Effects of Oxygen and Light Intensity on Transcriptome Expression in Rhodobacter sphaeroides 2.4.1

Roh, Jung Hyeob; Smith, William E.; Kaplan, Samuel

doi:10.1074/jbc.m311608200

Cited by 71 publications

(79 citation statements)

References 90 publications

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“…We and others have shown that changes in the R. sphaeroides transcriptome correlate well with the metabolic and physiological changes occurring in this bacterium (38,44). To ensure that the observed responses are stimulus specific, we used H 2 O 2 concentrations that do not severely impair cellular survival and growth.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome and Physiological Responses to Hydrogen Peroxide of the Facultatively Phototrophic Bacterium Rhodobacter sphaeroides

Zeller

Moskvin

et al. 2005

J Bacteriol

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The transcriptome responses to hydrogen peroxide, H 2 O 2 , of the facultatively phototrophic bacterium Rhodobacter sphaeroides grown under semiaerobic conditions were investigated. At 7 min after the addition of 1 mM H 2 O 2 , the expression of approximately 9% of all genes (total, 394) was changed reliably by at least twofold. At 30 min, the number of genes (total, 88) and the magnitude of expression changes were much lower, indicating rapid recovery from stress. Two types of responses were observed: (i) an H 2 O 2 stress response per se and (ii) a shift to high-oxygen metabolism. The former response involved the upregulation of genes for H 2 O 2 detoxification, protein folding and proteolysis, DNA damage repair, iron transport and storage, iron-sulfur cluster repair, and the downregulation of genes for protein translation, motility, and cell wall and lipopolysaccharide synthesis. The shift to high-oxygen metabolism was evident from the differential regulation of genes for aerobic electron transport chain components and the downregulation of tetrapyrrole biosynthesis and photosystem genes. The abundance of photosynthetic complexes was decreased upon prolonged exposure of R. sphaeroides to H 2 O 2 , thus confirming the physiological significance of the transcriptome data. The regulatory pathways mediating the shift to high-oxygen metabolism were investigated. They involved the anaerobic activator FnrL and the antirepressor-repressor AppA-PpsR system. The transcription of FnrL-dependent genes was down at 7 min, apparently due to the transient inactivation by H 2 O 2 of the iron-sulfur cluster of FnrL. The transcription of the AppA-PpsR-dependent genes was down at 30 min, apparently due to the significant decrease in appA mRNA.In natural environments, microorganisms have to cope with oxidative stress caused by reactive oxygen species (ROS). In aerobically growing bacteria, the autooxidation of the respiratory chain components is believed to be one of the main sources of endogenous ROS (16,20,30); however, additional sources exist (48). ROS are also produced by exposure of aerobically grown cells to metals, redox-active chemicals, or radiation. To cope with damage inflicted by ROS, bacteria induce oxidative stress defense systems. These include superoxide dismutases, catalases, and peroxidases directly involved in ROS detoxification and repair mechanisms. The ROS-oxidized cysteine and methionine residues of proteins are repaired (reduced) by the thioredoxin, glutathion/glutaredoxin, and methionine sulfoxide reductase systems. DNA is protected from damage by specific ROS-induced DNA-binding proteins, while damaged DNA is repaired via the SOS response (1, 8, 52).Rhodobacter sphaeroides is a facultatively phototrophic bacterium belonging to the alpha division of the proteobacteria that can use various pathways for energy generation. At high O 2 tension, it uses aerobic respiration and lacks photosynthetic complexes. When O 2 tension drops, the expression of the photosystem (PS) genes increases, resulting in the produ...

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Section: Resultsmentioning

confidence: 99%

Transcriptome and Physiological Responses to Hydrogen Peroxide of the Facultatively Phototrophic Bacterium Rhodobacter sphaeroides

Zeller

Moskvin

et al. 2005

J Bacteriol

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“…The wild-type was grown under five different growth conditions and the two mutant strains under one growth condition, a total of seven experiments. All strains, described in detail below, were grown as independent triplicate cultures (Roh et al, 2004). RNA was harvested from each culture, converted to cDNA, then applied to its own microarray chip.…”

Section: Methodsmentioning

confidence: 99%

“…A previously described RNA isolation procedure (Roh & Kaplan, 2002) was modified to optimize the isolation of intact mRNA for microarray analysis (Roh et al, 2004). We modified the earlier procedure by eliminating cell collection by centrifugation.…”

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confidence: 99%

Combining microarray and genomic data to predict DNA binding motifs

et al. 2005

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The ability to detect regulatory elements within genome sequences is important in understanding how gene expression is controlled in biological systems. In this work, microarray data analysis is combined with genome sequence analysis to predict DNA sequences in the photosynthetic bacterium Rhodobacter sphaeroides that bind the regulators PrrA, PpsR and FnrL. These predictions were made by using hierarchical clustering to detect genes that share similar expression patterns. The DNA sequences upstream of these genes were then searched for possible transcription factor recognition motifs that may be involved in their co-regulation. The approach used promises to be widely applicable for the prediction of cis-acting DNA binding elements. Using this method the authors were independently able to detect and extend the previously described consensus sequences that have been suggested to bind FnrL and PpsR. In addition, sequences that may be recognized by the global regulator PrrA were predicted. The results support the earlier suggestions that the DNA binding sequence of PrrA may have a variable-sized gap between its conserved block elements. Using the predicted DNA binding sequences, a whole-genome-scale analysis was performed to determine the relative importance of the interplay between the three regulators PpsR, FnrL and PrrA. Results of this analysis showed that, compared to the regulation by PpsR and FnrL, a much larger number of genes are candidates to be regulated by PrrA. The study demonstrates by example that integration of multiple data types can be a powerful approach for inferring transcriptional regulatory patterns in microbial systems, and it allowed the detection of photosynthesis-related regulatory patterns in R. sphaeroides.

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“…In the case of the most studied purple photosynthetic bacterium Rhodobacter sphaeroides, the LH complexes and RCs are only synthesized when the oxygen tension is below a critical value (11,12). Then if cells are grown at high light intensities, the PSU is dominated by LH1/RC core complexes (13,14).…”

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confidence: 99%

Tracking energy transfer between light harvesting complex 2 and 1 in photosynthetic membranes grown under high and low illumination

Lüer

Moulisová

Henry

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Energy transfer (ET) between B850 and B875 molecules in light harvesting complexes LH2 and LH1/RC (reaction center) complexes has been investigated in membranes of Rhodopseudomonas palustris grown under high-and low-light conditions. In these bacteria, illumination intensity during growth strongly affects the type of LH2 complexes synthesized, their optical spectra, and their amount of energetic disorder. We used a specially built femtosecond spectrometer, combining tunable narrowband pump with broadband white-light probe pulses, together with an analytical method based on derivative spectroscopy for disentangling the congested transient absorption spectra of LH1 and LH2 complexes. This procedure allows real-time tracking of the forward (LH2 → LH1) and backward (LH2 ← LH1) ET processes and unambiguous determination of the corresponding rate constants. In low-light grown samples, we measured lower ET rates in both directions with respect to high-light ones, which is explained by reduced spectral overlap between B850 and B875 due to partial redistribution of oscillator strength into a higher energetic exciton transition. We find that the low-light adaptation in R. palustris leads to a reduced elementary backward ET rate, in accordance with the low probability of two simultaneous excitations reaching the same LH1/RC complex under weak illumination. Our study suggests that backward ET is not just an inevitable consequence of vectorial ET with small energetic offsets, but is in fact actively managed by photosynthetic bacteria.bacteriochlorophylls | ultrafast spectroscopy

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Effects of Oxygen and Light Intensity on Transcriptome Expression in Rhodobacter sphaeroides 2.4.1

Cited by 71 publications

References 90 publications

Transcriptome and Physiological Responses to Hydrogen Peroxide of the Facultatively Phototrophic Bacterium Rhodobacter sphaeroides

Transcriptome and Physiological Responses to Hydrogen Peroxide of the Facultatively Phototrophic Bacterium Rhodobacter sphaeroides

Combining microarray and genomic data to predict DNA binding motifs

Tracking energy transfer between light harvesting complex 2 and 1 in photosynthetic membranes grown under high and low illumination

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