Article
Biochemical Research Methods
Mohammed Eslami, Amin Espah Borujeni, Hamed Eramian, Mark Weston, George Zheng, Joshua Urrutia, Carolyn Corbet, Diveena Becker, Paul Maschhoff, Katie Clowers, Alexander Cristofaro, Hamid Doost Hosseini, D. Benjamin Gordon, Yuval Dorfan, Jedediah Singer, Matthew Vaughn, Niall Gaffney, John Fonner, Joe Stubbs, Christopher A. Voigt, Enoch Yeung
Summary: The Host Response Model (HRM) combines high-throughput sequencing and machine learning to accurately predict the directionality of gene dysregulation to a combination of inducers. The use of prior knowledge of cell regulatory networks doubles the predictive performance of the HRM.
Article
Multidisciplinary Sciences
Abhishek Sinha, Vinson B. Fan, Aravinda-Bharathi Ramakrishnan, Nicole Engelhardt, Jennifer Kennell, Ken M. Cadigan
Summary: SOX9 promotes turnover of β-catenin independently of the destruction complex and proteasome in mammalian cell culture. This requires the activation of MAML2, which acts as a coactivator for SOX9 in antagonizing the Wnt/β-catenin pathway. This newly identified pathway provides a parallel mechanism for restricting Wnt/β-catenin signaling.
Article
Multidisciplinary Sciences
Alexander J. Moorhouse, Amy E. Loats, Kathryn F. Medler, Stefan G. E. Roberts
Summary: The transcriptional corepressor BASP1 requires N-terminal myristoylation for its activity and functions through interactions with nuclear lipids. Removal of active histone modifications H3K9ac and H3K4me3 by BASP1 requires N-terminal myristoylation, while placement of the repressive histone modification H3K27me3 does not require lipidation. BASP1 regulates activity of multiple transcription factors and induces extensive changes in chromatin accessibility, with about 50% of BASP1 target genes showing lipidation-dependent chromatin compaction and transcriptional repression.
Review
Biochemistry & Molecular Biology
Ryo Onishi, Soichiro Yamanaka, Mikiko C. Siomi
Summary: The piRNA pathway is a self-defense mechanism essential for maintaining germline genome integrity, suppressing transposons through RNA degradation and heterochromatinization. While showing conservation across species, there is clear biodiversity in the overall schemes of nuclear events.
Article
Biochemistry & Molecular Biology
Aleena L. Patel, Lili Zhang, Shannon E. Keenan, Christine A. Rushlow, Cecile Fradin, Stanislav Y. Shvartsman
Summary: This study investigates the dynamics of transcriptional repression by Capicua (Cic) in early Drosophila embryos, revealing the speed limit and mechanism of rapid gene repression by Cic. It sets quantitative constraints on potential mechanisms for gene regulation by Cic, providing insights for future studies in gene regulation mechanisms.
Article
Multidisciplinary Sciences
Jelle Jacobs, Michaela Pagani, Christoph Wenzl, Alexander Stark
Summary: This study finds that in Drosophila, most enhancers are repressed by only a subset of co-repressors (CoRs), and enhancers classified by CoR sensitivity show distinct chromatin features, function, TF motifs, and binding. Different TF motifs render enhancers more resistant or sensitive to specific CoRs, resulting in the additional layer of regulatory specificity for differential regulation at close genomic distances and indicative of distinct mechanisms of transcriptional repression.
Article
Plant Sciences
Jian Wang, Xiao-fen Liu, Hui-qin Zhang, Andrew C. Allan, Wen-qiu Wang, Xue-ren Yin
Summary: The study demonstrates that exogenous ASA treatment significantly reduces ethylene production and inhibits the activity of related enzymes in kiwifruit tissues. Transcriptome analysis and transcription factor screening reveal ASA-responsive regulators for ethylene biosynthetic genes. Additionally, abundantly expressed genes are found in both ASA-treated and control tissues. The findings suggest that ASA inhibits ethylene biosynthesis by regulating protein activity at a post-transcriptional level.
HORTICULTURE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
James K. Nunez, Jin Chen, Greg C. Pommier, J. Zachery Cogan, Joseph M. Replogle, Carmen Adriaens, Gokul N. Ramadoss, Quanming Shi, King L. Hung, Avi J. Samelson, Angela N. Pogson, James Y. S. Kim, Amanda Chung, Manuel D. Leonetti, Howard Y. Chang, Martin Kampmann, Bradley E. Bernstein, Volker Hovestadt, Luke A. Gilbert, Jonathan S. Weissman
Summary: CRISPRoff is a programmable epigenetic memory writer that can heritably alter gene expression by initiating specific DNA methylation and gene repression. The tool utilizes a single dead Cas9 fusion protein to establish these modifications, which are maintained through cell division and differentiation processes. By pairing CRISPRoff with genome-wide screens and analysis of chromatin marks, rules for heritable gene silencing can be established, with the tool capable of targeting a wide range of genes beyond canonical CpG islands.
Article
Biochemistry & Molecular Biology
Xin-Xin Kang, Qin-Qing Wang, Zhe Chi, Guang-Lei Liu, Zhong Hu, Zhen-Ming Chi
Summary: The study showed that by removing GATA-type transcriptional activator and repressor genes, as well as overexpressing mutated genes with specific residues, the pullulan production of Aureobasidium melanogenum P16 could be significantly increased.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Review
Biochemistry & Molecular Biology
Martin Anger, Lenka Radonova, Adela Horakova, Diana Sekach, Marketa Charousova
Summary: The onset of early development in mammals involves significant changes in cell morphology and behavior, including fertilization, genome merging, chromatin modifications, and gene expression initiation. Global transcriptional silencing during this period affects cellular activities controlled by translation and may impact chromosome segregation, potentially compromising further development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Aleksandra Anna Bonini, Stefano Maggi, Giulia Mori, Dario Carnuccio, Danila Delfino, Davide Cavazzini, Alberto Ferrari, Alessia Levante, Yoshihiro Yamaguchi, Claudio Rivetti, Claudia Folli
Summary: This study investigated the functional characteristics of DinJ-YafQ system in Lacticaseibacillus paracasei. The results showed that both YafQ orthologs can digest ribosomal RNA with different efficiencies, and their activity is neutralized by DinJ. Moreover, DinJ and DinJ-YafQ can cooperatively bind to the promoter of the TA operon, preventing RNA polymerase from binding. It was also found that a single amino acid substitution in DinJ abolishes its DNA binding ability.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Endocrinology & Metabolism
Agustin Romero, Ana C. Heidenreich, Carolina L. Roman, Macarena Alganaras, Ezequiel Nazer, Juan J. Gagliardino, Barbara Maiztegui, Luis E. Flores, Santiago A. Rodriguez-Segui
Summary: The study revealed the global transcriptional effects induced by short-term INGAP-PP treatment on adult rat pancreatic islets in vitro. Results showed that INGAP-PP treatment led to differential expression of numerous genes, including previously unannotated rat transcripts and novel lncRNAs. These findings help explain the enhancement of physiological effects on beta-cell mass and function by INGAP-PP, laying the groundwork for designing new therapies.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Virology
Mark R. Bruder, Sadru-Dean Walji, Marc G. Aucoin
Summary: The study compared the effectiveness of the CRISPR-Cas9 system for gene disruption and transcriptional repression, indicating its potential as an efficient tool for scrutinizing baculovirus genes.
Article
Biochemistry & Molecular Biology
Quancan Hou, Xueli An, Biao Ma, Suowei Wu, Xun Wei, Tingwei Yan, Yan Zhou, Taotao Zhu, Ke Xie, Danfeng Zhang, Ziwen Li, Lina Zhao, Canfang Niu, Yan Long, Chang Liu, Wei Zhao, Fei Ni, Jinping Li, Daolin Fu, Zhong-Nan Yang, Xiangyuan Wan
Summary: A previously unrecognized repressor, ZmMS1/ZmLBD30, was found to control pollen exine development in maize. It acts through an activation-feedback repression loop to regulate the proper level of exine.
Article
Immunology
Mariya London, Angelina M. Bilate, Tiago B. R. Castro, Tomohisa Sujino, Daniel Mucida
Summary: The study demonstrates that mesenteric lymph node T cells undergo tissue adaptation upon migrating to intestinal lamina propria and epithelium, with changes in transcription and chromatin. Cells occupying different gut layers have specific CD4 programming, and the transition to intraepithelial lymphocytes involves the shutdown of the T-reg cell program before accessibility to epithelium.
Review
Microbiology
Jiawei Sun, Steven T. Rutherford, Thomas J. Silhavy, Kerwyn Casey Huang
Summary: This review discusses the emerging physical and mechanical properties of the Gram-negative outer membrane, revealing a more expansive and versatile role in cellular physiology and viability. Recent studies have uncovered key molecular factors and interactions through experimental and computational research, while advancements in microfluidics and microscopy have contributed to a better understanding of the structural, rheological, and mechanical properties of the outer membrane. These findings suggest broader connections between cellular structure and physiology, with future prospects for elucidating the implications of outer membrane construction for cellular fitness and survival.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ashton N. Combs, Thomas J. Silhavy
Summary: This study reveals a novel role for the periplasmic chaperone Skp in the folding of outer membrane proteins (OMPs) in gram-negative bacteria. Skp removes membrane-integration-defective OMP substrates from the beta-barrel assembly machine (Bam) complex, allowing for clearance of stalled Bam-OMP complexes. Furthermore, Skp acts as an adaptor protein to facilitate the degradation of defective OMP substrates by the periplasmic protease DegP. These findings highlight the importance of Skp in ensuring efficient beta-barrel folding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Jackson Luu, Connor M. Mott, Olivia R. Schreiber, Holly M. Giovinco, Melanie Betchen, Valerie J. Carabetta
Summary: Bacillus subtilis produces highly resistant endospores in response to extreme environmental stresses or starvation. The spores can persist for many years without essential nutrients due to the protection of their chromosomal DNA. The acetylation state of the histone-like protein HBsu plays a role in regulating the process of sporulation and the resistance properties of mature spores.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Andrew S. Bray, Richard D. Smith, Andrew W. Hudson, Giovanna E. Hernandez, Taylor M. Young, Hannah E. George, Robert K. Ernst, M. Ammar Zafar
Summary: This study investigates the biological cost of colistin resistance in Klebsiella pneumoniae. It finds that while colistin resistance reduces the ability of the bacteria to colonize the gut, it enhances their survival outside the host and therefore increases their transmission between hosts.
Editorial Material
Microbiology
Valerie J. J. Carabetta, Julie Hardouin
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Infectious Diseases
Melanie Betchen, Holly M. Giovinco, Michael Curry, Jackson Luu, Henry Fraimow, Valerie J. Carabetta, Raquel Nahra
Summary: Acinetobacter baumannii hospital infections are difficult to treat due to the rapid emergence of multidrug-resistant strains. This study found that in addition to accumulating drug resistance determinants, these strains may also accumulate mutations that increase tolerance to microbicides. Interestingly, pan-susceptible strains were more likely to possess microbicide-resistance genes.
Review
Microbiology
Natividad Ruiz, Thomas J. Silhavy
Summary: Escherichia coli, as a well-studied organism, has played a significant role in the development of biochemical genetics and molecular biology. Its suitability for biochemical and genetic research, along with the conservation of processes found in complex organisms, contributed to its selection as a model organism.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Immunology
Andrew W. Hudson, Andrew J. Barnes, Andrew S. Bray, David A. Ornelles, M. Ammar Zafar
Summary: In this study, the researchers revealed that Klebsiella pneumoniae overcomes colonization resistance in the gut by utilizing fucose metabolism, which promotes its robust colonization. It was also found that fucose metabolism enhances hypermucoviscosity, autoaggregation, and biofilm formation of K. pneumoniae. These findings provide insights into the alternative carbon source utilization and the complex relationship between metabolism and virulence in K. pneumoniae.
INFECTION AND IMMUNITY
(2022)
Article
Infectious Diseases
Manas S. Deolankar, Rachel A. Carr, Rebecca Fliorent, Sean Roh, Henry Fraimow, Valerie J. Carabetta
Summary: The spread of multidrug-resistant Acinetobacter baumannii in critically ill, hospitalized patients has been a serious concern for decades. Traditional antibiotic therapies have failed to effectively treat this pathogen, prompting the introduction of new antibiotics such as eravacycline and omadacycline. In this study, the effectiveness of various antibiotics, including eravacycline and omadacycline, against susceptible and extensively drug-resistant A. baumannii strains was examined. The results showed that while monotherapies with certain antibiotics were largely ineffective, eravacycline showed high efficacy against these strains. Combination therapy with eravacycline or omadacycline and the aminoglycoside amikacin yielded the most promising results. This comprehensive characterization provides valuable guidance for the treatment of this deadly infection in hospitalized patients.
Article
Immunology
M. Ammar Zafar, Alicia Costa-Terryl, Taylor M. Young
Summary: The ability of Streptococcus pneumoniae to sense and respond quickly to the changing environment of the upper respiratory tract allows it to thrive as a pathogen. Two-component systems play a crucial role in this adaptation process. They have been found to promote pneumococcal colonization and virulence in the upper respiratory tract.
INFECTION AND IMMUNITY
(2023)
Review
Biochemistry & Molecular Biology
Aryanna Copling, Maxwell Akantibila, Raaha Kumaresan, Gilbert Fleischer, Dennise Cortes, Rahul S. S. Tripathi, Valerie J. J. Carabetta, Sebastian L. Vega
Summary: Advances in biomaterials have improved medical devices, but the introduction of foreign materials can lead to infections. Drug-resistant infections have become a concern due to overuse and improper use of antimicrobials. Recently, researchers have focused on developing novel antimicrobial biomaterials, such as AMP-tethered hydrogels, to overcome this problem. This article provides an update on innovations and discoveries made in the development of photopolymerizable, self-assembling, and AMP-releasing hydrogels in the last 5 years.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Randi L. Guest, Michael J. Lee, Wei Wang, Thomas J. Silhavy
Summary: The outer membrane of Gram-negative bacteria is unique and important for its structural and functional characteristics. The lipid asymmetry creates mechanical strength and lowers membrane permeability. The Mla pathway is responsible for removing mislocalized glycerophospholipids from the outer membrane. Pseudomonas aeruginosa has two proteins, PA2800 and PA3239, of the MlaA family.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Irina V. Mikheyeva, Jiawei Sun, Kerwyn Casey Huang, Thomas J. Silhavy
Summary: This study demonstrates that loss of BamD in Escherichia coli leads to reduction in outer membrane proteins (OMPs), weakening the outer membrane and altering cell shape. This results in outer membrane rupture in spent medium. In response to the loss of OMPs, phospholipids flip into the outer leaflet, creating tension between the membrane leaflets and contributing to membrane rupture. Suppressor mutations that halt phospholipid removal prevent rupture but do not restore membrane stiffness or normal cell shape, suggesting a possible connection between outer membrane stiffness and cell shape.
NATURE COMMUNICATIONS
(2023)
Letter
Multidisciplinary Sciences
Georgina Benn, Thomas J. Silhavy, Colin Kleanthous, Bart W. Hoogenboom
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Kathryn A. Macgillivray, Siu Lung Ng, Sophia Wiesenfeld, Randi L. Guest, Tahrima Jubery, Thomas J. Silhavy, William C. Ratcliff, Brian K. Hammer
Summary: The study reveals that populations of Escherichia coli, when subjected to T6SS attack by Vibrio cholerae, evolved to better survive the attack through two convergently evolved pathways. However, these mutations come with trade-offs, reducing cellular growth rates and increasing susceptibility to antibiotics and elevated pH.