Editorial Material
Cell Biology
Yuqing Lei, Ting Huang, Gaoyue Jiang, Yabin Zhang, Shiyan Liu, Huihui Li, Kefeng Lu
Summary: In yeast cells, the RNA polymerase II subunit Rpb9 upregulates the transcription of the autophagy gene ATG1 specifically and efficiently, with the mediation of Gcn4. This regulation is crucial for autophagic activities induced by starvation. Furthermore, the function of Rpb9 in autophagy and the activation of ATG1 transcription is conserved in mammalian cells.
Review
Biochemistry & Molecular Biology
Ken Ishikawa, Shigeaki Saitoh
Summary: Isolation and introduction of genetic mutations is a powerful approach to characterize gene functions in model yeasts, but not feasible for all genes. To overcome this difficulty, conditional and partial repression of target transcription is possible. This review summarizes gene perturbation technologies, including recent advances in methods based on CRISPR-Cas systems for Schizosaccharomyces pombe, and discusses how CRISPRi can promote fission yeast genetics.
Review
Cell Biology
Brittany J. Bisnett, Brett M. Condon, Caitlin H. Lamb, George R. Georgiou, Michael Boyce
Summary: COPII, an ancient and essential pathway in eukaryotes, mediates forward trafficking of protein and lipid cargoes from the endoplasmic reticulum. Despite its broad significance, major aspects of COPII trafficking remain incompletely understood. Recent studies have highlighted the role of post-transcriptional mechanisms in regulating the COPII pathway.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Plant Sciences
Sajjan Grover, Sanket Shinde, Heena Puri, Nathan Palmer, Gautam Sarath, Scott E. Sattler, Joe Louis
Summary: Plants undergo dynamic changes in the phenylpropanoid pathway to defend themselves against insect infestation. Flavonoids play a crucial role in enhancing resistance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biophysics
Daniel Schultz, Mirjana Stevanovic, Lev S. Tsimring
Summary: Cellular responses to toxic compounds require prompt expression of appropriate enzymes regulated by transcription factors. Different regulatory strategies are optimized based on selective pressures, with costs associated with drug, enzyme, and repressor concentrations influencing gene regulation.
BIOPHYSICAL JOURNAL
(2022)
Article
Plant Sciences
Chongmin Wang, Jun Li, Tao Zhou, Yongping Zhang, Haijun Jin, Xiaoqing Liu
Summary: This study analyzed the transcriptome of I. stachyodes roots to gain insights into the biosynthesis regulatory network of proanthocyanidins (PAs). It identified key structural genes and transcription factors involved in PA biosynthesis, and provided new insights into the molecular pathways underlying PA accumulation.
Article
Plant Sciences
Lin Chen, Qi Zeng, Jiahao Zhang, Chao Li, Xue Bai, Fengli Sun, Daniel J. Kliebenstein, Baohua Li
Summary: Aliphatic glucosinolates are important secondary metabolites in Brassicaceae plants, and their accumulation is regulated by numerous transcriptional regulators. This study successfully identified and validated 30 novel regulators that significantly influence the accumulation of aliphatic glucosinolates in Arabidopsis. The findings also revealed a balance between positive and negative effects of the regulators, indicating coordinated glucosinolate metabolism and plant development.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Cell Biology
Qiuqin Ma, Shihui Long, Zhending Gan, Gianluca Tettamanti, Kang Li, Ling Tian
Summary: Autophagy, a widely conserved process in eukaryotes, is regulated by nutrient deprivation, energy stress, and other unfavorable conditions through multiple pathways. It is primarily governed at the RNA and protein levels in a synergistic manner.
Review
Biochemistry & Molecular Biology
Guadalupe Cumplido-Laso, Dixan A. Benitez, Sonia Mulero-Navarro, Jose Maria Carvajal-Gonzalez
Summary: The airway epithelium is a crucial component of the respiratory system, serving as a barrier against inhaled pathogens and toxins. Chronic respiratory diseases can disrupt the cellular composition of the airway epithelium, leading to a decrease in multiciliated cells and an increase in secretory cells. Basal cells are identified as the primary stem cells in the airway epithelium, capable of differentiating into multiciliated cells and secretory cells. Recent advancements in single-cell RNA sequencing techniques have provided insights into the cellular composition of the airway epithelium, highlighting the importance of understanding cellular composition and differentiation processes for targeted therapies for respiratory diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Emilie Bourdonnay, Thomas Henry
Summary: Gasdermins (GSDM) are a family of proteins that play important roles in cell death, immune response, disease susceptibility, and treatment response. The expression of GSDM genes is influenced by various factors and has been associated with diseases such as asthma, inflammatory bowel disease, and cancer.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Microbiology
Alyssa C. Baugh, Cory Momany, Ellen L. Neidle
Summary: LysR-type transcriptional regulators (LTTRs) are a large family of bacterial regulators that contribute to various aspects of metabolism and physiology. They bind DNA in the presence or absence of a small-molecule ligand, undergo conformational changes in response to cellular signals, and can act as repressor-activators. This review updates on the molecular basis, regulatory complexity, and applications of LTTRs in biotechnology and medicine.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Article
Agronomy
Hongli Li, Gangshuai Liu, Daqi Fu
Summary: Tomato is a model plant for studying fruit ripening and quality formation. The ripening of tomato fruit is regulated by transcription factors, such as RIN, NOR, and CNR. Understanding the transcriptional network and regulatory patterns of ripening-related target genes in tomato has important biological significance.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Yanna Shi, Bai-Jun Li, Guanqing Su, Mengxue Zhang, Donald Grierson, Kun-Song Chen
Summary: Fleshy fruit texture is an important quality characteristic of ripe fruit, and softening is an irreversible process mainly caused by changes in cell wall, starch degradation, and flavonoid levels. Lignification of certain fruits negatively affects eating quality, and excessive softening can lead to physical damage and infection. Transcription factors play a crucial role in regulating fruit texture by controlling genes related to cell wall and starch metabolism. This review focuses on the transcriptional regulatory mechanisms governing fruit textural change and discusses potential targets for breeding and future research directions.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Rachel K. Lex, Weiqiang Zhou, Zhicheng Ji, Kristin N. Falkenstein, Kaleigh E. Schuler, Kathryn E. Windsor, Joseph D. Kim, Hongkai Ji, Steven A. Vokes
Summary: The study challenges the current understanding that GLI3 repression is established before Hedgehog (HH) signaling and demonstrates that GLI3 is inert in the limb bud before HH onset. The loss of Gli3 does not increase target gene expression or accessibility, contrasting with post-HH signaling. GLI repression is established independently of HH signaling, but after its onset.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Beiqin Yu, Wentao Dai, Li Pang, Qingqing Sang, Fangyuan Li, Junxian Yu, Haoran Feng, Jianfang Li, Junyi Hou, Chao Yan, Liping Su, Zhenggang Zhu, Yuan-Yuan Li, Bingya Liu
Summary: This study identified crucial transcription factors related to gastric cancer progression and proposed testable hypotheses on the differential regulation mechanisms of gastric carcinogenesis. Through cytological experiments and IHC staining, the dynamic changes of target genes regulated by one of the transcription factors were validated. The identified transcription factors and their targets may have potential therapeutic value.
MOLECULAR MEDICINE
(2022)
Article
Genetics & Heredity
Lucy Fang-I Chao, Meha Singh, James Thompson, John R. Yates, Kirsten A. Hagstrom
Article
Biochemical Research Methods
Hanhui Ma, Janel R. McLean, Lucy Fang-I Chao, Sebastian Mana-Capelli, Murugan Paramasivam, Kirsten A. Hagstrom, Kathleen L. Gould, Dannel McCollum
MOLECULAR & CELLULAR PROTEOMICS
(2012)
Article
Chemistry, Multidisciplinary
Miriam Linsenmeier, Marie R. G. Kopp, Fulvio Grigolato, Dany Liu, Dominik Zuercher, Maria Hondele, Karsten Weis, Umberto Capasso Palmiero, Paolo Arosio
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Biotechnology & Applied Microbiology
Tyler W. Doughty, Rosemary Yu, Lucy Fang- Chao, Zhongjun Qin, Verena Siewers, Jens Nielsen
Summary: The single chromosome strain exhibited poorer growth characteristics on non-fermentable carbon sources due to sirtuin-mediated silencing. Nicotinamide was able to rescue the diminished growth of the strain on ethanol.
Article
Multidisciplinary Sciences
Felix H. Lam, Burcu Turanli-Yildiz, Dany Liu, Michael G. Resch, Gerald R. Fink, Gregory Stephanopoulos
Summary: By engineering Saccharomyces cerevisiae, near-parity production can be achieved between inhibitor-laden and inhibitor-free feedstocks, and a single strain can be enhanced to tolerate diverse highly toxified feedstocks. Moreover, a lightweight design allows for seamless transferability to existing metabolically engineered chassis strains, demonstrating the potential for cost-effective, at-scale biomass utilization for cellulosic fuel and nonfuel products.
