Characterization of OmcA Mutants from Shewanella oneidensis MR-1 to Investigate the Molecular Mechanisms Underpinning Electron Transfer Across the Microbe-Electrode Interface

Fuel Cells ◽  
2017 ◽  
Vol 17 (5) ◽  
pp. 601-611 ◽  
Author(s):  
S. E. Neto ◽  
D. de Melo-Diogo ◽  
I. J. Correia ◽  
C. M. Paquete ◽  
R. O. Louro
Keyword(s):  
Electron Transfer ◽  
Molecular Mechanisms ◽  
Shewanella Oneidensis ◽  
Electrode Interface

The membrane-bound tetrahaem c-type cytochrome CymA interacts directly with the soluble fumarate reductase in Shewanella

2002 ◽  
Vol 30 (4) ◽  
pp. 658-662 ◽  
Author(s):  
C. Schwalb ◽  
S. K. Chapman ◽  
G. A. Reid
Keyword(s):  
Electron Transfer ◽  
Outer Membrane ◽  
Shewanella Oneidensis ◽  
Anaerobic Respiration ◽  
Fumarate Reductase ◽  
Sulphur Compounds ◽  
Sequence Alignments ◽  
Membrane Bound ◽  
Periplasmic Domain

Shewanella spp. demonstrate great variability in the use of terminal electron acceptors in anaerobic respiration; these include nitrate, fumarate, DMSO, trimethylamine oxide, sulphur compounds and metal oxides. These pathways open up possible applications in bioremediation. The wide variety of respiratory substrates for Shewanella is correlated with the evolution of several multi-haem membrane-bound, periplasmic and outer-membrane c-type cytochromes. The 21 kDa c-type cytochrome CymA of the freshwater strain Shewanella oneidensis MR-1 has an N-terminal membrane anchor and a globular tetrahaem periplasmic domain. According to sequence alignments, CymA is a member of the NapC/NirT family. This family of redox proteins is responsible for electron transfer from the quinone pool to periplasmic and outer-membrane-bound reductases. Prior investigations have shown that the absence of CymA results in loss of the ability to respire with Fe(III), fumarate and nitrate, indicating that CymA is involved in electron transfer to several terminal reductases. Here we describe the expression, purification and characterization of a soluble, truncated CymA (‘CymA). Potentiometric studies suggest that there are two pairs of haems with potentials of -175 and -261 mV and that ‘CymA is an efficient electron donor for the soluble fumarate reductase, flavocytochrome c3.

NETWORK ANALYSIS OF COMMON DIFFERENTIAL GENES IDENTIFIES KEY GENES AND IMPORTANT MODULES UNDERLYING EXTRACELLULAR ELECTRON TRANSFER PROCESSES

2019 ◽  
Vol 27 (01) ◽  
pp. 51-67
Author(s):  
DEWU DING
Keyword(s):  
Electron Transfer ◽  
Network Analysis ◽  
Molecular Mechanisms ◽  
Shewanella Oneidensis ◽  
Extracellular Electron Transfer ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
New Genes ◽  
Electron Transfer Processes ◽  
Insoluble Electron Acceptors

Electricigens can transfer electrons that produced in intracellular metabolic processes to cellular surface to restore extracellular insoluble electron acceptors (extracellular electron transfer, EET). To uncover the molecular mechanisms underlying EET processes, we integrated transcriptome changes accompanying such processes with molecular network. Firstly, time-series expression datasets for Shewanella oneidensis MR-1 under limited/changed [Formula: see text] conditions were obtained from the GEO database, and a total of 336 common differentially expressed genes (DEGs) were identified. Then, we constructed the protein–protein interaction (PPI) network that involved in EET processes from these DEGs. Furthermore, by using centralization analysis and community detection, network analysis of the PPI network was performed. Although the fundamental EET genes are similar to previous studies, important new genes have been discovered. Taking together, our study identified many literature-validated genes critical to EET processes, and also proposed some novel genes that were putatively involved in EET processes.

Metagenomic and metatranscriptomic characterization of a microbial community that catalyzes both energy-generating and energy-storing electrode reactions

2021 ◽  
Author(s):  
Rebecca L. Mickol ◽  
Brian J. Eddie ◽  
Anthony P. Malanoski ◽  
Matthew D. Yates ◽  
Leonard M. Tender ◽  
...  
Keyword(s):  
Gene Expression ◽  
Electron Transfer ◽  
Energy Storage ◽  
Electrode Potential ◽  
Molecular Mechanisms ◽  
Extracellular Electron Transfer ◽  
Rechargeable Battery ◽  
New Paradigm ◽  
Heterodisulfide Reductase

Electroactive bacteria are living catalysts, mediating energy-generating reactions at anodes or energy storage reactions at cathodes via extracellular electron transfer (EET). The Cathode-ANode (CANode) biofilm community was recently shown to facilitate both reactions, however, the identity of the primary constituents and underlying molecular mechanisms remain unknown. Here, we used metagenomics and metatranscriptomics to characterize the CANode biofilm. We show that a previously uncharacterized member of the family Desulfobulbaceae, Desulfobulbaceae -2, which had <1% relative abundance, had the highest relative gene expression and accounted for over 60% of all differentially expressed genes. At the anode potential, differential expression of genes for a conserved flavin oxidoreductase (Flx) and heterodisulfide reductase (Hdr) known to be involved in ethanol oxidation suggests a source of electrons for the energy-generating reaction. Genes for sulfate and carbon dioxide reduction pathways were expressed by Desulfobulbaceae -2 at both potentials and are the proposed energy storage reactions. Reduction reactions may be mediated by direct electron uptake from the electrode, or from hydrogen generated at the cathode potential. The Desulfobulbaceae -2 genome is predicted to encode at least 85 multi-heme (≥3 hemes) c -type cytochromes, some with as many as 26 heme-binding domains, that could facilitate reversible electron transfer with the electrode. Gene expression in other CANode biofilm species was also affected by the electrode potential, although to a lesser extent, and we cannot rule out their contribution to observed current. Results provide evidence of gene expression linked to energy storage and energy-generating reactions and will enable development of the CANode biofilm as a microbially-driven rechargeable battery. IMPORTANCE Microbial electrochemical technologies (METs) rely on electroactive bacteria to catalyze energy-generating and energy storage reactions at electrodes. Known electroactive bacteria are not equally capable of both reactions and METs are typically configured to be unidirectional. Here we report on genomic and transcriptomic characterization of a recently described microbial electrode community called the Cathode-ANode (CANode). The CANode community is able to generate or store electrical current based on the electrode potential. During periods where energy is not needed, electrons generated from a renewable source, such as solar power, could be converted into energy storage compounds to later be reversibly oxidized by the same microbial catalyst. Thus, the CANode system can be thought of as a living “rechargeable battery”. Results show that a single organism may be responsible for both reactions demonstrating a new paradigm for electroactive bacteria.

scholarly journals Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qian-Hao Zhu ◽  
Warwick Stiller ◽  
Philippe Moncuquet ◽  
Stuart Gordon ◽  
Yuman Yuan ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Agronomic Traits ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Wild Type ◽  
Calcium Dependent ◽  
Dependent Protein ◽  
Flanking Region ◽  
Comparative Transcriptomic Analysis

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

scholarly journals A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1

2021 ◽  
Vol 22 (14) ◽  
pp. 7390
Author(s):  
Nicole Wesch ◽  
Frank Löhr ◽  
Natalia Rogova ◽  
Volker Dötsch ◽  
Vladimir V. Rogov
Keyword(s):  
Cellular Localization ◽  
Molecular Mechanisms ◽  
Biochemical Characterization ◽  
Effective Interaction ◽  
Regulatory Region ◽  
Titration Calorimetry ◽  
Enzymatic Reactions ◽  
Cellular Processes ◽  
Mechanism Of Interaction

Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.

scholarly journals High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Betty Ha ◽  
Kevin P. Larsen ◽  
Jingji Zhang ◽  
Ziao Fu ◽  
Elizabeth Montabana ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Viral Entry ◽  
Reverse Transcription ◽  
Molecular Mechanisms ◽  
Dissociation Kinetics ◽  
Structural Mechanism ◽  
Medium Resolution ◽  
Kinetics Of ◽  
Hiv 1

AbstractReverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC–nevirapine, and RTIC–efavirenz complexes at 2.8, 3.1, and 2.9 Å, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA–tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

scholarly journals Hemolysis in the spleen drives erythrocyte turnover

Blood ◽  
2020 ◽  
Author(s):  
Thomas robert leon Klei ◽  
Jill Jasmine Dalimot ◽  
Benjamin Nota ◽  
Martijn Veldthuis ◽  
Erik Mul ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Matrix Proteins ◽  
Human Spleen ◽  
Erythrocyte Adhesion ◽  
Subsequent Degradation ◽  
Macrophage Subpopulations ◽  
Senescent Erythrocytes ◽  
Red Pulp

Red pulp macrophages of the spleen mediate turnover of billions of senescent erythrocytes per day. However, the molecular mechanisms involved in sequestration of senescent erythrocytes, their recognition and their subsequent degradation by red pulp macrophages remain unclear. In this study we provide evidence that the splenic environment is of substantial importance in facilitating erythrocyte turnover through induction of hemolysis. Upon isolating human spleen red pulp macrophages we noted a substantial lack of macrophages that were in the process of phagocytosing intact erythrocytes. Detailed characterization of erythrocyte and macrophage subpopulations from human spleen tissue led to the identification of erythrocytes that are devoid of hemoglobin, so-called erythrocyte ghosts. By in vivo imaging and transfusion experiments we further confirmed that senescent erythrocytes that are retained in the spleen are subject to hemolysis. Additionally, we show that erythrocyte adhesion molecules, which are specifically activated on aged erythrocytes, cause senescent erythrocytes to interact with extracellular matrix proteins that are exposed within the splenic architecture. Such adhesion molecule-driven retention of senescent erythrocytes, under low shear conditions, was found to result in steady shrinkage of the cell and ultimately resulted in hemolysis. In contrast to intact senescent erythrocytes, the remnant erythrocyte ghost shells were prone to recognition and breakdown by red pulp macrophages. These data identify hemolysis as a key event in the turnover of senescent erythrocytes, which alters our current understanding of how erythrocyte degradation is regulated.

Synthesis and Characterization of C70-Corrole—A New Electron Transfer Dyad

2014 ◽  
Vol 14 (7) ◽  
pp. 5370-5374 ◽  
Author(s):  
Youde Wang ◽  
Zhenzhen Wang ◽  
Xihong Guo ◽  
Rongli Cui ◽  
Xingfa Gao ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Synthesis And Characterization
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