A possible origin of newly-born bacterial genes: significance of GC-rich nonstop frame on antisense strand.
Base compositions were examined at every position in codons of more than 50 genes from taxonomically different bacteria and of the corresponding antisense sequences on the bacterial genes. We propose that the nonstop frame on antisense strand [NSF(a)] of GC-rich bacterial genes is the most promising sequence for newly-born genes. Reasons are: (i) NSF(a) frequently appears on the antisense strand of GC-rich bacterial genes; (ii) base compositions at three positions in the codon are nearly symmetrical between the gene having around 55% GC content and the corresponding NSF(a); (iii) amino acid compositions of actual proteins are also similar to those of hypothetical proteins from the GC-rich NSF(a); and (iv) proteins from NSF(a) of 60% or more GC content are flexible enough to adapt to various molecules encountered as novel substrates, due to the high glycine content. To support our proposition, using a computer we generated hypothetical antisense sequences with the same base compositions as of NSF(a) at each base position in the codon, and examined properties of resulting proteins encoded by the imaginary genes. It was confirmed that NSF(a) of GC-rich gene carrying about 60% GC content is competent enough for a newly-born gene.
Ikehara
K
K
Department of Chemistry, Faculty of Science, Nara Women's University, Kita-uoya Nishi-machi, Japan. ikehara@cc.nara-wu.ac.jp
Amada
F
F
Yoshida
S
S
Mikata
Y
Y
Tanaka
A
A
D000596:Amino Acids / Q000032:analysis; D001419:Bacteria / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D001482:Base Composition; D003062:Codon; D003198:Computer Simulation; D003596:Cytosine; D016373:DNA, Antisense / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D006147:Guanine; D008957:Models, Genetic; D010455:Peptides / Q000737:chemistry / Q000235:genetics
D000596:Amino Acids; D001426:Bacterial Proteins; D003062:Codon; D016373:DNA, Antisense; D004269:DNA, Bacterial; D010455:Peptides; D006147:Guanine; D003596:Cytosine