Postgenomic Adventures with <i>Rhodobacter sphaeroides</i>

MacKenzie, Cameron A.; Eraso, Jesus M.; Choudhary, Madhusudan; Roh, Jung Hyeob; Zeng, Xiaohua; Bruscella, Patrice; Puskás, Ágnes; Kaplan, Samuel

doi:10.1146/annurev.micro.61.080706.093402

Cited by 79 publications

(69 citation statements)

References 126 publications

(74 reference statements)

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“…However, based on the genome annotation, R. rubrum does not seem to have a specific sigma factor involved in general stress or entry into stationary phase such as RpoS. This has also been observed for the closely related a-proteobacterium, Rhodobacter sphaeroides 2.4.1 (Mackenzie et al, 2007). Thus, we can suspect these functions to be ascribed to another sigma factor or to non-sigma-factor-type regulator(s).…”

Section: Integrating Transcriptomics and Quantitative Proteomics Resultsmentioning

confidence: 80%

Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight

et al. 2009

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In view of long-haul space exploration missions, the European Space Agency initiated the MicroEcological Life Support System Alternative (MELiSSA) project targeting the total recycling of organic waste produced by the astronauts into oxygen, water and food using a loop of bacterial and higher plant bioreactors. In that purpose, the a-proteobacterium, Rhodospirillum rubrum S1H, was sent twice to the International Space Station and was analyzed post-flight using a newly developed R. rubrum whole genome oligonucleotide microarray and high throughput gel-free proteomics with Isotope-Coded Protein Label technology. Moreover, in an effort to identify a specific response of R. rubrum S1H to space flight, simulation of microgravity and space-ionizing radiation were performed on Earth under identical culture set-up and growth conditions as encountered during the actual space journeys. Transcriptomic and proteomic data were integrated and permitted to put forward the importance of medium composition and culture set-up on the response of the bacterium to space flight-related environmental conditions. In addition, we showed for the first time that a low dose of ionizing radiation (2 mGy) can induce a significant response at the transcriptomic level, although no change in cell viability and only a few significant differentially expressed proteins were observed. From the MELiSSA perspective, we could argue the effect of microgravity to be minimized, whereas R. rubrum S1H could be more sensitive to ionizing radiation during long-term space exploration mission.

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Section: Integrating Transcriptomics and Quantitative Proteomics Resultsmentioning

confidence: 80%

Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight

et al. 2009

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“…Some microbes that closely related to bacteria are able to convert light energy into chemical energy, also have the ability to regulate the nitrogen fixation pathways. For example, the Alphaproteobacteria R. sphaeroides possesses an extensive range of energy acquiring mechanisms including photosynthesis and lithotrophy, as well as the ability to use aerobic and anaerobic respiration (Mackenzie et al, 2007). Several species, such as actinobacteria use cyanobacteria biomasses for growth (Eiler and Bertilsson, 2004;Webster et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

Metagenome of microorganisms associated with the toxic Cyanobacteria Microcystis aeruginosa analyzed using the 454 sequencing platform

Zhang

et al. 2011

Chin. J. Ocean. Limnol.

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In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an average length of 248 bp. Running the 454 assembly algorithm over our sequences yielded 22 239 significant contigs. After excluding the M. aeruginosa sequences, we obtained 1 322 assembled contigs longer than 1 000 bp. Taxonomic analysis indicated that four kingdoms were represented in the community: Archaea (n = 9; 0.01%), Bacteria (n = 98 921; 99.6%), Eukaryota (n = 373; 3.7%), and Viruses (n = 18; 0.02%). The bacterial sequences were predominantly Alphaproteobacteria (n = 41 805; 83.3%), Betaproteobacteria (n = 5 254; 10.5%) and Gammaproteobacteria (n = 1 180; 2.4%). Gene annotations and assignment of COG (clusters of orthologous groups) functional categories indicate that a large number of the predicted genes are involved in metabolic, genetic, and environmental information processes. Our results demonstrate the extraordinary diversity of a microbial community in an ectosymbiotic system and further establish the tremendous utility of pyrosequencing.

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“…The mean of triplicate measurements (three Affymetrix GeneChips) was used to describe the expression level of a gene for each R. sphaeroides strain. For group comparisons, microarray data for the wild-type (21,28) and PrrA Ϫ (PRRA2) (11, 21) strains of R. sphaeroides grown under anaerobic-dark-DMSO conditions were used. The filtering criterion for the group means was a 1.2-fold change using the 90% confidence boundary for no change, which was calculated using the standard error of the group means (44).…”

Section: Methodsmentioning

confidence: 99%

“…The transition from high to low oxygen tension alone is an environmental alteration sufficient to induce the reversible physiological changes which accompany the formation of the intracytoplasmic membrane (ICM) (22). The ICM houses the pigment protein complexes used to gather light quanta, as well as the photosynthetic electron carriers that together constitute the photosynthetic apparatus (28). Formation of the ICM is precisely controlled via transcriptional and posttranslational regulatory processes.…”

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confidence: 99%

The Use of Chromatin Immunoprecipitation to Define PpsR Binding Activity in Rhodobacter sphaeroides 2.4.1

et al. 2008

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The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA (RegBA) two-component system, and the transcriptional repressor/antirepressor PpsR/AppA. Of the three regulators, PpsR appears to have the narrowest range of physiological effects, which are limited to effects on the structural and pigment biosynthetic activities involved in photosynthetic membrane function. Although a PrrA ؊ mutant is unable to grow under photosynthetic conditions, when a ppsR mutation was present, photosynthetic growth occurred. An examination of the double mutant under anaerobic-dark-dimethyl sulfoxide conditions using microarray analysis revealed the existence of an "extended" PpsR regulon and new physiological roles. To characterize the PpsR regulon and to better ascertain the significance of degeneracy within the PpsR binding sequence in vivo, we adapted the chromatin immunoprecipitation technique to R. sphaeroides. We demonstrated that in vivo there was direct and significant binding by PpsR to newly identified genes involved in microaerobic respiration and periplasmic stress resistance, as well as to photosynthesis genes. The new members of the PpsR regulon are located outside the photosynthesis gene cluster and have degenerate PpsR binding sequences. The possible interaction under physiologic conditions with degenerate binding sequences in the presence of other biologically relevant molecules is discussed with respect to its importance in physiological processes and to the existence of complex phenotypes associated with regulatory mutants. This study further defines the DNA structure necessary for PpsR binding in situ.

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Postgenomic Adventures with Rhodobacter sphaeroides

Cited by 79 publications

References 126 publications

Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight

Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight

Metagenome of microorganisms associated with the toxic Cyanobacteria Microcystis aeruginosa analyzed using the 454 sequencing platform

The Use of Chromatin Immunoprecipitation to Define PpsR Binding Activity in Rhodobacter sphaeroides 2.4.1

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