Article
Biochemical Research Methods
Nolan J. O'Connor, Antoni E. Bordoy, Anushree Chatterjee
Summary: Antisense transcription plays a widespread role in influencing gene expression through transcriptional interference (TI), and the processivity control of RNA polymerase (RNAP) can be used to tune TI and enhance gene repression, suggesting potential applications in synthetic biology. In this study, three distinct antitermination strategies were applied to control TI and design minimal genetic NAND and NOR logic gates, demonstrating the importance of processivity control for strong TI and highlighting TI's potential in synthetic biology.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Microbiology
Teppei Morita, Nadim Majdalani, Masahiro C. Miura, Rerina Inose, Taku Oshima, Masaru Tomita, Akio Kanai, Susan Gottesman
Summary: The regulatory function of many bacterial small RNAs (sRNAs) is dependent on the RNA chaperone Hfq binding to the 3' portion of the sRNA intrinsic terminator. This study identified several genes, including an sRNA gene (cyaR) and three protein-coding genes (cspD, ygjH, and rof), that attenuate the termination of SgrS in Escherichia coli. Overexpression of the protein attenuators CspD and Rof resulted in increased readthrough at terminators of SgrS and other sRNAs, reducing their regulatory effects on target mRNAs. Further analysis revealed the unexpected role of Rho in sRNA termination and the stabilizing effect of CspD on both terminated and readthrough transcripts. This study provides evidence of the modulation of intrinsic termination as an additional layer of regulation in sRNA signaling.
Article
Microbiology
Heung Jin Jeon, Monford Paul N. Abishek, Yonho Lee, Heon M. Lim
Summary: In this study, we demonstrate that Rho-dependent termination of transcription occurs stochastically at cistron junctions, generating a stable mRNA that is shorter than the full-length mRNA. We further show that the failure in translation initiation of the next gene, rather than the failure of translation termination of the preceding gene, causes the Rho-dependent termination. Additionally, we find that transcription pauses 130 nucleotides downstream from the site of translation termination, and this pause is necessary for Rho-dependent termination.
Article
Multidisciplinary Sciences
Mildred Delaleau, Eric Eveno, Isabelle Simon, Annie Schwartz, Marc Boudvillain
Summary: In this study, a screening scheme called Helicase-SELEX was developed to explore the requirements of helicases for substrates and cofactors on a global scale. Using the transcription termination helicase Rho of E.coli as a prototype, researchers generated a genome-wide map of Rho utilization sites and developed synthetic Rut sites. This study illustrates the potential and flexibility of Helicase-SELEX in fundamental and synthetic biology discovery.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Jillella Mallikarjun, L. SaiSree, P. Himabindu, K. Anupama, Manjula Reddy, J. Gowrishankar
Summary: Homologous recombination (HR) is essential for maintaining genome integrity in all cells. In this study, an isoform (IF2-1) of the translation initiation factor IF2 is identified as a novel facilitator of RecA's function during HR in Escherichia coli.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ezaz Ahmad, Anirban Mitra, Wareed Ahmed, Varsha Mahapatra, Shubhada R. Hegde, Claudia Sala, Stewart T. Cole, Valakunja Nagaraja
Summary: Intrinsic and Rho-dependent transcription termination mechanisms are important for regulating gene expression and recycling RNA polymerase in bacteria. This study highlights the dominance of Rho-dependent termination in mycobacteria, including Mycobacterium tuberculosis (Mtb), and validates Rho as a key regulatory factor. Rho affects the termination of both protein-coding and stable RNA genes in Mtb and its depletion impacts bacterial growth and transcription read-through.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2023)
Article
Multidisciplinary Sciences
Emilia Krypotou, Guy E. Townsend, Xiaohui Gao, Shoichi Tachiyama, Jun Liu, Nick D. Pokorzynski, Andrew L. Goodman, Eduardo A. Groisman
Summary: Therapeutic manipulation of the gut microbiota has great potential for human health. Bacteria in the gut use phase separation to enhance their fitness and this mechanism can be targeted for clinical intervention. The intrinsically disordered region (IDR) of the transcription termination factor Rho is crucial for phase separation and gene regulation in the gut. Phase separation is vital for host-commensal bacteria interactions and has implications for novel clinical applications.
Article
Biochemistry & Molecular Biology
Ezaz Ahmad, Varsha Mahapatra, V. M. Vanishree, Valakunja Nagaraja
Summary: The intrinsic and Rho-dependent mechanisms of transcription termination are important in bacteria to prevent transcriptional read-through. This study demonstrates the cooperation between intrinsic terminators and the Rho factor in ensuring efficient termination. The findings suggest the prevalence of this cooperation in various bacteria.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Yanfei Cheng, Hui Zhu, Zhengda Du, Xuena Guo, Chenyao Zhou, Zhaoyue Wang, Xiuping He
Summary: Enhanced eIF5A activity may improve acetic acid tolerance in Saccharomyces cerevisiae. eIF5A promotes the synthesis of Ume6p, leading to the up-regulation of target genes at the transcriptional level, especially under acetic acid stress. The eIF5A-Ume6p axis plays a crucial role in the adaptive response and tolerance to acetic acid in yeast cells.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Review
Pharmacology & Pharmacy
Sunil Kumar, Shashikanta Sau, Puja Kumari Agnivesh, Arnab Roy, Nitin Pal Kalia
Summary: This review provides an overview of the essentiality of Rho in Mycobacterium tuberculosis, making it an attractive drug target for inhibitor discovery.
DRUG DISCOVERY TODAY
(2023)
Article
Biochemistry & Molecular Biology
Maura Mittermeier, Bing Wang, Nelly Said, Daniela Gjorgjevikj, Markus C. Wahl, Irina Artsimovitch
Summary: Escherichia coli RfaH plays a role in abolishing Rho-mediated polarity in lipopolysaccharide core biosynthesis operons. A temperature-sensitive mutant rpoC397* was identified as a suppressor of SDS sensitivity, with 46 C-terminal residues of the RNA polymerase beta' subunit replaced by 23 residues carrying a net positive charge. The rpoC397* mutant mimics RfaH's resistance to Rho and exhibits similar responses to pause signals and Nus factors, while still binding to Rho and Nus factors in vivo.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Isabelle Simon, Mildred Delaleau, Annie Schwartz, Marc Boudvillain
Summary: Rho-dependent termination of transcription (RDTT) is a critical regulatory mechanism specific to bacteria, with the Rho factor containing a large, poorly conserved N-terminal insertion domain (NID) in some species. In this study, the biochemical characterization of a NID-bearing Rho factor from a low G + C bacterium was provided, revealing its behavior more like the NID-less Rho factor. This highlights the evolutionary plasticity of Rho's N-terminal region and how RDTT is adapted to distinct genomic contents.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Microbiology
Raphael Forquet, Xuejiao Jiang, William Nasser, Florence Hommais, Sylvie Reverchon, Sam Meyer
Summary: This study presents the first transcriptomic map of a Dickeya species, which can significantly contribute to the field of phytopathogenicity. It also demonstrates the application of long-read Nanopore native RNA-seq in prokaryotes. The findings provide insights into the coordination of transcription in bacteria and suggest that gene expression is controlled at the level of transcription units rather than operons. The results have implications for microbial research and challenge the traditional operon model.
Review
Genetics & Heredity
Evelyne Ng Kwan Lim, Charles Sasseville, Marie-Claude Carrier, Eric Masse
Summary: RNA binding proteins (RBPs) play crucial roles in a variety of regulatory events, ranging from direct gene expression regulation to guiding RNA modification. Over the past decade, the development of high-throughput methods has been instrumental in uncovering new functions of RBPs and elucidating the underlying molecular mechanisms of regulatory events.
TRENDS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Matthew S. Verosloff, William K. Corcoran, Taylor B. Dolberg, David Z. Bushhouse, Joshua N. Leonard, Julius B. Lucks
Summary: Through the newly developed in cellulo Pol III transcription termination assay, it was found that efficient Pol III termination requires the cooperation of poly-U tracts, RNA sequence, and structural elements in nascent RNA. Different promoter types have different requirements for transcription termination.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)