Alphaproteobacteria

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 (biology) 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]

Contents

  • Characteristics 1
  • Evolution and genomics 2
  • Phylogeny 3
  • References 4
  • External links 5

Characteristics

The Alphaproteobacteria is a diverse order and comprises several 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


?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

  1. ^ "Streamlining and core genome conservation among highly divergent members of the SAR11 clade.". MBio 3 (5): e00252–12. 2012.  
  2. ^ a b c d e f g h "New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability.". PLOS ONE 8 (12): e83383. 2013.  
  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.  
  4. ^ a b J.P. Euzéby. "Alphaproteobacteria".  
  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.  
  6. ^ "The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria.". PLOS ONE 7 (1): e30520. 2012.  
  7. ^ "Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade.". Mol Biol Evol 29 (2): 599–615. Feb 2012.  
  8. ^ "Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade.". PLOS ONE 8 (11): e78858. 2013.  
  9. ^ "Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion.". PLOS ONE 6 (9): e24857. 2011.  
  10. ^ "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade.". Sci Rep 1: 13. 2011.  
  11. ^ Williams KP, Sobral BW, Dickerman AW (July 2007). "A robust species tree for the alphaproteobacteria". Journal of Bacteriology 189 (13): 4578–86.  
  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.  
  14. ^ Gupta R.S. (2000). "Phylogeny of Proteobacteria: Relationships to other eubacterial phyla and to eukaryotes". FEMS Microbiol. Rev. 24 (4): 367–402.  
  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.  
  16. ^ Sayers; et al. "Alphaproteobacteria".  
  17. ^  

External links

  • Alphaproteobacteria at the US National Library of Medicine Medical Subject Headings (MeSH)
  • Bacterial (Prokaryotic) Phylogeny Webpage: Alpha Proteobacteria.