Article
Biochemistry & Molecular Biology
Janardan N. Gavade, Chris M. Puccia, S. Grace Herod, Jonathan C. Trinidad, Luke E. Berchowitz, Soni Lacefield
Summary: This study discovered six new regulators of meiotic commitment in budding yeast and revealed their multiple functions and mechanisms in the process of meiosis. The results demonstrate that the 14-3-3 proteins and Polo kinase play important regulatory roles in maintaining meiotic commitment.
Article
Biology
Farzan Ghanegolmohammadi, Shinsuke Ohnuki, Yoshikazu Ohya
Summary: Based on statistical principles, this study presents UNIMO as a reliable pipeline for the precise detection of subtle morphological changes in yeast cells. By assigning unimodal probability distributions to morphological features and using a probabilistic mixture model, UNIMO offers better predictions of the true values of morphological measurements. This approach allows for powerful downstream parametric analyses and provides biologically important information.
Review
Biochemistry & Molecular Biology
Alessandra Ferramosca, Vincenzo Zara
Summary: Yeast mitochondrial carriers play a crucial role in cellular metabolism by connecting mitochondrial and cytosolic reactions, contributing to various important metabolic pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Ahmed Elshobaky, Cathrine Lillo, Kristian Persson Hoden, Amr R. A. Kataya
Summary: Protein phosphatase 2A (PP2A) is a conserved serine/threonine phosphatase complex that plays a role in substrate specificity and localization in plants. In this study, the interactions between the PP2A-B'& zeta; subunit and enzymes related to mitochondrial energy flow were investigated. Through experiments in tobacco and onion cells, interactions were confirmed between the B'& zeta; subunit and several Krebs cycle proteins. Putative interacting candidates were also deduced from phosphoproteome analysis, shedding light on the role of PP2A in regulating energy metabolism in mitochondria.
Article
Biochemistry & Molecular Biology
Tiffany Yip Delormel, Liliana Avila-Ospina, Marlene Davanture, Michel Zivy, Julien Lang, Nicolas Valentin, Naganand Rayapuram, Heribert Hirt, Jean Colcombet, Marie Boudsocq
Summary: Calcium signaling plays a crucial role in plant developmental processes and stress responses. AtCPK5, a calcium-dependent protein kinase in Arabidopsis, regulates immunity and abiotic stress tolerance. Through a biochemical approach, researchers identified in vivo substrates of AtCPK5 and found 5 phosphorylated proteins that are direct targets of AtCPK5. Furthermore, interactions between the kinase and the candidates were detected in different cellular compartments, supporting the ubiquitous localization of AtCPK5. The study provides new insights into the biological functions of AtCPK5.
Review
Biochemistry & Molecular Biology
Antonio Casamayor, Joaquin Arino
Summary: Overexpression of yeast Ser/Thr protein phosphatase Ppz1 leads to a halt in cell proliferation due to changes in gene expression, altered phosphorylation state of proteins, and diverse cellular processes. However, overexpression of the Ppz1 regulatory subunit Hal3 can fully counteract the toxic effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Magdalena Boguta
Summary: The control of assembly of yeast RNA polymerases (RNAPs) is not well understood. A recent study suggests that the early-stage assembly of RNAP III complex may occur through a co-translational mechanism, with the involvement of the Rbs1 protein.
Article
Biotechnology & Applied Microbiology
Maria Cecilia Lerena, Andrea Susana Vargas-Trinidad, Javier Alonso del-Real, Maria Cecilia Rojo, Magali Lucia Gonzalez, Laura Analia Mercado, Diego Claudio Lijavetzky, Amparo Querol, Mariana Combina
Summary: Problematic fermentations in the winemaking industry can lead to economic losses and logistic problems. In this study, transcriptomic analysis was conducted on two yeast strains with different thermal responses to identify genes that can be used as biomarkers for early detection of sluggish fermentations associated with heat shock. Three genes (SSA1, MGA1, and OPI10) showed significantly increased expression after heat shock, indicating their potential for early detection of fermentation issues.
FERMENTATION-BASEL
(2023)
Article
Multidisciplinary Sciences
Li Cheng, Xuetong Yue, Zhaoyu Qin, Xiaogang Sun, Fuchu He, Junbiao Dai, Chen Ding
Summary: This study reports a genome-wide quantitative proteomic system that uses unique code peptides to achieve precise protein quantification. By systematically tagging and decoding 40 yeast proteins using mass spectrometry, the researchers successfully recovered all code peptides with a large and consistent quantitative dynamic range. Additionally, they verified the alterations in glucose and galactose metabolism pathways in yeast under different carbon source conditions.
Article
Food Science & Technology
Juan Antonio Porras-Aguera, Jaime Moreno-Garcia, Teresa Garcia-Martinez, Juan Moreno, Juan Carlos Mauricio
Summary: The prise de mousse stage during the elaboration of sparkling wine through the traditional method involves a second fermentation in a sealed bottle, which significantly contributes to the unique organoleptic properties of these wines. This study characterizes the mitochondrial response of Saccharomyces cerevisiae strains used in sparkling wine production and found that CO2 overpressure negatively affects mitochondrion-related proteins. However, proteins involved in wine aromas and respiratory chain are found to be over-represented in sealed bottles, with differences in concentrations observed depending on time and CO2 overpressure parameters. Ethanol content during fermentation may be a key factor in these proteomic changes, highlighting the importance of further research in this area.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2021)
Article
Food Science & Technology
Yen-Tso Lai, Chang-Wei Hsieh, Yi-Chen Lo, Bo-Kang Liou, Hui-Wen Lin, Chih-Yao Hou, Kuan-Chen Cheng
Summary: The study explored the enological characteristics of non-Saccharomyces yeast strains and their influence on aroma compound complexity during fermentation process, finding that they can provide more diverse flavors in wines.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Deepyaman Das, Hironmoy Sarkar, Soumita Podder
Summary: This study aims to explore the regulatory cross-talk that mediates the phase transition in MATa/MAT alpha budding yeasts, proposing a crucial role of pre-growth in glucose-starved condition in regulating the transition to meiosis, and identifying key transcription factors involved in the interaction between respiration and cellular preparation for meiosis. Abf1p and Adr1p have been identified as the master regulators of the integrated network in this process, which may help decipher the pre-meiotic initiation occurring in higher eukaryotes.
FEMS YEAST RESEARCH
(2021)
Article
Engineering, Environmental
Katarzyna Mizio, Donata Wawrzycka, Jacek Staszewski, Robert Wysocki, Ewa Maciaszczyk-Dziubinska
Summary: The Acr3 protein family is important for metalloid detoxification and consists of members from bacteria to higher plants. Most Acr3 transporters are specific for arsenite, but budding yeast Acr3 also has some capacity for antimonite transport. This study identified critical residues that determine substrate specificity, providing a valuable starting point for further research and potential applications in bioremediation.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biochemical Research Methods
Tomoya Niinae, Koshi Imami, Naoyuki Sugiyama, Yasushi Ishihama
Summary: Mass-spectrometry-based phosphoproteomics can identify over 10,000 phosphorylated sites in a single experiment, but understanding protein kinase-substrate relationships remains a challenge. This study presents a new method using a combination of techniques to identify endogenous substrates of kinases, successfully applied to CK2 and PKA. The approach extends our knowledge of physiological kinase-substrate networks and is particularly relevant for understanding cancer-related mutations affecting downstream signaling pathways.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Microbiology
Akihito Nakanishi, Kuan Zhang, Riri Matsumoto, Naotaka Yamamoto
Summary: In this study, glycerol-assimilating strains were isolated from S. cerevisiae BY4741, and the changes in biomass production, ethanol fermentation, and transcription levels related to glycolysis and the tricarboxylic acid cycle under aerobic and slightly anaerobic conditions were analyzed. The results showed differences in biomass production, ethanol yields, and transcription levels between wildtype and glycerol-assimilating strains under aerobic conditions. Differences in transcription levels downstream of glycolysis were also observed under slightly anaerobic conditions. The study suggests that redox imbalance in glycerol-acclimatized strains may hinder glycerol utilization.
Article
Biochemistry & Molecular Biology
Claudio Ponte de Albuquerque, Jason Liang, Nathaniel James Gaut, Huilin Zhou
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Article
Cell Biology
Jason Liang, Namit Singh, Christopher R. Carlson, Claudio P. Albuquerque, Kevin D. Corbett, Huilin Zhou
GENES & DEVELOPMENT
(2017)
Article
Biochemistry & Molecular Biology
Yuchao Gu, Claudio P. Albuquerque, Daniel Braas, Wei Zhang, Genaro R. Villa, Junfeng Bi, Shiro Ikegami, Kenta Masui, Beatrice Gini, Huijun Yang, Timothy C. Gahman, Andrew K. Shiau, Timothy F. Cloughesy, Heather R. Christofk, Huilin Zhou, Kun-Liang Guan, Paul S. Mischel
Article
Genetics & Heredity
Andrea Local, Hui Huang, Claudio P. Albuquerque, Namit Singh, Ah Young Lee, Wei Wang, Chaochen Wang, Judy E. Hsia, Andrew K. Shiau, Kai Ge, Kevin D. Corbett, Dong Wang, Huilin Zhou, Bing Ren
Article
Biochemistry & Molecular Biology
Claudio Ponte de Albuquerque, Raymond T. Suhandynata, Christopher R. Carlson, Wei-Tsung Yuan, Huilin Zhou
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Genetics & Heredity
Jason Liang, Bin-zhong Li, Alexander P. Tan, Richard D. Kolodner, Christopher D. Putnam, Huilin Zhou
Article
Genetics & Heredity
Raymond T. Suhandynata, Yun Quan, Yusheng Yang, Wei-Tsung Yuan, Claudio P. Albuquerque, Huilin Zhou
Article
Multidisciplinary Sciences
Raymond T. Suhandynata, Yong-Qi Gao, Ann L. Zhou, Yusheng Yang, Pang-Che Wang, Huilin Zhou
Summary: Protein sumoylation, particularly catalyzed by the Mms21 SUMO E3 ligase, plays a crucial role in suppressing duplication-mediated gross chromosomal rearrangements (dGCRs). Esc2, with SUMO-like domains (SLDs), recruits the Ubc9 SUMO conjugating enzyme to enhance Mms21-dependent sumoylation and suppress dGCRs accumulation. The D430R mutation in Esc2 disrupts its interaction with Ubc9, leading to growth defects and dGCRs accumulation, while not significantly affecting sensitivity to DNA damage or dGCRs caused by catalytically inactive mms21-CH.
Article
Cell Biology
Nataliia Serbyn, Ivona Bagdiul, Audrey Noireterre, Agnes H. Michel, Raymond T. Suhandynata, Huilin Zhou, Benoit Kornmann, Francoise Stutz
Summary: SUMO biogenesis factors play a crucial role in cell selection of DPC repair mechanisms, facilitating the repair of Top1cc or analogous DPC lesions. SUMO promotes Top1cc processing in the absence of Tdp1 and has an inhibitory role when cells additionally lack Wss1.
Article
Biochemistry & Molecular Biology
Fu-Long Li, Zhengming Wu, Yong-Qi Gao, Forrest Z. Bowling, J. Matthew Franklin, Chongze Hu, Raymond T. Suhandynata, Michael A. Frohman, Michael Airola, Huilin Zhou, Kun-Liang Guan
Summary: The Arf GTPase family plays a role in cellular regulation, and a proximity interaction network was generated to identify new interactors and provide clues for defining Arf pathway cell biological functions. The unexpected finding that PLD1 interacts with ARL11/14 to promote macrophage phagocytosis, and ARL5A/B interacts with PI4KB at trans-Golgi to promote PI4P synthesis and protein secretion.
Article
Genetics & Heredity
Yun Quan, Qian-Yi Zhang, Ann L. Zhou, Yuhao Wang, Jiaxi Cai, Yong-Qi Gao, Huilin Zhou
Summary: This study reveals a site-specific SUMO modification of the MCM complex, which plays a crucial role in regulating DNA replication and preventing gross chromosomal rearrangements (GCRs).
Correction
Multidisciplinary Sciences
Hannah E. E. Ledvina, Qiaozhen Ye, Yajie Gu, Ashley E. E. Sullivan, Yun Quan, Rebecca K. K. Lau, Huilin Zhou, Kevin D. D. Corbett, Aaron T. T. Whiteley
Article
Multidisciplinary Sciences
Hannah E. Ledvina, Qiaozhen Ye, Yajie Gu, Ashley E. Sullivan, Yun Quan, Rebecca K. Lau, Huilin Zhou, Kevin D. Corbett, Aaron T. Whiteley
Summary: In humans, the immune receptor cGAS detects viral infection and activates antiviral signalling. Bacteria have a similar system called CD-NTases, which detect bacteriophage infection. The protein Cap2 primes bacterial CD-NTases for activation through a ubiquitin transferase-like mechanism, leading to increased production of cGAMP.
Article
Biochemistry & Molecular Biology
Sunbin Deng, Jiaxi Cai, Stephen C. Harrison, Huilin Zhou, Stephen M. Hinshaw
Summary: Successful mitosis relies on the correct attachment of chromosomes to microtubules. The kinetochore plays a crucial role in this process by recognizing specific chromatin and ensuring the formation of only one kinetochore per chromatid at the correct location. The crystal structure of the Cse4 peptide bound to the inner kinetochore Okp1-Ame1 complex provides insights into centromere recognition and the organization of the inner kinetochore.
Article
Cell Biology
Yun Quan, Stephen M. Hinshaw, Pang-Che Wang, Stephen C. Harrison, Huilin Zhou
Summary: Chromosome segregation during cell division is controlled and adapted by kinetochores, which connect spindle microtubules to chromosomal centromeres. A mechanism that regulates kinetochore sumoylation has been identified, with a conserved surface of the Ctf3/CENP-I kinetochore protein providing a binding site for the SUMO chain-removing enzyme Ulp2. Disabling Ulp2 recruitment to kinetochores leads to defective chromosome segregation due to elevated sumoylation levels.
JOURNAL OF CELL BIOLOGY
(2021)