scholarly journals Genome Sequence of the Unusual Purple Photosynthetic Bacterium Phaeovibrio sulfidiphilus, Only Distantly Related to Rhodospirillaceae, Reveals Unique Genes for Respiratory Nitrate Reduction and Glycerol Metabolism

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
S. Dubey ◽  
T. E. Meyer ◽  
J. A. Kyndt
Keyword(s):  
Nitrate Reduction ◽  
Photosynthetic Bacteria ◽  
Photosynthetic Bacterium ◽  
Gene Clusters ◽  
Glycerol Metabolism ◽  
Freshwater Species ◽  
Content Type ◽  
Purple Photosynthetic Bacteria ◽  
Purple Photosynthetic Bacterium ◽  
Unique Genes

ABSTRACT Phaeovibrio sulfidiphilus was reported to be a divergent member of the purple photosynthetic bacteria with limited ability to metabolize organic compounds. Whole-genome-based analysis shows that it is indeed only distantly related to freshwater species of Rhodospirillaceae. Unexpectedly, the genome contains unique gene clusters for potential respiratory nitrate reduction and anaerobic glycerol metabolism.

scholarly journals Expression of Uptake Hydrogenase and Molybdenum Nitrogenase in Rhodobacter capsulatus Is Coregulated by the RegB-RegA Two-Component Regulatory System

2000 ◽  
Vol 182 (10) ◽  
pp. 2831-2837 ◽  
Author(s):  
Sylvie Elsen ◽  
Wanda Dischert ◽  
Annette Colbeau ◽  
Carl E. Bauer
Keyword(s):  
Photosynthetic Bacteria ◽  
Rhodobacter Capsulatus ◽  
Regulatory System ◽  
Photosynthetic Bacterium ◽  
Uptake Hydrogenase ◽  
Carbon And Nitrogen ◽  
Cellular Energy ◽  
Purple Photosynthetic Bacteria ◽  
Two Component

ABSTRACT Purple photosynthetic bacteria are capable of generating cellular energy from several sources, including photosynthesis, respiration, and H2 oxidation. Under nutrient-limiting conditions, cellular energy can be used to assimilate carbon and nitrogen. This study provides the first evidence of a molecular link for the coregulation of nitrogenase and hydrogenase biosynthesis in an anoxygenic photosynthetic bacterium. We demonstrated that molybdenum nitrogenase biosynthesis is under the control of the RegB-RegA two-component regulatory system in Rhodobacter capsulatus. Footprint analyses and in vivo transcription studies showed that RegA indirectly activates nitrogenase synthesis by binding to and activating the expression of nifA2, which encodes one of the two functional copies of the nif-specific transcriptional activator, NifA. Expression of nifA2 but notnifA1 is reduced in the reg mutants up to eightfold under derepressing conditions and is also reduced under repressing conditions. Thus, although NtrC is absolutely required fornifA2 expression, RegA acts as a coactivator ofnifA2. We also demonstrated that in regmutants, [NiFe]hydrogenase synthesis and activity are increased up to sixfold. RegA binds to the promoter of the hydrogenase gene operon and therefore directly represses its expression. Thus, the RegB-RegA system controls such diverse processes as energy-generating photosynthesis and H2 oxidation, as well as the energy-demanding processes of N2 fixation and CO2 assimilation.

scholarly journals Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes

mSystems ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Izabela Mujakić ◽  
Adrian-Ştefan Andrei ◽  
Tanja Shabarova ◽  
Lívia Kolesár Fecskeová ◽  
Michaela M. Salcher ◽  
...  
Keyword(s):  
Close Association ◽  
Gene Clusters ◽  
Gobi Desert ◽  
Rrna Gene ◽  
Natural Environments ◽  
Freshwater Species ◽  
Freshwater Lakes ◽  
Unique Type ◽  
Content Type ◽  
Bacterial Phyla

ABSTRACT Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota. They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes’ epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments. IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria. We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.

scholarly journals Draft Genome Sequence of Marine-Derived Streptomyces sp. Strain AA0539, Isolated from the Yellow Sea, China

2012 ◽  
Vol 194 (23) ◽  
pp. 6622-6623 ◽  
Author(s):  
Zhi-Qiang Xiong ◽  
Yong Wang
Keyword(s):  
Genome Sequence ◽  
Yellow Sea ◽  
Draft Genome ◽  
Gene Clusters ◽  
The Yellow Sea ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Small Genome ◽  
Streptomyces Sp ◽  
Unique Genes

ABSTRACTHere, we report the draft genome sequence ofStreptomycessp. strain AA0539, isolated from marine sediment of the Yellow Sea, China. Its small genome (∼5.8 Mb) contains large, unique genes and gene clusters for diverse secondary metabolites, suggesting great potential as a source for the discovery of novel natural products.

scholarly journals Draft Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodopseudomonas palustris XCP

2018 ◽  
Vol 7 (4) ◽  
Author(s):  
Amiera Rayyan ◽  
Terry Meyer ◽  
John Kyndt
Keyword(s):  
Genome Sequence ◽  
Rhodopseudomonas Palustris ◽  
Photosynthetic Bacterium ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Wide Range ◽  
Purple Photosynthetic Bacterium

Rhodopseudomonas palustris is known for its versatile metabolic capabilities and has been proposed for a wide range of innovative applications. Here, we report the genome sequence of strain XCP, as well as a whole-genome nucleotide comparison of R. palustris strains, which indicates the need for further differentiation of the known strains.

scholarly journals Structure-Guided Expansion of the Substrate Range of Methylmalonyl Coenzyme A Synthetase (MatB) of Rhodopseudomonas palustris

2012 ◽  
Vol 78 (18) ◽  
pp. 6619-6629 ◽  
Author(s):  
Heidi A. Crosby ◽  
Katherine C. Rank ◽  
Ivan Rayment ◽  
Jorge C. Escalante-Semerena
Keyword(s):  
Coenzyme A ◽  
Rhodopseudomonas Palustris ◽  
Photosynthetic Bacterium ◽  
Polyketide Biosynthesis ◽  
Content Type ◽  
Malonyl Coa ◽  
Purple Photosynthetic Bacterium ◽  
Important Building Block ◽  
Prime Target ◽  
Resolution Structure

ABSTRACTMalonyl coenzyme A (malonyl-CoA) and methylmalonyl-CoA are two of the most commonly used extender units for polyketide biosynthesis and are utilized to synthesize a vast array of pharmaceutically relevant products with antibacterial, antiparasitic, anticholesterol, anticancer, antifungal, and immunosuppressive properties. Heterologous hosts used for polyketide production such asEscherichia colioften do not produce significant amounts of methylmalonyl-CoA, however, requiring the introduction of other pathways for the generation of this important building block. Recently, the bacterial malonyl-CoA synthetase class of enzymes has been utilized to generate malonyl-CoA and methylmalonyl-CoA directly from malonate and methylmalonate. We demonstrate that in the purple photosynthetic bacteriumRhodopseudomonas palustris, MatB (RpMatB) acts as a methylmalonyl-CoA synthetase and is required for growth on methylmalonate. We report theapo(1.7-Å resolution) and ATP-bound (2.0-Å resolution) structure and kinetic analysis ofRpMatB, which shows similar activities for both malonate and methylmalonate, making it an ideal enzyme for heterologous polyketide biosynthesis. Additionally, rational, structure-based mutagenesis of the active site ofRpMatB led to substantially higher activity with ethylmalonate and butylmalonate, demonstrating that this enzyme is a prime target for expanded substrate specificity.

scholarly journals Redirection of Metabolism for Biological Hydrogen Production

2007 ◽  
Vol 73 (5) ◽  
pp. 1665-1671 ◽  
Author(s):  
Federico E. Rey ◽  
Erin K. Heiniger ◽  
Caroline S. Harwood
Keyword(s):  
Nitrogen Fixation ◽  
Hydrogen Production ◽  
Photosynthetic Bacteria ◽  
Rhodopseudomonas Palustris ◽  
Photosynthetic Bacterium ◽  
Selection Strategy ◽  
Wild Type ◽  
Purple Photosynthetic Bacteria ◽  
Mutant Strains ◽  
Different Strains

ABSTRACT A major route for hydrogen production by purple photosynthetic bacteria is biological nitrogen fixation. Nitrogenases reduce atmospheric nitrogen to ammonia with the concomitant obligate production of molecular hydrogen. However, hydrogen production in the context of nitrogen fixation is a rather inefficient process because about 75% of the reductant consumed by the nitrogenase is used to generate ammonia. In this study we describe a selection strategy to isolate strains of purple photosynthetic bacteria in which hydrogen production is necessary for growth and independent of nitrogen fixation. We obtained four mutant strains of the photosynthetic bacterium Rhodopseudomonas palustris that produce hydrogen constitutively, even in the presence of ammonium, a condition where wild-type cells do not accumulate detectable amounts of hydrogen. Some of these strains produced up to five times more hydrogen than did wild-type cells growing under nitrogen-fixing conditions. Transcriptome analyses of the hydrogen-producing mutant strains revealed that in addition to the nitrogenase genes, 18 other genes are potentially required to produce hydrogen. The mutations that caused constitutive hydrogen production mapped to four different sites in the NifA transcriptional regulator in the four different strains. The strategy presented here can be applied to the large number of diverse species of anoxygenic photosynthetic bacteria that are known to exist in nature to identify strains for which there are fitness incentives to produce hydrogen.

scholarly journals Peptide-Mediated Gene Transfer into Marine Purple Photosynthetic Bacteria

2020 ◽  
Vol 21 (22) ◽  
pp. 8625
Author(s):  
Mieko Higuchi-Takeuchi ◽  
Takaaki Miyamoto ◽  
Choon Pin Foong ◽  
Mami Goto ◽  
Kumiko Morisaki ◽  
...  
Keyword(s):  
Plasmid Dna ◽  
Photosynthetic Bacteria ◽  
Photosynthetic Bacterium ◽  
Dna Delivery ◽  
Transformation Method ◽  
Endosomal Escape ◽  
Purple Photosynthetic Bacteria ◽  
Rhodovulum Sulfidophilum ◽  
Wide Range ◽  
Plasmid Delivery

Use of photosynthetic organisms is one of the sustainable ways to produce high-value products. Marine purple photosynthetic bacteria are one of the research focuses as microbial production hosts. Genetic transformation is indispensable as a biotechnology technique. However, only conjugation has been determined to be an applicable method for the transformation of marine purple photosynthetic bacteria so far. In this study, for the first time, a dual peptide-based transformation method combining cell penetrating peptide (CPP), cationic peptide and Tat-derived peptide (dTat-Sar-EED) (containing D-amino acids of Tat and endosomal escape domain (EED) connected by sarcosine linkers) successfully delivered plasmid DNA into Rhodovulum sulfidophilum, a marine purple photosynthetic bacterium. The plasmid delivery efficiency was greatly improved by dTat-Sar-EED. The concentrations of dTat-Sar-EED, cell growth stage and recovery duration affected the efficiency of plasmid DNA delivery. The delivery was inhibited at 4 °C and by A22, which is an inhibitor of the actin homolog MreB. This suggests that the plasmid DNA delivery occurred via MreB-mediated energy dependent process. Additionally, this peptide-mediated delivery method was also applicable for E. coli cells. Thus, a wide range of bacteria could be genetically transformed by using this novel peptide-based transformation method.

scholarly journals Genes Involved in the Biosynthesis of Photosynthetic Pigments in the Purple Sulfur Photosynthetic Bacterium Thiocapsa roseopersicina

2003 ◽  
Vol 69 (6) ◽  
pp. 3093-3102 ◽  
Author(s):  
�kos T. Kov�cs ◽  
G�bor R�khely ◽  
Korn�l L. Kov�cs
Keyword(s):  
Mutant Strain ◽  
Photosynthetic Bacteria ◽  
Photosynthetic Reaction Center ◽  
Photosynthetic Bacterium ◽  
Chromosomal Locus ◽  
Reading Frame ◽  
Purple Photosynthetic Bacteria ◽  
Thiocapsa Roseopersicina ◽  
Photosynthetic Genes ◽  
General Arrangement

ABSTRACT A pigment mutant strain of the purple sulfur photosynthetic bacterium Thiocapsa roseopersicina BBS was isolated by plasposon mutagenesis. Nineteen open reading frame, most of which are thought to be genes involved in the biosynthesis of carotenoids, bacteriochlorophyll, and the photosynthetic reaction center, were identified surrounding the plasposon in a 22-kb-long chromosomal locus. The general arrangement of the photosynthetic genes was similar to that in other purple photosynthetic bacteria; however, the locations of a few genes occurring in this region were unusual. Most of the gene products showed the highest similarity to the corresponding proteins in Rubrivivax gelatinosus. The plasposon was inserted into the crtD gene, likely inactivating crtC as well, and the carotenoid composition of the mutant strain corresponded to the aborted spirilloxanthin pathway. Homologous and heterologous complementation experiments indicated a conserved function of CrtC and CrtD in the purple photosynthetic bacteria. The crtDC and crtE genes were shown to be regulated by oxygen, and a role of CrtJ in aerobic repression was suggested.

scholarly journals The Serratia marcescens Siderophore Serratiochelin Is Necessary for Full Virulence during Bloodstream Infection

2020 ◽  
Vol 88 (8) ◽  
Author(s):  
Danelle R. Weakland ◽  
Sara N. Smith ◽  
Bailey Bell ◽  
Ashootosh Tripathi ◽  
Harry L. T. Mobley
Keyword(s):  
Serratia Marcescens ◽  
Bloodstream Infection ◽  
Iron Acquisition ◽  
Gene Clusters ◽  
Clinical Isolates ◽  
Wild Type ◽  
Serratia Plymuthica ◽  
Content Type ◽  
Cas Assay ◽  
Essential Nutrient

ABSTRACT Serratia marcescens is a bacterium frequently found in the environment, but over the last several decades it has evolved into a concerning clinical pathogen, causing fatal bacteremia. To establish such infections, pathogens require specific nutrients; one very limited but essential nutrient is iron. We sought to characterize the iron acquisition systems in S. marcescens isolate UMH9, which was recovered from a clinical bloodstream infection. Using RNA sequencing (RNA-seq), we identified two predicted siderophore gene clusters (cbs and sch) that were regulated by iron. Mutants were constructed to delete each iron acquisition locus individually and in conjunction, generating both single and double mutants for the putative siderophore systems. Mutants lacking the sch gene cluster lost their iron-chelating ability as quantified by the chrome azurol S (CAS) assay, whereas the cbs mutant retained wild-type activity. Mass spectrometry-based analysis identified the chelating siderophore to be serratiochelin, a siderophore previously identified in Serratia plymuthica. Serratiochelin-producing mutants also displayed a decreased growth rate under iron-limited conditions created by dipyridyl added to LB medium. Additionally, mutants lacking serratiochelin were significantly outcompeted during cochallenge with wild-type UMH9 in the kidneys and spleen after inoculation via the tail vein in a bacteremia mouse model. This result was further confirmed by an independent challenge, suggesting that serratiochelin is required for full S. marcescens pathogenesis in the bloodstream. Nine other clinical isolates have at least 90% protein identity to the UMH9 serratiochelin system; therefore, our results are broadly applicable to emerging clinical isolates of S. marcescens causing bacteremia.

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