Current Genetics最新文献_第8页

Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology. 从耕地土壤中分离的铜绿假单胞菌菌株的全基因组测序和比较基因组分析揭示了重金属抗性和密码子生物学的新见解。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-08-01 Epub Date: 2022-06-28 DOI: 10.1007/s00294-022-01245-z

Jayanti Saha, Sourav Dey, Ayon Pal

{"title":"Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology.","authors":"Jayanti Saha, Sourav Dey, Ayon Pal","doi":"10.1007/s00294-022-01245-z","DOIUrl":"https://doi.org/10.1007/s00294-022-01245-z","url":null,"abstract":"Elevated concentration of non-essential persistent heavy metals and metalloids in the soil is detrimental to essential soil microbes and plants, resulting in diminished diversity and biomass. Thus, isolation, screening, and whole genomic analysis of potent strains of bacteria from arable lands with inherent capabilities of heavy metal resistance and plant growth promotion hold the key for bio remedial applications. This study is an attempt to do the same. In this study, a potent strain of Pseudomonas aeruginosa was isolated from paddy fields, followed by metabolic profiling using FTIR, metal uptake analysis employing ICP-MS, whole genome sequencing and comparative codon usage analysis. ICP-MS study provided insights into a high degree of Cd uptake during the exponential phase of growth under cumulative metal stress to Cd, Zn and Co, which was further corroborated by the detection of cadA gene along with czcCBA operon in the genome upon performing whole-genome sequencing. This potent strain of Pseudomonas aeruginosa also harboured genes, such as copA, chrA, znuA, mgtE, corA, and others conferring resistance against different heavy metals, such as Cd, Zn, Co, Cu, Cr, etc. A comparative codon usage bias analysis at the genomic and genic level, whereby several heavy metal resistant genes were considered in the backdrop of two housekeeping genes among 40 Pseudomonas spp. indicated the presence of a relatively strong codon usage bias in the studied strain. With this work, an effort was made to explore heavy metal-resistant bacteria (isolated from arable soil) and whole genome sequence analysis to get insight into metal resistance for future bio remedial applications.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":" ","pages":"481-503"},"PeriodicalIF":2.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40406707","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: 5

The vacuolar morphology protein VAC14 plays an important role in sexual development in the filamentous ascomycete Sordaria macrospora. 液泡形态蛋白VAC14在丝状子囊菌大孢子Sordaria macrospora的性发育中起重要作用。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-08-01 Epub Date: 2022-07-01 DOI: 10.1007/s00294-022-01244-0

Anika Groth, Svenja Ahlmann, Antonia Werner, Stefanie Pöggeler

{"title":"The vacuolar morphology protein VAC14 plays an important role in sexual development in the filamentous ascomycete Sordaria macrospora.","authors":"Anika Groth, Svenja Ahlmann, Antonia Werner, Stefanie Pöggeler","doi":"10.1007/s00294-022-01244-0","DOIUrl":"https://doi.org/10.1007/s00294-022-01244-0","url":null,"abstract":"The multiprotein Fab1p/PIKfyve-complex regulating the abundance of the phospholipid phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) is highly conserved among eukaryotes. In yeast/mammals, it is composed of the phosphatidylinositol 3-phosphate 5-kinase Fab1p/PIKfyve, the PtdIns(3,5)P2 phosphatase Fig4p/Sac3 and the scaffolding subunit Vac14p/ArPIKfyve. The complex is located to vacuolar membranes in yeast and to endosomal membranes in mammals, where it controls the synthesis and turnover of PtdIns(3,5)P2. In this study, we analyzed the role and function of the Fab1p/PIKfyve-complex scaffold protein SmVAC14 in the filamentous ascomycete Sordaria macrospora (Sm). We generated the Smvac14 deletion strain ∆vac14 and performed phenotypic analysis of the mutant. Furthermore, we conducted fluorescence microscopic localization studies of fluorescently labeled SmVAC14 with vacuolar and late endosomal marker proteins. Our results revealed that SmVAC14 is important for maintaining vacuolar size and appearance as well as proper sexual development in S. macrospora. In addition, SmVAC14 plays an important role in starvation stress response. Accordingly, our results propose that the turnover of PtdIns(3,5)P2 is of great significance for developmental processes in filamentous fungi.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":" ","pages":"407-427"},"PeriodicalIF":2.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40554289","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

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

How adaptive laboratory evolution can boost yeast tolerance to lignocellulosic hydrolyses 适应性实验室进化如何提高酵母对木质纤维素水解物的耐受性

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 DOI: 10.1007/s00294-022-01237-z

Y. A. Menegon, Jeferson Gross, A. Jacobus

引用次数: 7

Molecular characterization of lipase from a psychrotrophic bacterium Pseudomonas sp. CRBC14. 嗜冷细菌假单胞菌CRBC14脂肪酶的分子特性研究。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 Epub Date: 2021-11-27 DOI: 10.1007/s00294-021-01224-w

Saleem Farooq, Shabir Ahmad Ganai, Bashir Ahmad Ganai, Suma Mohan, Baba Uqab, Ruqeya Nazir

{"title":"Molecular characterization of lipase from a psychrotrophic bacterium Pseudomonas sp. CRBC14.","authors":"Saleem Farooq, Shabir Ahmad Ganai, Bashir Ahmad Ganai, Suma Mohan, Baba Uqab, Ruqeya Nazir","doi":"10.1007/s00294-021-01224-w","DOIUrl":"https://doi.org/10.1007/s00294-021-01224-w","url":null,"abstract":"Lipases from Pseudomonas species are particularly useful due to their broader biocatalytic applications and temperature activity. In this study, we amplified the gene encoding wild-type cold-active lipase from the genome of psychrotrophic bacterium isolated from the Himalayan glacier. The isolated CRBC14 strain was identified as Pseudomonas sp. based on the 16S rRNA gene sequence. Lipase activity was determined by observing the hydrolysis zone on nutrient agar containing tributyrin (1%, v/v). The sequence analysis of cold-active lipase revealed a protein of 611 amino acids with a calculated molecular mass of 63.71 kDa. The three-dimensional structure of this lipase was generated through template-supported modeling. Distinct techniques stamped the model quality, following which the binding free energies of tributyrin and oleic acid in the complex state with this enzymatic protein were predicted through molecular mechanics generalized born surface area (MMGBSA). A relative comparison of binding free energy values of these substrates indicated tributyrin's comparatively higher binding propensity towards the lipase. Using molecular docking, we evaluated the binding activity of cold-active lipase against tributyrin and oleic acid. Our docking analysis revealed that the lipase had a higher affinity for tributyrin than oleic acid, as evidenced by our measurement of the hydrolysis zone on two media plates. This study will help to understand the bacterial diversity of unexplored Himalayan glaciers and the possible application of their cold-adapted enzymes.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":" ","pages":"243-251"},"PeriodicalIF":2.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39783882","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: 6

Genome-wide analysis reveals a rhamnolipid-dependent modulation of flagellar genes in Pseudomonas aeruginosa PAO1. 全基因组分析揭示了铜绿假单胞菌PAO1中鞭毛基因的鼠李糖脂依赖性调节。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 Epub Date: 2022-01-30 DOI: 10.1007/s00294-021-01225-9

Michele R Castro, Graciela M Dias, Tiago S Salles, Nubia M Cabral, Danielly C O Mariano, Hadassa L Oliveira, Eliana S F W Abdelhay, Renata Binato, Bianca C Neves

{"title":"Genome-wide analysis reveals a rhamnolipid-dependent modulation of flagellar genes in Pseudomonas aeruginosa PAO1.","authors":"Michele R Castro, Graciela M Dias, Tiago S Salles, Nubia M Cabral, Danielly C O Mariano, Hadassa L Oliveira, Eliana S F W Abdelhay, Renata Binato, Bianca C Neves","doi":"10.1007/s00294-021-01225-9","DOIUrl":"https://doi.org/10.1007/s00294-021-01225-9","url":null,"abstract":"Pseudomonas aeruginosa is an opportunistic pathogen and an important model organism for the study of bacterial group behaviors, including cell motility and biofilm formation. Rhamnolipids play a pivotal role in biofilm formation and motility phenotypes in P. aeruginosa, possibly acting as wetting agents and mediating chemotactic stimuli. However, no biochemical mechanism or gene regulatory network has been investigated in regard to rhamnolipids' modulation of those group behaviors. Using DNA microarrays, we investigated the transcriptomic profiles in the stationary phase of growth of wild-type P. aeruginosa PAO1 and a rhlA-mutant strain, unable to produce rhamnolipids. A total of 134 genes were differentially expressed, comprising different functional categories, indicating a significant physiological difference between the rhamnolipid-producing and -non-producing strains. Interestingly, several flagellar genes are repressed in the mutant strain, which directly relates to the inability of the rhlA-minus strain to develop a swarming-motility phenotype. Supplementation with exogenous rhamnolipids has partially restored flagellar gene expression in the mutant strain. Our results show significant evidence that rhamnolipids, the major biosynthetic products of rhlABC pathway, seem to modulate gene expression in P. aeruginosa.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":" ","pages":"289-304"},"PeriodicalIF":2.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39871299","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