scholarly journals Meta-Analysis and Functional Validation of Nutritional Requirements of Solventogenic Clostridia Growing under Butanol Stress Conditions and Coutilization of d-Glucose and d-Xylose

2011 ◽  
Vol 77 (13) ◽  
pp. 4473-4485 ◽  
Author(s):  
Humberto Heluane ◽  
Matthew R. Evans ◽  
Sue F. Dagher ◽  
José M. Bruno-Bárcena
Keyword(s):  
Glucose Repression ◽  
Meta Analysis ◽  
Continuous Production ◽  
Clostridium Beijerinckii ◽  
Biofuel Production ◽  
Nutritional Requirements ◽  
Transcriptional Responses ◽  
Content Type ◽  
Butanol Stress ◽  
Solventogenic Clostridia

ABSTRACTRecent advances in systems biology, omics, and computational studies allow us to carry out data mining for improving biofuel production bioprocesses. Of particular interest are bioprocesses that center on microbial capabilities to biotransform both the hexose and pentose fractions present in crop residues. This called for a systematic exploration of the components of the media to obtain higher-density cultures and more-productive fermentation operations than are currently found. By using a meta-analysis approach of the transcriptional responses to butanol stress, we identified the nutritional requirements of solvent-tolerant strainClostridium beijerinckiiSA-1 (ATCC 35702). The nutritional requirements identified were later validated using the chemostat pulse-and-shift technique.C. beijerinckiiSA-1 was cultivated in a two-stage single-feed-stream continuous production system to test the proposed validated medium formulation, and the coutilization ofd-glucose andd-xylose was evaluated by taking advantage of the well-known ability of solventogenic clostridia to utilize a large variety of carbon sources such as mono-, oligo-, and polysaccharides containing pentose and hexose sugars. Our results indicated thatC. beijerinckiiSA-1 was able to coferment hexose/pentose sugar mixtures in the absence of a glucose repression effect. In addition, our analysis suggests that the solvent and acid resistance mechanisms found in this strain are differentially regulated compared to strain NRRL B-527 and are outlined as the basis of the analysis toward optimizing butanol production.

scholarly journals βγ-Crystallination Endows a Novel Bacterial Glycoside Hydrolase 64 with Ca2+-Dependent Activity Modulation

2019 ◽  
Vol 201 (23) ◽  
Author(s):  
Bal Krishnan ◽  
Shanti Swaroop Srivastava ◽  
Venu Sankeshi ◽  
Rupsi Garg ◽  
Sudhakar Srivastava ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Domain Architecture ◽  
Enzyme Reaction ◽  
Structural Features ◽  
Clostridium Beijerinckii ◽  
Biofuel Production ◽  
Carbohydrate Binding ◽  
Reaction Products ◽  
Vast Number ◽  
Content Type

ABSTRACT The prokaryotic βγ-crystallins are a large group of uncharacterized domains with Ca2+-binding motifs. We have observed that a vast number of these domains are found appended to other domains, in particular, the carbohydrate-active enzyme (CAZy) domains. To elucidate the functional significance of these prospective Ca2+ sensors in bacteria and this widespread domain association, we have studied one typical example from Clostridium beijerinckii, a bacterium known for its ability to produce acetone, butanol, and ethanol through fermentation of several carbohydrates. This novel glycoside hydrolase of family 64 (GH64), which we named glucanallin, is composed of a βγ-crystallin domain, a GH64 domain, and a carbohydrate-binding module 56 (CBM56). The substrates of GH64, β-1,3-glucans, are the targets for industrial biofuel production due to their plenitude. We have examined the Ca2+-binding properties of this protein, assayed its enzymatic activity, and analyzed the structural features of the β-1,3-glucanase domain through its high-resolution crystal structure. The reaction products resulting from the enzyme reaction of glucanallin reinforce the mixed nature of GH64 enzymes, in contrast to the prevailing notion of them being an exotype. Upon disabling Ca2+ binding and comparing different domain combinations, we demonstrate that the βγ-crystallin domain in glucanallin acts as a Ca2+ sensor and enhances the glycolytic activity of glucanallin through Ca2+ binding. We also compare the structural peculiarities of this new member of the GH64 family to two previously studied members. IMPORTANCE We have biochemically and structurally characterized a novel glucanase from the less studied GH64 family in a bacterium significant for fermentation of carbohydrates into biofuels. This enzyme displays a peculiar property of being distally modulated by Ca2+ via assistance from a neighboring βγ-crystallin domain, likely through changes in the domain interface. In addition, this enzyme is found to be optimized for functioning in an acidic environment, which is in line with the possibility of its involvement in biofuel production. Multiple occurrences of a similar domain architecture suggest that such a “βγ-crystallination”-mediated Ca2+ sensitivity may be widespread among bacterial proteins.

scholarly journals Crystal Structure and Biophysical Analysis of Furfural-Detoxifying Aldehyde Reductase fromClostridium beijerinckii

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
Alan F. Scott ◽  
Joel Cresser-Brown ◽  
Thomas L. Williams ◽  
Pierre J. Rizkallah ◽  
Yi Jin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Isotope Labeling ◽  
Docking Studies ◽  
Clostridium Beijerinckii ◽  
Biofuel Production ◽  
Aldehyde Reductase ◽  
Fermentation Inhibitors ◽  
Content Type ◽  
Rational Engineering ◽  
Substrate Tolerance

ABSTRACTMany aldehydes, such as furfural, are present in high quantities in lignocellulose lysates and are fermentation inhibitors, which makes biofuel production from this abundant carbon source extremely challenging. Cbei_3974 has recently been identified as an aldo-keto reductase responsible for partial furfural resistance inClostridium beijerinckii. Rational engineering of this enzyme could enhance the furfural tolerance of this organism, thereby improving biofuel yields. We report an extensive characterization of Cbei_3974 and a single-crystal X-ray structure of Cbei_3974 in complex with NADPH at a resolution of 1.75 Å. Docking studies identified residues involved in substrate binding, and an activity screen revealed the substrate tolerance of the enzyme. Hydride transfer, which is partially rate limiting under physiological conditions, occurs from the pro-Rhydrogen of NADPH. Enzyme isotope labeling revealed a temperature-independent enzyme isotope effect of unity, indicating that the enzyme does not use dynamic coupling for catalysis and suggesting that the active site of the enzyme is optimally configured for catalysis with the substrate tested.IMPORTANCEHere we report the crystal structure and biophysical properties of an aldehyde reductase that can detoxify furfural, a common inhibitor of biofuel fermentation found in lignocellulose lysates. The data contained here will serve as a guide for protein engineers to develop improved enzyme variants that would impart furfural resistance to the microorganisms used in biofuel production and thus lead to enhanced biofuel yields from this sustainable resource.

scholarly journals Ferrous-Iron-Activated Transcriptional Factor AdhR Regulates Redox Homeostasis in Clostridium beijerinckii

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Bin Yang ◽  
Xiaoqun Nie ◽  
Youli Xiao ◽  
Yang Gu ◽  
Weihong Jiang ◽  
...  
Keyword(s):  
Control Mechanism ◽  
Redox Homeostasis ◽  
Redox Status ◽  
Clostridium Beijerinckii ◽  
Cellular Redox ◽  
Content Type ◽  
Solvent Production ◽  
Alcohol Synthesis ◽  
Solventogenic Clostridia ◽  
Intracellular Redox

ABSTRACT The AdhR regulatory protein is an activator of σ54-dependent transcription of adhA1 and adhA2 genes, which are required for alcohol synthesis in Clostridium beijerinckii. Here, we identified the signal perceived by AdhR and determined the regulatory mechanism of AdhR activity. By assaying the activity of AdhR in N-terminally truncated forms, a negative control mechanism of AdhR activity was identified in which the central AAA+ domain is subject to repression by the N-terminal GAF and PAS domains. Binding of Fe2+ to the GAF domain was found to relieve intramolecular repression and stimulate the ATPase activity of AdhR, allowing the AdhR to activate transcription. This control mechanism enables AdhR to regulate transcription of adhA1 and adhA2 in response to cellular redox status. The mutants deficient in AdhR or σ54 showed large shifts in intracellular redox state indicated by the NADH/NAD+ ratio under conditions of increased electron availability or oxidative stress. We demonstrated that the Fe2+-activated transcriptional regulator AdhR and σ54 control alcohol synthesis to maintain redox homeostasis in clostridial cells. Expression of N-terminally truncated forms of AdhR resulted in improved solvent production by C. beijerinckii. IMPORTANCE Solventogenic clostridia are anaerobic bacteria that can produce butanol, ethanol, and acetone, which can be used as biofuels or building block chemicals. Here, we show that AdhR, a σ54-dependent transcriptional activator, senses the intracellular redox status and controls alcohol synthesis in Clostridium beijerinckii. AdhR provides a new example of a GAF domain coordinating a mononuclear non-heme iron to sense and transduce the redox signal. Our study reveals a previously unrecognized functional role of σ54 in control of cellular redox balance and provides new insights into redox signaling and regulation in clostridia. Our results reveal AdhR as a novel engineering target for improving solvent production by C. beijerinckii and other solventogenic clostridia.

scholarly journals Disentangling transcriptional responses in plant defense against arthropod herbivores

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alejandro Garcia ◽  
M. Estrella Santamaria ◽  
Isabel Diaz ◽  
Manuel Martinez
Keyword(s):  
Regulatory Networks ◽  
Pieris Rapae ◽  
Meta Analysis ◽  
Plant Response ◽  
Plant Responses ◽  
Transcriptional Responses ◽  
Crop Species ◽  
Physiological Processes ◽  
Meta Analyses ◽  
Plant Herbivore

AbstractThe success in the response of a plant to a pest depends on the regulatory networks that connect plant perception and plant response. Meta-analyses of transcriptomic responses are valuable tools to discover novel mechanisms in the plant/herbivore interplay. Considering the quantity and quality of available transcriptomic analyses, Arabidopsis thaliana was selected to test the ability of comprehensive meta-analyses to disentangle plant responses. The analysis of the transcriptomic data showed a general induction of biological processes commonly associated with the response to herbivory, like jasmonate signaling or glucosinolate biosynthesis. However, an uneven induction of many genes belonging to these biological categories was found, which was likely associated with the particularities of each specific Arabidopsis-herbivore interaction. A thorough analysis of the responses to the lepidopteran Pieris rapae and the spider mite Tetranychus urticae highlighted specificities in the perception and signaling pathways associated with the expression of receptors and transcription factors. This information was translated to a variable alteration of secondary metabolic pathways. In conclusion, transcriptomic meta-analysis has been revealed as a potent way to sort out relevant physiological processes in the plant response to herbivores. Translation of these transcriptomic-based analyses to crop species will permit a more appropriate design of biotechnological programs.

scholarly journals Simultaneous lipid biosynthesis and recovery for oleaginous yeast Yarrowia lipolytica

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Pratik Prashant Pawar ◽  
Annamma Anil Odaneth ◽  
Rajeshkumar Natwarlal Vadgama ◽  
Arvind Mallinath Lali
Keyword(s):  
Yarrowia Lipolytica ◽  
Oil Recovery ◽  
Oleaginous Yeast ◽  
Fermentation Broth ◽  
Continuous Production ◽  
Oil Production ◽  
Biofuel Production ◽  
Oil Yield ◽  
Microbial Oil

Abstract Background Recent trends in bioprocessing have underlined the significance of lignocellulosic biomass conversions for biofuel production. These conversions demand at least 90% energy upgradation of cellulosic sugars to generate renewable drop-in biofuel precursors (Heff/C ~ 2). Chemical methods fail to achieve this without substantial loss of carbon; whereas, oleaginous biological systems propose a greener upgradation route by producing oil from sugars with 30% theoretical yields. However, these oleaginous systems cannot compete with the commercial volumes of vegetable oils in terms of overall oil yields and productivities. One of the significant challenges in the commercial exploitation of these microbial oils lies in the inefficient recovery of the produced oil. This issue has been addressed using highly selective oil capturing agents (OCA), which allow a concomitant microbial oil production and in situ oil recovery process. Results Adsorbent-based oil capturing agents were employed for simultaneous in situ oil recovery in the fermentative production broths. Yarrowia lipolytica, a model oleaginous yeast, was milked incessantly for oil production over 380 h in a media comprising of glucose as a sole carbon and nutrient source. This was achieved by continuous online capture of extracellular oil from the aqueous media and also the cell surface, by fluidizing the fermentation broth over an adsorbent bed of oil capturing agents (OCA). A consistent oil yield of 0.33 g per g of glucose consumed, corresponding to theoretical oil yield over glucose, was achieved using this approach. While the incorporation of the OCA increased the oil content up to 89% with complete substrate consumptions, it also caused an overall process integration. Conclusion The nondisruptive oil capture mediated by an OCA helped in accomplishing a trade-off between microbial oil production and its recovery. This strategy helped in realizing theoretically efficient sugar-to-oil bioconversions in a continuous production process. The process, therefore, endorses a sustainable production of molecular drop-in equivalents through oleaginous yeasts, representing as an absolute microbial oil factory.

scholarly journals The impact of economic factors on the relationships between psychological contract breach and work outcomes: a meta-analysis

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Thushel Jayaweera ◽  
Matthijs Bal ◽  
Katharina Chudzikowski ◽  
Simon de Jong
Keyword(s):  
Job Performance ◽  
Unemployment Rate ◽  
Psychological Contract ◽  
Inflation Rate ◽  
Meta Analysis ◽  
Psychological Contract Breach ◽  
Contract Breach ◽  
Content Type ◽  
Outcome Relationship ◽  
The Impact

PurposeThe purpose of this paper is to explore the macroeconomic factors that may moderate the psychological contract breach (PCB) and work outcome relationship.Design/methodology/approachThis study conducted a meta-analysis based on data from 134 studies.FindingsThe study revealed that the inflation rate and the unemployment rate of a country moderated the association among employee PCB, job performance and turnover.Research limitations/implicationsThe availability of more detailed macroeconomic data against the PCB and outcome relationship for other countries and studies examining the impact of micro-economic data for PCB and outcome relationship would provide a better understanding of the context.Practical implicationsThe authors believe that the results highlight the importance of the national economy since it impacts individual outcomes following a breach.Social implicationsEmployment policies to capture the impact of macroeconomic circumstances as discussed.Originality/valueOne of the valuable contributions made by this paper is that the authors capture the current accumulative knowledge regarding the breach and performance and breach and turnover relationship. Second, the study examines how the inflation rate and unemployment rate could moderate the association between PCB and job performance and turnover.

Impact of economic and financial crimes on economic growth in emerging and developing countries

2019 ◽  
Vol 26 (3) ◽  
pp. 910-920 ◽  
Author(s):  
Sani Abubakar Saddiq ◽  
Abu Sufian Abu Bakar
Keyword(s):  
Systematic Review ◽  
Developing Countries ◽  
Negative Impact ◽  
Meta Analysis ◽  
Eligibility Criteria ◽  
Content Type ◽  
Research Reporting ◽  
Financial Crimes ◽  
Emerging And Developing Countries ◽  
The Impact

Purpose The purpose of the study is to investigate the impact of economic and financial crimes on the economies of emerging and developing countries. Design/methodology/approach Preferred Reporting Items for Systematic review and Meta-Analysis (PRISMA) guidelines and meta-analysis of economics research reporting guidelines were used to conduct a quantitative synthesis of empirical evidence on the impact of economic and financial crimes in developing and emerging countries. Findings A total of 103 studies were searched, out of which 6 met the selection/eligibility criteria of this systematic review. The six selected studies indicated that economic and financial crimes have a negative impact in emerging and developing countries. Originality/value To the best knowledge of the authors, no published systematic review of the impact of economic and financial crimes in developing countries has been conducted to date.

scholarly journals Endotoxemia as a Diagnostic Tool for Patients with Suspected Bacteremia Caused by Gram-Negative Organisms: a Meta-Analysis of 4 Decades of Studies

2015 ◽  
Vol 53 (4) ◽  
pp. 1183-1191 ◽  
Author(s):  
James C. Hurley ◽  
Piotr Nowak ◽  
Lars Öhrmalm ◽  
Charalambos Gogos ◽  
Apostolos Armaganidis ◽  
...  
Keyword(s):  
Confidence Interval ◽  
Meta Analysis ◽  
Inclusion Criteria ◽  
Summary Receiver Operating Characteristic ◽  
Detection Rates ◽  
Gram Negative ◽  
Content Type ◽  
E Coli ◽  
Patient Groups ◽  
Gram Negative Organisms

The clinical significance of endotoxin detection in blood has been evaluated for a broad range of patient groups in over 40 studies published over 4 decades. The influences of Gram-negative (GN) bacteremia species type and patient inclusion criteria on endotoxemia detection rates in published studies remain unclear. Studies were identified after a literature search and manual reviews of article bibliographies, together with a direct approach to authors of potentially eligible studies for data clarifications. The concordance between GN bacteremia and endotoxemia expressed as the summary diagnostic odds ratios (DORs) was derived for three GN bacteremia categories across eligible studies by using a hierarchical summary receiver operating characteristic (HSROC) method. Forty-two studies met broad inclusion criteria, with between 2 and 173 GN bacteremias in each study. Among all 42 studies, the DORs (95% confidence interval) were 3.2 (1.7 to 6.0) and 5.8 (2.4 to 13.7) in association with GN bacteremias withEscherichia coliand those withPseudomonas aeruginosa, respectively. Among 12 studies of patients with sepsis, the proportion of endotoxemia positivity (95% confidence interval) among patients withP. aeruginosabacteremia (69% [57 to 79%];P= 0.004) or withProteusbacteremia (76% [51 to 91%];P= 0.04) was significantly higher than that among patients without GN bacteremia (49% [33 to 64%]), but this was not so for patients bacteremic withE. coli(57% [40 to 73%];P= 0.55). Among studies of the sepsis patient group, the concordance of endotoxemia with GN bacteremia was surprisingly weak, especially forE. coliGN bacteremia.

scholarly journals Naturally Occurring Motility-Defective Mutants of Salmonella enterica Serovar Enteritidis Isolated Preferentially from Nonhuman Rather than Human Sources

2011 ◽  
Vol 77 (21) ◽  
pp. 7740-7748 ◽  
Author(s):  
Lucía Yim ◽  
Laura Betancor ◽  
Arací Martínez ◽  
Clare Bryant ◽  
Duncan Maskell ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Intestinal Epithelial ◽  
Salmonella Enterica Serovar Enteritidis ◽  
Transcriptional Responses ◽  
Content Type ◽  
Field Isolates ◽  
Specific Pcr ◽  
Human Intestinal Epithelial Cells ◽  
Natural Isolates ◽  
Cell Invasiveness

ABSTRACTSalmonellosis represents a worldwide health problem because it is one of the major causes of food-borne disease. Although motility is postulated as an importantSalmonellavirulence attribute, there is little information about variation in motility in natural isolates. Here we report the identification of a point mutation (T551 → G) inmotA, a gene essential for flagellar rotation, in severalSalmonella entericaserovar Enteritidis field isolates. This mutation results in bacteria that can biosynthesize structurally normal but paralyzed flagella and are impaired in their capacity to invade human intestinal epithelial cells. Introduction of a wild-type copy ofmotAinto one of these isolates restored both motility and cell invasiveness. ThemotAmutant triggered higher proinflammatory transcriptional responses than an aflagellate isolate in differentiated Caco-2 cells, suggesting that the paralyzed flagella are able to signal through pattern recognition receptors. A specific PCR was designed to screen for the T551 → G mutation in a collection of 266S. Enteritidis field isolates from a nationwide epidemic, comprising 194 from humans and 72 from other sources. We found that 72 of the 266 (27%) isolates were nonmotile, including 24.7% (48/194) of human and 33.3% (24/72) of food isolates. Among nonmotile isolates, 15 carried the T551 → G mutation and, significantly, 13 were recovered from food, including 7 from eggs, but only 2 were from human sources. These results suggest that the presence of paralyzed flagella may impair the ability ofS. Enteritidis to cause disease in the human host but does not prevent its ability to colonize chickens and infect eggs.

Does the good lives model work? A systematic review of the recidivism evidence

2021 ◽  
Vol 23 (3) ◽  
pp. 285-300
Author(s):  
Jenna Zeccola ◽  
Sally Fiona Kelty ◽  
Douglas Boer
Keyword(s):  
Meta Analysis ◽  
Future Research ◽  
Correct Treatment ◽  
Recidivism Rates ◽  
Good Lives Model ◽  
Content Type ◽  
Reducing Recidivism ◽  
Prison Community ◽  
Treatment Dosage ◽  
Good Lives

Purpose The purpose of this paper is to evaluate the efficacy of good lives model (GLM) interventions on the recidivism outcomes of convicted offenders. Design/methodology/approach The review adhered to preferred reporting items for systematic reviews and meta-analysis and Cochrane guidelines. Digital databases were searched and articles reporting outcomes of the GLM amongst convicted offenders and outcomes including recidivism data and pre-post measures of dynamic risk were included in a narrative synthesis. Findings Of 1,791 articles screened, only six studies met the criteria for review. Key findings were: in half the reviewed studies, GLM did not increase recidivism risk; in half the reviewed studies, only when the correct treatment dosage was applied that some evidence of risk reduction was found; there was limited support for GLM increasing or sustaining motivation for resistance from reoffending. Research for the review was limited and support for the GLM in reducing recidivism rates was not established. Practical implications In this 2021 review, the authors examined the efficacy of the GLM in reducing recidivism. This addresses a gap in the literature. The authors found that there is insufficient evidence to suggest that the GLM can reduce recidivism. This has implications for practitioners who wish to deliver evidence-based practices in prison/community settings. There is currently not enough peer-reviewed evidence to unequivocally confirm the efficacy of the GLM. The authors recommended additional quality programme outcome research be carried out. Originality/value To the best of the authors’ knowledge, this study is the first to assess quantitative and qualitative studies on the efficacy of the GLM and provides foundations for future research.

Sign in / Sign up

Export Citation Format

Share Document