scholarly journals The Crabtree Effect Shapes theSaccharomyces cerevisiaeLag Phase during the Switch between Different Carbon Sources

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Gemma Perez-Samper ◽  
Bram Cerulus ◽  
Abbas Jariani ◽  
Lieselotte Vermeersch ◽  
Nuria Barrajón Simancas ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Carbon Sources ◽  
Anaerobic Growth ◽  
Lag Phase ◽  
Crabtree Effect ◽  
Molecular Processes ◽  
Content Type ◽  
A Genome ◽  
Growth Experiments ◽  
Lag Phases

ABSTRACTWhen faced with environmental changes, microbes often enter a temporary growth arrest during which they reprogram the expression of specific genes to adapt to the new conditions. A prime example of such a lag phase occurs when microbes need to switch from glucose to other, less-preferred carbon sources. Despite its industrial relevance, the genetic network that determines the duration of the lag phase has not been studied in much detail. Here, we performed a genome-wide Bar-Seq screen to identify genetic determinants of theSaccharomyces cerevisiaeglucose-to-galactose lag phase. The results show that genes involved in respiration, and specifically those encoding complexes III and IV of the electron transport chain, are needed for efficient growth resumption after the lag phase. Anaerobic growth experiments confirmed the importance of respiratory energy conversion in determining the lag phase duration. Moreover, overexpression of the central regulator of respiration,HAP4, leads to significantly shorter lag phases. Together, these results suggest that the glucose-induced repression of respiration, known as the Crabtree effect, is a major determinant of microbial fitness in fluctuating carbon environments.IMPORTANCEThe lag phase is arguably one of the prime characteristics of microbial growth. Longer lag phases result in lower competitive fitness in variable environments, and the duration of the lag phase is also important in many industrial processes where long lag phases lead to sluggish, less efficient fermentations. Despite the immense importance of the lag phase, surprisingly little is known about the exact molecular processes that determine its duration. Our study uses the molecular toolbox ofS. cerevisiaecombined with detailed growth experiments to reveal how the transition from fermentative to respirative metabolism is a key bottleneck for cells to overcome the lag phase. Together, our findings not only yield insight into the key molecular processes and genes that influence lag duration but also open routes to increase the efficiency of industrial fermentations and offer an experimental framework to study other types of lag behavior.

scholarly journals GntR Family Regulator DasR Controls Acetate Assimilation by Directly Repressing the acsA Gene in Saccharopolyspora erythraea

2018 ◽  
Vol 200 (13) ◽  
Author(s):  
Di You ◽  
Bai-Qing Zhang ◽  
Bang-Ce Ye
Keyword(s):  
Environmental Changes ◽  
Carbon Sources ◽  
Saccharopolyspora Erythraea ◽  
Upstream Region ◽  
Acetate Metabolism ◽  
Acetyl Coa ◽  
Content Type ◽  
Acetate Assimilation ◽  
Responsive Element ◽  
Gntr Family

ABSTRACT The GntR family regulator DasR controls the transcription of genes involved in chitin and N -acetylglucosamine (GlcNAc) metabolism in actinobacteria. GlcNAc is catabolized to ammonia, fructose-6-phosphate (Fru-6P), and acetate, which are nitrogen and carbon sources. In this work, a DasR-responsive element ( dre ) was observed in the upstream region of acsA1 in Saccharopolyspora erythraea . This gene encodes acetyl coenzyme A (acetyl-CoA) synthetase (Acs), an enzyme that catalyzes the conversion of acetate into acetyl-CoA. We found that DasR repressed the transcription of acsA1 in response to carbon availability, especially with GlcNAc. Growth inhibition was observed in a dasR -deleted mutant (Δ dasR ) in the presence of GlcNAc in minimal medium containing 10 mM acetate, a condition under which Acs activity is critical to growth. These results demonstrate that DasR controls acetate assimilation by directly repressing the transcription of the acsA1 gene and performs regulatory roles in the production of intracellular acetyl-CoA in response to GlcNAc. IMPORTANCE Our work has identified the DasR GlcNAc-sensing regulator that represses the generation of acetyl-CoA by controlling the expression of acetyl-CoA synthetase, an enzyme responsible for acetate assimilation in S. erythraea . The finding provides the first insights into the importance of DasR in the regulation of acetate metabolism, which encompasses the regulatory network between nitrogen and carbon metabolism in actinobacteria, in response to environmental changes.

scholarly journals Novel DNA Binding and Regulatory Activities for σ54 (RpoN) in Salmonella enterica Serovar Typhimurium 14028s

2017 ◽  
Vol 199 (12) ◽  
Author(s):  
Ashley C. Bono ◽  
Christine E. Hartman ◽  
Sina Solaimanpour ◽  
Hao Tong ◽  
Steffen Porwollik ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Salmonella Enterica ◽  
Environmental Changes ◽  
Atp Hydrolysis ◽  
Content Type ◽  
Dna Binding Sites ◽  
A Genome ◽  
Serovar Typhimurium ◽  
Host Microbe Interactions

ABSTRACT The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. Salmonella enterica serovar Typhimurium utilizes the housekeeping σ70 and five alternative sigma factors, including σ54. The σ54-RNAP differs from other σ-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription. In S. Typhimurium, σ54-dependent promoters normally respond to one of 13 different bEBPs, each of which is activated under a specific growth condition. Here, we utilized a constitutively active, promiscuous bEBP to perform a genome-wide identification of σ54-RNAP DNA binding sites and the transcriptome of the σ54 regulon of S. Typhimurium. The position and context of many of the identified σ54 RNAP DNA binding sites suggest regulatory roles for σ54-RNAP that connect the σ54 regulon to regulons of other σ factors to provide a dynamic response to rapidly changing environmental conditions. IMPORTANCE The alternative sigma factor σ54 (RpoN) is required for expression of genes involved in processes with significance in agriculture, bioenergy production, bioremediation, and host-microbe interactions. The characterization of the σ54 regulon of the versatile pathogen S. Typhimurium has expanded our understanding of the scope of the σ54 regulon and how it links to other σ regulons within the complex regulatory network for gene expression in bacteria.

scholarly journals Phosphotransferase System-Dependent Extracellular Growth of Listeria monocytogenes Is Regulated by Alternative Sigma Factors σLand σH

2014 ◽  
Vol 80 (24) ◽  
pp. 7673-7682 ◽  
Author(s):  
Siyun Wang ◽  
Renato H. Orsi ◽  
Silin Tang ◽  
Wei Zhang ◽  
Martin Wiedmann ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Carbon Source ◽  
Parent Strain ◽  
Carbon Sources ◽  
Maximum Growth ◽  
Fine Tuning ◽  
Lag Phase ◽  
Phosphotransferase System ◽  
Phase Duration ◽  
Content Type

ABSTRACTAlternative sigma (σ) factors and phosphotransferase systems (PTSs) play pivotal roles in the environmental adaptation and virulence ofListeria monocytogenes. The growth of theL. monocytogenesparent strain 10403S and 15 isogenic alternative σ factor mutants was assessed in defined minimal medium (DM) with PTS-dependent or non-PTS-dependent carbon sources at 25°C or 37°C. Overall, our results suggested that the regulatory effect of alternative σ factors on the growth ofL. monocytogenesis dependent on the temperature and the carbon source. One-way analysis of variance (one-way ANOVA) showed that the factor “strain” had a significant effect on the maximum growth rate (μmax), lag phase duration (λ), and maximum optical density (ODmax) in PTS-dependent carbon sources (P< 0.05) but not in a non-PTS-dependent carbon source. Also, the ODmaxwas not affected by strain for any of the three PTS-dependent carbon sources at 25°C but was affected by strain at 37°C. Monitoring by quantitative real-time PCR (qRT-PCR) showed that transcript levels forlmo0027, a glucose-glucoside PTS permease (PTSGlc-1)-encoding gene, were higher in the absence of σL, and lower in the absence of σH, than in the parent strain. Our data thus indicate that σLnegatively regulateslmo0027and that the increased μmaxobserved for the ΔsigLstrain in DM with glucose may be associated with increased expression of PTSGlc-1 encoded bylmo0027. Our findings suggest that σHand σLmediate the PTS-dependent growth ofL. monocytogenesthrough complex transcriptional regulations and fine-tuning of the expression of specificptsgenes, includinglmo0027. Our findings also reveal a more important and complex role of alternative σ factors in the regulation of growth in different sugar sources than previously assumed.

scholarly journals Genome-scale metabolic modelling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism.

2021 ◽  
Author(s):  
Viviënne Mol ◽  
Martyn Bennett ◽  
Benjamín J. Sánchez ◽  
Beata K. Lisowska ◽  
Markus J. Herrgård ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Anaerobic Metabolism ◽  
Carbon Sources ◽  
Anaerobic Growth ◽  
Scale Model ◽  
High Yield ◽  
A Genome ◽  
Depth Analysis ◽  
Genome Scale ◽  
Parageobacillus Thermoglucosidasius

Parageobacillus thermoglucosidasius represents a thermophilic, facultative anaerobic bacterial chassis, with several desirable traits for metabolic engineering and industrial production. To further optimize strain productivity, a systems level understanding of its metabolism is needed, which can be facilitated by a genome-scale metabolic model. Here, we present p-thermo, the most complete, curated and validated genome-scale model (to date) of Parageobacillus thermoglucosidasius NCIMB 11955. It spans a total of 890 metabolites, 1175 reactions and 917 metabolic genes, forming an extensive knowledge base for P. thermoglucosidasius NCIMB 11955 metabolism. The model accurately predicts aerobic utilization of 22 carbon sources, and the predictive quality of internal fluxes was validated with previously published 13C-fluxomics data. In an application case, p-thermo was used to facilitate more in-depth analysis of reported metabolic engineering efforts, giving additional insight into fermentative metabolism. Finally, p-thermo was used to resolve a previously uncharacterised bottleneck in anaerobic metabolism, by identifying the minimal required supplemented nutrients (thiamin, biotin and iron(III)) needed to sustain anaerobic growth. This highlights the usefulness of p-thermo for guiding the generation of experimental hypotheses and for facilitating data-driven metabolic engineering, expanding the use of P. thermoglucosidasius as a high yield production platform.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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 Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Andrew Oliver ◽  
Brandon LaMere ◽  
Claudia Weihe ◽  
Stephen Wandro ◽  
Karen L. Lindsay ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Reproductive Health ◽  
Microbial Communities ◽  
Carbon Sources ◽  
Amplicon Sequencing ◽  
Vaginal Microbiome ◽  
Content Type ◽  
Healthy Women ◽  
Healthy Pregnancy ◽  
Tof Ms

ABSTRACT Microbes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well-adapted microbes which are able to survive in a narrow pH range and are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. We characterized the cervicovaginal microbiomes of 16 healthy women throughout the three trimesters of pregnancy. Additionally, we analyzed saliva and urine metabolomes using gas chromatography-time of flight mass spectrometry (GC-TOF MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) lipidomics approaches for samples from mothers and their infants through the first year of life. Amplicon sequencing revealed most women had either a simple community with one highly abundant species of Lactobacillus or a more diverse community characterized by a high abundance of Gardnerella, as has also been previously described in several independent cohorts. Integrating GC-TOF MS and lipidomics data with amplicon sequencing, we found metabolites that distinctly associate with particular communities. For example, cervicovaginal microbial communities dominated by Lactobacillus crispatus have high mannitol levels, which is unexpected given the characterization of L. crispatus as a homofermentative Lactobacillus species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal microbiome are dictated by the availability of host sugars, such as fructose, which is the most likely substrate being converted to mannitol. Overall, using a multi-“omic” approach, we begin to address the genetic and molecular means by which a particular vaginal microbiome becomes vulnerable to large changes in composition. IMPORTANCE Humans have a unique vaginal microbiome compared to other mammals, characterized by low diversity and often dominated by Lactobacillus spp. Dramatic shifts in vaginal microbial communities sometimes contribute to the presence of a polymicrobial overgrowth condition called bacterial vaginosis (BV). However, many healthy women lacking BV symptoms have vaginal microbiomes dominated by microbes associated with BV, resulting in debate about the definition of a healthy vaginal microbiome. Despite substantial evidence that the reproductive health of a woman depends on the vaginal microbiota, future therapies that may improve reproductive health outcomes are stalled due to limited understanding surrounding the ecology of the vaginal microbiome. Here, we use sequencing and metabolomic techniques to show novel associations between vaginal microbes and metabolites during healthy pregnancy. We speculate these associations underlie microbiome dynamics and may contribute to a better understanding of transitions between alternative vaginal microbiome compositions.

scholarly journals Calvin Cycle Flux, Pathway Constraints, and Substrate Oxidation State Together Determine the H2 Biofuel Yield in Photoheterotrophic Bacteria

mBio ◽  
2011 ◽  
Vol 2 (2) ◽  
Author(s):  
James B. McKinlay ◽  
Caroline S. Harwood
Keyword(s):  
Organic Compounds ◽  
Oxidation State ◽  
Rhodopseudomonas Palustris ◽  
Calvin Cycle ◽  
Substrate Oxidation ◽  
Hydrogen Gas ◽  
Anaerobic Growth ◽  
Anoxygenic Phototrophic Bacteria ◽  
Transportation Fuel ◽  
Content Type

ABSTRACTHydrogen gas (H2) is a possible future transportation fuel that can be produced by anoxygenic phototrophic bacteria via nitrogenase. The electrons for H2are usually derived from organic compounds. Thus, one would expect more H2to be produced when anoxygenic phototrophs are supplied with increasingly reduced (electron-rich) organic compounds. However, the H2yield does not always differ according to the substrate oxidation state. To understand other factors that influence the H2yield, we determined metabolic fluxes inRhodopseudomonas palustrisgrown on13C-labeled fumarate, succinate, acetate, and butyrate (in order from most oxidized to most reduced). The flux maps revealed that the H2yield was influenced by two main factors in addition to substrate oxidation state. The first factor was the route that a substrate took to biosynthetic precursors. For example, succinate took a different route to acetyl-coenzyme A (CoA) than acetate. As a result,R. palustrisgenerated similar amounts of reducing equivalents and similar amounts of H2from both succinate and acetate, even though succinate is more oxidized than acetate. The second factor affecting the H2yield was the amount of Calvin cycle flux competing for electrons. When nitrogenase was active, electrons were diverted away from the Calvin cycle towards H2, but to various extents, depending on the substrate. When Calvin cycle flux was blocked, the H2yield increased during growth on all substrates. In general, this increase in H2yield could be predicted from the initial Calvin cycle flux.IMPORTANCEPhotoheterotrophic bacteria, likeRhodopseudomonas palustris, obtain energy from light and carbon from organic compounds during anaerobic growth. Cells can naturally produce the biofuel H2as a way of disposing of excess electrons. Unexpectedly, feeding cells organic compounds with more electrons does not necessarily result in more H2. Despite repeated observations over the last 40 years, the reasons for this discrepancy have remained unclear. In this paper, we identified two metabolic factors that influence the H2yield, (i) the route taken to make biosynthetic precursors and (ii) the amount of CO2-fixing Calvin cycle flux that competes against H2production for electrons. We show that the H2yield can be improved on all substrates by using a strain that is incapable of Calvin cycle flux. We also contributed quantitative knowledge to the long-standing question of why photoheterotrophs must produce H2or fix CO2even on relatively oxidized substrates.

The impact of executives’ perceptions of environmental threats and organizational slack on innovation strategies

2016 ◽  
Vol 7 (2) ◽  
pp. 216-230 ◽  
Author(s):  
Chengyuan Wang ◽  
Biao Luo ◽  
Yong Liu ◽  
Zhengyun Wei
Keyword(s):  
Cognitive Theory ◽  
Environmental Changes ◽  
Ordinary Least Squares ◽  
Organizational Slack ◽  
Least Squares Regression ◽  
Content Type ◽  
Environmental Threats ◽  
Innovation Strategies ◽  
The Impact ◽  
The Relationship

Purpose The paper aims to study the relationship between executives’ perceptions of environmental threats and innovation strategies and investigate the moderating effect of contextual factor (i.e. organizational slack) on such relations. It proposes a dualistic relationship between executives’ perceptions of environmental threats and innovation strategies, in which different perceptions of environmental threats will lead to corresponding innovation strategies, and dyadic organizational slack can promote such processes. Design/methodology/approach The paper is based on a survey with 163 valid questionnaires, which were all completed by executives. Hierarchical ordinary least-squares regression analysis is used to test the hypotheses proposed in this paper. Findings The paper provides empirical insights about that executives tend to choose exploratory innovation when they perceive environmental changes as likely loss threats, yet adopt exploitative innovation when perceiving control-reducing threats. Furthermore, unabsorbed slack (e.g. financial redundancy) positively moderates both relationships, while absorbed slack (e.g. operational redundancy) merely positively influences the relationship between the perception of control-reducing threats and exploitative innovation. Originality/value The paper bridges the gap between organizational innovation and cognitive theory by proposing a dualistic relationship between executives’ perceptions of environmental threats and innovation strategies. The paper further enriches innovation studies by jointly considering both subjective and objective influence factors of innovation and argues that organizational slack can moderate such dualistic relationship.

scholarly journals The growth of Paracoccus halodenitrificans in a defined medium

1984 ◽  
Vol 30 (6) ◽  
pp. 837-840 ◽  
Author(s):  
Lawrence I. Hochstein ◽  
Geraldine A. Tomlinson
Keyword(s):  
Synthetic Medium ◽  
Carbon Sources ◽  
Defined Medium ◽  
Anaerobic Growth ◽  
Inorganic Salts ◽  
Vitamin B ◽  
Aerobic Growth ◽  
Methionine Biosynthesis ◽  
Dependent Pathway

A synthetic medium, consisting of inorganic salts and any of a number of carbon sources, supported the aerobic growth of Paracoccus halodenitrificans when supplemented with thiamine. The same medium plus an appropriate nitrogenous oxide supported anaerobic growth when additionally supplemented with methionine. The observation that vitamin B12 or betaine replaced methionine suggested that P. halodenitrificans had a defect in the cobalamin-dependent pathway for methionine biosynthesis, as well as the inability to synthesize betaine when growing anaerobically.

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