Mutational drift prevails over translational efficiency in Frankia nif operons

321-328Frankia is a Gram-positive actinomycete, fixing atmospheric nitrogen while making associations with a number of dicotyledonous plants. The most important operon of Frankia is the nif operon. Codon usage bias was investigated in three open reading frames and known genes of this organism from three different strains. Genes and ORFs show high biasness due to mutation pressure. Based on our results we conclude that mutational drift is more relevant over translational efficiency. The nif genes showed fairly high expression levels. Analysis of the result of codon indices and BLAST searches revealed that ORF3 might be a good candidate for expression

Proteome analysis reveals the influence of isoelectric point and amino acid usages on the lifestyle of nitrogen fixing microorganisms

88-97Biological nitrogen fixation is an important phenomenon in the ecosystem of our planet. Increasing number of complete proteomes for nitrogen fixing organisms has given scope to recognize characteristic features of protein functionality linked to nitrogen fixation and nature of the proteome. Physico-chemical aspects like isoelectric point (pI), protein energetic cost, aromaticity, hydropathicity and amino-acid adaptation index are significant in portraying the functions of microbes. The present work aims to recognize diversity in amino-acid usage patterns to understand the forces influencing them and to investigate association of pI with lifestyle of the organisms shaping its role in manipulating diversity across proteomes. Combination of in silico tools like DAMBE and CodonW were used for comparative analysis of properties and amino acid usage. Distributions of pI across different COGs (Cluster of orthologous groups) were compared. Proteomes of nitrogen fixing organisms show diversity at the interspecific and intraspecific level with tri-modal distribution for pI. Nitrogen fixation related proteins are more acidic in contrast to whole proteomes. Analysis of pI across COGs throws light upon the variation and lifestyle of organisms and substantiates the role of pI as a molecular signature. Proteomes show a shift towards acidity and are influenced by habitat and environmental adaptations. Acidic residues in COG functional groups belonging to cellular processes (Cp), metabolism (Me) and information storage and processing (Isp) play a significant role in shaping proteomes of nitrogen fixers. Methanogens and aquatic free living nitrogen fixing organisms are more acidic than others. Higher amino acid adaptation index (AAAI) values of proteomes imply their better adaptability in shaping frequency of amino acids. Hydropathicity and aromaticity are relevant for evaluating amino acid usage in these organisms

Role of Zinc in tRNA-acceptor Stem Binding by Glutamyl-tRNA Synthetase From E.coli: A Molecular Modeling Study

A model of the N-terminal half of glutamyl-tRNA synthetase from E. coli was constructed on the basis of similarity in sequence and function of Glutaminyl- and Glutamyl-tRNA synthetases. The glutaminyl-tRNA synthetase does not contain any zinc atom, but glutamyl-tRNA synthetase from E. coli contains one atom of zinc. The specific role of zinc is not yet known. In this article, molecular modeling is employed to show that the zinc atom is well outside the contact region of the acceptor stem of tRNA. The placement of a zinc atom at a significant distance from the tRNA acceptor stem indicates that the role of zinc is likely to be indirect and structural

Molecular Dynamics Simulation of Colchicinoids

Colchicine, a tricyclic alkaloid, has a remarkable range of biological activities. It binds with tubulin and prevents the formation of microtubules. This compound consists of a six membered aromatic ring (A ring), a seven membered troponoid ring (C ring) and another seven membered aliphatic ring (B ring). Using molecular mechanics and molecular dynamics simulations as tools, conformational analysis of colchicine and its several important analogs were done. Molecular mechanics studies show that conformational space of these molecules have one low energy region. Taking the low energy minima as the starting conformation, molecular dynamics simulation for 100 pico seconds is done for each of the analogs and molecular dynamics simulation in solution is done for three representative compounds colchicine, isocolchicine and A-C compound. Internal coordinate trajectories show that the value of the dihedral angle C9-C7-C1-C14 (phi), (C7-C1 bond connects the A and C ring), is within 40° to 50° for all the compounds with fluctuations less than 15°. These calculations indicate that there is an overall similarity in the dynamically averaged structure of all the drugs. The A ring and B ring of the compounds are more or less rigid. The C ring is somewhat flexible, the average conformation and motional properties show overall similarity. The potential energy curve and dynamics behaviour of colchicine and isocolchicine suggests that the difference in binding property of colchine and isocolchicine may originate from the positional difference of carbonyl oxygen and methoxy group of C ring, which is the only difference in the structures of the two compounds and this has no effect on the motional property and average conformations of these two compounds. From our study it is proposed that the movements occuring at various positions of the drug molecules are significantly correlated. It is suggested that such correlated motion may play an important role in the biological property of these compounds

Codon Count

The total codon counts for each of the 71 organsim per pathway

Codon pair ratio

The pathway/system -wise codon pair ratio data for all the species generated using Anaconda

All 71 genomes 5 pathways

This archive contains the different codon usage indices value for all the 71 species calculated separately for each of the five pathway systems and curated individually

Data from: Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly

A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature

Characterization of pseudogenes in members of the order Frankineae

Pseudogenes are defined as non-functional relatives of genes whose protein-coding abilities are lost and are no longer expressed within cells. They are an outcome of accumulation of mutations within a gene whose end product is not essential for survival. Proper investigation of the procedure of pseudogenization is relevant for estimating occurrence of duplications in genomes. Frankineae houses an interesting group of microorganisms, carving a niche in the microbial world. This study was undertaken with the objective of determining the abundance of pseudogenes, understanding strength of purifying selection, investigating evidence of pseudogene expression, and analysing their molecular nature, their origin, evolution and deterioration patterns amongst domain families. Investigation revealed the occurrence of 956 core pFAM families sharing common characteristics indicating co-evolution. WD40, Rve_3, DDE_Tnp_IS240 and phage integrase core domains are larger families, having more pseudogenes, signifying a probability of harmful foreign genes being disabled within transposable elements. High selective pressure depicted that gene families rapidly duplicating and evolving undoubtedly facilitated creation of a number of pseudogenes in Frankineae. Codon usage analysis between protein-coding genes and pseudogenes indicated a wide degree of variation with respect to different factors. Moreover, the majority of pseudogenes were under the effect of purifying selection. Frankineae pseudogenes were under stronger selective constraints, indicating that they were functional for a very long time and became pseudogenes abruptly. The origin and deterioration of pseudogenes has been attributed to selection and mutational pressure acting upon sequences for adapting to stressed soil environments

In silico Analysis of Chlorobium Genomes Divulge Insights into the Lifestyle of the Bacteria

The finished sequences of three Chlorobium genomes were examined and compared to each other for their synonymous codon usage. Codon usage by Chlorobium was moderately biased but a considerable amount of variation was observed. GC3 composition plays an important role in the codon usage variation among the genes in the studied genomes. Similar homologs of horizontally transferred nitrogen fixing and photosynthesis related genes having high identity levels indicated their co-evolution within the genus. Correlation of codon usage bias with tRNA content in Chlorobium genomes revealed the inability of the translation machinery in these bacteria to co-evolve with higher codon usage resulting in moderate bias. Arrangement of the genes in leading strand and lagging strand of replication had virtually no role in influencing synonymous codon usage variation in these bacteria. Whole genome alignment revealed the conserved nature of the genomes. Using codon adaptation index, a set of potentially highly expressed genes in Chlorobium was determined taking ribosomal protein genes as a reference. A sizeable fraction of the potentially highly expressed (PHX) genes in the COG categories were related to metabolism. Quite fascinatingly, some of the genes associated with nitrogen fixation and photosynthesis like hydrogenases, nitrogenase iron protein complexes, bacteriochlorophylls, chlorosomes etc. were also PHX. These results offer insights into the survival patterns of these bacteria thriving under stressed conditions and efficiently carrying out two important metabolic processes especially under reduced light and anoxic environments