Current Genetics最新文献_第10页

RNA modifications as a common denominator between tRNA and mRNA. RNA修饰是tRNA和mRNA之间的共同点。

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-08-01 Epub Date: 2021-03-08 DOI: 10.1007/s00294-021-01168-1

Ofri Levi, Yoav S Arava

引用次数: 6

Genetic barcodes allow traceability of CRISPR/Cas9-derived Aspergillus niger strains without affecting their fitness. 遗传条形码允许CRISPR/ cas9衍生的黑曲霉菌株的可追溯性，而不会影响它们的适应性。

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-08-01 Epub Date: 2021-03-16 DOI: 10.1007/s00294-021-01164-5

Sandra Garrigues, Roland S Kun, Ronald P de Vries

{"title":"Genetic barcodes allow traceability of CRISPR/Cas9-derived Aspergillus niger strains without affecting their fitness.","authors":"Sandra Garrigues, Roland S Kun, Ronald P de Vries","doi":"10.1007/s00294-021-01164-5","DOIUrl":"https://doi.org/10.1007/s00294-021-01164-5","url":null,"abstract":"Safe use of genetically modified organisms (GMOs) in biotechnology requires the ability to track the presence of these strains in any environment in which they are applied. For this, introduction of genetic barcodes within the editing site represents a valuable tool for the identification of microbial strains that have undergone genetic modifications. However, it is not known whether these barcodes would have any unexpected effect in the resulting strains or affect the efficiency of the genetic modification. CRISPR/Cas9 has become one of the fastest-growing technologies for genome editing in a range of organisms, including fungi. However, this technology enables the generation of scarless GMOs that are very difficult to distinguish from naturally occurring mutants or other modified organisms. In this study, we address this issue using the industrial workhorse Aspergillus niger as a test case. We applied CRISPR/Cas9 technology to delete the genes encoding the transcriptional regulators XlnR and AraR, involved in the production of plant biomass-degrading enzymes. We generated 20-bp barcoded and non-barcoded ΔxlnR and ΔaraR mutants and analyzed the traceability and fitness of the resulting strains, as well as the efficiency of the genetic modification. Results showed that both barcoded and non-barcoded mutants can be traced by routine PCR reactions when the specific CRISPR/Cas9 modification is known. Additionally, barcodes neither affected the efficiency of the genetic modification nor the growth or protein production of the resulting strains. These results confirm the suitability of genetic barcodes to trace CRISPR-derived GMOs without affecting the performance of the resulting strains.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"67 4","pages":"673-684"},"PeriodicalIF":2.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00294-021-01164-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25482072","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

Genetic characteristics and phylogenetic analysis of Brazilian clinical strains of Pseudomonas aeruginosa harboring CRISPR/Cas systems. 携带CRISPR/Cas系统的铜绿假单胞菌巴西临床菌株的遗传特征和系统发育分析。

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-08-01 Epub Date: 2021-03-22 DOI: 10.1007/s00294-021-01173-4

Ana Carolina de Oliveira Luz, Wilson José da Silva Junior, José Bandeira do Nascimento Junior, Julia Mariana Assis da Silva, Valdir de Queiroz Balbino, Tereza Cristina Leal-Balbino

{"title":"Genetic characteristics and phylogenetic analysis of Brazilian clinical strains of Pseudomonas aeruginosa harboring CRISPR/Cas systems.","authors":"Ana Carolina de Oliveira Luz, Wilson José da Silva Junior, José Bandeira do Nascimento Junior, Julia Mariana Assis da Silva, Valdir de Queiroz Balbino, Tereza Cristina Leal-Balbino","doi":"10.1007/s00294-021-01173-4","DOIUrl":"https://doi.org/10.1007/s00294-021-01173-4","url":null,"abstract":"The CRISPR-Cas are adaptive immune systems found in archaea and bacteria, responsible for providing sequence-specific resistance against foreign DNA. Strains of Pseudomonas aeruginosa may carry CRISPR/Cas system types I-F, I-E and/or I-C; however, several aspects related to the epidemiology and functionality of these systems have not yet been revealed. Here, we report 13 genomes of clinical strains of P. aeruginosa from Brazil that were positive for CRISPR/Cas system types I-F and I-E, a rare feature in this species. The phylogenetic tree, which was constructed with 161 other publicly available genomes, suggested no direct relationship between positive strains, and the various types of CRISPR/Cas systems were spread throughout the tree. Comparative analysis of the genetic locations of type I-F and a specific orphan CRISPR array (without cas genes), named the LES locus, showed sequence similarities between this orphan locus and type I-F, but these LES loci were inserted in a different genomic location. We also report the presence of prophages, the presence of anti-CRISPR genes, and possibly the presence of self-targeting spacers. Here, we conclude that CRISPR/Cas is highly associated with certain lineages and is spread throughout the phylogenetic tree, showing no clear pattern of evolutionary distribution. Moreover, the LES locus might be a CRISPR1 locus related to type I-F that may have been misplaced and maintained over time. Furthermore, strains carrying I-F and I-E are rare, and not all of them are closely related. Further functional work is needed to better comprehend if aspects reported in this study are functional, including the LES locus, self-targeting spacers, anti-CRISPR protection, and I-F/I-E-carrying lineages.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"67 4","pages":"663-672"},"PeriodicalIF":2.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00294-021-01173-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25504441","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 challenge of staying in shape: nuclear size matters. 保持体形的挑战:核尺寸很重要。

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-08-01 Epub Date: 2021-03-29 DOI: 10.1007/s00294-021-01176-1

Pallavi Deolal, Gurranna Male, Krishnaveni Mishra

引用次数: 5

Coordinated regulation of iron metabolism in Cryptococcus neoformans by GATA and CCAAT transcription factors: connections with virulence. GATA和CCAAT转录因子对新生隐球菌铁代谢的协同调节:与毒力的关系

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-08-01 Epub Date: 2021-03-24 DOI: 10.1007/s00294-021-01172-5

Won Hee Jung, Eddy Sánchez-León, James W Kronstad

{"title":"Coordinated regulation of iron metabolism in Cryptococcus neoformans by GATA and CCAAT transcription factors: connections with virulence.","authors":"Won Hee Jung, Eddy Sánchez-León, James W Kronstad","doi":"10.1007/s00294-021-01172-5","DOIUrl":"https://doi.org/10.1007/s00294-021-01172-5","url":null,"abstract":"Iron acquisition is critical for pathogenic fungi to adapt to and survive within the host environment. However, to same extent, the fungi must also avoid the detrimental effects caused by excess iron. The importance of iron has been demonstrated for the physiology and virulence of major fungal pathogens of humans including Aspergillus fumigatus, Candida albicans, and Cryptococcus neoformans. In particular, numerous studies have revealed that aspects of iron acquisition, metabolism, and homeostasis in the fungal pathogens are tightly controlled by conserved transcriptional regulators including a GATA-type iron transcription factor and the CCAAT-binding complex (CBC)/HapX orthologous protein complex. However, the specific downstream regulatory networks are slightly different in each fungus. In addition, roles have been proposed or demonstrated for other factors including monothiol glutaredoxins, BolA-like proteins, and Fe-S cluster incorporation on the GATA-type iron transcription factor and the CBC/HapX orthologous protein complex, although limited information is available. Here we focus on recent work on C. neoformans in the context of an emerging framework for fungal regulation of iron acquisition, metabolism, and homeostasis. Our specific goal is to summarize recent findings on transcriptional networks governed by the iron regulators Cir1 and HapX in C. neoformans.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"67 4","pages":"583-593"},"PeriodicalIF":2.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00294-021-01172-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25524751","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

Wake-up alarm: virtual time-lapse gene expression landscape illuminates mechanisms underlying dormancy breaking of germinating spores. 唤醒警报:虚拟延时基因表达景观阐明了发芽孢子休眠打破的机制。

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-08-01 Epub Date: 2021-03-29 DOI: 10.1007/s00294-021-01177-0

Hayato Tsuyuzaki, Ryosuke Ujiie, Masamitsu Sato

{"title":"Wake-up alarm: virtual time-lapse gene expression landscape illuminates mechanisms underlying dormancy breaking of germinating spores.","authors":"Hayato Tsuyuzaki, Ryosuke Ujiie, Masamitsu Sato","doi":"10.1007/s00294-021-01177-0","DOIUrl":"https://doi.org/10.1007/s00294-021-01177-0","url":null,"abstract":"Dormancy breaking is a common physiological phenomenon that is shared by eukaryotes. Germination of spores in fungi is one of the most representative cases of dormancy breaking. Understanding the mechanisms of spore germination is therefore fundamental to basic studies on the control of cell proliferation and differentiation, as well as agricultural applications and medical investigation of fungal pathogenesis. In fission yeast, spores are generated as a consequence of sexual differentiation under nutrient starvation, remaining dormant until further nourishment, but little is known about how dormant spores germinate in response to environmental change. In a breakthrough, methods for single-cell-based gene expression profiling have recently been introduced. Several mRNA expression profiles were assembled from single spore cells during dormancy or germination. Single-cell RNA-seq profiles were aligned sequentially according to their similarities. The alignment of transcriptomes visualised how gene expression varies over time upon dormancy breaking. In this review, we revisit knowledge from previous studies on germination, select candidate genes that may be involved in germination, and query their expression from the temporal transcriptomic dataset so that studies on S. pombe germination can be extended further.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"67 4","pages":"519-534"},"PeriodicalIF":2.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00294-021-01177-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25529223","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

Regulatory networking of the three RNA polymerases helps the eukaryotic cells cope with environmental stress. 三种RNA聚合酶的调控网络有助于真核细胞应对环境胁迫。

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-08-01 Epub Date: 2021-03-28 DOI: 10.1007/s00294-021-01179-y

Purnima Bhargava

{"title":"Regulatory networking of the three RNA polymerases helps the eukaryotic cells cope with environmental stress.","authors":"Purnima Bhargava","doi":"10.1007/s00294-021-01179-y","DOIUrl":"https://doi.org/10.1007/s00294-021-01179-y","url":null,"abstract":"Environmental stress influences the cellular physiology in multiple ways. Transcription by all the three RNA polymerases (Pols I, II, or III) in eukaryotes is a highly regulated process. With latest advances in technology, which have made many extensive genome-wide studies possible, it is increasingly recognized that all the cellular processes may be interconnected. A comprehensive view of the current research observations brings forward an interesting possibility that Pol II-associated factors may be directly involved in the regulation of expression from the Pol III-transcribed genes and vice versa, thus enabling a cross-talk between the two polymerases. An equally important cross-talk between the Pol I and Pol II/III has also been documented. Collectively, these observations lead to a change in the current perception that looks at the transcription of a set of genes transcribed by the three Pols in isolation. Emergence of an inclusive perspective underscores that all stress signals may converge on common mechanisms of transcription regulation, requiring an extensive cross-talk between the regulatory partners. Of the three RNA polymerases, Pol III turns out as the hub of these cross-talks, an essential component of the cellular stress-response under which the majority of the cellular transcriptional activity is shut down or re-aligned.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"67 4","pages":"595-603"},"PeriodicalIF":2.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00294-021-01179-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25527524","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

Who gets a license: DNA synthesis in quiescent cells re-entering the cell cycle. 谁获得许可:在静止细胞中重新进入细胞周期的DNA合成。

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-08-01 Epub Date: 2021-03-08 DOI: 10.1007/s00294-021-01170-7

Po-Hsuen Lee, Mary Ann Osley

{"title":"Who gets a license: DNA synthesis in quiescent cells re-entering the cell cycle.","authors":"Po-Hsuen Lee, Mary Ann Osley","doi":"10.1007/s00294-021-01170-7","DOIUrl":"https://doi.org/10.1007/s00294-021-01170-7","url":null,"abstract":"The precise regulation of the entry into S phase is critical for preventing genome instability. The first step in the initiation of eukaryotic DNA synthesis occurs in G1 phase cells and involves the loading of the conserved MCM helicase onto multiple origins of replication in a process known as origin licensing. In proliferating metazoan cells, an origin-licensing checkpoint delays initiation until high levels of MCM loading occur, with excess origins being licensed. One function of this checkpoint is to ensure that S phase can be completed in the face of replication stress by activation of dormant MCM bound origins. However, when both metazoan and yeast cells enter S phase from quiescence or G0 phase, a non-growing but reversible cell cycle state, origins are significantly under-licensed. In metazoan cells, under-licensing is the result of a compromised origin-licensing checkpoint. In budding yeast, our study has revealed that under-licensing can be attributed to the chromatin structure at a class of origins that is inhibitory to the binding of MCM. Thus, defects in multiple pathways may contribute to the failure to fully license origins in quiescent cells re-entering the cell cycle, thereby promoting a higher risk of genome instability.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"67 4","pages":"539-543"},"PeriodicalIF":2.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00294-021-01170-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25446257","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

Forkhead transcription factor Fkh1: insights into functional regulatory domains crucial for recruitment of Sin3 histone deacetylase complex. 叉头转录因子Fkh1:对Sin3组蛋白去乙酰化酶复合体募集至关重要的功能调控域的见解

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-06-01 Epub Date: 2021-02-26 DOI: 10.1007/s00294-021-01158-3

Rasha Aref, Marwa N M E Sanad, Hans-Joachim Schüller

{"title":"Forkhead transcription factor Fkh1: insights into functional regulatory domains crucial for recruitment of Sin3 histone deacetylase complex.","authors":"Rasha Aref, Marwa N M E Sanad, Hans-Joachim Schüller","doi":"10.1007/s00294-021-01158-3","DOIUrl":"https://doi.org/10.1007/s00294-021-01158-3","url":null,"abstract":"Transcription factors are inextricably linked with histone deacetylases leading to compact chromatin. The Forkhead transcription factor Fkh1 is mainly a negative transcriptional regulator which affects cell cycle control, silencing of mating-type cassettes and induction of pseudohyphal growth in the yeast Saccharomyces cerevisiae. Markedly, Fkh1 impinges chromatin architecture by recruiting large regulatory complexes. Implication of Fkh1 with transcriptional corepressor complexes remains largely unexplored. In this work we show that Fkh1 directly recruits corepressors Sin3 and Tup1 (but not Cyc8), providing evidence for its influence on epigenetic regulation. We also identified the specific domain of Fkh1 mediating Sin3 recruitment and substantiated that amino acids 51-125 of Fkh1 bind PAH2 of Sin3. Importantly, this part of Fkh1 overlaps with its Forkhead-associated domain (FHA). To analyse this domain in more detail, selected amino acids were replaced by alanine, revealing that hydrophobic amino acids L74 and I78 are important for Fkh1-Sin3 binding. In addition, we could prove Fkh1 recruitment to promoters of cell cycle genes CLB2 and SWI5. Notably, Sin3 is also recruited to these promoters but only in the presence of functional Fkh1. Our results disclose that recruitment of Sin3 to Fkh1 requires precisely positioned Fkh1/Sin3 binding sites which provide an extended view on the genetic control of cell cycle genes CLB2 and SWI5 and the mechanism of transcriptional repression by modulation of chromatin architecture at the G2/M transition.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"67 3","pages":"487-499"},"PeriodicalIF":2.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00294-021-01158-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25408203","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

How do small chromosomes know they are small? Maximizing meiotic break formation on the shortest yeast chromosomes. 小染色体如何知道自己很小？在最短的酵母染色体上最大限度地形成减数分裂断裂。

IF 2.5 4区生物学

Current Genetics Pub Date : 2021-06-01 Epub Date: 2021-02-18 DOI: 10.1007/s00294-021-01160-9

Hajime Murakami, Xiaojing Mu, Scott Keeney

{"title":"How do small chromosomes know they are small? Maximizing meiotic break formation on the shortest yeast chromosomes.","authors":"Hajime Murakami, Xiaojing Mu, Scott Keeney","doi":"10.1007/s00294-021-01160-9","DOIUrl":"10.1007/s00294-021-01160-9","url":null,"abstract":"The programmed formation of DNA double-strand breaks (DSBs) in meiotic prophase I initiates the homologous recombination process that yields crossovers between homologous chromosomes, a prerequisite to accurately segregating chromosomes during meiosis I (MI). In the budding yeast Saccharomyces cerevisiae, proteins required for meiotic DSB formation (DSB proteins) accumulate to higher levels specifically on short chromosomes to ensure that these chromosomes make DSBs. We previously demonstrated that as-yet undefined cis-acting elements preferentially recruit DSB proteins and promote higher levels of DSBs and recombination and that these intrinsic features are subject to selection pressure to maintain the hyperrecombinogenic properties of short chromosomes. Thus, this targeted boosting of DSB protein binding may be an evolutionarily recurrent strategy to mitigate the risk of meiotic mis-segregation caused by karyotypic constraints. However, the underlining mechanisms are still elusive. Here, we discuss possible scenarios in which components of the meiotic chromosome axis (Red1 and Hop1) bind to intrinsic features independent of the meiosis-specific cohesin subunit Rec8 and DNA replication, promoting preferential binding of DSB proteins to short chromosomes. We also propose a model where chromosome position in the nucleus, influenced by centromeres, promotes the short-chromosome boost of DSB proteins.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"67 3","pages":"431-437"},"PeriodicalIF":2.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141002/pdf/nihms-1676235.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25388157","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