Molecular evolution of PAS domain-containing proteins of filamentous cyanobacteria through domain shuffling and domain duplication

• Published in: DNA research Vol. 11; no. 2; pp. 69 - 81
• Main Authors: NARIKAWA, Rei, OKAMOTO, Shinobu, IKEUCHI, Masahiko, OHMORI, Masayuki
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 2004
• Subjects: Amino Acid Sequence; Anabaena; Anabaena - genetics; Bacterial Proteins - genetics; Biological and medical sciences; Cluster Analysis; Computational Biology; Conserved Sequence - genetics; Cyanobacterium; Databases, Genetic; Evolution, Molecular; Fundamental and applied biological sciences. Psychology; Genes. Genome; Genetics of eukaryotes. Biological and molecular evolution; Genome, Bacterial; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Nostoc; Nostoc punctiforme; Protein Structure, Tertiary - genetics; Sequence Alignment; Signal Transduction - genetics; Molecular evolution; PAS domain; Duplication; ortholog pair; Cyanobacteria; Bacteria; cyanobacterium; domain shuffling; Protein
• ISSN: 1340-2838; 1756-1663
• DOI: 10.1093/dnares/11.2.69

When the entire genome of a filamentous heterocyst-forming N2-fixing cyanobacterium, Anabaena sp. PCC 7120 (Anabaena) was determined in 2001, a large number of PAS domains were detected in signal-transducing proteins. The draft genome sequence is also available for the cyanobacterium, Nostoc punctiforme strain ATCC 29133 (Nostoc), that is closely related to Anabaena. In this study, we extracted all PAS domains from the Nostoc genome sequence and analyzed them together with those of Anabaena. Clustering analysis of all the PAS domains gave many specific pairings, indicative of evolutionary conservations. Ortholog analysis of PAS-containing proteins showed composite multidomain architecture in some cases of conserved domains and domains of disagreement between the two species. Further inspection of the domains of disagreement allowed us to trace them back in evolution. Thus, multidomain proteins could have been generated by duplication or shuffling in these cyanobacteria. The conserved PAS domains in the orthologous proteins were analyzed by structural fitting to the known PAS domains. We detected several subclasses with unique sequence features, which will be the target of experimental analysis.