المؤلفون: Xu, Melvin

المصدر: PloS one (Online), 2 May 2023; v.18 n.5:14p;sup.7p

URL الوصول: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0284978&type=printable

المؤلفون: Gui, Qian, Deng, Shuyun, Zhou, ZhenZhen, Cao, Waifang, Zhang, Xin, Shi, Wenjun, Cai, Xiujuan, Jiang, Wenbing, Cui, Zifeng, Hu, Zheng, Chen, Xiaoshu

المصدر: Molecular Biology & Evolution; Aug2021, Vol. 38 Issue 8, p3294-3307, 14p

مصطلحات موضوعية: TRANSCRIPTOMES, GENOMES, YEAST genetic engineering, YEAST fungi genetics, CHROMOSOMES

مستخلص: The activity of a gene newly integrated into a chromosome depends on the genomic context of the integration site. This "position effect" has been widely reported, although the other side of the coin, that is, how integration affects the local chromosomal environment, has remained largely unexplored, as have the mechanism and phenotypic consequences of this "externality" of the position effect. Here, we examined the transcriptome profiles of approximately 250 Saccharomyces cerevisiae strains, each with GFP integrated into a different locus of the wild-type strain. We found that in genomic regions enriched in essential genes, GFP expression tended to be lower, and the genes near the integration site tended to show greater expression reduction. Further joint analysis with public genome-wide histone modification profiles indicated that this effect was associated with H3K4me2. More importantly, we found that changes in the expression of neighboring genes, but not GFP expression, significantly altered the cellular growth rate. As a result, genomic loci that showed high GFP expression immediately after integration were associated with growth disadvantages caused by elevated expression of neighboring genes, ultimately leading to a low total yield of GFP in the long run. Our results were consistent with competition for transcriptional resources among neighboring genes and revealed a previously unappreciated facet of position effects. This study highlights the impact of position effects on the fate of exogenous gene integration and has significant implications for biological engineering and the pathology of viral integration into the host genome. [ABSTRACT FROM AUTHOR]

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المؤلفون: Vignogna, Ryan C, Buskirk, Sean W, Lang, Gregory I

المصدر: Molecular Biology & Evolution; Aug2021, Vol. 38 Issue 8, p3144-3152, 9p

مصطلحات موضوعية: SACCHAROMYCES cerevisiae, YEAST genetic engineering, MICROBIAL genetic engineering, YEAST fungi genetics, GENETIC variation

مستخلص: Understanding how genes interact is a central challenge in biology. Experimental evolution provides a useful, but underutilized, tool for identifying genetic interactions, particularly those that involve non-loss-of-function mutations or mutations in essential genes. We previously identified a strong positive genetic interaction between specific mutations in KEL1 (P344T) and HSL7 (A695fs) that arose in an experimentally evolved Saccharomyces cerevisiae population. Because this genetic interaction is not phenocopied by gene deletion, it was previously unknown. Using "evolutionary replay" experiments, we identified additional mutations that have positive genetic interactions with the kel1 -P344T mutation. We replayed the evolution of this population 672 times from six timepoints. We identified 30 populations where the kel1 -P344T mutation reached high frequency. We performed whole-genome sequencing on these populations to identify genes in which mutations arose specifically in the kel1 -P344T background. We reconstructed mutations in the ancestral and kel1 -P344T backgrounds to validate positive genetic interactions. We identify several genetic interactors with KEL1 , we validate these interactions by reconstruction experiments, and we show these interactions are not recapitulated by loss-of-function mutations. Our results demonstrate the power of experimental evolution to identify genetic interactions that are positive, allele specific, and not readily detected by other methods, shedding light on an underexplored region of the yeast genetic interaction network. [ABSTRACT FROM AUTHOR]

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المؤلفون: Su, Jie, Xu, Ran, Mongia, Piyusha, Toyofuku, Naoko, Nakagawa, Takuro

المصدر: PLoS Genetics; 7/22/2021, Vol. 17 Issue 7, p1-25, 25p

مصطلحات موضوعية: CHROMOSOMAL rearrangement, PROLIFERATING cell nuclear antigen, UBIQUITINATION, UBIQUITIN-conjugating enzymes, GENE conversion, UBIQUITIN ligases, LYSINE, YEAST fungi genetics

مستخلص: Gross chromosomal rearrangements (GCRs), including translocation, deletion, and inversion, can cause cell death and genetic diseases such as cancer in multicellular organisms. Rad51, a DNA strand exchange protein, suppresses GCRs by repairing spontaneous DNA damage through a conservative way of homologous recombination, gene conversion. On the other hand, Rad52 that catalyzes single-strand annealing (SSA) causes GCRs using homologous sequences. However, the detailed mechanism of Rad52-dependent GCRs remains unclear. Here, we provide genetic evidence that fission yeast Rad8/HLTF facilitates Rad52-dependent GCRs through the ubiquitination of lysine 107 (K107) of PCNA, a DNA sliding clamp. In rad51Δ cells, loss of Rad8 eliminated 75% of the isochromosomes resulting from centromere inverted repeat recombination, showing that Rad8 is essential for the formation of the majority of isochromosomes in rad51Δ cells. Rad8 HIRAN and RING finger mutations reduced GCRs, suggesting that Rad8 facilitates GCRs through 3' DNA-end binding and ubiquitin ligase activity. Mms2 and Ubc4 but not Ubc13 ubiquitin-conjugating enzymes were required for GCRs. Consistent with this, mutating PCNA K107 rather than the well-studied PCNA K164 reduced GCRs. Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs, as PCNA K107R, rad8, and rad52 mutations epistatically reduced GCRs. In contrast to GCRs, PCNA K107R did not significantly change gene conversion rates, suggesting a specific role of PCNA K107 ubiquitination in GCRs. PCNA K107R enhanced temperature-sensitive growth defects of DNA ligase I cdc17-K42 mutant, implying that PCNA K107 ubiquitination occurs when Okazaki fragment maturation fails. Remarkably, K107 is located at the interface between PCNA subunits, and an interface mutation D150E bypassed the requirement of PCNA K107 and Rad8 ubiquitin ligase for GCRs. These data suggest that Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs by changing the PCNA clamp structure. Author summary: Gross chromosomal rearrangements (GCRs), including translocation, can alter gene dosage and activity, resulting in genetic diseases such as cancer. However, GCRs can occur by some enzymes, including Rad52 recombinase, and result in chromosomal evolution. Therefore, GCRs are not only pathological but also physiological phenomena from an evolutionary point of view. However, the detailed mechanism of GCRs remains unclear. Here, using fission yeast, we show that the homolog of human HLTF, Rad8 causes GCRs through noncanonical ubiquitination of proliferating cellular nuclear antigen (PCNA) at a lysine 107 (K107). Rad51, a DNA strand exchange protein, suppresses the formation of isochromosomes whose arms mirror each another and chromosomal truncation. We found that, like Rad52, Rad8 is required for isochromosome formation but not chromosomal truncation in rad51Δ cells, showing a specific role of Rad8 in homology-mediated GCRs. Mutations in Rad8 ubiquitin E3 ligase RING finger domain, Mms2-Ubc4 ubiquitin-conjugating enzymes, and PCNA K107 reduced GCRs in rad51Δ cells, suggesting that Rad8-Mms2-Ubc4-dependent PCNA K107 ubiquitination facilitates GCRs. PCNA trimers form a DNA sliding clamp. The K107 residue is located at the PCNA-PCNA interface, and an interface mutation D150E restored GCRs in PCNA K107R mutant cells. This study provides genetic evidence that Rad8-dependent PCNA K107 ubiquitination facilitates GCRs by changing the PCNA clamp structure. [ABSTRACT FROM AUTHOR]

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المؤلفون: Chen, Piaopiao, Zhang, Jianzhi

المصدر: Molecular Biology & Evolution; Jul2021, Vol. 38 Issue 7, p2831-2842, 12p

مصطلحات موضوعية: YEAST fungi genetics, FUNGAL genetics, TRANSPOSONS, SACCHAROMYCES cerevisiae

مستخلص: Compared with asexual reproduction, sex facilitates the transmission of transposable elements (TEs) from one genome to another, but boosts the efficacy of selection against deleterious TEs. Thus, theoretically, it is unclear whether sex has a positive net effect on TE's proliferation. An empirical study concluded that sex is at the root of TE's evolutionary success because the yeast TE load was found to decrease rapidly in approximately 1,000 generations of asexual but not sexual experimental evolution. However, this finding contradicts the maintenance of TEs in natural yeast populations where sexual reproduction occurs extremely infrequently. Here, we show that the purported TE load reduction during asexual experimental evolution is likely an artifact of low genomic sequencing coverages. We observe stable TE loads in both sexual and asexual experimental evolution from multiple yeast data sets with sufficient coverages. To understand the evolutionary dynamics of yeast TEs, we turn to asexual mutation accumulation lines that have been under virtually no selection. We find that both TE transposition and excision rates per generation, but not their difference, tend to be higher in environments where yeast grows more slowly. However, the transposition rate is not significantly higher than the excision rate and the variance of the TE number among natural strains is close to its neutral expectation, suggesting that selection against TEs is at best weak in yeast. We conclude that the yeast TE load is maintained largely by a transposition–excision balance and that the influence of sex remains unclear. [ABSTRACT FROM AUTHOR]

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المؤلفون: Dodd, Sarah (Plant pathologist)

المصدر: New Zealand journal of forestry science, 2022; v.52 n.9:20p

URL الوصول: https://nzjforestryscience.nz/index.php/nzjfs/article/view/203/68
https://ndhadeliver.natlib.govt.nz/delivery/DeliveryManagerServlet?dps_pid=FL87474469

المؤلفون: Shivhare, Devendra, Musialak-Lange, Magdalena, Julca, Irene, Gluza, Pawel, Mutwil, Marek

المصدر: Scientific Reports; 3/9/2021, Vol. 11 Issue 1, p1-9, 9p

مصطلحات موضوعية: YEAST fungi genetics, BIOLOGICAL assay, PROMOTERS (Genetics), PROTEIN-protein interactions, YEAST physiology

مستخلص: Yeast-two-hybrid (Y2H) is widely used as a strategy to detect protein–protein interactions (PPIs). Recent advancements have made it possible to generate and analyse genome-wide PPI networks en masse by coupling Y2H with next-generation sequencing technology. However, one of the major challenges of yeast two-hybrid assay is the large amount of false-positive hits caused by auto-activators (AAs), which are proteins that activate the reporter genes without the presence of an interacting protein partner. Here, we have developed a negative selection to minimize these auto-activators by integrating the pGAL2-URA3 fragment into the yeast genome. Upon activation of the pGAL2 promoter by an AA, yeast cells expressing URA3 cannot grow in media supplemented with 5-Fluoroorotic acid (5-FOA). Hence, we selectively inhibit the growth of yeast cells expressing auto-activators and thus minimizing the amount of false-positive hits. Here, we have demonstrated that auto-activators can be successfully removed from a Marchantia polymorpha cDNA library using pGAL2-URA3 and 5-FOA treatment, in liquid and solid-grown cultures. Furthermore, since URA3 can also serve as a marker for uracil autotrophy, we propose that our approach is a valuable addition to any large-scale Y2H screen. [ABSTRACT FROM AUTHOR]

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المؤلفون: Gaikwad, Prashant, Joshi, Swanand, Mandlecha, Akshay, RaviKumar, Ameeta

المصدر: Scientific Reports; 3/9/2021, Vol. 11 Issue 1, p1-13, 13p

مصطلحات موضوعية: YEAST fungi genetics, YEAST physiology, PHENOTYPES, LIPASES, LOW temperatures

مستخلص: Yarrowia clade contains yeast species morphologically, ecologically, physiologically and genetically diverse in nature. Yarrowia lipolytica NCIM 3590 (NCIM 3590), a biotechnologically important strain, isolated from Scottish sea waters was reinvestigated for its phenotypic, biochemical, molecular and genomic properties as it exhibited characteristics unlike Y. lipolytica, namely, absence of extracellular lipolytic activity, growth at lower temperatures (less than 20 °C) and in high salt concentrations (10% NaCl). Molecular identification using ITS and D1/D2 sequences suggested NCIM 3590 to be 100% identical with reference strain Yarrowia bubula CBS 12934 rather than Y. lipolytica CBS 6124 (87% identity) while phylogenetic analysis revealed that it clustered with Y. bubula under a separate clade. Further, whole genome sequencing of NCIM 3590 was performed using Illumina NextSeq technology and the draft reported here. The overall genome relatedness values obtained by dDDH (94.1%), ANIb/ANIm (99.41/99.42%) and OrthoANI (99.47%) indicated proximity between NCIM 3590 and CBS 12934 as compared to the reference strain Y. lipolytica. No extracellular lipase activity could be detected in NCIM 3590 while LIP2 gene TBLASTN analysis suggests a low 42% identity with e value 2 e⁻⁷⁷ and 62% coverage. Hence molecular, phylogenetic, genomics, biochemical and microbial analyses suggests it belongs to Yarrowia bubula. [ABSTRACT FROM AUTHOR]

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المؤلفون: Eriksson, Peter R., Clark, David J.

المصدر: Scientific Reports; 2/18/2021, Vol. 11 Issue 1, p1-14, 14p

مصطلحات موضوعية: CHROMATIN, METHYLTRANSFERASES, ADENOSINE triphosphate, YEAST fungi genetics, GENETIC transcription

مستخلص: Isw1 and Chd1 are ATP-dependent nucleosome-spacing enzymes required to establish regular arrays of phased nucleosomes near transcription start sites of yeast genes. Cells lacking both Isw1 and Chd1 have extremely disrupted chromatin, with weak phasing, irregular spacing and a propensity to form close-packed dinucleosomes. The Isw1 ATPase subunit occurs in two different remodeling complexes: ISW1a (composed of Isw1 and Ioc3) and ISW1b (composed of Isw1, Ioc2 and Ioc4). The Ioc4 subunit of ISW1b binds preferentially to the H3-K36me3 mark. Here we show that ISW1b is primarily responsible for setting nucleosome spacing and resolving close-packed dinucleosomes, whereas ISW1a plays only a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution, such that neither enzyme is capable of resolving all dinucleosomes on its own. Loss of the Set2 H3-K36 methyltransferase partly phenocopies loss of Ioc4, resulting in increased dinucleosome levels with only a weak effect on nucleosome spacing, suggesting that Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation. The H4 tail domain is required for normal nucleosome spacing but not for dinucleosome resolution. We conclude that the nucleosome spacing and dinucleosome resolving activities of ISW1b and Chd1 are critical for normal global chromatin organisation. [ABSTRACT FROM AUTHOR]

: Copyright of Scientific Reports is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

المؤلفون: Chandelier, Anne, Hulin, Julie, San Martin, Gilles, Debode, Frédéric, Massart, Sébastien

المصدر: Phytopathology, 111 (3), 570-581 (2021-03)

مصطلحات موضوعية: FungiSearch, HTS, mycology techniques, real-time PCR, spore trap, surveillance, Fungi/genetics, High-Throughput Nucleotide Sequencing, Real-Time Polymerase Chain Reaction, Spores, Fungal, Ecosystem, Plant Diseases, Fungi, Agronomy and Crop Science, Plant Science, Life sciences, Biotechnology, Sciences du vivant, Biotechnologie

الوصف: Forest diseases caused by invasive fungal pathogens are becoming more common, sometimes with dramatic consequences to forest ecosystems. The development of early detection systems is necessary for efficient surveillance and to mitigate the impact of invasive pathogens. Windborne spores are an important pathway for introduction of fungal pathogens into new areas; the design of spore trapping devices adapted to forests, capable of collecting different types of spores, and aligned with development of efficient molecular methods for detection of the pathogen, should help forest managers anticipate new disease outbreaks. Two types of Rotorod samplers were evaluated for the collection of airborne inoculum of forest fungal pathogens with a range of spore sizes in five forest types. Detection was by specific quantitative PCR (qPCR) and by high-throughput sequencing (HTS) of amplified internal transcribed spacer sequences using a new bioinformatic pipeline, FungiSearch, developed for diagnostic purposes. Validation of the pipeline was conducted on mock communities of 10 fungal species belonging to different taxa. Although the sensitivity of the new HTS pipeline was lower than the specific qPCR, it was able to detect a wide variety of fungal pathogens. FungiSearch is easy to use, and the reference database is updatable, making the tool suitable for rapid identification of new pathogens. This new approach combining spore trapping and HTS detection is promising as a diagnostic tool for invasive fungal pathogens.

Relation: https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-02-20-0034-R; urn:issn:0031-949X; urn:issn:1943-7684

URL الوصول: https://orbi.uliege.be/handle/2268/291185