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Proteome Composition in Plasmodium falciparum: Higher Usage of GC-Rich Nonsynonymous Codons in Highly Expressed Genes

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Title Proteome Composition in Plasmodium falciparum: Higher Usage of GC-Rich
Nonsynonymous Codons in Highly Expressed Genes
 
Creator Chanda, Ipsita
Pan, Archana
Dutta, Chitra
 
Subject Molecular & Human Genetics
Structural Biology & Bioinformatics
 
Description 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.
 
Publisher Springer Verlag
 
Date 2005
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://www.eprints.iicb.res.in/319/1/fuJOURNAL_OF_MOLECULAR_EVOLUTION_61_(4_)_513%2D5232005[14].pdf
Chanda, Ipsita and Pan, Archana and Dutta, Chitra (2005) Proteome Composition in Plasmodium falciparum: Higher Usage of GC-Rich Nonsynonymous Codons in Highly Expressed Genes. Journal of Molecular Evolution, 61. pp. 513-523.
 
Relation http://dx.doi.org/10.1007/s00239-005-0023-5
http://www.eprints.iicb.res.in/319/