Alphaproteobacteria

Alphaproteobacteria is a class of

bacteria

in the phylum Proteobacteria (See also bacterial taxonomy). 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.

Characteristics

The Alphaproteobacteria are 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

). A species of technological interest is ''Rhizobium radiobacter'' (formerly ''Agrobacterium tumefaciens''): scientists often use this species to transfer foreign DNA into plant genomes. Aerobic anoxygenic phototrophic bacteria, such as ''Pelagibacter ubique'', are alphaproteobacteria that are a widely distributed and 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. The discord stems from the large difference in gene content (''e.g.'' genome streamlining in ''Pelagibacter ubique'') and the large difference in GC-content between members of several orders. Specifically, ''Pelagibacterales'', ''Rickettsiales'' and ''Holosporales'' contain 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. However, several studies disagree.

Furthermore, it has been found that the GC-content of ribosomal RNA (the traditional phylogenetic marker for prokaryotes) little reflects the GC-content of the genome. One example of this atypical decorrelation of ribosomal GC-content with phylogeny is that members of the '' Holosporales'' have a much higher ribosomal GC-content than members of the '' Pelagibacterales'' and ''Rickettsiales'', even though they are more closely related to species with high genomic GC-contents than to members of the latter two orders.

The Class ''Alphaproteobacteria'' is divided into three subclasses ''Magnetococcidae'', ''Rickettsidae'' and ''Caulobacteridae''. The basal group is ''Magnetococcidae'', which is composed by a large diversity of magnetotactic bacteria, but only one is described, ''Magnetococcus marinus''. 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 insertion-deletions (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. 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''.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S rRNA

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