Article
Multidisciplinary Sciences
Wenjing Liu, Xiaoai Zhou, Tao Jin, Yonghui Li, Bin Wu, Daoyuan Yu, Zongren Yu, Bomin Su, Ruirui Chen, Youzhi Feng, Manuel Delgado-Baquerizo
Summary: This study reveals the ecological and physiological features of microbial colonization on cultural relics, including multikingdom interactions and intrakingdom competition. These interactions are crucial for the long-term conservation of relics.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Saidi Wang, Amlan Talukder, Mingyu Cha, Xiaoman Li, Haiyan Hu
Summary: The identification of miRNA transcription start sites is crucial for understanding the functional roles of miRNA genes, and recent computational methods have advanced genome-wide miRNA TSS annotation significantly. This study compared and analyzed miRNA TSS annotations from 14 representative studies, and compiled a robust set of miRNA TSSs supported by multiple studies. Integration of genomic and epigenomic data revealed the features of miRNA TSSs and their relationships with protein-coding and long non-coding genes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
William J. Lu-Culligan, Leah J. Connor, Yixuan Xie, Babatunde E. Ekundayo, Brendan T. Rose, Martin Machyna, Andreas P. Pintado-Urbanc, Joshua T. Zimmer, Isaac W. Vock, Natarajan V. Bhanu, Megan C. King, Benjamin A. Garcia, Franziska Bleichert, Matthew D. Simon
Summary: Lysine residues can be modified by both methylation and acetylation to form N epsilon-acetyl-N epsilon-methyllysine (Kacme). Kacme is found on histone H4 across species and mammalian tissues and is associated with active chromatin.
Editorial Material
Plant Sciences
Ying Zhang, Xiao Yu, Bo Li
Summary: Appropriate spatiotemporal regulation of immune gene expression is crucial for defending against pathogens. Recent research has discovered that pathogen-associated molecular patterns (PAMPs) can induce widespread transcription initiation changes and an immediate wave of transcription factors, which are elements of immune gene reprogramming.
TRENDS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Yoshihiko Fujita, Takeru Kameda, Chingakham Ranjit Singh, Whitney Pepper, Ariana Cecil, Madelyn Hilgers, Mackenzie Thornton, Izumi Asano, Carter Moravek, Yuichi Togashi, Hirohide Saito, Katsura Asano
Summary: This study reveals that the combined modification of 5-cytosine methylation and pseudouridylation can enhance the initiation frequencies of GUG and UUG start codons in eukaryotes, making them more favorable than CUG initiation. Molecular dynamics simulations show that this modification increases the affinity between modified codons and tRNA, mitigating the discrimination against non-AUG codons. These findings suggest that chemical modifications of start codon bases can provide a new mechanism for regulating proteome diversity and therapeutic mRNA technology.
Article
Biochemistry & Molecular Biology
Eugeniya I. Bondar, Maxim E. Troukhan, Konstantin V. Krutovsky, Tatiana V. Tatarinova
Summary: This study utilized computational approaches to predict genome-wide TSS in four conifer species, laying the groundwork for future research on gene regulatory regions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Justus Niemeyer, Laura Fischer, Frank O'Neill Aylward, Michael Schroda
Summary: This study investigated the use of promoters from giant virus genomes in Chlamydomonas reinhardtii to drive gene expression. The results showed that the viral promoters were unable to effectively drive gene expression. Additionally, it was found that by mutating the start codons of mCherry and using the 5 '-UTR of beta TUB2, the problem of gene expression in Chlamydomonas could be overcome.
Editorial Material
Microbiology
Johanna Hoshizaki, Marcus C. S. Lee
Summary: This month's Genome Watch highlights approaches that enable high-resolution mapping of transcription start sites in apicomplexan parasites.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Daniel M. Sapozhnikov, Moshe Szyf
Summary: PROTECTOR is a novel approach that uses a nuclease-dead Cas protein to bind to off-target sites and interfere with Cas activity, reducing off-target mutation rates without compromising on-target activity. It can be used in combination with high-fidelity Cas enzymes to further decrease off-target editing, offering an ability to protect off-target sites with identical sequences to target sites.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Satoru Ishihara, Yohei Sasagawa, Takeru Kameda, Hayato Yamashita, Mana Umeda, Naoe Kotomura, Masayuki Abe, Yohei Shimono, Itoshi Nikaido
Summary: The 'open' and 'compact' regions of chromatin are implicated in active and silent transcription, respectively. However, this study suggests that transcription output is not only determined by the open-compact conversion of chromatin, but also by structural variations within chromatin itself. It was found that chromatin compaction plays a crucial role in transcription levels, with local states of chromatin compaction determining gene expression.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Masahide Seki, Yuta Kuze, Xiang Zhang, Ken-ichi Kurotani, Michitaka Notaguchi, Haruki Nishio, Hiroshi Kudoh, Takuya Suzaki, Satoko Yoshida, Sumio Sugano, Tomonao Matsushita, Yutaka Suzuki
Summary: TSS-seq2 is an improved method for detecting TSS, with higher accuracy and less bias compared to previous methods, achieved by introducing split ligation and other modifications. It can be conducted with as little as 5 ng of RNA and has been successfully applied to TSS analysis of four plant species.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Environmental Sciences
Pitchiah Sivaperumal, Kannan Kamala, Kumaran Subramanian, Wilson Aruni, Rajeshkumar Shanmugam, Rajendran Rajaram
Summary: Baseline assessments of marine microbial studies around Nuclear Power Plant (NPP) sites are limited. This study focused on the distribution and diversity of marine actinobacteria and their potential remediation ability. The results showed high diversity of marine actinobacteria, with dominance of the genus Streptomyces, and the identification of a potential strain capable of producing EPS and remediating uranium radionuclides.
ENVIRONMENTAL RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Tom Joshua Eisenack, Debora Broch Trentini
Summary: Proteins are versatile molecular machines that control and execute cellular processes. They go through a multilayered synthesis process with many opportunities for error, and must navigate a complex folding-energy landscape. Newly synthesized proteins are at increased risk of misfolding and toxic aggregation, but cells employ molecular chaperones and quality control factors to maintain proteostasis.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Ecology
Nathaniel J. Ennis, Dhanasekaran Dharumaduri, Julia G. Bryce, Louis S. Tisa
Summary: Stone surfaces, though seemingly uninhabitable, host microbial life that adapts to various harsh conditions by exhibiting resistance to environmental factors. Granite and granodiorite host distinct bacterial populations influenced by quartz mineral content, which plays a major role in structuring microbial communities. Other geochemical parameters such as ilmenite, albite, anorthite, and orthoclase components also impact community structure to a lesser degree than quartz. Core members of the stone microbiome community including Cyanobacteria, Rubrobacter, and Deinococcus were identified on both lithologies, with specific taxa like Sphingomonas, Geodermatophilus, and Truepera found predominantly in the granodiorite samples. Community diversity correlated with quartz mineral content indicates that microbial communities on quartz surfaces may be transient and regularly changing. This research expands our understanding of built-stone microbial community structure based on lithology and geochemistry.
Article
Biochemistry & Molecular Biology
Richard She, Jingchuan Luo, Jonathan S. Weissman
Summary: We conducted genome-wide CRISPRi screens in human K562 cells to identify modulators of translation initiation frequency at near-cognate start codons. Depletion of any eIF3 core subunit promoted near-cognate start codon usage, with different sensitivity thresholds to sgRNA-mediated depletion. eIF3D depletion enhanced near-cognate usage through canonical eIF4E cap-binding, and not through eIF2A or eIF2D-dependent tRNA initiation. Disruption of eIF3D's cap-binding properties had no effect on start codon selection accuracy. Depletion of eIF3D also activated TNF alpha signaling via NF-kappa B and the interferon gamma response, similar to knockdown of eIF1A and eIF4G2. Our study provides new insights into alternative start codon usage mechanisms and consequences.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Michael A. DeJesus, Thomas R. Ioerger
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2015)
Article
Microbiology
Jan Korte, Marina Alber, Carolina M. Trujillo, Karl Syson, Hendrik Koliwer-Brandl, Rene Deenen, Karl Koehrer, Michael A. DeJesus, Travis Hartman, William R. Jacobs, Stephen Bornemann, Thomas R. Ioerger, Sabine Ehrt, Rainer Kalscheuer
Article
Biochemical Research Methods
Michael A. DeJesus, Thomas R. Ioerger
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
(2016)
Article
Genetics & Heredity
Caitlin A. Orsini, Barry Setlow, Michael DeJesus, Stacy Galaviz, Kimberly Loesch, Thomas Ioerger, Deeann Wallis
MOLECULAR GENETICS & GENOMIC MEDICINE
(2016)
Article
Biochemistry & Molecular Biology
Michael A. DeJesus, Subhalaxmi Nambi, Clare M. Smith, Richard E. Baker, Christopher M. Sassetti, Thomas R. Ioerger
NUCLEIC ACIDS RESEARCH
(2017)
Article
Microbiology
Michael A. DeJesus, Elias R. Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E. Long, Cara C. Boutte, Eric J. Rubin, Dirk Schnappinger, Sabine Ehrt, Sarah M. Fortune, Christopher M. Sassetti, Thomas R. Ioerger
Article
Biochemical Research Methods
Siddharth Subramaniyam, Michael A. DeJesus, Anisha Zaveri, Clare M. Smith, Richard E. Baker, Sabine Ehrt, Dirk Schnappinger, Christopher M. Sassetti, Thomas R. Ioerger
BMC BIOINFORMATICS
(2019)
Article
Biochemistry & Molecular Biology
Barbara Bosch, Michael A. De Jesus, Nicholas C. Poulton, Wenzhu Zhang, Curtis A. Engelhart, Anisha Zaveri, Sophie Lavalette, Nadine Ruecker, Carolina Trujillo, Joshua B. Wallach, Shuqi Li, Sabine Ehrt, Brian T. Chait, Dirk Schnappinger, Jeremy M. Rock
Summary: The study suggests that traditional genetic approaches may not accurately identify high-value bacterial targets, while using CRISPR technology to modulate gene expression can help differentiate bacteria's vulnerability to gene inhibition, identifying both highly vulnerable genes and invulnerable essential genes.
Article
Multidisciplinary Sciences
Esha Dutta, Michael A. DeJesus, Nadine Ruecker, Anisha Zaveri, Eun-Ik Koh, Christopher M. Sassetti, Dirk Schnappinger, Thomas R. Ioerger
Summary: Chemical-genetics (C-G) experiments are used to identify interactions between inhibitory compounds and bacterial genes, potentially revealing drug targets or other functionally interacting genes and pathways. By constructing a library of hypomorphic strains, treating them with inhibitory compounds, and using high-throughput sequencing, changes in relative abundance of individual mutants can be quantified. A new statistical method called CGA-LMM is proposed for analyzing C-G data, capturing the dependence of gene abundance in the hypomorph library on increasing drug concentrations through slope coefficients. This method was applied to analyze interactions between Mycobacterium tuberculosis hypomorph libraries and antibiotics, successfully identifying known target genes or expected interactions for the majority of drugs tested.
Article
Microbiology
Gregory H. Babunovic, Michael A. DeJesus, Barbara Bosch, Michael R. Chase, Thibault Barbier, Amy K. Dickey, Bryan D. Bryson, Jeremy M. Rock, Sarah M. Fortune
Summary: The study found that the application of all-trans-retinoic acid (ATRA) can enhance the control of Mycobacterium tuberculosis (Mtb) by human macrophages, which is achieved by altering macrophage cholesterol trafficking and lipid metabolism. In addition, CRISPR interference screening was used to identify specific genes required for Mtb survival in ATRA-activated macrophages.
Article
Microbiology
Shuqi Li, Nicholas C. Poulton, Jesseon S. Chang, Zachary A. Azadian, Michael A. DeJesus, Nadine Ruecker, Matthew D. Zimmerman, Kathryn A. Eckartt, Barbara Bosch, Curtis A. Engelhart, Daniel F. Sullivan, Martin Gengenbacher, Veronique A. Dartois, Dirk Schnappinger, Jeremy M. Rock
Summary: This study utilized a CRISPR interference chemical-genetics platform to uncover various drug resistant mechanisms in Mycobacterium tuberculosis (Mtb) and identified a potential new drug for treating tuberculosis.
NATURE MICROBIOLOGY
(2022)
Article
Microbiology
Nicholas C. Poulton, Zachary A. Azadian, Michael A. DeJesus, Jeremy M. Rock
Summary: Tuberculosis is a fatal bacterial infection, causing 1.5 million deaths globally each year. Drug-resistant strains of Mycobacterium tuberculosis (Mtb) have emerged, leading to efforts in developing novel drugs. The arabinogalactan biosynthetic enzyme DprE1 in Mtb is a promising drug target, with over a dozen inhibitory compounds identified. Among them, BTZ043 and PBTZ169 have shown promise and are in clinical trials. A study using CRISPRi chemical-genetic screen with PBTZ169 identified rv0678 as a negative regulator of the mmpS5/L5 drug efflux pump, which confers resistance to PBTZ169. Mutations in rv0678 are associated with resistance to another drug, bedaquiline. These results highlight the importance of monitoring for rv0678 mutations in ongoing clinical trials of BTZ043 and PBTZ169.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Microbiology
Weizhen Xu, Michael A. DeJesus, Nadine Rucker, Curtis A. Engelhart, Meredith G. Wright, Claire Healy, Kan Lin, Ruojun Wang, Sae Woong Park, Thomas R. Ioerger, Dirk Schnappinger, Sabine Ehrt
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2017)
Article
Microbiology
Gregory H. Babunovic, Michael A. DeJesus, Barbara Bosch, Michael R. Chase, Thibault Barbier, Amy K. Dickey, Bryan D. Bryson, Jeremy M. Rock, Sarah M. Fortune
Summary: This study identifies that the treatment with ATRA can enhance the control ability of macrophages against Mycobacterium tuberculosis (Mtb) by affecting bacterial clearance through changes in macrophage cholesterol metabolism, and conducts the first Mtb CRISPR interference screen in the infection model, revealing certain Mtb genes specifically required to survive in ATRA-activated macrophages.
Article
Multidisciplinary Sciences
Esha Dutta, Michael A. DeJesus, Nadine Ruecker, Anisha Zaveri, Eun-Ik Koh, Christopher M. Sassetti, Dirk Schnappinger, Thomas R. Ioerger
Summary: Chemical-genetics experiments can identify interactions between inhibitory compounds and bacterial genes, revealing drug targets or functionally interacting genes. By using Linear Mixed Models, a statistical method known as CGA-LMM can analyze C-G data and detect candidate gene interactions based on their abundance changes with increasing drug concentrations.