Dataset Information

Proteomic comparison of photosynthetic reaction centre-light harvesting 1 complexes in wild-type, protein-W knockout and His-tagged protein-W strains of Rhodopseudomonas palustris.

ABSTRACT: Rhodopseudomonas palustris is a species of purple phototrophic bacterium. In these species, solar energy is captured by reaction centre-light harvesting 1 (RC-LH1) complexes which reside in membranes within the cells. The RC comprises three protein subunits: H, M, L and is encircled by a ring of LH1-α and LH1-β subunit pairs. Approximately 10% of these complexes in the wild-type (WT) strain include an additional subunit called protein-W. In this project, we have determined cryo-EM structures for RC-LH1 complexes both with and without protein-W. To enable the purification of RC-LH1-W with 100% occupancy of protein-W, strain expressing a C-terminally His-tagged W was engineered. For complexes lacking W, a knockout strain was used. Proteomic analysis was employed to validate these strains and establish that the WT and W-His expressed similar levels of W relative to RC-LH1.

INSTRUMENT(S):

ORGANISM(S): Rhodopseudomonas Palustris Cga009

SUBMITTER: Philip Jackson

LAB HEAD: Christopher Neil Hunter

PROVIDER: PXD020402 | Pride | 2021-09-09

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	20191118_PJ_DS_W-His-3-1.raw	Raw
	20191118_PJ_DS_W-His-3-2.raw	Raw
	20191118_PJ_DS_W-His-3-3.raw	Raw
	20191118_PJ_DS_delta-W-2-1.raw	Raw
	20191118_PJ_DS_delta-W-2-2.raw	Raw

Items per page:

1 - 5 of 11

Publications

Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels.

Swainsbury David J K DJK Qian Pu P Jackson Philip J PJ Faries Kaitlyn M KM Niedzwiedzki Dariusz M DM Martin Elizabeth C EC Farmer David A DA Malone Lorna A LA Thompson Rebecca F RF Ranson Neil A NA Canniffe Daniel P DP Dickman Mark J MJ Holten Dewey D Kirmaier Christine C Hitchcock Andrew A Hunter C Neil CN

Science advances 20210113 3

The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris A 2.65-Å resolution structure of the RC-LH114-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16- ...[more]

PMID: 33523887

Similar Datasets

Project description:Peripheral light harvesting (LH) antenna complexes have been studied extensively in the purple nonsulfur bacterium Rhodopseudomonas palustris because it produces different types of LH complexes under high light intensities (LH2 complex) and low light intensities (LH3 and LH4 complex). The ability of R. palustris to alter its peripheral LH complexes in response to changes in light intensity is attributed to the multiple operons that encode the a and b peptides that make up these complexes, whose expression is affected by light intensity, light quality, and oxygen tension. However, low resolution structures, amino acid similarities between the complexes, and a lack of transcriptional analysis made it difficult to determine the LH complexes composition and functions under different light intensities. It was also unclear how much diversity of the R. palustris LH complexes exists in nature.Results: To gain insight into the composition of the LH complexes, their function under high light intensities and low light intensities, and their prevalence in the environment we undertook an integrative genomics approach using 15 closely related R. palustris strains isolated from the environment and 5 R. palustris ecotypes whose genomes have been sequenced. We sequenced the genomes for the 15 closely related strains and using RNA-seq carried out transcriptomic analysis on all 20 strains grown under high light intensity and low light intensity. We were able to determine that even closely related R. palustris strains had differences in their pucBA gene content and expression, even under the same growth conditions. We also found that the LH2 complex could compensate for the lack of an LH4 complex under LL intensities but not under extremely LL intensities. Conclusions: This is the first time an integrative genomics approach has been used to study light harvesting in the environment. The variation observed in LH gene composition and expression in environmental isolates of R. palustris likely reflects how these strains have adapted to specific light conditions in the environment. We have also shown that there is redundancy between some of the LH complexes under certain light intensities, which may partially explain why multiple operons encoding LH complexes have evolved and been maintained in R. palustris. Examing the variation observed in LH gene composition and expression in various environmental isolates

Project description: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.

Dataset Information

Proteomic comparison of photosynthetic reaction centre-light harvesting 1 complexes in wild-type, protein-W knockout and His-tagged protein-W strains of Rhodopseudomonas palustris.

Dataset's files

Publications

Structures of <i>Rhodopseudomonas palustris</i> RC-LH1 complexes with open or closed quinone channels.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Dataset Information

Proteomic comparison of photosynthetic reaction centre-light harvesting 1 complexes in wild-type, protein-W knockout and His-tagged protein-W strains of Rhodopseudomonas palustris.

Dataset's files

Publications

Structures of &lt;i&gt;Rhodopseudomonas palustris&lt;/i&gt; RC-LH1 complexes with open or closed quinone channels.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Structures of <i>Rhodopseudomonas palustris</i> RC-LH1 complexes with open or closed quinone channels.