Current Genetics最新文献_第6页

Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae. 蜜环菌及Physalacriaceae其他物种非核糖体肽合成酶基因簇及nrpps依赖性铁载体合成酶预测特征

IF 2.5 4区生物学

Current Genetics Pub Date : 2023-02-01 DOI: 10.1007/s00294-022-01256-w

Deborah L Narh Mensah, Brenda D Wingfield, Martin P A Coetzee

{"title":"Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae.","authors":"Deborah L Narh Mensah, Brenda D Wingfield, Martin P A Coetzee","doi":"10.1007/s00294-022-01256-w","DOIUrl":"https://doi.org/10.1007/s00294-022-01256-w","url":null,"abstract":"Fungal secondary metabolites are often pathogenicity or virulence factors synthesized by genes contained in secondary metabolite gene clusters (SMGCs). Nonribosomal polypeptide synthetase (NRPS) clusters are SMGCs which produce peptides such as siderophores, the high affinity ferric iron chelating compounds required for iron uptake under aerobic conditions. Armillaria spp. are mostly facultative necrotrophs of woody plants. NRPS-dependent siderophore synthetase (NDSS) clusters of Armillaria spp. and selected Physalacriaceae were investigated using a comparative genomics approach. Siderophore biosynthesis by strains of selected Armillaria spp. was evaluated using CAS and split-CAS assays. At least one NRPS cluster and other clusters were detected in the genomes studied. No correlation was observed between the number and types of SMGCs and reported pathogenicity of the species studied. The genomes contained one NDSS cluster each. All NDSSs were multi-modular with the domain architecture (ATC)3(TC)2. NDSS clusters of the Armillaria spp. showed a high degree of microsynteny. In the genomes of Desarmillaria spp. and Guyanagaster necrorhizus, NDSS clusters were more syntenic with NDSS clusters of Armillaria spp. than to those of the other Physalacriaceae species studied. Three A-domain orthologous groups were identified in the NDSSs, and atypical Stachelhaus codes were predicted for the A3 orthologous group. In vitro biosynthesis of mainly hydroxamate and some catecholate siderophores was observed. Hence, Armillaria spp. generally contain one highly conserved, NDSS cluster although some interspecific variations in the products of these clusters is expected. Results from this study lays the groundwork for future studies to elucidate the molecular biology of fungal phyto-pathogenicity.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"69 1","pages":"7-24"},"PeriodicalIF":2.5,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10713453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA. 将 tRNA 基因水平转移到线粒体质粒有利于真菌线粒体 DNA 基因的丢失。

IF 1.8 4区生物学

Current Genetics Pub Date : 2023-02-01 Epub Date: 2022-11-30 DOI: 10.1007/s00294-022-01259-7

Mathijs Nieuwenhuis, Jeroen Groeneveld, Duur K Aanen

{"title":"Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA.","authors":"Mathijs Nieuwenhuis, Jeroen Groeneveld, Duur K Aanen","doi":"10.1007/s00294-022-01259-7","DOIUrl":"10.1007/s00294-022-01259-7","url":null,"abstract":"Fungal and plant mitochondria are known to exchange DNA with retroviral plasmids. Transfer of plasmid DNA to the organellar genome is best known and occurs through wholesale insertion of the plasmid. Less well known is the transfer of organellar DNA to plasmids, in particular tRNA genes. Presently, it is unknown whether fungal plasmids can adopt mitochondrial functions such as tRNA production through horizontal gene transfer. In this paper, we studied the exchange of DNA between fungal linear plasmids and fungal mtDNA, mainly focusing on the basidiomycete family Lyophyllaceae. We report at least six independent transfers of complete tRNA genes to fungal plasmids. Furthermore, we discovered two independent cases of loss of a tRNA gene from a fungal mitochondrial genome following transfer of such a gene to a linear mitochondrial plasmid. We propose that loss of a tRNA gene from mtDNA following its transfer to a plasmid creates a mutualistic dependency of the host mtDNA on the plasmid. We also find that tRNA genes transferred to plasmids encode codons that occur at the lowest frequency in the host mitochondrial genomes, possibly due to a higher number of unused transcripts. We discuss the potential consequences of mtDNA transfer to plasmids for both the host mtDNA and the plasmid.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"69 1","pages":"55-65"},"PeriodicalIF":1.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9925561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10736425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Novel determinants of cell size homeostasis in the opportunistic yeast Candida albicans. 机会性酵母菌白色念珠菌细胞大小稳态的新决定因素。

IF 2.5 4区生物学

Current Genetics Pub Date : 2023-02-01 DOI: 10.1007/s00294-022-01260-0

Julien Chaillot, Michael A Cook, Adnane Sellam

{"title":"Novel determinants of cell size homeostasis in the opportunistic yeast Candida albicans.","authors":"Julien Chaillot, Michael A Cook, Adnane Sellam","doi":"10.1007/s00294-022-01260-0","DOIUrl":"https://doi.org/10.1007/s00294-022-01260-0","url":null,"abstract":"The basis for commitment to cell division in late G1 phase, called Start in yeast, is a critical but still poorly understood aspect of eukaryotic cell proliferation. Most dividing cells accumulate mass and grow to a critical cell size before traversing the cell cycle. This size threshold couples cell growth to division and thereby establishes long-term size homeostasis. At present, mechanisms involved in cell size homeostasis in fungal pathogens are not well described. Our previous survey of the size phenome in Candida albicans focused on 279 unique mutants enriched mainly in kinases and transcription factors (Sellam et al. PLoS Genet 15:e1008052, 2019). To uncover novel size regulators in C. albicans and highlight potential innovation within cell size control in pathogenic fungi, we expanded our genetic survey of cell size to include 1301 strains from the GRACE (Gene Replacement and Conditional Expression) collection. The current investigation uncovered both known and novel biological processes required for cell size homeostasis in C. albicans. We also confirmed the plasticity of the size control network as few C. albicans size genes overlapped with those of the budding yeast Saccharomyces cerevisiae. Many new size genes of C. albicans were associated with biological processes that were not previously linked to cell size control and offer an opportunity for future investigation. Additional work is needed to understand if mitochondrial activity is a critical element of the metric that dictates cell size in C. albicans and whether modulation of the onset of actomyosin ring constriction is an additional size checkpoint.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"69 1","pages":"67-75"},"PeriodicalIF":2.5,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10710463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nab3 nuclear granule accumulation is driven by respiratory capacity. Nab3核颗粒的积累受呼吸能力的驱动。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-12-01 DOI: 10.1007/s00294-022-01248-w

Katherine M Hutchinson, Jeremy C Hunn, Daniel Reines

{"title":"Nab3 nuclear granule accumulation is driven by respiratory capacity.","authors":"Katherine M Hutchinson, Jeremy C Hunn, Daniel Reines","doi":"10.1007/s00294-022-01248-w","DOIUrl":"https://doi.org/10.1007/s00294-022-01248-w","url":null,"abstract":"Numerous biological processes involve proteins capable of transiently assembling into subcellular compartments necessary for cellular functions. One process is the RNA polymerase II transcription cycle which involves initiation, elongation, co-transcriptional modification of nascent RNA, and termination. The essential yeast transcription termination factor Nab3 is required for termination of small non-coding RNAs and accumulates into a compact nuclear granule upon glucose removal. Nab3 nuclear granule accumulation varies in penetrance across yeast strains and a higher Nab3 granule accumulation phenotype is associated with petite strains, suggesting a possible ATP-dependent mechanism for granule disassembly. Here, we demonstrate the uncoupling of mitochondrial oxidative phosphorylation by drug treatment or deletions of nuclear-encoded ATP synthase subunit genes were sufficient to increase Nab3 granule accumulation and led to an inability to proliferate during prolonged glucose deprivation, which requires respiration. Additionally, by enriching for respiration competent cells from a petite-prone strain, we generated a low granule-accumulating strain from a relatively high one, providing another link between respiratory competency and Nab3 granules. Consistent with the resulting idea that ATP is involved in granule accumulation, the addition of extracellular ATP to semi-permeabilized cells was sufficient to reduce Nab3 granule accumulation. Deleting the SKY1 gene, which encodes a kinase that phosphorylates nuclear SR repeat-containing proteins and is involved in efficient stress granule disassembly, also resulted in increased granule accumulation. This observation implicates Sky1 in Nab3 granule biogenesis. Taken together, these findings suggest there is normally an equilibrium between termination factor granule assembly and disassembly mediated by ATP-requiring nuclear machinery.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"68 5-6","pages":"581-591"},"PeriodicalIF":2.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9887517/pdf/nihms-1857372.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10643763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Variable penetrance of Nab3 granule accumulation quantified by a new tool for high-throughput single-cell granule analysis. 高通量单细胞颗粒分析新工具定量测定Nab3颗粒积累的可变外显率。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-08-01 DOI: 10.1007/s00294-022-01234-2

Jeremy C Hunn, Katherine M Hutchinson, Joshua B Kelley, Daniel Reines

{"title":"Variable penetrance of Nab3 granule accumulation quantified by a new tool for high-throughput single-cell granule analysis.","authors":"Jeremy C Hunn, Katherine M Hutchinson, Joshua B Kelley, Daniel Reines","doi":"10.1007/s00294-022-01234-2","DOIUrl":"https://doi.org/10.1007/s00294-022-01234-2","url":null,"abstract":"Reorganization of cellular proteins into subcellular compartments, such as the concentration of RNA-binding proteins into cytoplasmic stress granules and P-bodies, is a well-recognized, widely studied physiological process currently under intense investigation. One example of this is the induction of the yeast Nab3 transcription termination factor to rearrange from its pan-nucleoplasmic distribution to a granule at the nuclear periphery in response to nutrient limitation. Recent work in many cell types has shown that protein condensation in the nucleus is functionally important for transcription initiation, RNA processing, and termination. However, little is known about how subnuclear compartments form. Here, we have quantitatively analyzed this dynamic process in living yeast using a high-throughput computational tool and fluorescence microscopy. This analysis revealed that Nab3 granule accumulation varies in penetrance across yeast strains. A concentrated single granule is formed from at least a quarter of the nuclear Nab3 drawn from the rest of the nucleus. Levels of granule accumulation were inversely correlated with a growth defect in the absence of glucose. Importantly, the basis for some of the variation in penetrance was attributable to a defect in mitochondrial function. This publicly available computational tool provides a rigorous, reproducible, and unbiased examination of Nab3 granule accumulation that should be widely applicable to a variety of fluorescent images. Thousands of live cells can be readily examined enabling rigorous statistical verification of significance. With it, we describe a new feature of inducible subnuclear compartment formation for RNA-binding transcription factors and an important determinant of granule biogenesis.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"68 3-4","pages":"467-480"},"PeriodicalIF":2.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9283369/pdf/nihms-1815149.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9700016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

New destination vectors facilitate Modular Cloning for Chlamydomonas. 新的目的载体为衣藻的模块化克隆提供了便利。

IF 1.8 4区生物学

Current Genetics Pub Date : 2022-08-01 Epub Date: 2022-04-16 DOI: 10.1007/s00294-022-01239-x

Justus Niemeyer, Michael Schroda

{"title":"New destination vectors facilitate Modular Cloning for Chlamydomonas.","authors":"Justus Niemeyer, Michael Schroda","doi":"10.1007/s00294-022-01239-x","DOIUrl":"10.1007/s00294-022-01239-x","url":null,"abstract":"Synthetic Biology is revolutionizing biological research by introducing principles of mechanical engineering, including the standardization of genetic parts and standardized part assembly routes. Both are realized in the Modular Cloning (MoClo) strategy. MoClo allows for the rapid and robust assembly of individual genes and multigene clusters, enabling iterative cycles of gene design, construction, testing, and learning in short time. This is particularly true if generation times of target organisms are short, as is the case for the unicellular green alga Chlamydomonas reinhardtii. Testing a gene of interest in Chlamydomonas with MoClo requires two assembly steps, one for the gene of interest itself and another to combine it with a selection marker. To reduce this to a single assembly step, we constructed five new destination vectors. They contain genes conferring resistance to commonly used antibiotics in Chlamydomonas and a site for the direct assembly of basic genetic parts. The vectors employ red/white color selection and, therefore, do not require costly compounds like X-gal and IPTG. mCherry expression is used to demonstrate the functionality of these vectors.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"68 1","pages":"531-536"},"PeriodicalIF":1.8,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51750167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Suggestion for a new bacteriophage genus for the Klebsiella pneumoniae phage vB_KpnS-Carvaje 肺炎克雷伯菌噬菌体vB_KpnS-Carvaje新噬菌体属的建议

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-06-06 DOI: 10.1007/s00294-022-01242-2

J. C. Sousa, S. Sillankorva, A. Faustino, C. Carvalho

引用次数: 0

Synthetic negative genome screen of the GPN-loop GTPase NPA3 in Saccharomyces cerevisiae 酿酒酵母gpn环GTPase NPA3的合成阴性基因组筛选

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-06-04 DOI: 10.1007/s00294-022-01243-1

Martín Mora-García, Diana Ascencio, Tania Félix-Pérez, Judith Ulloa-Calzonzin, A. Juárez-Reyes, K. Robledo-Márquez, Yolanda Rebolloso-Gómez, L. Riego-Ruiz, A. DeLuna, M. R. Calera, R. Sánchez-Olea

引用次数: 2

Cold-adaptive traits identified by comparative genomic analysis of a lipase-producing Pseudomonas sp. HS6 isolated from snow-covered soil of Sikkim Himalaya and molecular simulation of lipase for wide substrate specificity 从锡金喜马拉雅地区积雪土壤分离的产脂肪酶假单胞菌HS6的比较基因组分析和广泛底物特异性脂肪酶的分子模拟鉴定了其冷适应特性

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-05-09 DOI: 10.1007/s00294-022-01241-3

Loreni Chiring Phukon, Rounak Chourasia, S. Padhi, M. Abedin, Tharangattumana Krishnan Godan, Binod Parameswaran, Sudhir P. Singh, A. Rai

引用次数: 1

A positive genetic selection for transmembrane domain mutations in HRD1 underscores the importance of Hrd1 complex integrity during ERAD. HRD1跨膜结构域突变的阳性遗传选择强调了HRD1复合物完整性在ERAD中的重要性。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 DOI: 10.1007/s00294-022-01227-1

Kunio Nakatsukasa, Sylvia Wigge, Yuki Takano, Tomoyuki Kawarasaki, Takumi Kamura, Jeffrey L Brodsky

{"title":"A positive genetic selection for transmembrane domain mutations in HRD1 underscores the importance of Hrd1 complex integrity during ERAD.","authors":"Kunio Nakatsukasa, Sylvia Wigge, Yuki Takano, Tomoyuki Kawarasaki, Takumi Kamura, Jeffrey L Brodsky","doi":"10.1007/s00294-022-01227-1","DOIUrl":"https://doi.org/10.1007/s00294-022-01227-1","url":null,"abstract":"Misfolded proteins in the endoplasmic reticulum (ER) are retrotranslocated to the cytosol for ubiquitination and degradation by the proteasome. During this process, known as ER-associated degradation (ERAD), the ER-embedded Hrd1 ubiquitin ligase plays a central role in recognizing, ubiquitinating, and retrotranslocating scores of lumenal and integral membrane proteins. To better define the mechanisms underlying Hrd1 function in Saccharomyces cerevisiae, several model substrates have been developed. One substrate is Sec61-2, a temperature sensitive allele of the Sec61 translocation channel. Cells expressing Sec61-2 grow at 25 °C because the protein is stable, but sec61-2 yeast are inviable at 38 °C because the mutated protein is degraded in a Hrd1-dependent manner. Therefore, deleting HRD1 stabilizes Sec61-2 and hence sec61-2hrd1∆ double mutants are viable at 38 °C. This unique phenotype allowed us to perform a non-biased screen for loss-of-function alleles in HRD1. Based on its importance in mediating substrate retrotranslocation, the screen was also developed to focus on mutations in sequences encoding Hrd1's transmembrane-rich domain. Ultimately, a group of recessive mutations was identified in HRD1, including an ensemble of destabilizing mutations that resulted in the delivery of Hrd1 to the ERAD pathway. A more stable mutant resided in a buried transmembrane domain, yet the Hrd1 complex was disrupted in yeast expressing this mutant. Together, these data confirm the importance of Hrd1 complex integrity during ERAD, suggest that allosteric interactions between transmembrane domains regulate Hrd1 complex formation, and provide the field with new tools to define the dynamic interactions between ERAD components during substrate retrotranslocation.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"68 2","pages":"227-242"},"PeriodicalIF":2.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9036396/pdf/nihms-1796626.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9232527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3