scholarly journals Genetic mapping of a bioethanol yeast strain reveals new targets for aldehyde- and thermotolerance

2021 ◽  
Author(s):  
Fellipe da Silveira Bezerra de Mello ◽  
Alessandro L V Coradini ◽  
Marcelo Falsarella Carazzolle ◽  
Carla Maneira ◽  
Monique Furlan ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Intracellular Signaling ◽  
Yeast Strain ◽  
Laboratory Strain ◽  
Genetic Network ◽  
Nucleotide Polymorphisms ◽  
Yeast Robustness ◽  
Stress Mediators ◽  
Chromosome Ii ◽  
Harsh Conditions

Current technology that enables bioethanol production from agricultural biomass imposes harsh conditions for Saccharomyces cerevisiae's metabolism. In this work, the genetic architecture of industrial bioethanol yeast strain SA-1 was evaluated. SA-1 segregant FMY097 was previously described as highly aldehyde resistant and here also as thermotolerant: two important traits for the second-generation industry. A Quantitative Trait Loci (QTL) mapping of 5-hydroxymethylfurfural (HMF) -resistant segregants of hybrid FMY097/BY4742 disclosed a region in chromosome II bearing alleles with uncommon non-synonymous (NS) single nucleotide polymorphisms (SNPs) in FMY097: MIX23, PKC1, SEA4, and SRO77. Allele swap to susceptible laboratory strain BY4742 revealed that SEA4FMY097 enhances robustness towards HMF, but the industrial fitness could not be fully recovered. The genetic network arising from the causative genes in the QTL window suggests that intracellular signaling TOR (Target of Rapamycin) and CWI (Cell Wall Integrity) pathways are regulators of this phenotype in FMY097. Because the QTL mapping did not result in one major allelic contribution to the evaluated trait, a background effect in FMY097's HMF resistance is expected. Quantification of NADPH - cofactor implied in endogenous aldehyde detoxification reactions - supports the former hypothesis, given its high availability in FMY097. Regarding thermotolerance, SEA4FMY097 grants BY4742 ability to grow in temperatures as high as 38 °C in liquid, while allele PKC1FMY097 allows growth up to 40 °C in solid medium. Both SEA4FMY097 and PKC1FMY097 encode rare NS SNPs, not found in other >1,013 S. cerevisiae. Altogether, these findings point towards crucial membrane and stress mediators for yeast robustness.

scholarly journals BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology

2013 ◽  
Vol 10 (2) ◽  
pp. 103-116 ◽  
Author(s):  
Goksel Misirli ◽  
Anil Wipat ◽  
Joseph Mullen ◽  
Katherine James ◽  
Matthew Pocock ◽  
...  
Keyword(s):  
Laboratory Strain ◽  
Nucleotide Polymorphisms ◽  
Genetic Circuits ◽  
Positive Bacterium ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Data Resource ◽  
Data Integration System ◽  
Bacterium Bacillus Subtilis ◽  
Bacterium Bacillus

Summary BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 SNPs with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that BacillOndex is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism.

scholarly journals GWAS Discovery Of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 803 ◽  
Author(s):  
Wang ◽  
Yan ◽  
Li ◽  
Li ◽  
Zhao ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Market Demand ◽  
Oil Crops ◽  
A Genome ◽  
Genomic Regions

Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

scholarly journals IL-12 and IL-23—Close Relatives with Structural Homologies but Distinct Immunological Functions

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2184
Author(s):  
Doreen M. Floss ◽  
Jens M. Moll ◽  
Jürgen Scheller
Keyword(s):  
Protein Interactions ◽  
Intracellular Signaling ◽  
Signaling Cascades ◽  
Structural Knowledge ◽  
Nucleotide Polymorphisms ◽  
Protein Protein Interactions ◽  
Single Nucleotide ◽  
Mediated Effects ◽  
Protein Functions ◽  
Close Relatives

Cytokines of the IL-12 family show structural similarities but have distinct functions in the immune system. Prominent members of this cytokine family are the pro-inflammatory cytokines IL-12 and IL-23. These two cytokines share cytokine subunits and receptor chains but have different functions in autoimmune diseases, cancer and infections. Accordingly, structural knowledge about receptor complex formation is essential for the development of new therapeutic strategies preventing and/or inhibiting cytokine:receptor interaction. In addition, intracellular signaling cascades can be targeted to inhibit cytokine-mediated effects. Single nucleotide polymorphisms can lead to alteration in the amino acid sequence and thereby influencing protein functions or protein–protein interactions. To understand the biology of IL-12 and IL-23 and to establish efficient targeting strategies structural knowledge about cytokines and respective receptors is crucial. A highly efficient therapy might be a combination of different drugs targeting extracellular cytokine:receptor assembly and intracellular signaling pathways.

scholarly journals Integrated Information as a Measure of Cognitive Processes in Coupled Genetic Repressilators

Entropy ◽  
2019 ◽  
Vol 21 (4) ◽  
pp. 382
Author(s):  
Luis Abrego ◽  
Alexey Zaikin
Keyword(s):  
Cognitive Processes ◽  
Intracellular Signaling ◽  
Genetic Network ◽  
Functional Differentiation ◽  
Cell Fates ◽  
Dynamical Complexity ◽  
Collective Interaction ◽  
Open Question ◽  
Insight Into ◽  
Integrated Information

Intercellular communication and its coordination allow cells to exhibit multistability as a form of adaptation. This conveys information processing from intracellular signaling networks enabling self-organization between other cells, typically involving mechanisms associated with cognitive systems. How information is integrated in a functional manner and its relationship with the different cell fates is still unclear. In parallel, drawn originally from studies on neuroscience, integrated information proposes an approach to quantify the balance between integration and differentiation in the causal dynamics among the elements in any interacting system. In this work, such an approach is considered to study the dynamical complexity in a genetic network of repressilators coupled by quorum sensing. Several attractors under different conditions are identified and related to proposed measures of integrated information to have an insight into the collective interaction and functional differentiation in cells. This research particularly accounts for the open question about the coding and information transmission in genetic systems.

scholarly journals Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Adam Kawalek ◽  
Karolina Kotecka ◽  
Magdalena Modrzejewska ◽  
Jan Gawor ◽  
Grazyna Jagura-Burdzy ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequence ◽  
Dna Methyltransferase ◽  
Laboratory Strain ◽  
Mercury Resistance ◽  
Nucleotide Polymorphisms ◽  
Modification System ◽  
Restriction Modification System ◽  
Integrative Conjugative Element ◽  
Restriction Modification

Abstract Background Pseudomonas aeruginosa is a cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies demonstrated differences in the genomes and phenotypes of derivatives from different laboratories. Results Here we report the genome sequence of P. aeruginosa PAO1161 laboratory strain, a leu-, RifR, restriction-modification defective PAO1 derivative, described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury. Comparison of PAO1161 genome with PAO1-UW sequence revealed lack of an inversion of a large genome segment between rRNA operons and 100 nucleotide polymorphisms, short insertions and deletions. These included a change in leuA, resulting in E108K substitution, which caused leucine auxotrophy and a mutation in rpoB, likely responsible for the rifampicin resistance. Nonsense mutations were detected in PA2735 and PA1939 encoding a DNA methyltransferase and a putative OLD family endonuclease, respectively. Analysis of revertants in these two genes showed that PA2735 is a component of a restriction-modification system, independent of PA1939. Moreover, a 12 kb RPG42 prophage and a novel 108 kb PAPI-1 like integrative conjugative element (ICE) encompassing a mercury resistance operon were identified. The ICEPae1161 was transferred to Pseudomonas putida cells, where it integrated in the genome and conferred the mercury resistance. Conclusions The high-quality P. aeruginosa PAO1161 genome sequence provides a reference for further research including e.g. investigation of horizontal gene transfer or comparative genomics. The strain was found to carry ICEPae1161, a functional PAPI-1 family integrative conjugative element, containing loci conferring mercury resistance, in the past attributed to the FP2 plasmid of IncP-8 incompatibility group. This indicates that the only known member of IncP-8 is in fact an ICE.

scholarly journals QTL mapping and genome-wide prediction of heat tolerance in multiple connected populations of temperate maize

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Delphine Van Inghelandt ◽  
Felix P. Frey ◽  
David Ries ◽  
Benjamin Stich
Keyword(s):  
Qtl Mapping ◽  
Heat Tolerance ◽  
Prediction Models ◽  
Genotypic Diversity ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
Prediction Ability ◽  
Specific Pcr ◽  
Genome Wide ◽  
Trait Locus

Abstract Climate change will lead to increasing heat stress in the temperate regions of the world. The objectives of this study were the following: (I) to assess the phenotypic and genotypic diversity of traits related to heat tolerance of maize seedlings and dissect their genetic architecture by quantitative trait locus (QTL) mapping, (II) to compare the prediction ability of genome-wide prediction models using various numbers of KASP (Kompetitive Allele Specific PCR genotyping) single nucleotide polymorphisms (SNPs) and RAD (restriction site-associated DNA sequencing) SNPs, and (III) to examine the prediction ability of intra-, inter-, and mixed-pool calibrations. For the heat susceptibility index of five of the nine studied traits, we identified a total of six QTL, each explaining individually between 7 and 9% of the phenotypic variance. The prediction abilities observed for the genome-wide prediction models were high, especially for the within-population calibrations, and thus, the use of such approaches to select for heat tolerance at seedling stage is recommended. Furthermore, we have shown that for the traits examined in our study, populations created from inter-pool crosses are suitable training sets to predict populations derived from intra-pool crosses.

scholarly journals An RpoB Mutation Confers Dual Heteroresistance to Daptomycin and Vancomycin in Staphylococcus aureus

2010 ◽  
Vol 54 (12) ◽  
pp. 5222-5233 ◽  
Author(s):  
Longzhu Cui ◽  
Taisuke Isii ◽  
Minoru Fukuda ◽  
Tomonori Ochiai ◽  
Hui-min Neoh ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Cell Surface ◽  
Ribosomal Proteins ◽  
Laboratory Strain ◽  
Genome Comparison ◽  
Nucleotide Position ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding

ABSTRACT We have previously reported the establishment of a Staphylococcus aureus laboratory strain, 10*3d1, having reduced susceptibility to daptomycin and heterogeneous vancomycin-intermediate S. aureus (VISA) phenotype. The strain was generated in vitro by serial daptomycin selection (Camargo, I. L., H. M. Neoh, L. Cui, and K. Hiramatsu, Antimicrob. Agents Chemother. 52:4289-4299, 2008). Here we explored the genetic mechanism of resistance in the strain by whole-genome sequencing and by producing gene-replaced strains. By genome comparison between 10*3d1 and its parent methicillin-resistant Staphylococcus aureus (MRSA) strain N315ΔIP, we identified five nonsynonymous single nucleotide polymorphisms (SNPs). One of the five mutations was found in the rpoB gene encoding the RNA polymerase β subunit. The mutation at nucleotide position 1862 substituted the 621st alanine by glutamic acid. The replacement of the intact rpoB with the mutated rpoB, designated rpoB(A621E), conferred N315ΔIP with the phenotypes of reduced susceptibility to daptomycin and hetero-VISA. The rpoB(A621E)-mediated resistance conversion was accompanied by a thickened cell wall and reduction of the cell surface negative charge. Being consistent with these phenotypic changes, microarray data showed that the expression of the dlt operon, which increases the cell surface positive charge, was enhanced in the rpoB(A621E) mutant. Other remarkable findings of microarray analysis of the rpoB(A621E) mutant included repression of metabolic pathways of purine, pyrimidine, arginine, the urea cycle, and the lac operon, enhancement of the biosynthetic pathway of vitamin B2, K1, and K2, and cell wall metabolism. Finally, mutations identified in rplV and rplC, encoding 50S ribosomal proteins L22 and L3, respectively, were found to be associated with the slow growth, but not with the phenotype of decreased susceptibility to vancomycin and daptomycin, of 10*3d1.

scholarly journals Mapping a double flower phenotype-associated gene DcAP2L in Dianthus chinensis

2020 ◽  
Vol 71 (6) ◽  
pp. 1915-1927 ◽  
Author(s):  
Qijian Wang ◽  
Xiaoni Zhang ◽  
Shengnan Lin ◽  
Shaozong Yang ◽  
Xiuli Yan ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Dianthus Caryophyllus ◽  
Flower Formation ◽  
Nucleotide Polymorphisms ◽  
Double Flower ◽  
Major Qtls ◽  
Horticultural Traits ◽  
Organ Identity ◽  
Number Variation ◽  
Trait Locus

Abstract The double flower is a highly important breeding trait that affects the ornamental value in many flowering plants. To get a better understanding of the genetic mechanism of double flower formation in Dianthus chinensis, we have constructed a high-density genetic map using 140 F2 progenies derived from a cross between a single flower genotype and a double flower genotype. The linkage map was constructed using double-digest restriction site-associated DNA sequencing (ddRAD-seq) with 2353 single nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) mapping analysis was conducted for 12 horticultural traits, and major QTLs were identified for nine of the 12 traits. Among them, two major QTLs accounted for 20.7% and 78.1% of the total petal number variation, respectively. Bulked segregant RNA-seq (BSR-seq) was performed to search accurately for candidate genes associated with the double flower trait. Integrative analysis of QTL mapping and BSR-seq analysis using the reference genome of Dianthus caryophyllus suggested that an SNP mutation in the miR172 cleavage site of the A-class flower organ identity gene APETALA2 (DcAP2L) is responsible for double flower formation in Dianthus through regulating the expression of DcAG genes.

scholarly journals Influence of TLR-8 Gene Polymorphisms (rs3764880 and rs3788935) Associated to Pulmonary Tuberculosis in Kupang, Indonesia

2021 ◽  
Vol 9 (1) ◽  
pp. 9
Author(s):  
Afandi Charles ◽  
Simeon Penggoam ◽  
Ani Melani Maskoen ◽  
Edhyana Sahiratmadja
Keyword(s):  
Pulmonary Tuberculosis ◽  
Intracellular Signaling ◽  
Gene Polymorphisms ◽  
Pathogenic Bacteria ◽  
Nucleotide Polymorphisms ◽  
Toll Like Receptor ◽  
Single Nucleotide ◽  
Significant Difference ◽  
Hardy Weinberg Equilibrium ◽  
Control Study

Toll-like receptor 8 (TLR-8) is known as part of intracellular signaling transduction for bacterial phagocytosis. Mycobacterium tuberculosis (Mtb) is intracellular pathogenic bacteria that is recognized by this receptor, and genetic variation of TLR-8 might alter susceptibility of the host towards pulmonary tuberculosis (PTB). This study aimed to determine whether TLR-8 gene polymorphisms were associated to PTB in Kupang, Indonesia. This case-control study compared demographic and clinical data between 115 PTB patients and 115 controls, then two TLR-8 single nucleotide polymorphisms (rs3764880 and rs3788935) were explored using the GoldenGate® Genotyping for VeraCode® / BeadXpress Illumina®. There is no significant difference between sex distribution of patient vs control groups. The polymorphisms (rs3764880 and rs3788935) are in Hardy-Weinberg Equilibrium in this population (p > 0.05). The distribution of major vs minor genotypes and alleles of TLR-8 polymorphisms in PTB patients were as followed: rs3764880 (GG vs GA vs AA, 50.0% vs 21.4% vs 28.6% ; G vs A, 60.9% vs 39.1% ) and rs3788935 (GG vs GA vs AA, 53.0% vs 21.7% vs 25.3%; G vs A, 62.9% vs 37.1%). Neither genotypes nor alleles were associated with PTB in this population (P > 0.05). Besides, when the analyses were stratified by gender, none of the alleles of polymorphism in both genders were associated with PTB cases. None of the TLR-8 polymorphisms have associated the risk of developing PTB in Kupang, East Nusa Tenggara population (as opposed to other studies in different ethnic groups). These might reflect the diversity of genetic polymorphisms in eastern Indonesia populations, suggesting different genetic backgrounds with western part of Indonesia. 

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