PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families

Oruganty, Krishnadev; Rekha, Nambudiry; Pandit, Shashi Bhushan; Abhiman, Saraswathi; Mohanty, Smita; Swapna, Lakshmipuram S.; Gore, Swanand; Srinivasan, Narayanaswamy

doi:10.1093/nar/gki474

Cited by 10 publications

(5 citation statements)

References 39 publications

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“…Domain architectures have been also used to detect homology between multidomain protein families and were shown to achieve a very good performance. 18,19 For example, Krishnamurthy et al 20 clustered sequences sharing similar domain architectures to detect homologous proteins while the method introduced by Krishnadev et al 21 allowed identification of circular permutations in the evolution of multidomain protein families.…”

Section: Introductionmentioning

confidence: 99%

Evolution of domain promiscuity in eukaryotic genomes—a perspective from the inferred ancestral domain architectures

et al. 2011

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Most eukaryotic proteins are composed of two or more domains. These assemble in a modular manner to create new proteins usually by the acquisition of one or more domains to an existing protein. Promiscuous domains which are found embedded in a variety of proteins and co-exist with many other domains are of particular interest and were shown to have roles in signaling pathways and mediating network communication. The evolution of domain promiscuity is still an open problem, mostly due to the lack of sequenced ancestral genomes. Here we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. We find an increase in average promiscuity along many branches of the eukaryotic tree. Moreover, domain promiscuity can proceed at almost a steady rate over long evolutionary time or exhibit lineage-specific acceleration. We also observe that many signaling and regulatory domains gained domain promiscuity around the Bilateria divergence. In addition we show that those domains that played a role in the creation of two body axes and existed before the divergence of the bilaterians from fungi/metazoan achieve a boost in their promiscuities during the bilaterian evolution.

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Section: Introductionmentioning

confidence: 99%

Evolution of domain promiscuity in eukaryotic genomes—a perspective from the inferred ancestral domain architectures

et al. 2011

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“…Two parameters were employed to estimate sequence divergence: variability in composition and order of sequence domains and percent sequence identity. Pfam [ 10 ] domain assignments of the different subunits of RNA polymerase complex of bacterial organisms with known genome sequences were extracted from the PRODOC [ 11 ] database. Greater than 100 sequences were obtained for alpha (121), beta (138) and betaprime (127) subunits each.…”

Section: Methodsmentioning

confidence: 99%

Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly

Swapna¹,

Rekha²,

Srinivasan³

2012

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Evolutionarily divergent proteins have been shown to change their interacting partners. RNA polymerase assembly is one of the rare cases which retain its component proteins in the course of evolution. This ubiquitous molecular assembly, involved in transcription, consists of four core subunits (alpha, beta, betaprime, and omega), which assemble to form the core enzyme. Remarkably, the orientation of the four subunits in the complex is conserved from prokaryotes to eukaryotes although their sequence similarity is low. We have studied how the sequence divergence of the core subunits of RNA polymerase is accommodated in the formation of the multi-molecular assembly, with special reference to eubacterial species. Analysis of domain composition and order of the core subunits in >85 eubacterial species indicates complete conservation. However, sequence analysis indicates that interface residues of alpha and omega subunits are more divergent than those of beta, betaprime, and sigma70 subunits. Although beta and betaprime are generally well-conserved, residues involved in interaction with divergent subunits are not conserved. Insertions/deletions are also observed near interacting regions even in case of the most conserved subunits, beta and betaprime. Homology modelling of three divergent RNA polymerase complexes, from Helicobacter pylori, Mycoplasma pulmonis and Onion yellows phytoplasma, indicates that insertions/deletions can be accommodated near the interface as they generally occur at the periphery. Evaluation of the modeled interfaces indicates that they are physico-chemically similar to that of the template interfaces in Thermus thermophilus, indicating that nature has evolved to retain the obligate complex in spite of substantial substitutions and insertions/deletions.

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“…Detecting a fusion event of a protein of unknown function with a sequence involved in a known metabolic pathway or regulatory network may accordingly help to narrow the possibilities of its putative functions and thus facilitate hypothesis building. Many computational approaches to detect such gene fusion events were undertaken in the past [80][81][82]. FusionDB is a public database that allows detecting such gene fusion events [83,84].…”

Section: Fusiondbmentioning

confidence: 99%

The Role of the COG Database in Comparative and Functional Genomics

Kaufmann

2006

CBIO

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A major breakthrough in classifying proteins from different microbial genomes in terms of sequence similarity was the development of the COG concept by Tatusov et al. in 1997. The authors defined clusters of orthologous groups of proteins (COGs) by strictly applying all against all BLAST alignments of protein sequences from completely sequenced microbial genomes. The latest update of the COG database already covered 66 microbial genomes and additionally included the KOG database, an equivalent consisting of seven eukaryotic genomes. Although excellent web-based software tools designed to analyze this huge amount of data were initially provided by the authors, many other groups independently developed more specialized or extended programs making use of COG data for diverse purposes. Here a brief introduction is given to the concept behind COGs and their potentials in the field of comparative and functional genomics are discussed. The review then is focused on the multitude of recently developed web services aimed at mining the COG database. Their capabilities to solve diverse problems in biochemistry are addressed. In order to illustrate the broad field of possible applications, a compilation of recently published findings, implementing information derived from comparative genomics with emphasis on data retrieved from the COG database, is given.

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PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families

Cited by 10 publications

References 39 publications

Evolution of domain promiscuity in eukaryotic genomes—a perspective from the inferred ancestral domain architectures

Evolution of domain promiscuity in eukaryotic genomes—a perspective from the inferred ancestral domain architectures

Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly

The Role of the COG Database in Comparative and Functional Genomics

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