ArticleBioinformatics and biology insights2011
Functional Annotation Analytics of Rhodopseudomonas palustris Genomes.
Article in Bioinformatics and biology insights, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- Structural and functional characterization of aquaporin 4 from the freshwater gastropod Pomacea canaliculata under temperature stress.Molecular biology reports · 2026Article
- The draft genome of Andean Rhodopseudomonas sp. strain AZUL predicts genome plasticity and adaptation to chemical homeostasis.BMC microbiology · 2022Article
- The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome.BMC genomics · 2021Article
- Transparent polyvinyl-alcohol cryogel as immobilisation matrix for continuous biohydrogen production by phototrophic bacteria.Biotechnology for biofuels · 2020Article
- Photosynthetic bacterium Rhodopseudomonas palustris GJ-22 induces systemic resistance against viruses.Microbial biotechnology · 2017Article
- Secondary Data Analytics of Aquaporin Expression Levels in Glioblastoma Stem-Like Cells.Cancer informatics · 2015Article
- Evolution of mitochondria reconstructed from the energy metabolism of living bacteria.PloS one · 2014Article
- GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes.BMC genomics · 2013Article
- Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium.Bioinformatics and biology insights · 2012Article
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. The availability of the finished genome sequences of six R. palustris strains (BisA53, BisB18, BisB5, CGA009, HaA2 and TIE-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological lifestyles of the bacteria species. The purpose of this investigation was to compare the functional annotations available for multiple R. palustris genomes to identify annotations that can be further investigated for strain-specific or uniquely shared phenotypic characteristics. A total of 2,355 protein family Pfam domain annotations were clustered based on presence or absence in the six genomes. The clustering process identified groups of functional annotations including those that could be verified as strain-specific or uniquely shared phenotypes. For example, genes encoding water/glycerol transport were present in the genome sequences of strains CGA009 and BisB5, but absent in strains BisA53, BisB18, HaA2 and TIE-1. Protein structural homology modeling predicted that the two orthologous 240 aa R. palustris aquaporins have water-specific transport function. Based on observations in other microbes, the presence of aquaporin in R. palustris strains may improve freeze tolerance in natural conditions of rapid freezing such as nitrogen fixation at low temperatures where access to liquid water is a limiting factor for nitrogenase activation. In the case of adaptive loss of aquaporin genes, strains may be better adapted to survive in conditions of high-sugar content such as fermentation of biomass for biohydrogen production. Finally, web-based resources were developed to allow for interactive, user-defined selection of the relationship between protein family annotations and the R. palustris genomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.