SUMMARY
A survey of the already characterized and potential two-component
protein sequences that exist in the nine complete and seven partially
annotated cyanobacterial genome sequences available (as of May 2005)
showed that the cyanobacteria possess a much larger repertoire of such
proteins than most other bacteria. By analysis of the domain structure
of the 1,171 potential histidine kinases, response regulators, and
hybrid kinases, many various arrangements of about thirty different
modules could be distinguished. The number of two-component proteins is
related in part to genome size but also to the variety of physiological
properties and ecophysiologies of the different strains. Groups of
orthologues were defined, only a few of which have representatives with
known physiological functions. Based on comparisons with the proposed
phylogenetic relationships between the strains, the orthology groups
show that (i) a few genes, some of them clustered on the genome, have
been conserved by all species, suggesting their very ancient origin and
an essential role for the corresponding proteins, and (ii)
duplications, fusions, gene losses, insertions, and deletions, as well
as domain shuffling, occurred during evolution, leading to the extant
repertoire. These mechanisms are put in perspective with the different
genetic properties that cyanobacteria have to achieve genome
plasticity. This review is designed to serve as a basis for orienting
further research aimed at defining the most ancient regulatory
mechanisms and understanding how evolution worked to select and keep
the most appropriate systems for cyanobacteria to develop in the quite
different environments that they have successfully
colonized.
The numbers of potential response regulator genes were determined from the complete and annotated genome sequences of Archaea and Bacteria. The numbers of each class of response regulators are shown for each organism, determined principally from BLASTP searches, but with reference to the gene category lists where available. The survey shows that for Bacteria there is a link between the total number of potential response regulator genes and both the genome complexity (number of potential protein-coding genes) and the organism's lifestyle/habitat. Increasingly complex lifestyles and genome complexities are matched by an increase in the average number of potential response regulator genes per genome, indicating that a higher degree of complexity requires a higher level of control of gene expression and cellular activity. Detailed results of this study are available online at and.
The publicly available annotated archaeal genome sequences (23 complete and three partial annotations, October 2005) were searched for the presence of potential two-component open reading frames (ORFs) using gene category lists and BLASTP. A total of 489 potential two-component genes were identified from the gene category lists and BLASTP. Two-component genes were found in 14 of the 21 Euryarchaeal sequences (October 2005) and in neither the Crenarchaeota nor the Nanoarchaeota. A total of 20 predicted protein domains were identified in the putative two-component ORFs that, in addition to the histidine kinase and receiver domains, also includes sensor and signalling domains. The detailed structure of these putative proteins is shown, as is the distribution of each class of two-component genes in each species. Potential members of orthologous groups have been identified, as have any potential operons containing two or more two-component genes. The number of two-component genes in those Euryarchaeal species which have them seems to be linked more to lifestyle and habitat than to genome complexity, with most examples being found in Methanospirillum hungatei, Haloarcula marismortui, Methanococcoides burtonii and the mesophilic Methanosarcinales group. The large numbers of two-component genes in these species may reflect a greater requirement for internal regulation. Phylogenetic analysis of orthologous groups of five different protein classes, three probably involved in regulating taxis, suggests that most of these ORFs have been inherited vertically from an ancestral Euryarchaeal species and point to a limited number of key horizontal gene transfer events.
Within the photosynthetic gene cluster of Rhodobacter sphaeroides the genes encoding light-harvesting LHI and reaction-centre complexes are transcriptionally linked in the order pufBALMX. The region stretching 1.6 kb upstream of pufB has been examined by DNA sequencing and by complementation/deletion analysis. These studies demonstrate that three open reading frames are located upstream of pufB. One open reading frame, designated bchA, terminates just inside pufQ, which is located proximal to pufB. BchA contains a 37 bp region that functions as the oxygen-regulated promoter for pufQ, and probably for the puf operon as a whole. We also demonstrate that the protein encoded by pufQ appears to play a role in bacteriochlorophyll biosynthesis.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.