scholarly journals Structural and Functional Analyses of Photosynthetic Regulatory Genes regA and regBfrom Rhodovulum sulfidophilum, Roseobacter denitrificans, and Rhodobacter capsulatus

1999 ◽  
Vol 181 (14) ◽  
pp. 4205-4215 ◽  
Author(s):  
Shinji Masuda ◽  
Yumi Matsumoto ◽  
Kenji V. P. Nagashima ◽  
Keizo Shimada ◽  
Kazuhito Inoue ◽  
...  
Keyword(s):  
Photosynthetic Bacteria ◽  
Rhodobacter Capsulatus ◽  
Photosynthetic Apparatus ◽  
Anaerobic Growth ◽  
Binding Motif ◽  
Sequence Information ◽  
Sensor Kinase ◽  
Rhodovulum Sulfidophilum ◽  
High Level ◽  
Aerobic And Anaerobic

ABSTRACT Genes coding for putative RegA, RegB, and SenC homologues were identified and characterized in the purple nonsulfur photosynthetic bacteria Rhodovulum sulfidophilum and Roseobacter denitrificans, species that demonstrate weak or no oxygen repression of photosystem synthesis. This additional sequence information was then used to perform a comparative analysis with previously sequenced RegA, RegB, and SenC homologues obtained fromRhodobacter capsulatus and Rhodobacter sphaeroides. These are photosynthetic bacteria that exhibit a high level of oxygen repression of photosystem synthesis controlled by the RegA-RegB two-component regulatory system. The response regulator, RegA, exhibits a remarkable 78.7 to 84.2% overall sequence identity, with total conservation within a putative helix-turn-helix DNA-binding motif. The RegB sensor kinase homologues also exhibit a high level of sequence conservation (55.9 to 61.5%) although these additional species give significantly different responses to oxygen. ARhodovulum sulfidophilum mutant lacking regA orregB was constructed. These mutants produced smaller amounts of photopigments under aerobic and anaerobic conditions, indicating that the RegA-RegB regulon controls photosynthetic gene expression in this bacterium as it does as in Rhodobacterspecies. Rhodobacter capsulatus regA- orregB-deficient mutants recovered the synthesis of a photosynthetic apparatus that still retained regulation by oxygen tension when complemented with reg genes fromRhodovulum sulfidophilum and Roseobacter denitrificans. These results suggest that differential expression of photosynthetic genes in response to aerobic and anaerobic growth conditions is not the result of altered redox sensing by the sensor kinase protein, RegB.

Isolation and Identification of Photosynthetic Bacteria and their Hydrogen Production Characterization

2012 ◽  
Vol 512-515 ◽  
pp. 527-533
Author(s):  
Yan Yan Zhu ◽  
Quan Guo Zhang ◽  
Bin Xu Han ◽  
Yan Yan Jing
Keyword(s):  
Hydrogen Production ◽  
Photosynthetic Bacteria ◽  
Culture Medium ◽  
Gene Sequence ◽  
Rhodospirillum Rubrum ◽  
Rhodobacter Capsulatus ◽  
Solid Medium ◽  
Production Capacity ◽  
Sequence Information ◽  
Isolation And Identification

Using special culture medium, dominant photosynthetic bacterias were enriched from sewage silt and paddy fields with plentiful light and organic compounds. Five strains of photosynthetic bacteria capable of producing hydrogen were purified and isolated by gradual dilution and double—deck solid medium. The analysis of the gene sequence information of 1 6SrDNA was carried out, and the five strains were identified as Rhodospirillum rubrum,R.capsulata, R.pulastris, Rhodobacter capsulatus, Rhodobacter capsulatus . Moreover, it was found that with Optimized medium formula, hydrogen production can be achieved 204h, the maximum hydrogen production capacity of 3.41L, the maximum hydrogen production rate was 44.17ml / (L • h),the highest hydrogen content of 46.73%.

scholarly journals Regulation of Aerobic and Anaerobic d-Malate Metabolism of Escherichia coli by the LysR-Type Regulator DmlR (YeaT)

2010 ◽  
Vol 192 (10) ◽  
pp. 2503-2511 ◽  
Author(s):  
Hanna Lukas ◽  
Julia Reimann ◽  
Ok Bin Kim ◽  
Jan Grimpo ◽  
Gottfried Unden
Keyword(s):  
Escherichia Coli ◽  
Malate Dehydrogenase ◽  
Major Effect ◽  
Anaerobic Growth ◽  
Two Component System ◽  
E Coli ◽  
High Level ◽  
K 12 ◽  
Aerobic And Anaerobic ◽  
Malate Metabolism

ABSTRACT Escherichia coli K-12 is able to grow under aerobic conditions on d-malate using DctA for d-malate uptake and the d-malate dehydrogenase DmlA (formerly YeaU) for converting d-malate to pyruvate. Induction of dmlA encoding DmlA required an intact dmlR (formerly yeaT) gene, which encodes DmlR, a LysR-type transcriptional regulator. Induction of dmlA by DmlR required the presence of d-malate or l- or meso-tartrate, but only d-malate supported aerobic growth. The regulator of general C4-dicarboxylate metabolism (DcuS-DcuR two-component system) had some effect on dmlA expression. The anaerobic l-tartrate regulator TtdR or the oxygen sensors ArcB-ArcA and FNR did not have a major effect on dmlA expression. DmlR has a high level of sequence identity (49%) with TtdR, the l- and meso-tartrate-specific regulator of l-tartrate fermentation in E. coli. dmlA was also expressed at high levels under anaerobic conditions, and the bacteria had d-malate dehydrogenase activity. These bacteria, however, were not able to grow on d-malate since the anaerobic pathway for d-malate degradation has a predicted yield of ≤0 ATP/mol d-malate. Slow anaerobic growth on d-malate was observed when glycerol was also provided as an electron donor, and d-malate was used in fumarate respiration. The expression of dmlR is subject to negative autoregulation. The network for regulation and coordination of the central and peripheral pathways for C4-dicarboxylate metabolism by the regulators DcuS-DcuR, DmlR, and TtdR is discussed.

scholarly journals Maturation of Rhodobacter capsulatus Multicopper Oxidase CutO Depends on the CopA Copper Efflux Pathway and Requires the cutF Product

2021 ◽  
Vol 12 ◽  
Author(s):  
Yavuz Öztürk ◽  
Crysten E. Blaby-Haas ◽  
Noel Daum ◽  
Andreea Andrei ◽  
Juna Rauch ◽  
...  
Keyword(s):  
Rhodobacter Capsulatus ◽  
Growth Conditions ◽  
Anaerobic Growth ◽  
Binding Motif ◽  
Catalytic Center ◽  
Domains Of Life ◽  
Cu Homeostasis ◽  
Cu Resistance ◽  
Efflux Pathway ◽  
Detoxification Pathway

Copper (Cu) is an essential cofactor required for redox enzymes in all domains of life. Because of its toxicity, tightly controlled mechanisms ensure Cu delivery for cuproenzyme biogenesis and simultaneously protect cells against toxic Cu. Many Gram-negative bacteria contain extracytoplasmic multicopper oxidases (MCOs), which are involved in periplasmic Cu detoxification. MCOs are unique cuproenzymes because their catalytic center contains multiple Cu atoms, which are required for the oxidation of Cu1+ to the less toxic Cu2+. Hence, Cu is both substrate and essential cofactor of MCOs. Here, we investigated the maturation of Rhodobacter capsulatus MCO CutO and its role in periplasmic Cu detoxification. A survey of CutO activity of R. capsulatus mutants with known defects in Cu homeostasis and in the maturation of the cuproprotein cbb3-type cytochrome oxidase (cbb3-Cox) was performed. This revealed that CutO activity is largely independent of the Cu-delivery pathway for cbb3-Cox biogenesis, except for the cupric reductase CcoG, which is required for full CutO activity. The most pronounced decrease of CutO activity was observed with strains lacking the cytoplasmic Cu chaperone CopZ, or the Cu-exporting ATPase CopA, indicating that CutO maturation is linked to the CopZ-CopA mediated Cu-detoxification pathway. Our data demonstrate that CutO is important for cellular Cu resistance under both aerobic and anaerobic growth conditions. CutO is encoded in the cutFOG operon, but only CutF, and not CutG, is essential for CutO activity. No CutO activity is detectable when cutF or its putative Cu-binding motif are mutated, suggesting that the cutF product serves as a Cu-binding component required for active CutO production. Bioinformatic analyses of CutF-like proteins support their widespread roles as putative Cu-binding proteins for several Cu-relay pathways. Our overall findings show that the cytoplasmic CopZ-CopA dependent Cu detoxification pathway contributes to providing Cu to CutO maturation, a process that strictly relies on cutF.

scholarly journals Programmed spatial organization of biomacromolecules into discrete, coacervate-based protocells

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Wiggert J. Altenburg ◽  
N. Amy Yewdall ◽  
Daan F. M. Vervoort ◽  
Marleen H. M. E. van Stevendaal ◽  
Alexander F. Mason ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Nitrilotriacetic Acid ◽  
Binding Motif ◽  
Biologically Relevant ◽  
Enzyme Cascade ◽  
Synthetic Cell ◽  
Synthetic Cells ◽  
Membrane Bound ◽  
High Concentrations ◽  
High Level

AbstractThe cell cytosol is crowded with high concentrations of many different biomacromolecules, which is difficult to mimic in bottom-up synthetic cell research and limits the functionality of existing protocellular platforms. There is thus a clear need for a general, biocompatible, and accessible tool to more accurately emulate this environment. Herein, we describe the development of a discrete, membrane-bound coacervate-based protocellular platform that utilizes the well-known binding motif between Ni2+-nitrilotriacetic acid and His-tagged proteins to exercise a high level of control over the loading of biologically relevant macromolecules. This platform can accrete proteins in a controlled, efficient, and benign manner, culminating in the enhancement of an encapsulated two-enzyme cascade and protease-mediated cargo secretion, highlighting the potency of this methodology. This versatile approach for programmed spatial organization of biologically relevant proteins expands the protocellular toolbox, and paves the way for the development of the next generation of complex yet well-regulated synthetic cells.

scholarly journals BGFE: A Deep Learning Model for ncRNA-Protein Interaction Predictions Based on Improved Sequence Information

2019 ◽  
Vol 20 (4) ◽  
pp. 978 ◽  
Author(s):  
Zhao-Hui Zhan ◽  
Li-Na Jia ◽  
Yong Zhou ◽  
Li-Ping Li ◽  
Hai-Cheng Yi
Keyword(s):  
Deep Learning ◽  
Protein Interactions ◽  
Prediction Accuracy ◽  
Sparse Matrices ◽  
Protein Sequences ◽  
Biological Research ◽  
Sequence Information ◽  
Feature Extraction Method ◽  
Cellular Processes ◽  
High Level

The interactions between ncRNAs and proteins are critical for regulating various cellular processes in organisms, such as gene expression regulations. However, due to limitations, including financial and material consumptions in recent experimental methods for predicting ncRNA and protein interactions, it is essential to propose an innovative and practical approach with convincing performance of prediction accuracy. In this study, based on the protein sequences from a biological perspective, we put forward an effective deep learning method, named BGFE, to predict ncRNA and protein interactions. Protein sequences are represented by bi-gram probability feature extraction method from Position Specific Scoring Matrix (PSSM), and for ncRNA sequences, k-mers sparse matrices are employed to represent them. Furthermore, to extract hidden high-level feature information, a stacked auto-encoder network is employed with the stacked ensemble integration strategy. We evaluate the performance of the proposed method by using three datasets and a five-fold cross-validation after classifying the features through the random forest classifier. The experimental results clearly demonstrate the effectiveness and the prediction accuracy of our approach. In general, the proposed method is helpful for ncRNA and protein interacting predictions and it provides some serviceable guidance in future biological research.

High-level transcription of large gene regions: a novel T7 RNA-polymerase-based system for expression of functional hydrogenases in the phototrophic bacterium Rhodobacter capsulatus

2005 ◽  
Vol 33 (1) ◽  
pp. 56-58 ◽  
Author(s):  
T. Drepper ◽  
S. Arvani ◽  
F. Rosenau ◽  
S. Wilhelm ◽  
K.-E. Jaeger
Keyword(s):  
Rna Polymerase ◽  
Rhodobacter Capsulatus ◽  
Expression System ◽  
Active Form ◽  
T7 Rna Polymerase ◽  
High Level Synthesis ◽  
Phototrophic Bacterium ◽  
Large Gene ◽  
High Level ◽  
Complex Enzymes

High-level synthesis of complex enzymes like bacterial [NiFe] hydrogenases, in general, requires an expression system that allows concerted expression of a large number of genes. So far, it has not been possible to overproduce a hydrogenase in a stable and active form by using a customary expression system. Therefore we started to establish a new, T7-based expression system in the phototrophic bacterium Rhodobacter capsulatus. The beneficial properties of this bacterial host in combination with the unique capacity of T7 RNA polymerase to synthesize long transcripts will allow the high-level synthesis and assembly of active hydrogenase as well as other complex enzymes in the near future.

scholarly journals Constitutive Expression of Escherichia coli tat Genes Indicates an Important Role for the Twin-Arginine Translocase during Aerobic and Anaerobic Growth

2001 ◽  
Vol 183 (5) ◽  
pp. 1801-1804 ◽  
Author(s):  
Rachael L. Jack ◽  
Frank Sargent ◽  
Ben C. Berks ◽  
Gary Sawers ◽  
Tracy Palmer
Keyword(s):  
Constitutive Expression ◽  
Protein Export ◽  
The Other ◽  
Anaerobic Growth ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Expression Studies ◽  
Twin Arginine Translocase ◽  
Aerobic And Anaerobic Growth ◽  
Aerobic And Anaerobic

ABSTRACT The transcription start sites for the tatABCD andtatE loci, encoding components of the Tat (twin-arginine translocase) protein export pathway, have been identified. Expression studies indicate that the tatABCD and tatEtranscription units are expressed constitutively. Translational fusion experiments suggest that TatA is synthesized at a much higher level than the other Tat proteins.

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