Bioinformatics Analysis Of Genes That Encode Photosynthetic NAD(P)H Dehydrogenase Complex

Photosynthetic NAD(P)H dehydrogenase (NDH) is an important membrane protein complex that is essential to CO2 uptake, photosystem I-dependent cyclic electron transport and cellular respiration. Up to now, NDH complex comprises of at least 15 subunits, which are encoded by genes homologous between cyanobacteria and higher plants. However, during the plant evolution, certain of these 15 ndh encoding genes had a considerable change. For examples, in contrast to cyanobacteria, ndhL–O genes of higher plants transferred from chloroplasts to nuclear genomes, and several copies of ndhF gene lost. In this study, bioinformatics analysis of the genes that encode the NDH complex attempted to reveal the reason why photosynthetic NDH complex changed during the evolution and the correlative applications.First, by the comparison of the synonymous (dS) and nonsynonymous (dN) nucleotide substitiution rates in cyanobacteria and higher plants, it was found that in cyanobacterial cells, there were no significant differenences between the ndhA–K and ndhL–O genes. In contrast, in higher plants, the dS and dN values in nuclear-encoded ndhL–O were much higher than those in chloroplast-encoded ndhA–K. Such situation also similarly occurred in chloroplast– and nuclear–encoded genes of other photosynthetic complexes. According to the Muller's ratchet effect, high mutation frequency was suggested to be required for the transfer of genes of photosynthetic complexes, at least ndhL–O, from chloroplasts to nuclear genomes. The probability of transfer of ndhA–K in chloroplasts to nuclear genomes in the future was discussed by judging the dS and dN values.Secondly, by the analysis of the several criteria as molecular marker proposed during the plant phylogeny, and molecular characteristics of cyanobacterial ndh genes, classification standard of cyanobacterial morphology and other molecular markers suitable for cyanobacteria, ndhH gene was found to be a novel molecular marker applicable to the study on cyanobacterial phylogeny. Further, such novel molecular marker was only suitable for the phylogenetic study in cyanobacteria and not in higher plants. In contrast, those molecular markers of ndh genes such as ndhA, D and F applicable to the phylogenetic research of higher plants were not suitable for that cyanobacterial study. Therefore, the application category as the molecular markers of ndh genes in cyanobacteria and higher plants was different.In conclusion, bioinformatics analysis of 15 genes that encode the NDH complex in cyanobacteria and higher plants indicated the possible reason for the transfer of ndhL–O of higher plants to nucleus, and that ndhH gene was a novel molecular marker suitable for phylogenetic research in cyanobacteria.