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https://www.readbyqxmd.com/read/28335590/roles-of-budding-yeast-hrr25-in-recombination-and-sporulation
#1
Min-Su Lee, Jeong Hwan Joo, Keunpil Kim
Hrr25, a casein kinase 1 δ/ε homolog in budding yeast, is essential to set up mono-orientation of sister kinetochores during meiosis. Hrr25 kinase activity coordinates sister chromatid cohesion via cohesin phosphorylation. Here, we investigated the prophase roles of Hrr25 using the auxin-inducible degron system and by ectopic expression of Hrr25 during yeast meiosis. Hrr25 mediates nuclear division in meiosis I but does not affect DNA replication. We also found that initiation of meiotic double-strand breaks as well as joint molecule formation were normal in HRR25-deficient cells...
March 24, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28335026/melting-temperature-highlights-functionally-important-rna-structure-and-sequence-elements-in-yeast-mrna-coding-regions
#2
Fei Qi, Dmitrij Frishman
Secondary structure elements in the coding regions of mRNAs play an important role in gene expression and regulation, but distinguishing functional from non-functional structures remains challenging. Here we investigate the dependence of sequence-structure relationships in the coding regions on temperature based on the recent PARTE data by Wan et al. Our main finding is that the regions with high and low thermostability (high Tm and low Tm regions) are under evolutionary pressure to preserve RNA secondary structure and primary sequence, respectively...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334975/apricot-an-integrated-computational-pipeline-for-the-sequence-based-identification-and-characterization-of-rna-binding-proteins
#3
Malvika Sharan, Konrad U Förstner, Ana Eulalio, Jörg Vogel
RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches...
March 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334955/the-schizosaccharomyces-pombe-ppr-protein-ppr10-associates-with-a-novel-protein-mpa1-and-acts-as-a-mitochondrial-translational-activator
#4
Yirong Wang, Jianhua Yan, Qingzhen Zhang, Xuting Ma, Juan Zhang, Minghui Su, Xiaojun Wang, Ying Huang
The pentatricopeptide repeat (PPR) proteins characterized by tandem repeats of a degenerate 35-amino-acid motif function in all aspects of organellar RNA metabolism, many of which are essential for organellar gene expression. In this study, we report the characterization of a fission yeast Schizosaccharomyces pombe PPR protein, Ppr10 and a novel Ppr10-associated protein, designated Mpa1. The ppr10 deletion mutant exhibits growth defects in respiratory media, and is dramatically impaired for viability during the late-stationary phase...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334931/rgf1p-rho1p-gef-is-required-for-double-strand-break-repair-in-fission-yeast
#5
Elvira Manjón, Tomás Edreira, Sofía Muñoz, Yolanda Sánchez
Rho GTPases are conserved molecules that control cytoskeletal dynamics. These functions are expedited by Rho GEFs that stimulate the release of GDP to enable GTP binding, thereby allowing Rho proteins to initiate intracellular signaling. How Rho GEFs and Rho GTPases protect cells from DNA damage is unknown. Here, we explore the extreme sensitivity of a deletion mutation in the Rho1p exchange factor Rgf1p to the DNA break/inducing antibiotic phleomycin (Phl). The Rgf1p mutant cells are defective in reentry into the cell cycle following the induction of severe DNA damage...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334887/avoidance-of-apobec3b-induced-mutation-by-error-free-lesion-bypass
#6
James I Hoopes, Amber L Hughes, Lauren A Hobson, Luis M Cortez, Alexander J Brown, Steven A Roberts
APOBEC cytidine deaminases mutate cancer genomes by converting cytidines into uridines within ssDNA during replication. Although uracil DNA glycosylases limit APOBEC-induced mutation, it is unknown if subsequent base excision repair (BER) steps function on replication-associated ssDNA. Hence, we measured APOBEC3B-induced CAN1 mutation frequencies in yeast deficient in BER endonucleases or DNA damage tolerance proteins. Strains lacking Apn1, Apn2, Ntg1, Ntg2 or Rev3 displayed wild-type frequencies of APOBEC3B-induced canavanine resistance (CanR)...
March 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334827/yeast-hrq1-shares-structural-and-functional-homology-with-the-disease-linked-human-recq4-helicase
#7
Cody M Rogers, Joseph Che-Yen Wang, Hiroki Noguchi, Tsuyoshi Imasaki, Yuichiro Takagi, Matthew L Bochman
The five human RecQ helicases participate in multiple processes required to maintain genome integrity. Of these, the disease-linked RecQ4 is the least studied because it poses many technical challenges. We previously demonstrated that the yeast Hrq1 helicase displays similar functions to RecQ4 in vivo, and here, we report the biochemical and structural characterization of these enzymes. In vitro, Hrq1 and RecQ4 are DNA-stimulated ATPases and robust helicases. Further, these activities were sensitive to DNA sequence and structure, with the helicases preferentially unwinding D-loops...
February 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334815/gcn5-mediated-rph1-acetylation-regulates-its-autophagic-degradation-under-dna-damage-stress
#8
Feng Li, Liang-De Zheng, Xin Chen, Xiaolu Zhao, Scott D Briggs, Hai-Ning Du
Histone modifiers regulate proper cellular activities in response to various environmental stress by modulating gene expression. In budding yeast, Rph1 transcriptionally represses many DNA damage or autophagy-related gene expression. However, little is known how Rph1 is regulated during these stress conditions. Here, we report that Rph1 is degraded upon DNA damage stress conditions. Notably, this degradation occurs via the autophagy pathway rather than through 26S proteasome proteolysis. Deletion of ATG genes or inhibition of vacuole protease activity compromises Rph1 turnover...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334785/amino-acid-substitution-equivalent-to-human-chorea-acanthocytosis-i2771r-in-yeast-vps13-protein-affects-its-binding-to-phosphatidylinositol-3-phosphate
#9
Weronika Rzepnikowska, Krzysztof Flis, Joanna Kaminska, Marcin Grynberg, Agnieszka Urbanek, Kathryn R Ayscough, Teresa Zoladek
The rare human disorder chorea-acanthocytosis (ChAc) is caused by mutations in hVPS13A gene. The hVps13A protein interacts with actin and regulates the level of phosphatidylinositol 4-phosphate (PI4P) in the membranes of neuronal cells. Yeast Vps13 is involved in vacuolar protein transport and, like hVps13A, participates in PI4P metabolism. Vps13 proteins are conserved in eukaryotes, but their molecular function remains unknown. One of the mutations found in ChAc patients causes amino acids substitution I2771R which affects the localization of hVps13A in skeletal muscles...
March 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334755/tracking-fluctuation-hotspots-on-the-yeast-ribosome-through-the-elongation-cycle
#10
Suna P Gulay, Sujal Bista, Amitabh Varshney, Serdal Kirmizialtin, Karissa Y Sanbonmatsu, Jonathan D Dinman
Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334329/metabolomics-of-pichia-pastoris-impact-of-buffering-conditions-on-the-kinetics-and-nature-of-metabolite-loss-during-quenching
#11
Matthias Mattanovich, Hannes Rußmayer, Theresa Scharl-Hirsch, Verena Puxbaum, Jonas Burgard, Diethard Mattanovich, Stephan Hann
Mass spectrometry based metabolomic profiling is a powerful strategy to quantify the concentrations of numerous primary metabolites in parallel. To avoid distortion of metabolite concentrations, quenching is applied to stop the cellular metabolism instantly. For yeasts, cold methanol quenching is accepted to be the most suitable method to stop metabolism, while keeping the cells intact for separation from the supernatant. During this treatment, metabolite loss may occur while the cells are suspended in the quenching solution...
March 15, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28334322/evaluation-of-food-lures-for-capture-and-monitoring-of-anastrepha-fraterculus-diptera-tephritidae-on-temperate-fruit-trees
#12
J M da Rosa, C J Arioli, J P Dos Santos, A C Menezes-Netto, M Botton
The Anastrepha fraterculus (Wiedemann) (Diptera: Tephritidae) is the main pest of fruit trees grown in temperate climates in the southern region of Brazil. The objective of this work was to evaluate the efficiency of the major commercial food lures used in Brazil for trapping and monitoring of A. fraterculus in plum, pear, and feijoa orchards. The assessed lures were hydrolyzed proteins of animal origin (CeraTrap) and plant origin (BioAnastrepha), torula yeast + borax (Torula), and grape juice. Response variables included the rate of adult capture (flies per trap per day, FTD) and the percentage of females captured...
March 16, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28334215/systematic-inference-of-functional-phosphorylation-events-in-yeast-metabolism
#13
Yu Chen, Yonghong Wang, Jens Nielsen
Motivation: Protein phosphorylation is a post-translational modification that affects proteins by changing their structure and conformation in a rapid and reversible way, and it is an important mechanism for metabolic regulation in cells. Phosphoproteomics enables high-throughput identification of phosphorylation events on metabolic enzymes, but identifying functional phosphorylation events still requires more detailed biochemical characterization. Therefore, development of computational methods for investigating unknown functions of a large number of phosphorylation events identified by phosphoproteomics has received increased attention...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334169/characterization-of-saccharomyces-uvarum-beijerinck-1898-and-related-hybrids-assessment-of-molecular-markers-that-predict-the-parent-and-hybrid-genomes-and-a-proposal-to-name-yeast-hybrids
#14
Huu-Vang Nguyen, Teun Boekhout
The use of the nuclear-DNA re-association technique has led taxonomists to consider Saccharomyces uvarum a synonym of S. bayanus. The latter, however, is not a species but a hybrid harbouring S. eubayanus (Seu) and S. uvarum (Su) sub-genomes with a minor DNA contribution from S. cerevisiae (Sc). To recognize genetically pure lines of S. uvarum and putative interspecies hybrids among so-called S. bayanus strains present in public culture collections, we propose the use of four markers that were defined from the S...
March 3, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28334164/transcription-factor-mxr1-promotes-the-expression-of-aox1-by-repressing-glycerol-transporter-1-in-pichia-pastoris
#15
Chunjun Zhan, Yankun Yang, Zhenyang Zhang, Xiang Li, Xiuxia Liu, Zhonghu Bai
In methylotrophic yeast Pichia pastoris (P. pastoris), the efficient promoter of alcohol oxidase (PAox1) is induced by methanol and repressed by glycerol, but the molecular mechanism is not clear. In this study, the relationship between alcohol oxidase 1 (aox1), methanol expression regulator 1 (mxr1) and glycerol transporter 1 (gt1) was studied. By RT-PCR, it was found that the overexpression of gt1 could increase the glycerol content in cells and repress the expression of mxr1 and aox1, and the deletion of gt1 reduced the glycerol content in cells and promoted the expression of aox1 ...
March 3, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28334119/climbing-the-yeast-cell-wall
#16
Enrico Cabib
Here is a life in three countries, with different cultures, different political structures and even different skies. The constant through all these changes is the addiction of the subject of this story to science and laboratory work. Perhaps the tale that unfolds here will show to some beginners in research that persistence, seasoned with a little luck, can bring results and satisfaction in the long run.
February 25, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28334092/the-cuticle-protein-gene-mpcp4-of-myzus-persicae-homoptera-aphididae-plays-a-critical-role-in-cucumber-mosaic-virus-acquisition
#17
Yan Liang, Xi-Wu Gao
Myzus persicae (Sulzer) (Homoptera: Aphididae) is one of the most important agricultural pests worldwide. In addition to sucking phloem sap, M. persicae also transmits Cucumber mosaic virus (CMV) as a vector in a nonpersistent manner. At present, the infection mechanism remains unclear, especially the process of aphid virus acquisition. In this study, we isolated four M. persicae cuticle protein genes (MPCP1, MPCP2, MPCP4, and MPCP5) from M. persicae. The relative amount of the gene encoding Cucumber mosaic virus capsid protein (CMV CP) and the transcript levels of these four cuticle protein genes were investigated in aphid virus acquisition by feeding the tobacco preinfested by CMV...
February 19, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28333944/mechanisms-of-glycosylase-induced-genomic-instability
#18
Daniel E Eyler, Kylie A Burnham, Thomas E Wilson, Patrick J O'Brien
Human alkyladenine DNA glycosylase (AAG) initiates base excision repair (BER) to guard against mutations by excising alkylated and deaminated purines. Counterintuitively, increased expression of AAG has been implicated in increased rates of spontaneous mutation in microsatellite repeats. This microsatellite mutator phenotype is consistent with a model in which AAG excises bulged (unpaired) bases, altering repeat length. To directly test the role of base excision in AAG-induced mutagenesis, we conducted mutation accumulation experiments in yeast overexpressing different variants of AAG and detected mutations via high-depth genome resequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28333638/a-comparative-study-for-identifying-the-chromosome-wide-spatial-clusters-from-high-throughput-chromatin-conformation-capture-data
#19
Xiangtao Li, Ka-Chun Wong
In the past years, the high-throughput sequencing technologies have enabled massive insights into genomic annotations. In contrast, the full-scale three-dimensional arrangements of genomic regions are relatively unknown. Thanks to the recent breakthroughs in High-throughput Chromosome Conformation Capture (Hi-C) techniques, non-negative matrix factorization (NMF) has been adopted to identify local spatial clusters of genomic regions from Hi-C data. However, such non-negative matrix factorization entails a high-dimensional non-convex objective function to be optimized with non-negative constraints...
March 20, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28333434/measurement-of-in-vivo-protein-binding-affinities-in-a-signaling-network-with-mass-spectrometry
#20
Mumun Gencoglu, Alexander Schmidt, Attila Becskei
Protein interaction networks play a key role in signal processing. Despite the progress in identifying the interactions, the quantification of their strengths lags behind. Here we present an approach to quantify the in vivo binding of proteins to their binding partners in signaling-transcriptional networks, by the pairwise genetic isolation of each interaction and by varying the concentration of the interacting components over time. The absolute quantification of the protein concentrations was performed with targeted mass spectrometry...
March 23, 2017: ACS Synthetic Biology
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