Proteobacteria is broadly divided in different groups–alpha,beta, gamma, delta, epsilon, and zeta. Evolution shows that beta and gamma are paralogous and considered unique as compared to other members. Moreover, focusing precisely on the cell division machinary, again both these groups (beta and gamma) have unique proteins that lack any reportable homologs in other groups. So what makes beta and or gammaproteobacteria unique? Is this related to adaptive evolution as they are relatively "younger" than others. Or is there any other specific reason for this, as cell division is a fundamental process and should be highly conserved. What could be the reason for inclusion of unique or species specific members.?
The class Gammaproteobacteria - one of the largest groups within bacteria, is currently distinguished from other bacteria solely on the basis of its branching in phylogenetic trees. No biochemical characteristic is known that is unique to the class Gammaproteobacteria or its different subgroups (orders). The analyses by Gao B, Mohan R, Gupta RS. ( Phylogenomics and protein signatures elucidating the
evolutionary relationships among the Gammaproteobacteria. Int J Syst Evol
Microbiol. 2009 Feb;59(Pt 2):234-47. doi: 10.1099/ijs.0.002741-0). identified 75 proteins that were unique to most members of the class Gammaproteobacteria
yes i am aware of prof gupta's work. But as i have mentioned the eg of cell division protein that are unique to this order, why such difference especially to such a fundamental process majority of the proteins are conserved
Manan,
1) Any taxonomical system is artificial and build based on analysis of small part of genotype and phenotype properties. Use of complete genome analysis sometimes show disagreement to SSU or MLST phylogenetic tree. But, large part of genes in bacterial genome has still unkown function, so we cannot compare two strains in content of their functional homologues. So, "true" gama proteobacteria can include some distant linages and closely related groups can be included into other taxons.
2) The difference between gamma and betta proteobacteria is not always obvious. For instance Xanthomonas and Ralstonia have a lot of similar genetic properties.
3) We hardly can find one gene or operon unique to gamma proteobacteria. Some works show presence of regulons typical for this group of bacteria:
1: Augustus AM, Spicer LD. The MetJ regulon in gammaproteobacteria determined by
comparative genomics methods. BMC Genomics. 2011 Nov 14;12:558. doi:
10.1186/1471-2164-12-558. PubMed PMID: 22082356; PubMed Central PMCID:
PMC3228920.
2: Ravcheev DA, Gel'fand MS, Mironov AA, Rakhmaninova AB. [Purine regulon of
gamma-proteobacteria: a detailed description]. Genetika. 2002 Sep;38(9):1203-14.
Russian. PubMed PMID: 12391881.
3: Suvorova IA, Tutukina MN, Ravcheev DA, Rodionov DA, Ozoline ON, Gelfand MS.
Comparative genomic analysis of the hexuronate metabolism genes and their
regulation in gammaproteobacteria. J Bacteriol. 2011 Aug;193(15):3956-63. doi:
10.1128/JB.00277-11. Epub 2011 May 27. PubMed PMID: 21622752; PubMed Central
PMCID: PMC3147527.
4: Rodionov DA, Gelfand MS, Hugouvieux-Cotte-Pattat N. Comparative genomics of
the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria.
Microbiology. 2004 Nov;150(Pt 11):3571-90. PubMed PMID: 15528647.
5: Rodionov DA, Gelfand MS, Mironov AA, Rakhmaninova AB. Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in
gamma-proteobacteria. J Mol Microbiol Biotechnol. 2001 Apr;3(2):319-24. PubMed
PMID: 11321589.
I would consider tonB genes and tonB-dependent receptors system as unique and very important for aquatic life of gammaproteobactera:
Blanvillain S, Meyer D, Boulanger A, Lautier M, Guynet C, Denancé N, Vasse J,
Lauber E, Arlat M. Plant carbohydrate scavenging through tonB-dependent
receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS One.
2007 Feb 21;2(2):e224.
Considering the idea about quasispecies that are large groups of related genotypes that exist in an environment of high mutation rate, where a large fraction of offspring are expected to contain mutations\gene gain or gene deletion relative to the parent, it is possible to say, that bacteria in one taxone must have a common mechanism that reduce horizontal gene transfer from distant organisms but allow it for close relatives.
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