Review
Cell Biology
Jee Whu Lee, Eugene Boon Beng Ong
Summary: Cellular senescence, triggered by nucleic acid damage and genetic alterations, is one of the pathways leading to aging. Telomere erosion and ribosomal DNA instability can also result in cellular senescence. Lessons from budding yeast provide insights into the molecular mechanisms linking telomere length homeostasis and ribosomal DNA stability to cellular senescence and longevity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xiang Meng, Alan Reed, Sandie Lai, Juraj Szavits-Nossan, John E. G. McCarthy
Summary: Gene expression stochasticity is an inherent feature of biological systems, creating non-genetic cellular variation and influencing various processes. In this study, the researchers discovered a distinct form of non-transcriptional noise associated with the translation machinery and mRNA 5'UTR of the GCN4 gene in yeast. They characterized the heterogeneity of translation initiation mediated by GCN4-5'UTR using different techniques and found a subpopulation of cells that consistently exhibited enhanced GCN4 translation under non-starvation conditions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Food Science & Technology
Gang Du, Xingyu Zhang, Yuting Gao, Cunying Sun, Liwen Wang, Wei Zhao, Dan Meng, Wenqiang Guan, Hui Zhao
Summary: Ginger is commonly used in traditional Chinese medicine as a natural remedy for cold, and it has thermogenic effects when consumed. This study revealed that ginger oleoresin stress and heat stress had similar effects on yeast and shared genes. The transcription factor Hsf1 was found to be phosphorylated and activated in response to ginger oleoresin stress, leading to increased expression of heat shock proteins.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Cell Biology
Stefan Bresson, Vadim Shchepachev, David Tollervey
Summary: The fungal cell wall is a crucial target for antifungal compounds, and the cell wall integrity (CWI) pathway regulates transcriptional responses to cell wall damage. In addition, RNA-binding proteins Mrn1 and Nab6 play a complementary role by stabilizing cell wall-related mRNAs. Lack of Nab6 leads to downregulation of these mRNAs, while CWI signaling and Nab6 work together to maintain appropriate cell wall gene expression during stress. Deletion of MRN1 partially alleviates the growth defects associated with Delta nab6, indicating an opposing function in mRNA destabilization. Our findings highlight the importance of a posttranscriptional pathway in cellular resistance to antifungal compounds.
Article
Biochemistry & Molecular Biology
Ana I. Garrido-Godino, Abel Cuevas-Bermudez, Francisco Gutierrez-Santiago, Maria del Carmen Mota-Trujillo, Francisco Navarro
Summary: Rtr1 plays a critical role in RNA pol II assembly and mRNA decay regulation by mediating the association between RNA pol II and Rpb4/7. This study reveals new mechanisms in gene regulation and the crosstalk between mRNA synthesis and decay.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Food Science & Technology
Yanru Chen, Yili Yang, Wenqin Cai, Jiali Zeng, Na Liu, Yin Wan, Guiming Fu
Summary: This article summarizes the environmental stress factors that affect the growth and fermentation characteristics of S. cerevisiae during the brewing process, as well as the adaptation mechanisms of S. cerevisiae to these stress factors. The article also introduces strategies and methods to improve the stress tolerance of S. cerevisiae during brewing.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Food Science & Technology
Andrea Caridi, Antonella Nicolo, Antonino Modafferi, Alessandra De Bruno
Summary: This study investigated the use of pomegranate as a protective agent in winemaking and found that it can improve the quality of wine under high sugar and high acidity conditions. The addition of pomegranate reduced acetic acid content and increased color intensity, total phenolic content, and antioxidant activity.
EUROPEAN FOOD RESEARCH AND TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zachari Turgeon, Thomas Sierocinski, Cedric A. Brimacombe, Yiqiong Jin, Brittany Goldhawke, Jessica M. Swanson, John Husnik, Matthew S. Dahabieh
Summary: Lager beer is produced by a natural hybrid yeast, and lack of strain diversity has driven research to create new lager hybrids with unique genomic compositions. A novel breeding strategy has successfully produced de novo lager hybrids with fermentation characteristics similar to commercial strains but without undesirable brewing attributes of wild strains. These novel lager hybrids are immediately suitable for industrial lager beer production and may lead to the creation of additional diverse commercial lager strains.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Harry J. Harvey, Mykyta Chubynsky, James E. Sprittles, Leslie M. Shor, Sacha J. Mooney, Ricky D. Wildman, Simon Avery
Summary: This study investigated the impact of micrometre-scale structure on microbial stress sensing, and found that structure plays an important role in microbial responses to their chemical environment. Predictive modelling of these interactions can depend on the complexity of the system.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Agriculture, Dairy & Animal Science
S. E. Sivinski, K. E. Meier, L. K. Mamedova, B. A. Saylor, J. E. Shaffer, A. Sauls-Hiesterman, I. Yoon, B. J. Bradford
Summary: This study evaluated the effects of a dietary Saccharomyces cerevisiae fermentation product on oxidative status, inflammation, and immune responses in dairy cattle during the transition period. The results showed that the product did not significantly affect oxidative, inflammatory, or immune parameters in the cows.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Matthew P. Swaffer, Georgi K. Marinov, Huan Zheng, Lucas Fuentes Valenzuela, Crystal Yee Tsui, Andrew W. Jones, Jessica Greenwood, Anshul Kundaje, William J. Greenleaf, Rodrigo Reyes-Lamothe, Jan M. Skotheim
Summary: A fundamental feature of cellular growth is that protein and RNA amounts increase with cell size to maintain constant concentrations. In budding yeast, RNA polymerase II (RNAPII) is identified as the limiting factor scaling mRNA transcription with cell size. The global RNAPII transcription is determined by the mass action recruitment kinetics of unengaged nucle-oplasmic RNAPII to the genome. However, this increase in transcription with size is partially compensated for by a decrease in mRNA decay rates as cells enlarge.
Article
Microbiology
Yeong Hyeock Kim, Ji-In Ryu, Mayur Nimbadas Devare, Juhye Jung, Jeong-Yoon Kim
Summary: This study investigated the molecular mechanism underlying the altered stress susceptibilities in Saccharomyces cerevisiae due to the absence of Sir2. The absence of Sir2 increased sensitivity to H2O2 during the post-diauxic phase but increased resistance during the exponential growth phase. Transcriptome analysis revealed lower expression levels of several oxidative defense genes in the sir2 Delta strain, potentially explaining its increased susceptibility to H2O2. Interestingly, the sir2 Delta ras2 Delta double mutant exhibited greater resistance to H2O2 than the ras2 Delta single mutant, and the regulation of the cytoplasmic catalase encoded by CTT1 was critical for this increased resistance.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Energy & Fuels
Hamidreza Shafaei, Ahmad Taghizadeh-Alisaraei, Ahmad Abbaszadeh-Mayvan, Aliasghar Tatari
Summary: In this study, the use of giant reed as a substrate for bioethanol production was investigated. The effects of sodium hydroxide concentration, temperature, and pretreatment duration on bioethanol concentration and yield were studied and optimized using response surface methodology. The results showed significant effects of the variables on bioethanol production, and the optimal conditions for bioethanol production were determined. These findings highlight the potential of giant reed biomass as a suitable raw material for bioethanol production.
BIOMASS CONVERSION AND BIOREFINERY
(2023)
Article
Biochemistry & Molecular Biology
Jinfan Wang, Byung-Sik Shin, Carlos Alvarado, Joo-Ran Kim, Jonathan Bohlen, Thomas E. Dever, Joseph D. Puglisi
Summary: Through real-time single-molecule fluorescence spectroscopy, it has been found that the eukaryotic 43S preinitiation complex engages with mRNA through a slow, ATP-dependent process and proceeds to scan rapidly and directionally along the 5' untranslated region (5' UTR). Scanning ribosomes can traverse RNA secondary structures, but hairpin structures near the start codons drive them backward in the 5' direction, requiring rescanning.
Review
Microbiology
Nicole Robbins, Leah E. Cowen
Summary: In the past few decades, there has been a significant increase in drug-resistant fungal infections, posing a serious threat to human health. However, scientific advancements have provided hope for the discovery of new antifungal drugs. The use of chemical-genomic assays in Saccharomyces cerevisiae and molecular biology techniques in fungal pathogens has allowed for the identification and study of target genes for drug candidates, as well as the understanding of virulence attributes in diverse fungal pathogens, thus strengthening the development of antifungal drugs.
ANNUAL REVIEW OF MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Marina Barba-Aliaga, Paula Alepuz
Summary: The eukaryotic translation initiation factor 5A (eIF5A) plays a crucial role in translation and cellular processes. It has been associated with various diseases and proposed as an anti-aging factor. Recent research has revealed its important function in maintaining healthy mitochondria, although the precise mechanisms are still unclear. This review discusses the link between eIF5A and mitochondria, speculates on its role in regulating mitochondrial homeostasis, and highlights its potential as a target in diseases related to energy metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Antonio Casamayor, Diego Velazquez, Carlos Santolaria, Marcel Albacar, Morten I. Rasmussen, Peter Hojrup, Joaquin Arino
Summary: Type 1 Ser/Thr protein phosphatases, represented by PP1 and PPZ, have distinct functions and regulations in fungi. PP1c enzymes are more conserved than PPZs. Specific residues in the catalytic domains of PP1 and PPZ have been identified, some of which likely affect the protein's surface charges. Hal3 is a specific inhibitor of PPZ phosphatases in many fungi, but the basis for their interaction is still unclear. The D566 and D615 residues in ScPpz1 may play a crucial role in the regulation of both enzymes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Antonia Maria Romero, Jose Garcia-Martinez, Jose Enrique Perez-Ortin, Maria Teresa Martinez-Pastor, Sergi Puig
Summary: Eukaryotic cells rely on iron for various biological functions. In response to iron deficiency, yeast regulates iron metabolism through transcription and posttranscriptional mechanisms. The stability of ribosomal protein transcripts increases when iron bioavailability diminishes, and the mRNA-binding protein Pub1 plays a critical role in their stabilization.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Biochemistry & Molecular Biology
Marina Barba-Aliaga, Paula Alepuz
Summary: Mitochondrial activity is crucially regulated by the translation elongation factor eIF5A, whose dysfunction is associated with ageing and human diseases. The study demonstrates how the yeast transcription factor Hap1 plays a role in regulating the expression of eIF5A isoforms, adapting them to the functional status of mitochondria.
Article
Biochemistry & Molecular Biology
Marcel Albacar, Diego Velazquez, Antonio Casamayor, Joaquin Arino
Summary: Overexpression of protein phosphatase Ppz1 in Saccharomyces cerevisiae strongly inhibits cell growth. However, overexpression of its subunit Hal3 can completely counteract the toxic effects caused by excess Ppz1. Hal3 not only inhibits the enzymatic activity of Ppz1, but also recruits the phosphatase to internal structures.
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
Biochemistry & Molecular Biology
Jose E. Perez-Ortin, Sebastian Chavez
Summary: Gene expression is a highly regulated process that adapts RNA and protein content to the cellular environment. RBPs can shuttle between the nucleus and cytoplasm to regulate transcription, mRNA degradation, and translation, acting as potential coordinators of mRNA metabolism.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Biochemistry & Molecular Biology
Carlos Santolaria, Diego Velazquez, Marcel Albacar, Antonio Casamayor, Joaquin Arino
Summary: The function of the Ppz1 phosphatase in Saccharomyces cerevisiae is controlled by its inhibitory subunit Hal3. Hal3 is a moonlighting protein involved in the CoA biosynthetic pathway. Deletion or specific mutations in a region of Hal3's N-terminal extension compromise its function as a Ppz1 inhibitor without affecting its ability to interact with the phosphatase. The presence of a specific sequence explains the unexpected ability of Cab3 to regulate Ppz1 function in Candida albicans. This study contributes to our understanding of Ppz phosphatase regulation and its importance in pathogenic fungi.
Article
Multidisciplinary Sciences
Vicente Arnau, Marina Barba-Aliaga, Gaurav Singh, Javier Ferri, Jose Garcia-Martinez, Jose E. Perez-Ortin
Summary: rDNA copy number is controlled by cell volume via a feedback circuit that senses cell volume by means of the concentration of the free upstream activator factor (UAF). Cells regulate rDNA copy number to reach an optimal level through a self-regulatory mechanism. The study shows that this evolutionary process can amplify rDNA repeats independently of the selective advantage.
Review
Microbiology
Antonio Casamayor, Joaquin Arino
Summary: Hal3 is a yeast protein with dual functions as a regulatory subunit and an enzyme catalyst. The structure and functions of Hal3 vary in different fungi, and recent findings may provide insights into predicting its moonlighting properties.
Article
Endocrinology & Metabolism
Irene Bravo-Alonso, Matias Morin, Laura Arribas-Carreira, Mar Alvarez, Consuelo Pedron-Giner, Lucia Soletto, Carlos Santolaria, Santiago Ramon-Maiques, Magdalena Ugarte, Pilar Rodriguez-Pombo, Joaquin Arino, Miguel Angel Moreno-Pelayo, Belen Perez
Summary: Coenzyme A (CoA) is an essential cofactor synthesized from vitamin B5 and involved in various metabolic pathways. This study identified biallelic variants of PPCDC gene in two sisters, leading to a severe inborn error of metabolism with a fatal cardiac phenotype. The variants significantly affected the function of PPCDC enzyme and resulted in reduced CoA levels and energy deficiency in patient-derived cells. The findings highlight the importance of PPCDC in CoA biosynthesis and its role in cardiac function.
JOURNAL OF INHERITED METABOLIC DISEASE
(2023)
Article
Multidisciplinary Sciences
Shiladitya Chattopadhyay, Jose Garcia-Martinez, Gal Haimovich, Jonathan Fischer, Aya Khwaja, Oren Barkai, Silvia Gabriela Chuartzman, Maya Schuldiner, Ron Elran, Miriam Rosenberg, Shira Urim, Shubham Deshmukh, Katherine E. Bohnsack, Markus T. Bohnsack, Jose E. Perez-Ortin, Mordechai Choder
Summary: This study reveals the crucial role of nucleocytoplasmic shuttling of yeast mRNA decay factors in regulating both transcription and mRNA decay. The shuttling process is controlled by decaying RNA and is essential for coping with environmental changes.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jose Garcia-Martinez, Abhyudai Singh, Daniel Medina, Sebastian Chavez, Jose E. Perez-Ortin
Summary: In recent years, it has become increasingly clear that gene expression in eukaryotes is a circular process where mRNA levels are controlled by crosstalk between transcription and mRNA decay pathways. This crosstalk can result in either buffering or enhanced gene expression regulation, depending on whether transcription and mRNA degradation act at compensatory rates or additively. The study shows that certain proteins presumed to be only involved in transcription or mRNA decay may actually be RNA-binding proteins (RBPs) that have specific crosstalk effects, enhancing the control of mRNA levels.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2023)
Article
Biochemistry & Molecular Biology
Abdelghani Zekhnini, Marcel Albacar, Antonio Casamayor, Joaquin Arino
Summary: The Saccharomyces cerevisiae ENA1 gene, encoding a Na+-ATPase, is transcriptionally regulated by multiple signaling pathways in response to alkalinization and changes in amino acid composition. The Stp1/2 transcription factors of the SPS pathway play a role in ENA1 promoter activity. Deletion of STP1 or STP2 decreases the ENA1 promoter response to alkalinization and changes in amino acid composition. The SPS pathway may participate in the regulation of a subset of alkali-inducible genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Marcel Albacar, Abdelghani Zekhnini, Jorge Perez-Valle, Jose L. Martinez, Antonio Casamayor, Joaquin Arino
Summary: In this study, the transcriptional impact of moderate alkalinization on Komagataella phaffii yeast was explored, searching for suitable novel promoters for transcription response to the pH signal. Results showed significant changes in mRNA levels of over 700 genes when cultures shifted from pH 5.5 to 8.0 or 8.2. Alkalinization provoked oxidative stress and induced the expression of Na+/Pi cotransporter PHO89 through a calcium-mediated signal.
MICROBIAL CELL FACTORIES
(2023)
Article
Biochemistry & Molecular Biology
Damien Marchese, Florent Guislain, Tamara Pringels, Laure Bridoux
Summary: Homopolymeric amino acid repeats are common in human proteins, particularly in transcription factors and kinases. This study focuses on homopolymeric histidine repeats (polyH) and their role in regulating embryonic development. Through bioinformatic analysis, the study identifies that polyH-containing proteins interact with cysteine-rich proteins and proteins containing cysteine repeats. The study further investigates the HOXA1 protein, a transcription factor with a long polyH motif, and finds that the polyH motif is necessary for its interaction with cysteine-rich proteins. Additionally, the study discovers that metal ions are required for the HOXA1-MDFI interaction and identifies three polyH interactors that down-regulate the transcriptional activity of HOXA1.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2024)
