# Protein Signatures Distinctive of Alpha Proteobacteria and Its Subgroups and a Model for α –Proteobacterial Evolution

@article{Gupta2005ProteinSD,
title={Protein Signatures Distinctive of Alpha Proteobacteria and Its Subgroups and a Model for $\alpha$ –Proteobacterial Evolution},
journal={Critical Reviews in Microbiology},
year={2005},
volume={31},
pages={101 - 135}
}
• Radhey S. Gupta
• Published 1 January 2005
• Biology, Medicine
• Critical Reviews in Microbiology
Alpha (α) proteobacteria comprise a large and metabolically diverse group. No biochemical or molecular feature is presently known that can distinguish these bacteria from other groups. The evolutionary relationships among this group, which includes numerous pathogens and agriculturally important microbes, are also not understood. Shared conserved inserts and deletions (i.e., indels or signatures) in molecular sequences provide a powerful means for identification of different groups in clear…
Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups
The use of these signatures in conjunction with phylogenomic analyses, summarized here, is leading to a holistic picture concerning the branching order and evolutionary relationships among the above groups of photosynthetic bacteria.
Signature proteins that are distinctive of alpha proteobacteria
• Biology, Medicine
BMC Genomics
• 2005
The identified proteins provide novel means for defining and identifying the α-proteobacteria and many of its subgroups in clear molecular terms and in understanding the evolution of this group of species.
Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups
• Biology, Medicine
Antonie van Leeuwenhoek
• 2006
The analyses have identified 233 actinobacteria-specific proteins, homologues of which are generally not present in any other bacteria, which provide novel molecular means for defining and circumscribing the Actinob bacteria phylum and a number of subgroups within it.
Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups
• Biology, Medicine
BMC Microbiology
• 2007
The α-proteobacteria-specific proteins and indels described here provide novel and powerful means for the taxonomic, biochemical and molecular biological studies on these bacteria.
Evolutionary placement of Xanthomonadales based on conserved protein signature sequences.
• Biology, Medicine
Molecular phylogenetics and evolution
• 2010
The data presented clearly support the Xanthomonadales group as an independent subdivision, and constitute one of the deepest branching lineage within the gamma-proteobacteria clade.
Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades
• Biology, Medicine
Antonie van Leeuwenhoek
• 2011
The identification of two distinct clades within the Pasteurellales, which are supported by both phylogenetic analyses and by multiple highly specific molecular markers, strongly argues for and provides potential means for the division of various genera from this order into a minimum of two families.
Chapter 8 – Identification of Conserved Indels that are Useful for Classification and Evolutionary Studies
The usefulness of CSIs for evolutionary and systematic studies is discussed and the methods that are being used to discover them are described, and how the results obtained from these studies should be interpreted are described.
Molecular signatures in protein sequences that are characteristics of the phylum Aquificae.
• Biology, Medicine
International journal of systematic and evolutionary microbiology
• 2006
Six conserved inserts and deletions (indels or signature sequences) in four widely distributed proteins that are distinctive features of species from the phylum Aquificae are described and may prove useful for functional studies aimed at understanding the unique biochemical and physiological characteristics of these species.
A new alpha-proteobacterial clade of Bdellovibrio-like predators: implications for the mitochondrial endosymbiotic theory.
• Biology, Medicine
Environmental microbiology
• 2006
A scenario based on the BALO feeding-mode is proposed to hypothesize a mechanism at play at the origin of the mitochondrial endosymbiosis, and suggests that their peculiar mode of parasitism maybe an ancestral character in this proteobacterial class.
dnaJ is a useful phylogenetic marker for alphaproteobacteria.
• Biology, Medicine
International journal of systematic and evolutionary microbiology
• 2008
It is suggested that the dnaJ gene is a good phylogenetic marker, particularly for the class Alphaproteobacteria, since its phylogeny is consistent with phylogenies based on multilocus approaches.

## References

SHOWING 1-10 OF 129 REFERENCES
The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes.
• R. Gupta
• Biology, Medicine
FEMS microbiology reviews
• 2000
An unexpected but important aspect of the relationship deduced here is that the main eubacterial phyla are related to each other linearly rather than in a tree-like manner, suggesting that the major evolutionary changes within Bacteria have taken place in a directional manner.
Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes
• Radhey S. Gupta
• Biology, Medicine
Microbiology and Molecular Biology Reviews
• 1998
Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria and suggests that this evolution occurred in response to antibiotic selection pressures, and an alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed.
The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins
• R. Gupta
• Biology, Medicine
International microbiology : the official journal of the Spanish Society for Microbiology
• 2001
The results strongly vindicate the usefulness of the signature sequence approach to understanding phylogeny within the Bacteria and show that it provides a reliable and internally consistent means for the placement of bacterial species into different groups and for determining the relative branching order of the groups.
Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales.
• Biology, Medicine
International microbiology : the official journal of the Spanish Society for Microbiology
• 2004
The results provide strong and consistent evidence that the Aquificales diverged after the branching of Firmicutes, Actinob bacteria, Thermotoga, Deinococcus-Thermus, green nonsulfur bacteria, Cyanobacteria, Spirochetes, Chlamydiae, and CFBG group, but before the emergence of the Proteobacteria.
The Phylogeny and Signature Sequences Characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes
Signatures in a number of other proteins provide evidence that the FCB group of bacteria diverged at a similar time as the Chlamydiae group, and that the Spirochetes and Aquificales groups are its closest relatives.
Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum
• Medicine, Biology
Journal of bacteriology
• 2004
The presence of these signatures in various species from all three known genera within this phylum, viz., Deinococcus, Thermus, and Meiothermus, provide evidence that they are likely distinctive characteristics of the entire phylum which were introduced in a common ancestor of this group.
Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons.
• Biology, Medicine
International journal of systematic bacteriology
• 1994
The general observations suggest that GroEL proteins provide valuable evolutionary tools for defining evolutionary relationships among the eubacterial lineage of life.
The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species
• J. Eisen
• Biology, Medicine
Journal of Molecular Evolution
• 2004
Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust and have similar resolving power for close, medium, and deep branches in the history of bacteria.
Evolutionary relationships among photosynthetic bacteria
All main groups within bacteria can now be defined in clear molecular terms and their relative branching orders logically deduced using the indel model.
Critical issues in bacterial phylogeny.
• Biology, Medicine
Theoretical population biology
• 2002
A new approach, based on shared conserved inserts and deletions (indels or signature sequences) found in various proteins, that provides a reliable and internally consistent means for understanding various critical and long outstanding issues in bacterial phylogeny.