Current Genetics最新文献_第7页

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":null,"pages":null},"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

Emerging roles of SWI/SNF remodelers in fungal pathogens. SWI/SNF重塑因子在真菌病原体中的新作用

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 Epub Date: 2022-01-10 DOI: 10.1007/s00294-021-01219-7

Vinutha K Balachandra, Santanu K Ghosh

引用次数: 1

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":null,"pages":null},"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

Histone 3 lysine 4 monomethylation supports activation of transcription in S. cerevisiae during nutrient stress. 组蛋白3赖氨酸4单甲基化支持酿酒酵母在营养胁迫下的转录激活。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 Epub Date: 2022-01-18 DOI: 10.1007/s00294-022-01226-2

Neha Deshpande, Rachel Jordan, Michelle Henderson Pozzi, Mary Bryk

{"title":"Histone 3 lysine 4 monomethylation supports activation of transcription in S. cerevisiae during nutrient stress.","authors":"Neha Deshpande, Rachel Jordan, Michelle Henderson Pozzi, Mary Bryk","doi":"10.1007/s00294-022-01226-2","DOIUrl":"https://doi.org/10.1007/s00294-022-01226-2","url":null,"abstract":"Mono-methylation of the fourth lysine on the N-terminal tail of histone H3 was found to support the induction of RNA polymerase II transcription in S. cerevisiae during nutrient stress. In S. cerevisiae, the mono-, di- and tri-methylation of lysine 4 on histone H3 (H3K4) is catalyzed by the protein methyltransferase, Set1. The three distinct methyl marks on H3K4 act in discrete ways to regulate transcription. Nucleosomes enriched with tri-methylated H3K4 are usually associated with active transcription whereas di-methylated H3K4 is associated with gene repression. Mono-methylated H3K4 has been shown to repress gene expression in S. cerevisiae and is detected at enhancers and promoters in eukaryotes. S. cerevisiae set1Δ mutants unable to methylate H3K4 exhibit growth defects during histidine starvation. The growth defects are rescued by either a wild-type allele of SET1 or partial-function alleles of set1, including a mutant that predominantly generates H3K4me1 and not H3K4me3. Rescue of the growth defect is associated with induction of the HIS3 gene. Growth defects observed when set1Δ cultures were starved for isoleucine and valine were also rescued by wild-type SET1 or partial-function set1 alleles. The results show that H3K4me1, in the absence of H3K4me3, supports transcription of the HIS3 gene and expression of one or more of the genes required for biosynthesis of isoleucine and valine during nutrient stress. Set1-like methyltransferases are evolutionarily conserved, and research has linked their functions to developmental gene regulation and several cancers in higher eukaryotes. Identification of mechanisms of H3K4me1-mediated activation of transcription in budding yeast will provide insight into gene regulation in all eukaryotes.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8976815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39705995","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: 5

Investigating cell autonomy in microorganisms. 研究微生物的细胞自主性。

IF 1.8 4区生物学

Current Genetics Pub Date : 2022-04-01 Epub Date: 2022-02-04 DOI: 10.1007/s00294-022-01231-5

Sarah Piccirillo, Andrew P Morgan, Andy Y Leon, Annika L Smith, Saul M Honigberg

{"title":"Investigating cell autonomy in microorganisms.","authors":"Sarah Piccirillo, Andrew P Morgan, Andy Y Leon, Annika L Smith, Saul M Honigberg","doi":"10.1007/s00294-022-01231-5","DOIUrl":"10.1007/s00294-022-01231-5","url":null,"abstract":"Cell-cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell-cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell-cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell-cell signaling in microbial processes.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9101301/pdf/nihms-1802249.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9595524","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

The yeast Dbf4 Zn²⁺ finger domain suppresses single-stranded DNA at replication forks initiated from a subset of origins. 酵母Dbf4 Zn2+手指结构域抑制从一个起源子集发起的复制叉上的单链DNA。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 Epub Date: 2022-02-11 DOI: 10.1007/s00294-022-01230-6

Jeff Bachant, Elizabeth A Hoffman, Chris Caridi, Constance I Nugent, Wenyi Feng

{"title":"The yeast Dbf4 Zn2+ finger domain suppresses single-stranded DNA at replication forks initiated from a subset of origins.","authors":"Jeff Bachant, Elizabeth A Hoffman, Chris Caridi, Constance I Nugent, Wenyi Feng","doi":"10.1007/s00294-022-01230-6","DOIUrl":"https://doi.org/10.1007/s00294-022-01230-6","url":null,"abstract":"Dbf4 is the cyclin-like subunit for the Dbf4-dependent protein kinase (DDK), required for activating the replicative helicase at DNA replication origin that fire during S phase. Dbf4 also functions as an adaptor, targeting the DDK to different groups of origins and substrates. Here we report a genome-wide analysis of origin firing in a budding yeast mutant, dbf4-zn, lacking the Zn2+ finger domain within the C-terminus of Dbf4. At one group of origins, which we call dromedaries, we observe an unanticipated DNA replication phenotype: accumulation of single-stranded DNA spanning ± 5kbp from the center of the origins. A similar accumulation of single-stranded DNA at origins occurs more globally in pri1-m4 mutants defective for the catalytic subunit of DNA primase and rad53 mutants defective for the S phase checkpoint following DNA replication stress. We propose the Dbf4 Zn2+ finger suppresses single-stranded gaps at replication forks emanating from dromedary origins. Certain origins may impose an elevated requirement for the DDK to fully initiate DNA synthesis following origin activation. Alternatively, dbf4-zn may be defective for stabilizing/restarting replication forks emanating from dromedary origins during replication stress.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8976809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39910034","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

Yeast Stn1 promotes MCM to circumvent Rad53 control of the S phase checkpoint. 酵母Stn1促进MCM绕过Rad53对S期检查点的控制。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 Epub Date: 2022-02-12 DOI: 10.1007/s00294-022-01228-0

Hovik Gasparayan, Chris Caridi, Jeff Julius, Wenyi Feng, Jeff Bachant, Constance I Nugent

{"title":"Yeast Stn1 promotes MCM to circumvent Rad53 control of the S phase checkpoint.","authors":"Hovik Gasparayan, Chris Caridi, Jeff Julius, Wenyi Feng, Jeff Bachant, Constance I Nugent","doi":"10.1007/s00294-022-01228-0","DOIUrl":"https://doi.org/10.1007/s00294-022-01228-0","url":null,"abstract":"Treating yeast cells with the replication inhibitor hydroxyurea activates the S phase checkpoint kinase Rad53, eliciting responses that block DNA replication origin firing, stabilize replication forks, and prevent premature extension of the mitotic spindle. We previously found overproduction of Stn1, a subunit of the telomere-binding Cdc13-Stn1-Ten1 complex, circumvents Rad53 checkpoint functions in hydroxyurea, inducing late origin firing and premature spindle extension even though Rad53 is activated normally. Here, we show Stn1 overproduction acts through remarkably similar pathways compared to loss of RAD53, converging on the MCM complex that initiates origin firing and forms the catalytic core of the replicative DNA helicase. First, mutations affecting Mcm2 and Mcm5 block the ability of Stn1 overproduction to disrupt the S phase checkpoint. Second, loss of function stn1 mutations compensate rad53 S phase checkpoint defects. Third Stn1 overproduction suppresses a mutation in Mcm7. Fourth, stn1 mutants accumulate single-stranded DNA at non-telomeric genome locations, imposing a requirement for post-replication DNA repair. We discuss these interactions in terms of a model in which Stn1 acts as an accessory replication factor that facilitates MCM activation at ORIs and potentially also maintains MCM activity at replication forks advancing through challenging templates.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8976814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39912109","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: 1

Development of versatile and efficient genetic tools for the marine-derived fungus Aspergillus terreus RA2905. 海洋源真菌地曲霉RA2905多功能高效遗传工具的开发。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 Epub Date: 2022-01-19 DOI: 10.1007/s00294-021-01218-8

Guangshan Yao, Xiaofeng Chen, Yijuan Han, Huawei Zheng, Zonghua Wang, Jianming Chen

{"title":"Development of versatile and efficient genetic tools for the marine-derived fungus Aspergillus terreus RA2905.","authors":"Guangshan Yao, Xiaofeng Chen, Yijuan Han, Huawei Zheng, Zonghua Wang, Jianming Chen","doi":"10.1007/s00294-021-01218-8","DOIUrl":"https://doi.org/10.1007/s00294-021-01218-8","url":null,"abstract":"Marine-derived Aspergillus terreus produces a variety of structurally novel secondary metabolites, most of which show unique biological activities. However, the lack of efficient genetic tools limits the discovery of new compounds, the elucidation of involved biosynthesis mechanism, as well as the strain engineering efforts. Therefore, in this study, we first established both an effective PEG-mediated chemical transformation system of protoplasts and an electroporation system of conidia in a marine-derived fungus A. terreus RA2905. To overcome the insensitivity of RA2905 to fungicides, the uracil auxotrophy strain (pyrG gene deletion mutant, ΔpyrG) was constructed using PEG-mediated transformation system, and using ΔpyrG as the genetic background, the methyltransferase gene laeA-overexpression transformants were further constructed through both PEG- and electroporation-mediated transformations, which showed enhanced terrein production. Besides, in this study, an efficient CRISPR/Cas9 genome-editing system was established for the first time in A. terreus, and a higher gene deletion efficiency of 71% for APSES transcription factor gene stuA could be achieved when using short homologous arms compared with conventional long homologous ones. In addition, using a non-integrative Cas9 plasmid, another efficient and marker-free genome-editing system was established, which allowing repeatable and unlimited genetic manipulation in A. terreus. Using the marker-free genome-editing system, we successfully developed the ΔpyrGΔku70 double-deletion mutant in RA2905, which could further improve gene deletion efficiency. In conclusion, efficient genetic manipulation systems along with a variety of functional mutants were developed in this study, which would significantly expedite both theoretical and applied researches in not only A. terreus but also other marine-derived filamentous fungi.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39830749","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: 11

Prophage-encoded gene VpaChn25_0734 amplifies ecological persistence of Vibrio parahaemolyticus CHN25. 噬菌体编码基因VpaChn25_0734增强副溶血性弧菌CHN25的生态持久性。

IF 2.5 4区生物学

Current Genetics Pub Date : 2022-04-01 Epub Date: 2022-01-22 DOI: 10.1007/s00294-022-01229-z

Yingwei Xu, Lianzhi Yang, Yaping Wang, Zhuoying Zhu, Jizhou Yan, Si Qin, Lanming Chen

{"title":"Prophage-encoded gene VpaChn25_0734 amplifies ecological persistence of Vibrio parahaemolyticus CHN25.","authors":"Yingwei Xu, Lianzhi Yang, Yaping Wang, Zhuoying Zhu, Jizhou Yan, Si Qin, Lanming Chen","doi":"10.1007/s00294-022-01229-z","DOIUrl":"https://doi.org/10.1007/s00294-022-01229-z","url":null,"abstract":"Vibrio parahaemolyticus is a waterborne pathogen that can cause acute gastroenteritis, wound infection, and septicemia in humans. The molecular basis of its pathogenicity is not yet fully understood. Phages are found most abundantly in aquatic environments and play a critical role in horizontal gene transfer. Nevertheless, current literature on biological roles of prophage-encoded genes remaining in V. parahaemolyticus is rare. In this study, we characterized one such gene VpaChn25_0734 (543-bp) in V. parahaemolyticus CHN25 genome. A deletion mutant ΔVpaChn25_0734 (543-bp) was obtained by homologous recombination, and a revertant ΔVpaChn25_0734-com (543-bp) was also constructed. The ΔVpaChn25_0734 (543-bp) mutant was defective in growth and swimming mobility particularly at lower temperatures and/or pH 7.0-8.5. Cell surface hydrophobicity and biofilm formation were significantly decreased in the ΔVpaChn25_0734 (543-bp) mutant (p < 0.05). Based on the in vitro Caco-2 cell model, the deletion of VpaChn25_0734 (543-bp) gene significantly reduced the cytotoxicity of V. parahaemolyticus CHN25 to human intestinal epithelial cells (p < 0.05). Comparative secretomic and transcriptomic analyses revealed a slightly increased extracellular proteins, and thirteen significantly changed metabolic pathways in the ΔVpaChn25_0734 (543-bp) mutant, showing down-regulated carbon source transport and utilization, biofilm formation, and type II secretion system (p < 0.05), consistent with the observed defective phenotypes. Taken, the prophage-encoded gene VpaChn25_0734 (543-bp) enhanced V. parahaemolyticus CHN25 fitness for survival in the environment and the host. The results in this study facilitate better understanding of pathogenesis and genome evolution of V. parahaemolyticus, the leading sea foodborne pathogen worldwide.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8783578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39725239","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: 4