4 research outputs found
Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes
Background: The study of survival and communication of pathogenic bacteria is important to combat diseases
caused by such micro-organisms. Bacterial cells communicate with each other using a density-dependent cell-cell
communication process called Quorum Sensing (QS). LuxS protein is an important member of interspecies quorumsensing
system, involved in the biosynthesis of Autoinducer-2 (AI-2), and has been identified as a drug target.
Despite the above mentioned significance, their evolution has not been fully studied, particularly from a structural
perspective.
Results: Search for LuxS in the non-redundant database of protein sequences yielded 3106 sequences. Phylogenetic
analysis of these sequences revealed grouping of sequences into five distinct clusters belonging to different phyla and
according to their habitat. A majority of the neighbouring genes of LuxS have been found to be hypothetical proteins.
However, gene synteny analyses in different bacterial genomes reveal the presence of few interesting gene
neighbours. Moreover, LuxS gene was found to be a component of an operon in only six out of 36 genomes. Analysis
of conserved motifs in representative LuxS sequences of different clusters revealed the presence of conserved motifs
common to sequences of all the clusters as well as motifs unique to each cluster. Homology modelling of LuxS protein
sequences of each cluster revealed few structural features unique to protein of each cluster. Analyses of surface
electrostatic potentials of the homology models of each cluster showed the interactions that are common to all the
clusters, as well as cluster-specific potentials and therefore interacting partners, which may be unique to each cluster.
Conclusions: LuxS protein evolved early during the course of bacterial evolution, but has diverged into five subtypes.
Analysis of sequence motifs and homology models of representative members reveal cluster-specific structural
properties of LuxS. Further, it is also shown that LuxS protein may be involved in various protein-protein or proteinRNA
interactions, which may regulate the activity of LuxS proteins in bacteria
Revisiting Myosin Families through Large-scale Sequence Searches Leads to the Discovery of New Myosins
Myosins are actin-based motor proteins involved in many cellular movements. It is interesting to study the evolutionary patterns and the functional attributes of various types of myosins. Computational search algorithms were performed to identify putative myosin members by phylogenetic analysis, sequence motifs, and coexisting domains. This study is aimed at understanding the distribution and the likely biological functions of myosins encoded in various taxa and available eukaryotic genomes. We report here a phylogenetic analysis of around 4,064 myosin motor domains, built entirely from complete or near-complete myosin repertoires incorporating many unclassified, uncharacterized sequences and new myosin classes, with emphasis on myosins from Fungi, Haptophyta, and other Stramenopiles, Alveolates, and Rhizaria (SAR). The identification of large classes of myosins in Oomycetes, Cellular slime molds, Choanoflagellates, Pelagophytes, Eustigmatophyceae, Fonticula, Eucoccidiorida, and Apicomplexans with novel myosin motif variants that are conserved and thus presumably functional extends our knowledge of this important family of motor proteins. This work provides insights into the distribution and probable function of myosins including newly identified myosin classes