Dataset Information

Proteomic analysis of Rhodopsedomonas palustris longevity

ABSTRACT: Proteomics analysis of Rhodopseudomonas palustris 6 and 20 days after growth arrest.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Rhodopseudomonas Palustris Cga009

SUBMITTER: Ernesto Nakayasu

LAB HEAD: Ernesto Nakayasu

PROVIDER: PXD013729 | Pride | 2019-10-02

REPOSITORIES: pride

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Dataset's files

Source:

			Action	DRS
	Biodiversity_R_palustris_long_WT_Ar_20d_01_QEP_20Aug18_Wally_18-07-04.raw	Raw
	Biodiversity_R_palustris_long_WT_Ar_20d_02_QEP_20Aug18_Wally_18-07-04.raw	Raw
	Biodiversity_R_palustris_long_WT_Ar_20d_03_QEP_20Aug18_Wally_18-07-04.raw	Raw
	Biodiversity_R_palustris_long_WT_Ar_6d_01_QEP_20Aug18_Wally_18-07-04.raw	Raw
	Biodiversity_R_palustris_long_WT_Ar_6d_02_QEP_20Aug18_Wally_18-07-04.raw	Raw

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Publications

Bacterial Longevity Requires Protein Synthesis and a Stringent Response.

Yin Liang L Ma Hongyu H Nakayasu Ernesto S ES Payne Samuel H SH Morris David R DR Harwood Caroline S CS

mBio 20191015 5

Gram-negative bacteria in infections, biofilms, and industrial settings often stop growing due to nutrient depletion, immune responses, or environmental stresses. Bacteria in this state tend to be tolerant to antibiotics and are often referred to as dormant. <i>Rhodopseudomonas palustris</i>, a phototrophic alphaproteobacterium, can remain fully viable for more than 4 months when its growth is arrested. Here, we show that protein synthesis, specific proteins involved in translation, and a string ...[more]

PMID: 31615958

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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