Article
Microbiology
Paula Mondragon, Sungmin Hwang, Lakshmi Kasirajan, Rebecca Oyetoro, Angelina Nasthas, Emily Winters, Ricardo L. Couto-Rodriguez, Amy Schmid, Julie A. Maupin-Furlow
Summary: This study identifies a TrmB-like protein (OxsR) that functions as a thiol-based transcriptional regulator in response to oxidative stress, particularly hypochlorite stress. OxsR binds to specific regions of DNA during hypochlorite stress, which are proximal to oxidative stress operons. Further analysis reveals that OxsR acts as both a transcriptional activator and repressor during hypochlorite stress. The presence of a conserved cysteine residue and a CG-rich motif in the promoter region suggests a widespread redox signaling mechanism in archaea.
Review
Microbiology
Katie E. Shalvarjian, Dipti D. Nayak
Summary: Methanogenesis is a significant metabolic process carried out by methanogens in the Archaea domain. Although genes involved in methanogenic metabolism have been identified and characterized, the regulation of methane production in response to various signals remains less understood.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ruoyao Lin, Xiaoming Zhong, Yongli Zhou, Huichao Geng, Qingxi Hu, Zhihao Huang, Jun Hu, Xiang-Dong Fu, Liang Chen, Jia-Yu Chen
Summary: R-loopBase integrates high-quality genome-wide R-loop mapping datasets and comprehensive literature information to provide high-confidence R-loop localization and a comprehensive list of regulatory proteins, helping to reveal a global regulatory network of R-loop dynamics and its potential links to cancer and neurological diseases.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Plant Sciences
Angeles Aroca, Inmaculada Garcia-Diaz, Margarita Garcia-Calderon, Cecilia Gotor, Antonio J. Marquez, Marco Betti
Summary: Photorespiration plays a fundamental role in plant metabolism and its regulation, including transcriptional and post-translational regulation, has been a topic of interest. The interconnections between photorespiration and nitrogen and sulfur metabolism have also been explored. Recent findings on sulfide signaling and protein persulfidation are discussed.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Plant Sciences
Kathlyn N. Woolfson, Mina Esfandiari, Mark A. Bernards
Summary: Suberin is a specialized cell wall polymer that is deposited in below-ground and above-ground tissues of plants. It helps prevent water loss and pathogen infection. Suberin is composed of phenolic and fatty acid monomers, and its deposition is important for the skin maturation and storage longevity of tuber crops like potato. The deposition of suberin follows a temporal pattern, with phenolics being polymerized before other components like fatty acids.
Article
Biochemistry & Molecular Biology
Sanjit K. Dhar, Timothy Scott, Chi Wang, Teresa W. M. Fan, Daret K. St Clair
Summary: This study reveals the regulatory role of mitochondrial-generated superoxide radicals in gene expression and establishes a new paradigm that recognizes O2· as an initiator of metabolic reprogramming and epigenetic regulation in response to mitochondrial dysfunction.
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Article
Cell Biology
Wenju Li, Aiping Duan, Yuexian Xing, Li Xu, Jingping Yang
Summary: The study showed that HIF1α activation affects lipid metabolism in tubular cells by suppressing fatty acid mobilization and oxidation, leading to lipid accumulation and compositional changes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Plant Sciences
Huan Han, Caini Wang, Xiaoyan Yang, Lina Wang, Jiabao Ye, Feng Xu, Yongling Liao, Weiwei Zhang
Summary: This study provides an overview of the structure, classification, regulatory mechanisms, and biological functions of basic leucine zipper transcription factors (bZIPs) and their molecular mechanisms in the biosynthesis of various secondary metabolites. bZIPs are highly conserved transcription factors in eukaryotic organisms and play crucial roles in plant growth and development, stress response, and secondary metabolism. The paper elaborates on the structure, classification, biological function, and regulatory mechanisms of bZIPs, as well as their molecular mechanisms in regulating the biosynthesis of flavonoids, terpenoids, alkaloids, phenolic acids, and lignin. This review is significant for understanding the molecular mechanisms of bZIPs in secondary metabolite synthesis and plant molecular breeding.
Article
Cell Biology
Lorela Ciraku, Emily M. Esquea, Mauricio J. Reginato
Summary: O-GlcNAcylation is a post-translational modification affecting protein stability, interactions, and phosphorylation, playing a crucial role in nutrient sensing and regulation of cancer signaling pathways. Its elevated levels have been linked to various cancers, making it a potential target for cancer treatment.
CELLULAR SIGNALLING
(2022)
Review
Plant Sciences
Paula da Fonseca-Pereira, Paulo V. L. Souza, Alisdair R. Fernie, Stefan Timm, Danilo M. Daloso, Wagner L. Araujo
Summary: Thioredoxins play a crucial role in the redox regulation of plant metabolism, activating photosynthesis and adjusting mitochondrial photorespiratory metabolism. Mitochondrial TRX o1 has been identified as a regulator for alternative oxidase and enzymes associated with the tricarboxylic acid cycle, as well as being involved in photorespiration and branched chain amino acid degradation.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Review
Immunology
Hunter Bennett, Ty D. Troutman, Mashito Sakai, Christopher K. Glass
Summary: Kupffer cells are the resident macrophages of the liver, playing important roles in responses to tissue damage and specialized activities such as iron scavenging. Recent studies have focused on the epigenetic pathways that establish Kupffer cell identity and function.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
German A. Ashniev, Natalia Sernova, Aleksei E. Shevkoplias, Ivan D. Rodionov, Irina A. Rodionova, Alexey G. Vitreschak, Mikhail S. Gelfand, Dmitry A. Rodionov
Summary: Using a comparative genomic approach, this study identified a novel DNA-binding transcription factor (HisR) and RNA regulatory elements (T-box riboswitches and RNA attenuators) involved in the regulation of histidine metabolism and transport genes in various bacterial taxa. The distribution of HisR and these regulatory mechanisms across over 600 species of Firmicutes were discussed from functional and evolutionary perspectives.
Article
Biochemistry & Molecular Biology
Shivani Nanda, Marc-Antoine Jacques, Wen Wang, Chad L. Myers, L. Safak Yilmaz, Albertha J. M. Walhout
Summary: A new study reveals that three-quarters of metabolic genes in the nematode Caenorhabditis elegans are transcriptionally regulated, and generates a co-regulated subpathway map of metabolism. The researchers also develop a web application to query gene associations with metabolic pathways. This study sheds light on the ubiquity of transcriptional regulation in metabolism and provides a blueprint for similar studies in other organisms.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Cell Biology
Li Xia, Tiejian Nie, Fangfang Lu, Lu Huang, Xiaolong Shi, Dongni Ren, Jianjun Lu, Xiaobin Li, Tuo Xu, Bozhou Cui, Qing Wang, Guodong Gao, Qian Yang
Summary: This study discovered a transcriptional regulatory mechanism of MTORC1 involving MEF2A and MEF2D. MEF2A and MEF2D control the cyto-lysosome shutting of MTORC1 by regulating the transcription of FNIP1 and FNIP2, and tyrosine phosphorylation of MEF2D by SRC/c-Src enhances its transcriptional activity and is necessary for MTORC1 activation. The protein and tyrosine phosphorylation levels of MEF2D are elevated in pancreatic cancer and positively correlated with MTORC1 activity.
Article
Immunology
Chenshen Huang, Na Zhang, Hao Xiong, Ning Wang, Zhizhong Chen, Zhizhan Ni, Xiaohong Liu, Boxu Lin, Bujun Ge, Bing Du, Qi Huang
Summary: This study aims to explore a novel method for transcriptional regulation and proposes a new pipeline for analyzing the role of GPRC5B in COAD. By using RNA-seq, ATAC-seq, and ChIP-seq, researchers found the correlation between GPRC5B and macrophages and identified TF GATA4 as a key upstream factor.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maxwell L. Neal, Ling Wei, Eliza Peterson, Mario L. Arrieta-Ortiz, Samuel A. Danziger, Nitin S. Baliga, Alexis Kaushansky, John D. Aitchison
Summary: Researchers developed a gene regulatory network model for Plasmodium falciparum using machine learning, which accurately predicted gene expression levels across diverse datasets. By investigating gene expression coherence, they found that artemisinin resistance in the parasite is associated with incoherent expression across multiple regulatory programs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Environmental Sciences
Jacob J. Valenzuela, Justin Ashworth, Allison Cusick, Raffaela M. Abbriano, E. Virginia Armbrust, Mark Hildebrand, Monica Orellana, Nitin S. Baliga
Summary: This study identified a potential bioindicator for the resilience shift of diatoms under ocean acidification conditions, which is a putative Na+(K+)/H+ antiporter localized in plastid membrane that may play an important role in maintaining pH homeostasis. The differential in transcript levels of this antiporter between nighttime and daytime could serve as an indicator for the resilience shift of diatoms in response to high CO2 conditions in marine environments.
FRONTIERS IN MARINE SCIENCE
(2021)
Correction
Cell Biology
Eliza J. R. Peterson, Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga
Review
Oncology
James H. Park, Adrian Lopez Garcia de Lomana, Diego M. Marzese, Tiffany Juarez, Abdullah Feroze, Parvinder Hothi, Charles Cobbs, Anoop P. Patel, Santosh Kesari, Sui Huang, Nitin S. Baliga
Summary: Pronounced differences between individuals and cell-cell heterogeneity within tumors are major obstacles in effective brain tumor treatment, necessitating a personalized precision medicine approach. A systems biology approach is crucial for developing a multiscale understanding of disease mechanisms. Integrating patient tumor analysis with clinical medicine can optimize treatment strategies.
Article
Multidisciplinary Sciences
Charlotte Cooper, Eliza J. R. Peterson, Rebeca Bailo, Min Pan, Albel Singh, Patrick Moynihan, Makoto Nakaya, Nagatoshi Fujiwara, Nitin Baliga, Apoorva Bhatt
Summary: This study reveals that the mycolic acid desaturase regulator (MadR) controls mycolic acid desaturation and biosynthesis in response to cell envelope stress. This unique regulation mechanism is distinct to other regulators and MadR acts as a key regulatory checkpoint during infection to coordinate mycolic acid remodeling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Lidia dos Passos Lima, Juliana Biar Pereira, Anthony Jhoao Fasabi Flores, Alan Pericles Rodrigues Lorenzetti, Ana Laura Boechat, Maria Claudia Pereda, Sophia Gualtieri, Daniele Ferreira do Prado, Diego Rocha, Lucas de Moraes Ceseti, Regina Lucia Baldini, Chuck S. Farah, Tie Koide, Celso Eduardo Benedetti, Cristina E. Alvarez-Martinez
Summary: The genus Xanthomonas includes multiple phytopathogenic species that infect various plants and cause significant crop diseases. This study characterizes a sigma(ECF) factor called EcfL in Xanthomonas citri, showing its involvement in the virulence and adaptation of the bacterium to citrus plants. EcfL regulates an operon containing three genes and is induced in response to acid stress.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lidia dos Passos Lima, Eliane Silva de Santana, Alan Pericles Rodrigues Lorenzetti, Rogerio Ferreira Lourenco, Lucas de Moraes Ceseti, Luana Riva, Ethel Bayer-Santos, Ana Laura Boechat, Regina Lucia Baldini, Chuck Shaker Farah, Tie Koide, Cristina Elisa Alvarez-Martinez
Summary: This study uncovers the regulatory mechanism of X. citri T6SS. Overexpression of a constitutively active EcfK activates the transcription factor TagK, which induces the expression of T6SS genes. TagK binds directly to T6SS gene promoters and promotes T6SS expression upon contact with amoeba cells.
MOLECULAR MICROBIOLOGY
(2022)
Article
Microbiology
Mario L. Arrieta-Ortiz, Min Pan, Amardeep Kaur, Evan Pepper-Tunick, Vivek Srinivas, Ananya Dash, Selva Rupa Christinal Immanuel, Aaron N. Brooks, Tyson R. Shepherd, Nitin S. Baliga
Summary: There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Researchers found that tetracycline-resistant Escherichia coli undergo metabolic and transcriptional remodeling to support antibiotic resistance. They also discovered that sertraline, a drug, can resensitize tetracycline-resistant E. coli to the antibiotic.
Article
Microbiology
Evelyn Ayumi Onga, Ricardo Z. N. Vencio, Tie Koide
Summary: Through transcriptomic analysis of Halobacterium salinarum NRC-1 under different salt concentrations, we identified differentially expressed genes and validated three important biological processes with differential expression. We also found consistency and differences between the transcriptome and proteome, highlighting potential post-transcriptional regulation candidates.
Article
Microbiology
Alan P. R. Lorenzetti, Ulrike Kusebauch, Livia S. Zaramela, Wei-Ju Wu, Joao P. P. de Almeida, Serdar Turkarslan, Adrian L. G. de Lomana, Jose V. Gomes-Filho, Ricardo Z. N. Vencio, Robert L. Moritz, Tie Koide, Nitin S. Baliga
Summary: In this study, we investigated the scale of post-transcriptional regulation in the halophilic archaeon Halobacterium salinarum NRC-1. Our integrated analysis revealed that a large number of protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for post-transcriptional processing and regulation. Additionally, we found evidence for the conditional post-transcriptional regulation of a subset of genes involved in stressful environment acclimation. These findings provide valuable insights into the role of post-transcriptional regulation in environmental adaptation and are made available as an interactive atlas for further research.
Article
Multidisciplinary Sciences
Ulrike Kusebauch, Alan P. R. Lorenzetti, David S. Campbell, Min Pan, David Shteynberg, Charu Kapil, Mukul K. Midha, Adrian Lopez Garcia de Lomana, Nitin S. Baliga, Robert L. Moritz
Summary: Researchers have reported a comprehensive spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, which enables the measurement of a large fraction of its proteome. This library provides a valuable resource for confidently measuring and quantifying any protein of this archaeon.
Article
Microbiology
Hugo L. de Araujo, Beatriz A. Picinato, Alan P. R. Lorenzetti, Nisansala S. Muthunayake, I. W. Rathnayaka-Mudiyanselage, Naara M. dos Santos, Jared Schrader, Tie Koide, Marilis V. Marques
Summary: The absence of the RNA helicase RhlB in Caulobacter crescentus causes important changes in gene expression and cell physiology. These changes are likely due, at least in part, to inefficient RNA processing by the RNA degradosome, especially at low-temperature conditions.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemical Research Methods
Vivek Srinivas, Rene A. Ruiz, Min Pan, Selva Rupa Christinal Immanuel, Eliza J. R. Peterson, Nitin S. Baliga
Summary: The study presents a method named DRonA and MLSynergy, which uses transcriptome signature to detect drug responses of Mycobacterium tuberculosis and predict their cell killing effects, providing a new framework for rapid monitoring of drug effects and discovery of effective drug combinations.
CELL REPORTS METHODS
(2021)
Article
Oncology
Matthew A. Wall, Serdar Turkarslan, Wei-Ju Wu, Samuel A. Danziger, David J. Reiss, Mike J. Mason, Andrew P. Dervan, Matthew W. B. Trotter, Douglas Bassett, Robert M. Hershberg, Adrian Lopez Garcia de Lomana, Alexander V. Ratushny, Nitin S. Baliga
Summary: This study reports a transcriptional regulatory network inferred from multi-omics data that accurately predicts disease progression risk in multiple myeloma patients and provides insights into possible mechanisms and therapeutic vulnerabilities.
NPJ PRECISION ONCOLOGY
(2021)
