Alphaproteobacteria

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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 most members of the Proteobacteria, most of its members are Gram-negative and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.[3][4]

Characteristics[edit]

The Alphaproteobacteria is a diverse order and comprises several phototrophic genera, several genera metabolising C1-compounds (e.g., Methylobacterium spp.), symbionts of plants (e.g., Rhizobium spp.), endosymbionts of arthopods (Wolbachia) and intracellular pathogens (eg. 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[edit]

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 (eg. 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[edit]

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



?FurvibacterLee et al. 2007



?Kopriimonas byunsanensisKwon et al. 2005



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



?Micavibrio aeruginosavorusLambina et al. 1983



?Polymorphum gilvumCai 2010



?Reyranella massiliensis Pagnier et al. 2011



?Ronia tepidophila



?Subaequorebacter tamlenseLee 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)

References[edit]

  1. ^ PubMed
  2. ^ a b c d e f g h PubMed
  3. ^ a b 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. ^ a b J.P. Euzéby. "Alphaproteobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN) [1]. Retrieved 2011-11-17. 
  5. ^ Chilton MD, Drummond MH, Merio DJ, Sciaky D, Montoya AL, Gordon MP, Nester EW., Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis, Cell. 1977 Jun;11(2):263-71.
  6. ^ PubMed
  7. ^ PubMed
  8. ^ PubMed
  9. ^ PubMed
  10. ^ PubMed
  11. ^ PubMed
  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: Protein signatures distinctive of Alphaproteobacteria and its subgroups and a model for Alpha proteobacterial evolution. Crit Rev Microbiol 2005, 31: 135. PMID 15986834
  14. ^ Gupta, R.S. (2000) Phylogeny of Proteobacteria: Relationships to other eubacterial phyla and to eukaryotes. FEMS Microbiol. Rev. 24: 367-402.
  15. ^ Gupta, R.S. and 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: 90-100.
  16. ^ Sayers et al. "Alphaproteobacteria". National Center for Biotechnology Information (NCBI) taxonomy database [2]. Retrieved 2011-06-05. 
  17. ^ 'The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)". Silva Comprehensive Ribosomal RNA Database [3]. Retrieved 2011-11-17. 

External links[edit]