5 research outputs found
Analysis of the genome and proteome composition of Bdellovibrio bacteriovorus: Indication for recent prey-derived horizontal gene transfer
AbstractThe genome/proteome composition of Bdellovibrio bacteriovorus, the predatory microorganism that preys on other Gram-negative bacteria, has been analyzed. The study elucidates that translational selection plays a major role in genome compositional variation with higher intensity compared to other deltaproteobacteria. Other sources of variations having relatively minor contributions are local GC-bias, horizontal gene transfer and strand-specific mutational bias. The study identifies a group of AT-rich genes with distinct codon composition that is presumably acquired by Bdellovibrio recently from Gram-negative prey-bacteria other than deltaproteobacteria. The proteome composition of this species is influenced by various physico-chemical factors, viz, alcoholicity, residue-charge, aromaticity and hydropathy. Cell-wall-surface-anchor-family (CSAPs) and transporter proteins with distinct amino acid composition and specific secondary-structure also contribute notably to proteome compositional variation. CSAPs, which are low molecular-weight, outer-membrane proteins with highly disordered secondary-structure, have preference toward polar-uncharged residues and cysteine that presumably help in prey-predator interaction by providing particular bonds of attachment
Comparative Codon and Amino Acid Composition Analysis of Tritryps-Conspicuous Features of Leishmania Major
Comparative analyses of codon/amino acid usage in
Leishmania major, Trypanosoma brucei and Trypanosoma cruzi
reveal that gene expressivity and GC-bias play key roles in shaping the gene composition of all three parasites, and protein composition of L. major only. In T. brucei and T. cruzi, the major contributors to the variation in protein composition are hydropathy and/or aromaticity. Principle of Cost Minimization is followed by T. brucei, disregarded by T. cruzi and opposed by L. major. Slowly evolving highly expressed gene-products of L. major bear signatures of relatively AT-rich ancestor, while faster evolution under GC-bias has characterized the lowly expressed genes of the species by higher GC12-conten
Proteome Composition in Plasmodium falciparum: Higher Usage of GC-Rich Nonsynonymous Codons in Highly Expressed Genes
The parasite Plasmodium falciparum,
responsible for the most deadly form of human malaria,
is one of the extremely AT-rich genomes sequenced
so far and known to possess many atypical
characteristics. Using multivariate statistical approaches,
the present study analyzes the amino acid
usage pattern in 5038 annotated protein-coding sequences
in P. falciparum clone 3D7. The amino acid
composition of individual proteins, though dominated
by the directional mutational pressure, exhibits
wide variation across the proteome. The Asn content,
expression level, mean molecular weight, hydropathy,
and aromaticity are found to be the major sources of
variation in amino acid usage. At all stages of
development, frequencies of residues encoded by GCrich
codons such as Gly, Ala, Arg, and Pro increase
significantly in the products of the highly expressed
genes. Investigation of nucleotide substitution patterns
in P. falciparum and other Plasmodium species
reveals that the nonsynonymous sites of highly expressed
genes are more conserved than those of the
lowly expressed ones, though for synonymous sites,
the reverse is true. The highly expressed genes are,
therefore, expected to be closer to their putative
ancestral state in amino acid composition, and a
plausible reason for their sequences being GC-rich at
nonsynonymous codon positions could be that their
ancestral state was less AT-biased. Negative correlation
of the expression level of proteins with respective molecular weights supports the notion that
P. falciparum, in spite of its intracellular parasitic
lifestyle, follows the principle of cost minimization