ProOpDB: Prokaryotic Operon DataBase

Taboada, Blanca; Ciria, Ricardo; Martinez-Guerrero, Cristian E.; Merino, Enrique

doi:10.1093/nar/gkr1020

Cited by 158 publications

(149 citation statements)

References 20 publications

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“…The bioinformatic predictions for CcsR1 target mRNAs were performed by IntaRNA and RNApredator. For analysis of operons, ProOpDB was used (40). putative carbon monoxide dehydrogenase subunits coxL (RSP_2877) and RSP_2876, the pyruvate dehydrogenase subunit pdhB (RSP_4050), and pqqA (RSP_6132) encoding the PQQ coenzyme synthesis protein.…”

Section: Resultsmentioning

confidence: 99%

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A Cluster of Four Homologous Small RNAs Modulates C ₁ Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions

et al. 2015

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In bacteria, regulatory RNAs play an important role in the regulation and balancing of many cellular processes and stress responses. Among these regulatory RNAs, trans-encoded small RNAs (sRNAs) are of particular interest since one sRNA can lead to the regulation of multiple target mRNAs. In the purple bacterium Rhodobacter sphaeroides, several sRNAs are induced by oxidative stress. In this study, we focused on the functional characterization of four homologous sRNAs that are cotranscribed with the gene for the conserved hypothetical protein RSP_6037, a genetic arrangement described for only a few sRNAs until now. Each of the four sRNAs is characterized by two stem-loops that carry CCUCCUCCC motifs in their loops. They are induced under oxidative stress, as well as by various other stress conditions, and were therefore renamed here sRNAs CcsR1 to CcsR4 (CcsR1-4) for conserved CCUCCUCCC motif stress-induced RNAs 1 to 4. Increased CcsR1-4 expression decreases the expression of genes involved in C 1 metabolism or encoding components of the pyruvate dehydrogenase complex either directly by binding to their target mRNAs or indirectly. One of the CcsR1-4 target mRNAs encodes the transcriptional regulator FlhR, an activator of glutathione-dependent methanol/formaldehyde metabolism. Downregulation of this glutathione-dependent pathway increases the pool of glutathione, which helps to counteract oxidative stress. The FlhR-dependent downregulation of the pyruvate dehydrogenase complex reduces a primary target of reactive oxygen species and reduces aerobic electron transport, a main source of reactive oxygen species. Our findings reveal a previously unknown strategy used by bacteria to counteract oxidative stress. IMPORTANCEPhototrophic organisms have to cope with photo-oxidative stress due to the function of chlorophylls as photosensitizers for the formation of singlet oxygen. Our study assigns an important role in photo-oxidative stress resistance to a cluster of four homologous sRNAs in the anoxygenic phototrophic bacterium Rhodobacter sphaeroides. We reveal a function of these regulatory RNAs in the fine-tuning of C 1 metabolism. A model that relates oxidative stress defense to C 1 metabolism is presented. The purple bacterium Rhodobacter sphaeroides is able to adapt its life-style to changing environmental conditions by making use of many different metabolic pathways like aerobic and anaerobic respiration, fermentation, and anaerobic anoxygenic photosynthesis. Major determinants of the life-style of R. sphaeroides are light quality and quantity, as well as oxygen tension. Under microaerobic conditions, R. sphaeroides produces photosynthetic complexes in the dark, while light inhibits their formation (1, 2). In addition to the intricate transcriptional regulation of photosynthesis genes by diverse protein regulators, photosynthetic complex formation is also based on oxygen-dependent mRNA stability for photosynthetically relevant genes and control by sRNAs (3, 4). Light-dependent inhibition of photosynthetic com...

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Section: Resultsmentioning

confidence: 99%

“…The top 50 results of each search were subjected to further analysis. For analysis of operons, the Prokaryotic Operon DataBase (ProOpDB) was used (40).…”

Section: Construction Of Lacz Reporter Plasmidsmentioning

confidence: 99%

A Cluster of Four Homologous Small RNAs Modulates C ₁ Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions

et al. 2015

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“…Because the 5= and 3= ends of most genes in B. burgdorferi have not been mapped, the operon configurations were predicted (Fig. 4) using the Prokaryotic Operon Database (48) and Microbes Online Operon Predictions (49) and modified by 5= end mapping data for rpoS (50) and rpsM (data not shown). We observed variability in the time scale of decay of genes that are expected to be found on a polycistronic transcript.…”

Section: Discussionmentioning

confidence: 99%

Measurements of mRNA Degradation in Borrelia burgdorferi

et al. 2013

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The importance of gene regulation in the enzootic cycle of Borrelia burgdorferi, the spirochete that causes Lyme disease, is well established. B. burgdorferi regulates gene expression in response to changes in environmental stimuli associated with changing hosts. In this study, we monitored mRNA decay in B. burgdorferi following transcriptional arrest with actinomycin D. The timedependent decay of transcripts encoding RNA polymerase subunits (rpoA and rpoS), ribosomal proteins (rpsD, rpsK, rpsM, rplQ, and rpsO), a nuclease (pnp), outer surface lipoproteins (ospA and ospC), and a flagellar protein (flaB) have different profiles and indicate half-lives ranging from approximately 1 min to more than 45 min in cells cultured at 35°C. Our results provide a first step in characterizing mRNA decay in B. burgdorferi and in investigating its role in gene expression and regulation.

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“…Each mutant was then verified by Illumina whole-genome sequencing to confirm the expected deletion of each gene of interest and to ascertain that no secondary mutations had occurred. Three of the genes selected for mutagenesis, bapA, rpiR, and bpss2248, are located within predicted operons, while tex and bspl1728 do not have any downstream genes located within the same reading frame (39). Due to the nature of our mutagenesis strategy, we did not expect to see polar effects from any of the mutants we constructed, including those with mutations in genes within operons.…”

Section: Resultsmentioning

confidence: 99%

Characterization of New Virulence Factors Involved in the Intracellular Growth and Survival of Burkholderia pseudomallei

et al. 2016

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dBurkholderia pseudomallei, the causative agent of melioidosis, has complex and poorly understood extracellular and intracellular lifestyles. We used transposon-directed insertion site sequencing (TraDIS) to retrospectively analyze a transposon library that had previously been screened through a BALB/c mouse model to identify genes important for growth and survival in vivo. This allowed us to identify the insertion sites and phenotypes of negatively selected mutants that were previously overlooked due to technical constraints. All 23 unique genes identified in the original screen were confirmed by TraDIS, and an additional 105 mutants with various degrees of attenuation in vivo were identified. Five of the newly identified genes were chosen for further characterization, and clean, unmarked bpsl2248, tex, rpiR, bpsl1728, and bpss1528 deletion mutants were constructed from the wild-type strain K96243. Each of these mutants was tested in vitro and in vivo to confirm their attenuated phenotypes and investigate the nature of the attenuation. Our results confirm that we have identified new genes important to in vivo virulence with roles in different stages of B. pseudomallei pathogenesis, including extracellular and intracellular survival. Of particular interest, deletion of the transcription accessory protein Tex was shown to be highly attenuating, and the tex mutant was capable of providing protective immunity against challenge with wild-type B. pseudomallei, suggesting that the genes identified in our TraDIS screen have the potential to be investigated as live vaccine candidates. Burkholderia pseudomallei is a Gram-negative, motile saprophytic bacterium that is the causative agent of melioidosis. This emerging human pathogen is endemic to the soil and water of tropical areas, including Thailand, Singapore, and northern Australia, and can cause infection through contact with broken skin or through ingestion or inhalation of the bacterium (1). The resulting disease can manifest as a localized skin ulcer or can progress to a systemic infection that is associated with mortality rates as high as 50% in some regions of endemicity (2). There is currently no licensed vaccine against B. pseudomallei available, and it is highly resistant to most antibiotics, severely limiting treatment options (3). Due to the virulent nature of the pathogen, potential for aerosol transmission, and lack of therapeutic options, B. pseudomallei is listed as a Tier 1 bioterrorism threat by the Centers for Disease Control and Prevention (4).B. pseudomallei is a facultative intracellular pathogen capable of invading and replicating within both epithelial cells and macrophages (5). While B. pseudomallei is capable of extracellular growth and survival and is highly resistant to complement-mediated killing in human sera, intracellular growth is essential for virulence (2, 6). When B. pseudomallei enters the host cell, either through phagocytosis or by inducing its own uptake into nonphagocytic cells, it is able to escape from the phagosome or endocyt...

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ProOpDB: Prokaryotic Operon DataBase

Cited by 158 publications

References 20 publications

A Cluster of Four Homologous Small RNAs Modulates C ₁ Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions

A Cluster of Four Homologous Small RNAs Modulates C ₁ Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions

Measurements of mRNA Degradation in Borrelia burgdorferi

Characterization of New Virulence Factors Involved in the Intracellular Growth and Survival of Burkholderia pseudomallei

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ProOpDB: Prokaryotic Operon DataBase

Cited by 158 publications

References 20 publications

A Cluster of Four Homologous Small RNAs Modulates C 1 Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions

A Cluster of Four Homologous Small RNAs Modulates C 1 Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions

Measurements of mRNA Degradation in Borrelia burgdorferi

Characterization of New Virulence Factors Involved in the Intracellular Growth and Survival of Burkholderia pseudomallei

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A Cluster of Four Homologous Small RNAs Modulates C ₁ Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions

A Cluster of Four Homologous Small RNAs Modulates C ₁ Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions