scholarly journals Retromer Complex and PI3K Complex II-Related Genes Mediate the Yeast (Saccharomyces cerevisiae) Sodium Metabisulfite Resistance Response

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3512
Author(s):  
Xuejiao Jin ◽  
Huihui Zhao ◽  
Min Zhou ◽  
Jie Zhang ◽  
Tingting An ◽  
...  
Keyword(s):  
Wine Industry ◽  
Cellular Damage ◽  
Sodium Metabisulfite ◽  
Yeast Saccharomyces Cerevisiae ◽  
Resistance Response ◽  
Complex Ii ◽  
Retromer Complex ◽  
A Genome ◽  
Tolerance Response ◽  
Cytotoxicity Effects

Sodium metabisulfite (Na2S2O5) is widely used as a preservative in the food and wine industry. However, it causes varying degrees of cellular damage to organisms. In order to improve our knowledge regarding its cyto-toxicity, a genome-wide screen using the yeast single deletion collection was performed. Additionally, a total of 162 Na2S2O5-sensitive strains and 16 Na2S2O5-tolerant strains were identified. Among the 162 Na2S2O5 tolerance-related genes, the retromer complex was the top enriched cellular component. Further analysis demonstrated that retromer complex deletion leads to increased sensitivity to Na2S2O5, and that Na2S2O5 can induce mislocalization of retromer complex proteins. Notably, phosphatidylinositol 3-monophosphate kinase (PI3K) complex II, which is important for retromer recruitment to the endosome, might be a potential regulator mediating retromer localization and the yeast Na2S2O5 tolerance response. Na2S2O5 can decrease the protein expressions of Vps34, which is the component of PI3K complex. Therefore, Na2S2O5-mediated retromer redistribution might be caused by the effects of decreased Vps34 expression levels. Moreover, both pharmaceutical inhibition of Vps34 functions and deletions of PI3K complex II-related genes affect cell tolerance to Na2S2O5. The results of our study provide a global picture of cellular components required for Na2S2O5 tolerance and advance our understanding concerning Na2S2O5-induced cytotoxicity effects.

scholarly journals Signal Peptide-Dependent Protein Transport inBacillus subtilis: a Genome-Based Survey of the Secretome

2000 ◽  
Vol 64 (3) ◽  
pp. 515-547 ◽  
Author(s):  
Harold Tjalsma ◽  
Albert Bolhuis ◽  
Jan D. H. Jongbloed ◽  
Sierd Bron ◽  
Jan Maarten van Dijl
Keyword(s):  
Protein Secretion ◽  
Molecular Mechanisms ◽  
Protein Transport ◽  
Transport Systems ◽  
Future Research ◽  
Yeast Saccharomyces Cerevisiae ◽  
Transport Pathways ◽  
Amino Terminal ◽  
Cell Factories ◽  
A Genome

SUMMARY One of the most salient features of Bacillus subtilis and related bacilli is their natural capacity to secrete a variety of proteins into their environment, frequently to high concentrations. This has led to the commercial exploitation of bacilli as major “cell factories” for secreted enzymes. The recent sequencing of the genome of B. subtilis has provided major new impulse for analysis of the molecular mechanisms underlying protein secretion by this organism. Most importantly, the genome sequence has allowed predictions about the composition of the secretome, which includes both the pathways for protein transport and the secreted proteins. The present survey of the secretome describes four distinct pathways for protein export from the cytoplasm and approximately 300 proteins with the potential to be exported. By far the largest number of exported proteins are predicted to follow the major “Sec” pathway for protein secretion. In contrast, the twin-arginine translocation “Tat” pathway, a type IV prepilin-like export pathway for competence development, and ATP-binding cassette transporters can be regarded as “special-purpose” pathways, through which only a few proteins are transported. The properties of distinct classes of amino-terminal signal peptides, directing proteins into the various protein transport pathways, as well as the major components of each pathway are discussed. The predictions and comparisons in this review pinpoint important differences as well as similarities between protein transport systems in B. subtilis and other well-studied organisms, such as Escherichia coli and the yeast Saccharomyces cerevisiae. Thus, they may serve as a lead for future research and applications.

scholarly journals Sensory domain of the cell cycle kinase CckA inCaulobacter crescentusregulates the differential DNA binding activity of the master regulator CtrA

2018 ◽  
Author(s):  
Sharath Narayanan ◽  
Lokesh Kumar ◽  
Sunish Kumar Radhakrishnan
Keyword(s):  
Cell Cycle ◽  
Dna Binding ◽  
Caulobacter Crescentus ◽  
Point Mutations ◽  
Signal Transduction Pathway ◽  
Binding Activity ◽  
Cellular Damage ◽  
Bacterial Cells ◽  
Topoisomerase Iv ◽  
A Genome

Sophisticated signaling mechanisms allow bacterial cells to cope with environmental and intracellular challenges. Activation of specific pathways facilitates the cells to overcome cellular damage and thereby warrant integrity. Here we demonstrate the pliability of the CckA-CtrA two component signaling system in the freshwater bacteriumCaulobacter crescentus. Our forward genetic screen to analyse suppressor mutations that can negate the chromosome segregation block induced by the topoisomerase IV inhibitor, NstA, yielded various point mutations in the cell cycle histidine kinase, CckA. Notably, we identified a point mutation in the PAS-B domain of CckA, which resulted in increased levels of phosphorylated CtrA (CtrA~P), the master cell cycle regulator. Surprisingly, this increase in CtrA~P levels did not translate into a genome-wide increase in the DNA occupancy of CtrA, but specifically enriched its affinity to the chromosomal origin of replication, Cori, and a very small sub-set of CtrA regulated promoters. We show that through this enhanced binding of CtrA to the Cori, cells are able to overcome the toxic defects rendered by stable NstA through a possible slow down in the chromosome cycle. Taken together, our work opens up an unexplored and intriguing aspect of the CckA-CtrA signal transduction pathway. The distinctive DNA binding nature of CtrA and its regulation by CckA might also be crucial for pathogenesis because of the highly conserved nature of CckA-CtrA pathway in alphaproteobacteria.

scholarly journals Genomic Dissection of Anthracnose (Colletotrichum sublineolum) Resistance Response in Sorghum Differential Line SC112-14

2020 ◽  
Vol 10 (4) ◽  
pp. 1403-1412
Author(s):  
Clara M. Cruet-Burgos ◽  
Hugo E. Cuevas ◽  
Louis K. Prom ◽  
Joseph E. Knoll ◽  
Lauren R. Stutts ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Genome Scan ◽  
The United States ◽  
Resistance Locus ◽  
Chromosome 5 ◽  
Resistance Response ◽  
Colletotrichum Sublineolum ◽  
A Genome

Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum, is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.

scholarly journals Assortment of Phosphatidylinositol 3-Kinase Complexes—Atg14p Directs Association of Complex I to the Pre-autophagosomal Structure in Saccharomyces cerevisiae

2006 ◽  
Vol 17 (4) ◽  
pp. 1527-1539 ◽  
Author(s):  
Keisuke Obara ◽  
Takayuki Sekito ◽  
Yoshinori Ohsumi
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Complex I ◽  
Regulatory Subunit ◽  
Biological Processes ◽  
Phosphatidylinositol 3 Kinase ◽  
Yeast Saccharomyces Cerevisiae ◽  
Complex Ii ◽  
Vacuolar Protein ◽  
Vacuolar Membranes ◽  
Phosphatidylinositol 3

In the yeast Saccharomyces cerevisiae, two similar phosphatidylinositol 3-kinase complexes (complexes I and II) function in distinct biological processes, complex I in autophagy and complex II in the vacuolar protein sorting via endosomes. Atg14p is only integrated into complex I, likely facilitating the function of complex I in autophagy. Deletion analysis of Atg14p revealed that N-terminal region containing the coiled-coil structures was essential and sufficient for autophagy. Atg14p localized to pre-autophagosomal structure (PAS) and vacuolar membranes, whereas Vps38p, a component specific to complex II, localized to endosomes and vacuolar membranes. Vps34p and Vps30p, components shared by the two complexes, localized to the PAS, vacuolar membranes, and several punctate structures that included endosomes. The localization of these components to the PAS was Atg14p dependent but not dependent on Vps38p. Conversely, localization of these proteins to endosomes required Vps38p but not Atg14p. Vps15p, regulatory subunit of the Vps34p complexes, localized to the PAS, vacuolar membranes, and punctate structures independent of both Atg14p and Vps38p. Together, these results indicate that complexes I and II function in distinct biological processes by localizing to specific compartments in a manner mediated by specific components of each complex, Atg14p and Vps38p, respectively.

scholarly journals Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance

2020 ◽  
Author(s):  
Helena M. van Tol ◽  
E. Virginia Armbrust
Keyword(s):  
Organic Matter ◽  
Sulfur Metabolism ◽  
Reducing Power ◽  
Metabolic Model ◽  
Redox Balance ◽  
Thalassiosira Pseudonana ◽  
Cellular Damage ◽  
Marine Microorganisms ◽  
A Genome ◽  
Genome Scale

AbstractDiatoms are unicellular photosynthetic algae known to secrete organic matter that fuels secondary production in the ocean, though our knowledge of how their physiology impacts the character of dissolved organic matter remains limited. Like all photosynthetic organisms, their use of light for energy and reducing power creates the challenge of avoiding cellular damage. To better understand the interplay between redox balance and organic matter secretion, we reconstructed a genome-scale metabolic model of Thalassiosira pseudonana strain CCMP 1335, a model for diatom molecular biology and physiology, with a 60-year history of studies. The model simulates the metabolic activities of 1,432 genes via a network of 2,792 metabolites produced through 6,079 reactions distributed across six subcellular compartments. Growth was simulated under different steady-state light conditions (5-200 μmol photons m−2 s−1) and in a batch culture progressing from exponential growth to nitrate-limitation and nitrogen-starvation. We used the model to examine the dissipation of reductants generated through light-dependent processes and found that when available, nitrate assimilation is an important means of dissipating reductants in the plastid; under nitrate-limiting conditions, sulfate assimilation plays a similar role. The use of either nitrate or sulfate uptake to balance redox reactions leads to the secretion of distinct organic nitrogen and sulfur compounds. Such compounds can be accessed by bacteria in the surface ocean. The model of the diatom Thalassiosira pseudonana provides a mechanistic explanation for the production of ecologically and climatologically relevant compounds that may serve as the basis for intricate, cross-kingdom microbial networks. Diatom metabolism has an important influence on global biogeochemistry; metabolic models of marine microorganisms link genes to ecosystems and may be key to integrating molecular data with models of ocean biogeochemistry.

scholarly journals Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0241960
Author(s):  
Helena M. van Tol ◽  
E. Virginia Armbrust
Keyword(s):  
Organic Matter ◽  
Sulfur Metabolism ◽  
Reducing Power ◽  
Metabolic Model ◽  
Redox Balance ◽  
Thalassiosira Pseudonana ◽  
Cellular Damage ◽  
Marine Microorganisms ◽  
A Genome ◽  
Genome Scale

Diatoms are unicellular photosynthetic algae known to secrete organic matter that fuels secondary production in the ocean, though our knowledge of how their physiology impacts the composition of dissolved organic matter remains limited. Like all photosynthetic organisms, their use of light for energy and reducing power creates the challenge of avoiding cellular damage. To better understand the interplay between redox balance and organic matter secretion, we reconstructed a genome-scale metabolic model of Thalassiosira pseudonana strain CCMP 1335, a model for diatom molecular biology and physiology, with a 60-year history of studies. The model simulates the metabolic activities of 1,432 genes via a network of 2,792 metabolites produced through 6,079 reactions distributed across six subcellular compartments. Growth was simulated under different steady-state light conditions (5–200 μmol photons m-2 s-1) and in a batch culture progressing from exponential growth to nitrate-limitation and nitrogen-starvation. We used the model to examine the dissipation of reductants generated through light-dependent processes and found that when available, nitrate assimilation is an important means of dissipating reductants in the plastid; under nitrate-limiting conditions, sulfate assimilation plays a similar role. The use of either nitrate or sulfate uptake to balance redox reactions leads to the secretion of distinct organic nitrogen and sulfur compounds. Such compounds can be accessed by bacteria in the surface ocean. The model of the diatom Thalassiosira pseudonana provides a mechanistic explanation for the production of ecologically and climatologically relevant compounds that may serve as the basis for intricate, cross-kingdom microbial networks. Diatom metabolism has an important influence on global biogeochemistry; metabolic models of marine microorganisms link genes to ecosystems and may be key to integrating molecular data with models of ocean biogeochemistry.

scholarly journals Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance

2011 ◽  
Vol 43 (14) ◽  
pp. 855-872 ◽  
Author(s):  
Ajit N. Shah ◽  
Daniela Cadinu ◽  
R. Michael Henke ◽  
Xiantong Xin ◽  
Ranita Ghosh Dastidar ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Molecular Mechanisms ◽  
Specific Protein ◽  
Hypoxia Tolerance ◽  
Deletion Mutants ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild ◽  
Induced Changes

Hypoxia is a widely occurring condition experienced by diverse organisms under numerous physiological and disease conditions. To probe the molecular mechanisms underlying hypoxia responses and tolerance, we performed a genome-wide screen to identify mutants with enhanced hypoxia tolerance in the model eukaryote, the yeast Saccharomyces cerevisiae . Yeast provides an excellent model for genomic and proteomic studies of hypoxia. We identified five genes whose deletion significantly enhanced hypoxia tolerance. They are RAI1, NSR1, BUD21, RPL20A, and RSM22, all of which encode functions involved in ribosome biogenesis. Further analysis of the deletion mutants showed that they minimized hypoxia-induced changes in polyribosome profiles and protein synthesis. Strikingly, proteomic analysis by using the iTRAQ profiling technology showed that a substantially fewer number of proteins were changed in response to hypoxia in the deletion mutants, compared with the parent strain. Computational analysis of the iTRAQ data indicated that the activities of a group of regulators were regulated by hypoxia in the wild-type parent cells, but such regulation appeared to be diminished in the deletion strains. These results show that the deletion of one of the genes involved in ribosome biogenesis leads to the reversal of hypoxia-induced changes in gene expression and related regulators. They suggest that modifying ribosomal function is an effective mechanism to minimize hypoxia-induced specific protein changes and to confer hypoxia tolerance. These results may have broad implications in understanding hypoxia responses and tolerance in diverse eukaryotes ranging from yeast to humans.

scholarly journals Gene-for-Gene Tolerance to Bacterial Wilt in Arabidopsis

2013 ◽  
Vol 26 (4) ◽  
pp. 398-406 ◽  
Author(s):  
Liesl Van der Linden ◽  
Jane Bredenkamp ◽  
Sanushka Naidoo ◽  
Joanne Fouché-Weich ◽  
Katherine J. Denby ◽  
...  
Keyword(s):  
Bacterial Wilt ◽  
Gene Interaction ◽  
Model System ◽  
Economic Importance ◽  
Arms Race ◽  
In Planta ◽  
Resistance Response ◽  
Tolerance Response ◽  
Highly Virulent ◽  
Gene For Gene

Bacterial wilt caused by Ralstonia solanacearum is a disease of widespread economic importance that affects numerous plant species, including Arabidopsis thaliana. We describe a pathosystem between A. thaliana and biovar 3 phylotype I strain BCCF402 of R. solanacearum isolated from Eucalyptus trees. A. thaliana accession Be-0 was susceptible and accession Kil-0 was tolerant. Kil-0 exhibited no wilting symptoms and no significant reduction in fitness (biomass, seed yield, and germination efficiency) after inoculation with R. solanacearum BCCF402, despite high bacterial numbers in planta. This was in contrast to the well-characterized resistance response in the accession Nd-1, which limits bacterial multiplication at early stages of infection and does not wilt. R. solanacearum BCCF402 was highly virulent because the susceptible accession Be-0 was completely wilted after inoculation. Genetic analyses, allelism studies with Nd-1, and RRS1 cleaved amplified polymorphic sequence marker analysis showed that the tolerance phenotype in Kil-0 was dependent upon the resistance gene RRS1. Knockout and complementation studies of the R. solanacearum BCCF402 effector PopP2 confirmed that the tolerance response in Kil-0 was dependent upon the RRS1–PopP2 interaction. Our data indicate that the gene-for-gene interaction between RRS1 and PopP2 can contribute to tolerance, as well as resistance, which makes it a useful model system for evolutionary studies of the arms race between plants and bacterial pathogens. In addition, the results alert biotechnologists to the risk that deployment of RRS1 in transgenic crops may result in persistence of the pathogen in the field.

scholarly journals Generation of a Non-Transgenic Genetically Improved Yeast Strain for Wine Production from Nitrogen-Deficient Musts

2020 ◽  
Vol 8 (8) ◽  
pp. 1194 ◽  
Author(s):  
Eduardo Kessi-Pérez ◽  
Jennifer Molinet ◽  
Verónica García ◽  
Omayra Aguilera ◽  
Fernanda Cepeda ◽  
...  
Keyword(s):  
Nitrogen Sources ◽  
Direct Consequence ◽  
Nitrogen Addition ◽  
Wine Industry ◽  
Economic Losses ◽  
Improvement Program ◽  
Yeast Saccharomyces Cerevisiae ◽  
Wine Production ◽  
Grape Must ◽  
Improved Strain

The yeast Saccharomyces cerevisiae is the main species responsible for the process that involves the transformation of grape must into wine, with the initial nitrogen in the grape must being vital for it. One of the main problems in the wine industry is the deficiency of nitrogen sources in the grape must, leading to stuck or sluggish fermentations, and generating economic losses. In this scenario, an alternative is the isolation or generation of yeast strains with low nitrogen requirements for fermentation. In the present study, we carry out a genetic improvement program using as a base population a group of 70 strains isolated from winemaking environments mainly in Chile and Argentina (F0), making from it a first and second filial generation (F1 and F2, respectively) based in different families and hybrids. It was found that the trait under study has a high heritability, obtaining in the F2 population strains that consume a minor proportion of the nitrogen sources present in the must. Among these improved strains, strain “686” specially showed a marked drop in the nitrogen consumption, without losing fermentative performance, in synthetic grape must at laboratory level. When using this improved strain to produce wine from a natural grape must (supplemented and non-supplemented with ammonium) at pilot scale under wine cellar conditions, a similar fermentative capacity was obtained between this strain and a widely used commercial strain (EC1118). However, when fermented in a non-supplemented must, improved strain “686” showed the presence of a marked floral aroma absent for EC1118 strain, this difference being probably a direct consequence of its different pattern in amino acid consumption. The combination of the capacity of improved strain “686” to ferment without nitrogen addition and produce floral aromas may be of commercial interest for the wine industry.

scholarly journals Novel Organ-Specific Genetic Factors for Quantitative Resistance to Late Blight in Potato

2019 ◽  
Author(s):  
Deissy Katherine Juyo Rojas ◽  
Johana Carolina Soto Sedano ◽  
Agim Ballvora ◽  
Jens Léon ◽  
Teresa Mosquera Vásquez
Keyword(s):  
Late Blight ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Quantitative Resistance ◽  
Genotyping By Sequencing ◽  
Phenotypic Variance ◽  
Resistance Response ◽  
Genome Wide ◽  
A Genome ◽  
Organ Specific

AbstractPotato, Solanum tuberosum, is one of the highest consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain from 13.7% to 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including one leucine-rich repeat kinase.

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