large difference in GC-richness between members of several order.[2] Specifically,Pelagibacterales, Rickettsiales and Holosporales contains species with AT-rich genomes. It has been argued that it could be a case of convergent evolution that would result in an artefactual clustering.[6][7][8] However, several studies disagree,.[2][9][10][11] Furthermore, it has been found that the GC-content of ribosomal RNA, the traditional phylogenetic marker, little reflects the GC-content of the genome: for example, members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales, which have similarly low genomic GC-content, because they are more closely related to species with high genomic GC-contents than to members of the latter two orders[2]

The Class Alphaproteobacteria is divided into three subclasses Magnetococcidae, Rickettsidae and Caulobacteridae.[2] The basal group is Magnetococcidae, which is composed by a large diversity of magnetotactic bacteria, but only one is described, Magnetococcus marinus.[12] The Rickettsidae is composed of the intracellular Rickettsiales and the free-living Pelagibacterales. The Caulobacteridae is composed of the Holosporales, Rhodospirillales, Sphingomonadales, Rhodobacterales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales.

Comparative analyses of the sequenced genomes have also led to discovery of many conserved indels in widely distributed proteins and whole proteins (i.e. signature proteins) that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae). These molecular signatures provide novel means for the circumscription of these taxonomic groups and for identification/assignment of new species into these groups.[13] Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and Classes of Bacteria except Betaproteobacteria and Gammaproteobacteria.[14][15]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [4] and National Center for Biotechnology Information (NCBI)[16] and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project [17]

?Aquaspirillum polymorphum ♠ (Williams and Rittenberg 1957) Hylemon et al. 1973

?Furvibacter ♠ Lee et al. 2007

?Kopriimonas byunsanensis ♠ Kwon et al. 2005

?Magnetococcus marinus Bazylinski et al. 2012 (in press)

?Micavibrio aeruginosavorus ♠ Lambina et al. 1983

?Polymorphum gilvum ♠ Cai 2010

?Reyranella massiliensis Pagnier et al. 2011

?Ronia tepidophila ♠



?Subaequorebacter tamlense ♠ Lee 2006

?Tuberoidobacter mutans ♠



?Vibrio adaptatus Muir et al. 1990

?Vibrio cyclosites Muir et al. 1990

Rhodovibrio

Rhodospirillaceae 2


Tistrella

Rhodospirillaceae 3

Rhodospirillaceae 4

Defluviicoccus vanus Maszenan et al. 2005

Elioraea tepidiphila Albuquerque et al. 2008

Acetobacteraceae

Rickettsiales [incl. Mitochondrion]

Sneathiella

Sphingomonadaceae [incl. Erythrobacteraceae, Caulobacter leidyi, Asticcacaulis]


Rhodothalassium salexigens (Drews 1982) Imhoff et al. 1998

Kordiimonas

Rhodospirillaceae 1 [incl. Roseospirillum parvum, Kiloniella laminariae, Terasakiella pusilla]

Rhizobiales [incl. Caulobacteraceae, Rhodobacteraceae, Parvularcula & Streptomyces longisporoflavus]










Notes:
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN)

Natural genetic transformation

Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens,[18] Methylobacterium organophilum,[19] and Bradyrhizobium japonicum.[20] Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium, and the integration of the donor sequence into the recipient genome by homologous recombination.

References

  1. ↑ "Streamlining and core genome conservation among highly divergent members of the SAR11 clade.". MBio. 3 (5): e00252–12. 2012. doi:10.1128/mBio.00252-12. PMC 3448164Freely accessible. PMID 22991429.
  2. 1 2 3 4 5 6 7 8 "New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability". PLOS ONE. 8 (12): e83383. 2013. doi:10.1371/journal.pone.0083383. PMC 3859672Freely accessible. PMID 24349502.
  3. 1 2 Brenner, Don J.; Krieg, Noel R.; Staley, James T. (July 26, 2005) [1984(Williams & Wilkins)]. George M. Garrity, ed. The Proteobacteria. Bergey's Manual of Systematic Bacteriology. 2C (2nd ed.). New York: Springer. p. 1388. ISBN 978-0-387-24145-6. British Library no. GBA561951.
  4. 1 2 J.P. Euzéby. "Alphaproteobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2011-11-17.
  5. ↑ Chilton MD, Drummond MH, Merio DJ, Sciaky D, Montoya AL, Gordon MP, Nester EW (1977). "Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis". Cell. 11 (2): 263–71. doi:10.1016/0092-8674(77)90043-5. PMID 890735.
  6. ↑ "The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria.". PLOS ONE. 7 (1): e30520. 2012. doi:10.1371/journal.pone.0030520. PMC 3264578Freely accessible. PMID 22291975.
  7. ↑ "Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade.". Mol Biol Evol. 29 (2): 599–615. Feb 2012. doi:10.1093/molbev/msr203. PMID 21900598.
  8. ↑ "Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade.". PLOS ONE. 8 (11): e78858. 2013. doi:10.1371/journal.pone.0078858. PMC 3815206Freely accessible. PMID 24223857.
  9. ↑ "Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion.". PLOS ONE. 6 (9): e24857. 2011. doi:10.1371/journal.pone.0024857. PMC 3177885Freely accessible. PMID 21957463.
  10. ↑ "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade.". Sci Rep. 1: 13. 2011. doi:10.1038/srep00013. PMID 22355532.
  11. ↑ Williams KP, Sobral BW, Dickerman AW (July 2007). "A robust species tree for the alphaproteobacteria". Journal of Bacteriology. 189 (13): 4578–86. doi:10.1128/JB.00269-07. PMC 1913456Freely accessible. PMID 17483224.
  12. ↑ Bazylinski DA, Williams TJ, Lefèvre CT, Berg RJ, Zhang CL, Bowser SS, Dean AJ, Beveridge TJ. (2012) Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov.; Magnetococcales ord. nov.) at the base of the Alphaproteobacteria. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.038927-0
  13. ↑ Gupta RS (2005). "Protein signatures distinctive of Alphaproteobacteria and its subgroups and a model for Alpha proteobacterial evolution". Crit Rev Microbiol. 31 (2): 135. doi:10.1080/10408410590922393. PMID 15986834.
  14. ↑ Gupta R.S. (2000). "Phylogeny of Proteobacteria: Relationships to other eubacterial phyla and to eukaryotes". FEMS Microbiol. Rev. 24 (4): 367–402. doi:10.1111/j.1574-6976.2000.tb00547.x. PMID 10978543.
  15. ↑ Gupta R.S.; Sneath P.H.A. (2007). "Application of the Character compatibility approach to generalized molecular sequence data: Branching order of the Proteobacterial subdivisions". J. Mol. Evol. 64 (1): 90–100. doi:10.1007/s00239-006-0082-2.
  16. ↑ Sayers; et al. "Alphaproteobacteria". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2011-06-05.
  17. ↑ 'The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2011-11-17.
  18. ↑ Demanèche S, Kay E, Gourbière F, Simonet P (2001). "Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil". Appl. Environ. Microbiol. 67 (6): 2617–21. doi:10.1128/AEM.67.6.2617-2621.2001. PMC 92915Freely accessible. PMID 11375171.
  19. ↑ O'Connor M, Wopat A, Hanson RS (1977). "Genetic transformation in Methylobacterium organophilum". J. Gen. Microbiol. 98 (1): 265–72. doi:10.1099/00221287-98-1-265. PMID 401866.
  20. ↑ Raina JL, Modi VV (1972). "Deoxyribonucleate binding and transformation in Rhizobium jpaonicum". J. Bacteriol. 111 (2): 356–60. PMC 251290Freely accessible. PMID 4538250.

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