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Chung S, Lerner E, Jin Y, Kim S, Alhadid Y, Grimaud LW, Zhang IX, Knobler CM, Gelbart WM, Weiss S. The effect of macromolecular crowding on single-round transcription by Escherichia coli RNA polymerase. Nucleic Acids Res 2019; 47:1440-1450. [PMID: 30590739 PMCID: PMC6379708 DOI: 10.1093/nar/gky1277] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 12/01/2018] [Accepted: 12/13/2018] [Indexed: 01/09/2023] Open
Abstract
Previous works have reported significant effects of macromolecular crowding on the structure and behavior of biomolecules. The crowded intracellular environment, in contrast to in vitro buffer solutions, likely imparts similar effects on biomolecules. The enzyme serving as the gatekeeper for the genome, RNA polymerase (RNAP), is among the most regulated enzymes. Although it was previously demonstrated that macromolecular crowding affects association of RNAP to DNA, not much is known about how crowding acts on late initiation and promoter clearance steps, which are considered to be the rate-determining steps for many promoters. Here, we demonstrate that macromolecular crowding enhances the rate of late initiation and promoter clearance using in vitro quenching-based single-molecule kinetics assays. Moreover, the enhancement's dependence on crowder size notably deviates from predictions by the scaled-particle theory, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions could be affected by crowded conditions in the cellular milieu.
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Affiliation(s)
- SangYoon Chung
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Eitan Lerner
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yan Jin
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Soohong Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yazan Alhadid
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
| | - Logan Wilson Grimaud
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Irina X Zhang
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Present address: Irina X. Zhang, Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute (MBI), University of California Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Correspondence may also be addressed to William M. Gelbart. Tel: +1 310 825 2005; Fax: +1 310 206 4038;
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute (MBI), University of California Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, CA 90095, USA
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
- To whom correspondence should be addressed. Tel: +1 310 794 0093; Fax: +1 310 267 4672;
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Lemay G. Synthesis and Translation of Viral mRNA in Reovirus-Infected Cells: Progress and Remaining Questions. Viruses 2018; 10:E671. [PMID: 30486370 PMCID: PMC6315682 DOI: 10.3390/v10120671] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/23/2018] [Accepted: 11/25/2018] [Indexed: 12/11/2022] Open
Abstract
At the end of my doctoral studies, in 1988, I published a review article on the major steps of transcription and translation during the mammalian reovirus multiplication cycle, a topic that still fascinates me 30 years later. It is in the nature of scientific research to generate further questioning as new knowledge emerges. Our understanding of these fascinating viruses thus remains incomplete but it seemed appropriate at this moment to look back and reflect on our progress and most important questions that still puzzle us. It is also essential of being careful about concepts that seem so well established, but could still be better validated using new approaches. I hope that the few reflections presented here will stimulate discussions and maybe attract new investigators into the field of reovirus research. Many other aspects of the viral multiplication cycle would merit our attention. However, I will essentially limit my discussion to these central aspects of the viral cycle that are transcription of viral genes and their phenotypic expression through the host cell translational machinery. The objective here is not to review every aspect but to put more emphasis on important progress and challenges in the field.
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Affiliation(s)
- Guy Lemay
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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Ghosh S, Malik YS, Kobayashi N. Therapeutics and Immunoprophylaxis Against Noroviruses and Rotaviruses: The Past, Present, and Future. Curr Drug Metab 2018; 19:170-191. [PMID: 28901254 PMCID: PMC5971199 DOI: 10.2174/1389200218666170912161449] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/25/2016] [Accepted: 03/19/2017] [Indexed: 12/20/2022]
Abstract
Background: Noroviruses and rotaviruses are important viral etiologies of severe gastroenteritis. Noroviruses are the primary cause of nonbacterial diarrheal outbreaks in humans, whilst rotaviruses are a major cause of childhood diarrhea. Although both enteric pathogens substantially impact human health and economies, there are no approved drugs against noroviruses and rotaviruses so far. On the other hand, whilst the currently licensed rotavirus vaccines have been successfully implemented in over 100 countries, the most advanced norovirus vaccine has recently completed phase-I and II trials. Methods: We performed a structured search of bibliographic databases for peer-reviewed research litera-ture on advances in the fields of norovirus and rotavirus therapeutics and immunoprophylaxis. Results: Technological advances coupled with a proper understanding of viral morphology and replication over the past decade has facilitated pioneering research on therapeutics and immunoprophylaxis against noroviruses and rotaviruses, with promising outcomes in human clinical trials of some of the drugs and vaccines. This review focuses on the various developments in the fields of norovirus and rotavirus thera-peutics and immunoprophylaxis, such as potential antiviral drug molecules, passive immunotherapies (oral human immunoglobulins, egg yolk and bovine colostral antibodies, llama-derived nanobodies, and anti-bodies expressed in probiotics, plants, rice grains and insect larvae), immune system modulators, probiot-ics, phytochemicals and other biological substances such as bovine milk proteins, therapeutic nanoparti-cles, hydrogels and viscogens, conventional viral vaccines (live and inactivated whole virus vaccines), and genetically engineered viral vaccines (reassortant viral particles, virus-like particles (VLPs) and other sub-unit recombinant vaccines including multi-valent viral vaccines, edible plant vaccines, and encapsulated viral particles). Conclusions: This review provides important insights into the various approaches to therapeutics and im-munoprophylaxis against noroviruses and rotaviruses..
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Affiliation(s)
- Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts and Nevis, West Indies.,Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Yashpal Singh Malik
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
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Engineering recombinant reoviruses with tandem repeats and a tetravirus 2A-like element for exogenous polypeptide expression. Proc Natl Acad Sci U S A 2013; 110:E1867-76. [PMID: 23630248 DOI: 10.1073/pnas.1220107110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We tested a strategy for engineering recombinant mammalian reoviruses (rMRVs) to express exogenous polypeptides. One important feature is that these rMRVs are designed to propagate autonomously and can therefore be tested in animals as potential vaccine vectors. The strategy has been applied so far to three of the 10 MRV genome segments: S3, M1, and L1. To engineer the modified segments, a 5' or 3' region of the essential, long ORF in each was duplicated, and then exogenous sequences were inserted between the repeats. The inner repeat and exogenous insert were positioned in frame with the native protein-encoding sequences but were separated from them by an in-frame "2A-like" sequence element that specifies a cotranslational "stop/continue" event releasing the exogenous polypeptide from the essential MRV protein. This design preserves a terminal region of the MRV genome segment with essential activities in RNA packaging, assortment, replication, transcription, and/or translation and alters the encoded MRV protein to a limited degree. Recovery of rMRVs with longer inserts was made more efficient by wobble-mutagenizing both the inner repeat and the exogenous insert, which possibly helped via respective reductions in homologous recombination and RNA structure. Immunogenicity of a 300-aa portion of the simian immunodeficiency virus Gag protein expressed in mice by an L1-modified rMRV was confirmed by detection of Gag-specific T-cell responses. The engineering strategy was further used for mapping the minimal 5'-terminal region essential to MRV genome segment S3.
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