scholarly journals Energy Conservation Model Based on Genomic and Experimental Analyses of a Carbon Monoxide-Utilizing, Butyrate-Forming Acetogen, Eubacterium limosum KIST612

2015 ◽  
Vol 81 (14) ◽  
pp. 4782-4790 ◽  
Author(s):  
Jiyeong Jeong ◽  
Johannes Bertsch ◽  
Verena Hess ◽  
Sunju Choi ◽  
In-Geol Choi ◽  
...  
Keyword(s):  
Carbon Monoxide ◽  
Atp Synthesis ◽  
Binding Motif ◽  
Oxidation Of Co ◽  
Co Dehydrogenase ◽  
Content Type ◽  
A Genome ◽  
Eubacterium Limosum ◽  
The One ◽  
Conservation Model

ABSTRACTEubacterium limosumKIST612 is one of the few acetogens that can produce butyrate from carbon monoxide. We have used a genome-guided analysis to delineate the path of butyrate formation, the enzymes involved, and the potential coupling to ATP synthesis. Oxidation of CO is catalyzed by the acetyl-coenzyme A (CoA) synthase/CO dehydrogenase and coupled to the reduction of ferredoxin. Oxidation of reduced ferredoxin is catalyzed by the Rnf complex and Na+dependent. Consistent with the finding of a Na+-dependent Rnf complex is the presence of a conserved Na+-binding motif in thecsubunit of the ATP synthase. Butyrate formation is from acetyl-CoA via acetoacetyl-CoA, hydroxybutyryl-CoA, crotonyl-CoA, and butyryl-CoA and is consistent with the finding of a gene cluster that encodes the enzymes for this pathway. The activity of the butyryl-CoA dehydrogenase was demonstrated. Reduction of crotonyl-CoA to butyryl-CoA with NADH as the reductant was coupled to reduction of ferredoxin. We postulate that the butyryl-CoA dehydrogenase uses flavin-based electron bifurcation to reduce ferredoxin, which is consistent with the finding ofetfAandetfBgenes next to it. The overall ATP yield was calculated and is significantly higher than the one obtained with H2+ CO2. The energetic benefit may be one reason that butyrate is formed only from CO but not from H2+ CO2.

scholarly journals Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism inCarboxydothermus pertinaxRevealed by Comparative Genome Analysis

2018 ◽  
Vol 84 (14) ◽  
Author(s):  
Yuto Fukuyama ◽  
Kimiho Omae ◽  
Yasuko Yoneda ◽  
Takashi Yoshida ◽  
Yoshihiko Sako
Keyword(s):  
Carbon Monoxide ◽  
Co Oxidation ◽  
Gene Cluster ◽  
Genome Analysis ◽  
Transcriptional Analysis ◽  
Comparative Genome Analysis ◽  
Co Dehydrogenase ◽  
Comparative Genome ◽  
Content Type ◽  
Energy Converting

ABSTRACTCarboxydothermusspecies are some of the most studied thermophilic carboxydotrophs. Their varied carboxydotrophic growth properties suggest distinct strategies for energy conservation via carbon monoxide (CO) metabolism. In this study, we used comparative genome analysis of the genusCarboxydothermusto show variations in the CO dehydrogenase-energy-converting hydrogenase gene cluster, which is responsible for CO metabolism with H2production (hydrogenogenic CO metabolism). Indeed, the ability or inability to produce H2with CO oxidation is explained by the presence or absence of this gene cluster inCarboxydothermus hydrogenoformans,Carboxydothermus islandicus, andCarboxydothermus ferrireducens. Interestingly, despite its hydrogenogenic CO metabolism,Carboxydothermus pertinaxlacks the Ni-CO dehydrogenase catalytic subunit (CooS-I) and its transcriptional regulator-encoding genes in this gene cluster, probably due to inversion. Transcriptional analysis inC. pertinaxshowed that the Ni-CO dehydrogenase gene (cooS-II) and distantly encoded energy-converting-hydrogenase-related genes were remarkably upregulated with 100% CO. In addition, when thiosulfate was available as a terminal electron acceptor in 100% CO, the maximum cell density and maximum specific growth rate ofC. pertinaxwere 3.1-fold and 1.5-fold higher, respectively, than when thiosulfate was absent. The amount of H2produced was only 62% of the amount of CO consumed, less than expected according to hydrogenogenic CO oxidation (CO + H2O → CO2+ H2). Accordingly,C. pertinaxwould couple CO oxidation by Ni-CO dehydrogenase II with simultaneous reduction of not only H2O but also thiosulfate when grown in 100% CO.IMPORTANCEAnaerobic hydrogenogenic carboxydotrophs are thought to fill a vital niche by scavenging potentially toxic CO and producing H2as an available energy source for thermophilic microbes. This hydrogenogenic carboxydotrophy relies on a Ni-CO dehydrogenase-energy-converting hydrogenase gene cluster. This feature is thought to be common to these organisms. However, the hydrogenogenic carboxydotrophCarboxydothermus pertinaxlacks the gene for the Ni-CO dehydrogenase catalytic subunit encoded in the gene cluster. Here, we performed a comparative genome analysis of the genusCarboxydothermus, a transcriptional analysis, and a cultivation study in 100% CO to prove the hydrogenogenic CO metabolism. Results revealed thatC. pertinaxcould couple Ni-CO dehydrogenase II alternatively to the distal energy-converting hydrogenase. Furthermore,C. pertinaxrepresents an example of the functioning of Ni-CO dehydrogenase that does not always correspond to its genomic context, owing to the versatility of CO metabolism and the low redox potential of CO.

scholarly journals CO Metabolism in the Thermophilic Acetogen Thermoanaerobacter kivui

2016 ◽  
Vol 82 (8) ◽  
pp. 2312-2319 ◽  
Author(s):  
Marie Charlotte Weghoff ◽  
Volker Müller
Keyword(s):  
Carbon Monoxide ◽  
Atp Synthesis ◽  
Gene Clusters ◽  
Hydrogenase Activity ◽  
Resting Cells ◽  
Acetate Production ◽  
Content Type ◽  
Crude Extracts ◽  
Acetogenic Bacterium ◽  
Thermoanaerobacter Kivui

ABSTRACTThe thermophilic acetogenic bacteriumThermoanaerobacter kivui, previously described not to use carbon monoxide as a carbon and energy source, was adapted to grow on CO. This was achieved by using a preculture grown on H2plus CO2and by increasing the CO concentration in small, 10% increments.T. kivuiwas finally able to grow within a 100% CO atmosphere. Growth on CO was found in complex and mineral media, and vitamins were not required. Carbon monoxide consumption was accompanied by acetate and hydrogen production. Cells also grew on synthesis gas (syngas) with the simultaneous use of CO and H2coupled to acetate production. CO oxidation in resting cells was coupled to hydrogen and acetate production and accompanied by the synthesis of ATP. A protonophore abolished ATP synthesis but stimulated H2production, which is consistent with a chemiosmotic mechanism of ATP synthesis. Hydrogenase activity was highest in crude extracts of CO-grown cells, and carbon monoxide dehydrogenase (CODH) activity was highest in H2-plus-CO2- or CO-grown cells. The genome ofT. kivuiharbors two CODH gene clusters, and both CODH proteins were present in crude extracts, but one CODH was more prevalent in crude extracts from CO-grown cells.

scholarly journals Physiological and Metabolic Effects of Carbon Monoxide Oxidation in the Model Marine Bacterioplankton Ruegeria pomeroyi DSS-3

2012 ◽  
Vol 79 (2) ◽  
pp. 738-740 ◽  
Author(s):  
Michael Cunliffe
Keyword(s):  
Carbon Monoxide ◽  
Nmr Spectra ◽  
Metabolic Effects ◽  
Co Dehydrogenase ◽  
Ecosystem Models ◽  
Content Type ◽  
Marine Bacterioplankton ◽  
Metabolite Profiles ◽  
Ruegeria Pomeroyi ◽  
Cellular Metabolite

ABSTRACTRuegeria pomeroyiexpresses carbon monoxide (CO) dehydrogenase and oxidizes CO; however, CO has no effect on growth. Nuclear magnetic resonance (NMR) spectra showed that CO has no effect on cellular metabolite profiles. These data support ecosystem models proposing that, even though bacterioplankton CO oxidation is biogeochemically significant, it has an insignificant effect on bacterioplankton productivity.

How Phillips saw the light

2020 ◽  
Vol 36 (8) ◽  
pp. 29-31
Keyword(s):  
Design Methodology ◽  
Reading Time ◽  
Daily Basis ◽  
Business World ◽  
Content Type ◽  
Freak Show ◽  
The World ◽  
Pertinent Information ◽  
The One ◽  
Practical Implications

Purpose Reviews the latest management developments across the globe and pinpoints practical implications from cutting-edge research and case studies. Design/methodology/approach This briefing is prepared by an independent writer who adds their own impartial comments and places the articles in context. Findings The problem with developing a reputation of being something of an oracle in the business world is that all of a sudden, everyone expects you to pull off the trick of interpreting the future on a daily basis. Like a freak show circus act or one-hit wonder pop singer, people expect you to perform when they see you, and they expect you to perform the thing that made you famous, even if it is the one thing in the world you don’t want to do. And when you fail to deliver on these heightened expectations, you are dismissed as a one trick pony, however good that trick is in the first place. Originality/value The briefing saves busy executives and researchers hours of reading time by selecting only the very best, most pertinent information and presenting it in a condensed and easy-to-digest format.

PROMETHEE-based ranking of project managers based on the five personality traits

Kybernetes ◽  
2019 ◽  
Vol 49 (4) ◽  
pp. 1083-1102
Author(s):  
Georgios N. Aretoulis ◽  
Jason Papathanasiou ◽  
Fani Antoniou
Keyword(s):  
Personality Traits ◽  
Questionnaire Survey ◽  
Multicriteria Decision Making ◽  
Project Managers ◽  
Preference Ranking ◽  
Infrastructure Projects ◽  
Public Infrastructure ◽  
Content Type ◽  
The One ◽  
Selection Of

Purpose This paper aims to rank and identify the most efficient project managers (PMs) based on personality traits, using Preference Ranking Organization METHod for Enrichment Evaluations (PROMETHEE) methodology. Design/methodology/approach The proposed methodology relies on the five personality traits. These were used as the selection criteria. A questionnaire survey among 82 experienced engineers was used to estimate the required weights per personality trait. A second two-part questionnaire survey aimed at recording the PMs profile and assess the performance of personality traits per PM. PMs with the most years of experience are selected to be ranked through Visual PROMETHEE. Findings The findings suggest that a competent PM is the one that scores low on the “Neuroticism” trait and high especially on the “Conscientiousness” trait. Research limitations/implications The research applied a psychometric test specifically designed for Greek people. Furthermore, the proposed methodology is based on the personality characteristics to rank the PMs and does not consider the technical skills. Furthermore, the type of project is not considered in the process of ranking PMs. Practical implications The findings could contribute in the selection of the best PM that maximizes the project team’s performance. Social implications Improved project team communication and collaboration leading to improved project performance through better communication and collaboration. This is an additional benefit for the society, especially in the delivery of public infrastructure projects. A lot of public infrastructure projects deviate largely as far as cost and schedule is concerned and this is an additional burden for public and society. Proper project management through efficient PMs would save people’s money and time. Originality/value Identification of the best PMbased on a combination of multicriteria decision-making and psychometric tests, which focus on personality traits.

scholarly journals A Genome-Wide Analysis of Pathogenesis-Related Protein-1 (PR-1) Genes from Piper nigrum Reveals Its Critical Role during Phytophthora capsici Infection

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1007
Author(s):  
Divya Kattupalli ◽  
Asha Sreenivasan ◽  
Eppurathu Vasudevan Soniya
Keyword(s):  
Phytophthora Capsici ◽  
Regulatory Elements ◽  
Piper Nigrum ◽  
Binding Motif ◽  
Altered Expression ◽  
Genome Wide ◽  
A Genome ◽  
Pathogenesis Related Protein ◽  
Pathogenesis Related

Black pepper (Piper nigrum L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. Phytophthora capsici, the causative agent of footrot disease, causes a drastic constraint in P. nigrum cultivation and productivity. To counterattack various biotic and abiotic stresses, plants employ a broad array of mechanisms that includes the accumulation of pathogenesis-related (PR) proteins. Through a genome-wide survey, eleven PR-1 genes that belong to a CAP superfamily protein with a caveolin-binding motif (CBM) and a CAP-derived peptide (CAPE) were identified from P. nigrum. Despite the critical functional domains, PnPR-1 homologs differ in their signal peptide motifs and core amino acid composition in the functional protein domains. The conserved motifs of PnPR-1 proteins were identified using MEME. Most of the PnPR-1 proteins were basic in nature. Secondary and 3D structure analyses of the PnPR-1 proteins were also predicted, which may be linked to a functional role in P. nigrum. The GO and KEGG functional annotations predicted their function in the defense responses of plant-pathogen interactions. Furthermore, a transcriptome-assisted FPKM analysis revealed PnPR-1 genes mapped to the P. nigrum-P. capsici interaction pathway. An altered expression pattern was detected for PnPR-1 transcripts among which a significant upregulation was noted for basic PnPR-1 genes such as CL10113.C1 and Unigene17664. The drastic variation in the transcript levels of CL10113.C1 was further validated through qRT-PCR and it showed a significant upregulation in infected leaf samples compared with the control. A subsequent analysis revealed the structural details, phylogenetic relationships, conserved sequence motifs and critical cis-regulatory elements of PnPR-1 genes. This is the first genome-wide study that identified the role of PR-1 genes during P. nigrum-P. capsici interactions. The detailed in silico experimental analysis revealed the vital role of PnPR-1 genes in regulating the first layer of defense towards a P. capsici infection in Panniyur-1 plants.

scholarly journals Evaluation of a Genome-ScaleIn SilicoMetabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

2012 ◽  
Vol 78 (24) ◽  
pp. 8735-8742 ◽  
Author(s):  
Yilin Fang ◽  
Michael J. Wilkins ◽  
Steven B. Yabusaki ◽  
Mary S. Lipton ◽  
Philip E. Long
Keyword(s):  
Proteomic Analysis ◽  
In Silico ◽  
Field Experiments ◽  
Metabolic Model ◽  
Geobacter Metallireducens ◽  
Content Type ◽  
Proteomic Data ◽  
Subsurface Environment ◽  
A Genome ◽  
Genome Scale

ABSTRACTAccurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within anin silicomodel using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model ofGeobacter metallireducens—specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-basedin silicomodelof G. metallireducensrelates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637G. metallireducensproteins detected during the 2008 experiment were associated with specific metabolic reactions in thein silicomodel. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through thein silicomodel reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in thein silicomodel that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.

scholarly journals Beyond agency and stewardship theory: shareholder–manager relationships and governance structures in family firms

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Ann Sophie K. Löhde ◽  
Giovanna Campopiano ◽  
Andrea Calabrò
Keyword(s):  
Social Exchange ◽  
Family Business ◽  
Social Exchange Theory ◽  
Family Firms ◽  
Governance Structure ◽  
Managerial Behavior ◽  
Exchange System ◽  
Content Type ◽  
The One ◽  
Over Time

PurposeChallenging the static view of family business governance, we propose a model of owner–manager relationships derived from the configurational analysis of managerial behavior and change in governance structure.Design/methodology/approachStemming from social exchange theory and building on the 4C model proposed by Miller and Le Breton-Miller (2005), we consider the evolving owner–manager relationship in four main configurations. On the one hand, we account for family businesses shifting from a generalized to a restricted exchange system, and vice versa, according to whether a family manager misbehaves in a stewardship-oriented governance structure or a nonfamily manager succeeds in building a trusting relationship in an agency-oriented governance structure. On the other hand, we consider that family firms will strengthen a generalized exchange system, rather than a restricted one, according to whether a family manager contributes to the stewardship-oriented culture in the business or a nonfamily manager proves to be driven by extrinsic rewards. Four scenarios are analyzed in terms of the managerial behavior and governance structure that characterize the phases of the relationship between owners and managers.FindingsVarious factors trigger managerial behavior, making the firm deviate from or further build on what is assumed by stewardship and agency theories (i.e. proorganizational versus opportunistic behavior, respectively), which determine the governance structure over time. Workplace deviance, asymmetric altruism and patriarchy on the one hand, and proorganizational behavior, relationship building and long-term commitment on the other, are found to determine how the manager behaves and thus characterize the owner's reactions in terms of governance mechanisms. This enables us to present a dynamic view of governance structures, which adapt to the actual attitudes and behaviors of employed managers.Research limitations/implicationsAs time is a relevant dimension affecting individual behavior and triggering change in an organization, one must consider family business governance as being dynamic in nature. Moreover, it is not family membership that determines the most appropriate governance structure but the owner–manager relationship that evolves over time, thus contributing to the 4C model.Originality/valueThe proposed model integrates social exchange theory and the 4C model to predict changes in governance structure, as summarized in the final framework we propose.

scholarly journals Structural and Functional Insights into Peptidoglycan Access for the Lytic Amidase LytA of Streptococcus pneumoniae

mBio ◽  
2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Peter Mellroth ◽  
Tatyana Sandalova ◽  
Alexey Kikhney ◽  
Francisco Vilaplana ◽  
Dusan Hesek ◽  
...  
Keyword(s):  
Cell Wall ◽  
Streptococcus Pneumoniae ◽  
Solution Structure ◽  
Substrate Binding ◽  
Substrate Recognition ◽  
Lytic Activity ◽  
Site Directed Mutagenesis ◽  
Binding Motif ◽  
Content Type ◽  
Peptidoglycan Synthesis

ABSTRACT The cytosolic N-acetylmuramoyl-l-alanine amidase LytA protein of Streptococcus pneumoniae, which is released by bacterial lysis, associates with the cell wall via its choline-binding motif. During exponential growth, LytA accesses its peptidoglycan substrate to cause lysis only when nascent peptidoglycan synthesis is stalled by nutrient starvation or β-lactam antibiotics. Here we present three-dimensional structures of LytA and establish the requirements for substrate binding and catalytic activity. The solution structure of the full-length LytA dimer reveals a peculiar fold, with the choline-binding domains forming a rigid V-shaped scaffold and the relatively more flexible amidase domains attached in a trans position. The 1.05-Å crystal structure of the amidase domain reveals a prominent Y-shaped binding crevice composed of three contiguous subregions, with a zinc-containing active site localized at the bottom of the branch point. Site-directed mutagenesis was employed to identify catalytic residues and to investigate the relative impact of potential substrate-interacting residues lining the binding crevice for the lytic activity of LytA. In vitro activity assays using defined muropeptide substrates reveal that LytA utilizes a large substrate recognition interface and requires large muropeptide substrates with several connected saccharides that interact with all subregions of the binding crevice for catalysis. We hypothesize that the substrate requirements restrict LytA to the sites on the cell wall where nascent peptidoglycan synthesis occurs. IMPORTANCE Streptococcus pneumoniae is a human respiratory tract pathogen responsible for millions of deaths annually. Its major pneumococcal autolysin, LytA, is required for autolysis and fratricidal lysis and functions as a virulence factor that facilitates the spread of toxins and factors involved in immune evasion. LytA is also activated by penicillin and vancomycin and is responsible for the lysis induced by these antibiotics. The factors that regulate the lytic activity of LytA are unclear, but it was recently demonstrated that control is at the level of substrate recognition and that LytA required access to the nascent peptidoglycan. The present study was undertaken to structurally and functionally investigate LytA and its substrate-interacting interface and to determine the requirements for substrate recognition and catalysis. Our results reveal that the amidase domain comprises a complex substrate-binding crevice and needs to interact with a large-motif epitope of peptidoglycan for catalysis.

Subaltern mediators in the digital landscape

Target ◽  
2017 ◽  
Vol 29 (2) ◽  
pp. 319-338 ◽  
Author(s):  
Teresa Iribarren
Keyword(s):  
Cultural Capital ◽  
Web 2.0 ◽  
The Other ◽  
The Internet ◽  
Lingua Franca ◽  
Content Type ◽  
For Profit ◽  
Long Run ◽  
The One ◽  
Digital Landscape

This article explores translational literary Web 2.0 practices and user-generated cultural creations on the Internet, focusing on video poetry that re-creates canonical poets’ bodies of work. It will be argued that the use of for-profit platforms like YouTube and Vimeo by indie creators and translators of video poetry favours the emergence of new translational attitudes, practices and objects that have positive but also contentious effects. One the one hand, these online mediators explore new poetic expressions and tend to make the most of the potential for dissemination of poetic heritage, providing visibility to non-hegemonic literatures. On the other hand, however, these translational digitally-born practices and creations by voluntary and subaltern mediators might reinforce the hegemonic position of large American Internet corporations at the risk of commodifying cultural capital, consolidating English as a lingua franca and perhaps, in the long run, even fostering a potentially monocultural and internationally homogeneous aesthetics.

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