title: Molecular evolution of ldpA, a gene mediating the circadian input signal in cyanobacteria.
abstract: The ldpA gene is an element of the cyanobacterial circadian system and mediates input to the clock. Using complete prokaryotic genomes from various public databases, I analyzed the structure and phylogeny of the ldpA genes. This gene belongs to the large superfamily of ferredoxins and has a HycB domain as a core element of its structure. In addition to this domain, ldpA has two conserved terminal domains that are specific to this gene and have no homologs in the databases. All three domains are under different selective constraints. The ldpA tree topology features two very distinct clades that are essentially the same as those in the previously reported trees of the sasA gene and the kaiBC operon, two other elements of the circadian system. The data on the ldpA polymorphism and evolutionary patterns give further support to the existence of two types of the system, kaiABC- and kaiBC-based, respectively. Each type has specific functional and selective constraints, which have likely been attained through highly concordant evolution of the system's components.
authors.affiliation: Osteoporosis Research Center and Department of Biomedical Sciences, Creighton University, 601 North 30th Street, Suite 6730, Omaha, NE 68131, USA. dvornyk@creighton.edu
authors.forename: Volodymyr
authors.initials: V
authors.lastname: Dvornyk
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics* / Q000502:physiology; D001665:Binding Sites / Q000235:genetics; D002940:Circadian Rhythm / Q000502:physiology*; D000458:Cyanobacteria / Q000145:classification / Q000235:genetics* / Q000502:physiology; D019143:Evolution, Molecular; D007506:Iron-Sulfur Proteins / Q000235:genetics* / Q000502:physiology; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D012641:Selection, Genetic; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D015398:Signal Transduction
chemical_list: D001426:Bacterial Proteins; D007506:Iron-Sulfur Proteins