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Lang M, Ganapathy US, Mann L, Seidel RW, Goddard R, Erdmann F, Dick T, Richter A. Synthesis and in vitro Metabolic Stability of Sterically Shielded Antimycobacterial Phenylalanine Amides. ChemMedChem 2024; 19:e202300593. [PMID: 38329388 DOI: 10.1002/cmdc.202300593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/09/2024]
Abstract
Nα-aroyl-N-aryl-phenylalanine amides (AAPs) are RNA polymerase inhibitors with activity against Mycobacterium tuberculosis and non-tuberculous mycobacteria. We observed that AAPs rapidly degrade in microsomal suspensions, suggesting that avoiding hepatic metabolism is critical for their effectiveness in vivo. As both amide bonds are potential metabolic weak points of the molecule, we synthesized 16 novel AAP analogs in which the amide bonds are shielded by methyl or fluoro substituents in close proximity. Some derivatives show improved microsomal stability, while being plasma-stable and non-cytotoxic. In parallel with the metabolic stability studies, the antimycobacterial activity of the AAPs against Mycobacterium tuberculosis, Mycobacterium abscessus, Mycobacterium avium and Mycobacterium intracellulare was determined. The stability data are discussed in relation to the antimycobacterial activity of the panel of compounds and reveal that the concept of steric shielding of the anilide groups by a fluoro substituent has the potential to improve the stability and bioavailability of AAPs.
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Affiliation(s)
- Markus Lang
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Uday S Ganapathy
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, 07110, Nutley, New Jersey, USA
| | - Lea Mann
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Rüdiger W Seidel
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Richard Goddard
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Frank Erdmann
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, 07110, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, 123 Metro Blvd, 07110, Nutley, New Jersey, USA
- Department of Microbiology and Immunology, Georgetown University, 3900 Reservoir Road, N.W., 20007, Washington DC, USA
| | - Adrian Richter
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
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2
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Papastavrou N, Horning DP, Joyce GF. RNA-catalyzed evolution of catalytic RNA. Proc Natl Acad Sci U S A 2024; 121:e2321592121. [PMID: 38437533 PMCID: PMC10945747 DOI: 10.1073/pnas.2321592121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/25/2024] [Indexed: 03/06/2024] Open
Abstract
An RNA polymerase ribozyme that was obtained by directed evolution can propagate a functional RNA through repeated rounds of replication and selection, thereby enabling Darwinian evolution. Earlier versions of the polymerase did not have sufficient copying fidelity to propagate functional information, but a new variant with improved fidelity can replicate the hammerhead ribozyme through reciprocal synthesis of both the hammerhead and its complement, with the products then being selected for RNA-cleavage activity. Two evolutionary lineages were carried out in parallel, using either the prior low-fidelity or the newer high-fidelity polymerase. The former lineage quickly lost hammerhead functionality as the population diverged toward random sequences, whereas the latter evolved new hammerhead variants with improved fitness compared to the starting RNA. The increase in fitness was attributable to specific mutations that improved the replicability of the hammerhead, counterbalanced by a small decrease in hammerhead activity. Deep sequencing analysis was used to follow the course of evolution, revealing the emergence of a succession of variants that progressively diverged from the starting hammerhead as fitness increased. This study demonstrates the critical importance of replication fidelity for maintaining heritable information in an RNA-based evolving system, such as is thought to have existed during the early history of life on Earth. Attempts to recreate RNA-based life in the laboratory must achieve further improvements in replication fidelity to enable the fully autonomous Darwinian evolution of RNA enzymes as complex as the polymerase itself.
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do Prado PFV, Ahrens FM, Liebers M, Ditz N, Braun HP, Pfannschmidt T, Hillen HS. Structure of the multi-subunit chloroplast RNA polymerase. Mol Cell 2024; 84:910-925.e5. [PMID: 38428434 DOI: 10.1016/j.molcel.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression.
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Affiliation(s)
- Paula F V do Prado
- University Medical Center Göttingen, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Research Group Structure and Function of Molecular Machines, Am Fassberg 11, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Frederik M Ahrens
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Monique Liebers
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Noah Ditz
- Institute of Plant Genetics, Plant Molecular Biology and Plant Proteomics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Plant Molecular Biology and Plant Proteomics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Thomas Pfannschmidt
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Hauke S Hillen
- University Medical Center Göttingen, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Research Group Structure and Function of Molecular Machines, Am Fassberg 11, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Research Group Structure and Function of Molecular Machines, University of Göttingen, 37077 Göttingen, Germany.
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4
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Silver BD, Willett CG, Maher KA, Wang D, Deal RB. Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements. G3 (Bethesda) 2024; 14:jkae016. [PMID: 38253712 PMCID: PMC10917500 DOI: 10.1093/g3journal/jkae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/10/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
Transcriptional initiation is among the first regulated steps controlling eukaryotic gene expression. High-throughput profiling of fungal and animal genomes has revealed that RNA Polymerase II often initiates transcription in both directions at the promoter transcription start site, but generally only elongates productively into the gene body. Additionally, Pol II can initiate transcription in both directions at cis-regulatory elements such as enhancers. These bidirectional RNA Polymerase II initiation events can be observed directly with methods that capture nascent transcripts, and they are also revealed indirectly by the presence of transcription-associated histone modifications on both sides of the transcription start site or cis-regulatory elements. Previous studies have shown that nascent RNAs and transcription-associated histone modifications in the model plant Arabidopsis thaliana accumulate mainly in the gene body, suggesting that transcription does not initiate widely in the upstream direction from genes in this plant. We compared transcription-associated histone modifications and nascent transcripts at both transcription start sites and cis-regulatory elements in A. thaliana, Drosophila melanogaster, and Homo sapiens. Our results provide evidence for mostly unidirectional RNA Polymerase II initiation at both promoters and gene-proximal cis-regulatory elements of A. thaliana, whereas bidirectional transcription initiation is observed widely at promoters in both D. melanogaster and H. sapiens, as well as cis-regulatory elements in Drosophila. Furthermore, the distribution of transcription-associated histone modifications around transcription start sites in the Oryza sativa (rice) and Glycine max (soybean) genomes suggests that unidirectional transcription initiation is the norm in these genomes as well. These results suggest that there are fundamental differences in transcriptional initiation directionality between flowering plant and metazoan genomes, which are manifested as distinct patterns of chromatin modifications around RNA polymerase initiation sites.
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Affiliation(s)
- Brianna D Silver
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA
| | - Courtney G Willett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA
| | - Kelsey A Maher
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dongxue Wang
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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5
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Wu XX, Mu WH, Li F, Sun SY, Cui CJ, Kim C, Zhou F, Zhang Y. Cryo-EM structures of the plant plastid-encoded RNA polymerase. Cell 2024; 187:1127-1144.e21. [PMID: 38428393 DOI: 10.1016/j.cell.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 03/03/2024]
Abstract
Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast biogenesis from proplastids and functions as the predominant RNA polymerase in mature chloroplasts. The PEP-centered transcription apparatus comprises a bacterial-origin PEP core and more than a dozen eukaryotic-origin PEP-associated proteins (PAPs) encoded in the nucleus. Here, we determined the cryo-EM structures of Nicotiana tabacum (tobacco) PEP-PAP apoenzyme and PEP-PAP transcription elongation complexes at near-atomic resolutions. Our data show the PEP core adopts a typical fold as bacterial RNAP. Fifteen PAPs bind at the periphery of the PEP core, facilitate assembling the PEP-PAP supercomplex, protect the complex from oxidation damage, and likely couple gene transcription with RNA processing. Our results report the high-resolution architecture of the chloroplast transcription apparatus and provide the structural basis for the mechanistic and functional study of transcription regulation in chloroplasts.
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Affiliation(s)
- Xiao-Xian Wu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen-Hui Mu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Fan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shu-Yi Sun
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao-Jun Cui
- University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS. Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase. Proc Natl Acad Sci U S A 2024; 121:e2311480121. [PMID: 38354263 PMCID: PMC10895346 DOI: 10.1073/pnas.2311480121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish them from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β'1 and β'2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spanning approximately half of the β'2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP in the absence of iNTP bound at the active site and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG, or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms and organelle.
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Affiliation(s)
- M. Zuhaib Qayyum
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
| | - Masahiko Imashimizu
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba305-8565, Japan
| | - Miron Leanca
- The Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Rishi K. Vishwakarma
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
| | - Amber Riaz-Bradley
- The Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Yulia Yuzenkova
- The Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
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Sabsay KR, te Velthuis AJ. Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships. bioRxiv 2024:2024.02.16.580771. [PMID: 38405982 PMCID: PMC10888975 DOI: 10.1101/2024.02.16.580771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Negative sense RNA viruses (NSV) include some of the most detrimental human pathogens, including the influenza, Ebola and measles viruses. NSV genomes consist of one or multiple single-stranded RNA molecules that are encapsidated into one or more ribonucleoprotein (RNP) complexes. Current evolutionary relationships within the NSV phylum are based on alignment of conserved RNA-dependent RNA polymerase (RdRp) domain amino acid sequences. However, the RdRp-based phylogeny does not address whether other core proteins in the NSV genome evolved along the same trajectory. Moreover, the current classification of NSVs does not consistently match the segmented and non-segmented nature of negative-sense virus genomes. Viruses belonging to e.g. the Serpentovirales have a segmented genome but are classified among the non-segmented negative-sense RNA viruses. We hypothesized that RNA genome segmentation is not coupled to the RdRp domain, but rather to the nucleocapsid protein (NP) that forms RNP complexes with the viral RNA. Because NP sequences are too short to infer robust phylogenetic relationships, we here used experimentally-obtained and AlphaFold 2.0-predicted NP structures to probe whether evolutionary relationships can be estimated using NSV NP sequences and potentially improve our understanding of the relationships between NSV subphyla and the NSV genome organization. Following flexible structure alignments of modeled structures, we find that the structural homology of the NSV NPs reveals phylogenetic clusters that are consistent with the currently accepted NSV taxonomy based on RdRp sequences with one key difference: the NPs of the segmented Serpentovirales cluster with the other segmented NSV. In addition, we were able to assign viruses for which RdRp sequences are currently missing to phylogenetic clusters. Overall, our results suggest that the NSV RdRp and NP genes largely evolved along similar trajectories, that NP-based clustering is better correlated with the NSV genome structure organization, and that even short pieces of genetic, protein-coding information can be used to infer evolutionary relationships, potentially making metagenomic analyses more valuable.
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Affiliation(s)
- Kimberly R. Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
- Sigler Institute, Princeton University, Princeton, NJ 08544, United States
| | - Aartjan J.W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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8
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Wang L. RNA polymerase collisions and their role in transcription. Transcription 2024:1-10. [PMID: 38357902 DOI: 10.1080/21541264.2024.2316972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
RNA polymerases are the central enzymes of gene expression and function frequently in either a head-on or co-directional manner on the busy DNA track. Whether and how these collisions between RNA polymerases contribute to transcriptional regulation is mysterious. Increasing evidence from biochemical and single-molecule studies suggests that RNA polymerase collisions function as an important regulator to fine-tune transcription, rather than creating deleterious "traffic jams". This review summarizes the recent progress on elucidating the consequences of RNA polymerase collisions during transcription and highlights the significance of cooperation and coordination between RNA polymerases.
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Affiliation(s)
- Ling Wang
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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9
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Ye J, Kan CH, Zheng Y, Tsang TF, Chu AJ, Chan KH, Yang X, Ma C. Sulfonamidyl derivatives of sigmacidin: Protein-protein interaction inhibitors targeting bacterial RNA polymerase and sigma factor interaction exhibiting antimicrobial activity against antibiotic-resistant bacteria. Bioorg Chem 2024; 143:106983. [PMID: 38016396 DOI: 10.1016/j.bioorg.2023.106983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/12/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023]
Abstract
RNA polymerase is an essential enzyme involved in bacterial transcription, playing a crucial role in RNA synthesis. However, it requires the association with sigma factors to initiate this process. In our previous work, we utilized a structure-based drug discovery approach to create benzoyl and benzyl benzoic acid compounds. These compounds were designed based on the amino acid residues within the key binding site of sigma factors, which are crucial for their interaction with RNA polymerase. By inhibiting bacterial transcription, these compounds exhibited notable antimicrobial activity, and we coined them as sigmacidins to highlight their resemblance to sigma factors and the benzoic acid structure. In this study, we further modified the compound scaffolds and developed a series of sulfonamidyl benzoic acid derivatives. These derivatives displayed potent antimicrobial activity, with minimum inhibitory concentrations (MICs) as low as 1 µg/mL, demonstrating their efficacy against bacteria. Furthermore, these compounds demonstrated low cytotoxicity, indicating their potential as safe antimicrobial agents. To ascertain their mechanism of action in interfering with bacterial transcription, we conducted biochemical and cellular assays. Overall, this study showcases the effectiveness of sulfonamidyl benzoic acid derivatives as antimicrobial agents by targeting protein-protein interactions involving RNA polymerase and sigma factors. Their strong antimicrobial activity and low cytotoxicity implicate their potential in combating antibiotic-resistant bacteria.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region; School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Cheuk Hei Kan
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region
| | - Yingbo Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Tsz Fung Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region
| | - Adrian Jun Chu
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region
| | - King Hong Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region.
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region.
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Wu M, Vadlakonda S, El-Kattan Y, Ghosh A, Lin TH, Chambers-Wilson R, Cheng X, Bantia S, Kellogg-Yelder D, Chand P, Babu YS, Kotian PL. Synthesis and biological evaluation of Ribo 7-N/O/S pyrimidine 9-deaza C-nucleoside analogs as new antiviral agents for inhibiting HCV RNA-dependent RNA polymerases. Eur J Med Chem 2024; 264:115991. [PMID: 38118393 DOI: 10.1016/j.ejmech.2023.115991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/22/2023]
Abstract
Hepatitis C infection is caused by the bloodborne pathogen hepatitis C virus (HCV) and can lead to serious liver diseases and, ultimately, death if the treatment is ineffective. This work reports the synthesis and preclinical evaluation of 7 novel 9-O/N/S pyrimidine nucleosides, including compound 12, the triphosphate of known compound 7b. The nucleosides are 9-deaza modifications of adenosine and guanosine with β-2'-C-methyl substituent on the ribose. Within this series of compounds, a 9-deaza furopyrimidine analog of adenosine, compound 7b, showed high anti-HCV activity in vitro, good stability, low toxicity, and low genotoxicity when administrated in low doses, and an adequate pharmacokinetics profile. An improved synthesis of compound 7b compared to a previous study is also reported. Compound 12 was synthesized as a control to verify phosphorylation of 7b occurred in vivo.
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Affiliation(s)
- Minwan Wu
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA
| | - Satish Vadlakonda
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA
| | - Yahya El-Kattan
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA
| | - Ajit Ghosh
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA.
| | - Tsu-Hsing Lin
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA
| | - Ramanda Chambers-Wilson
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA
| | - Xiaogang Cheng
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA
| | - Shanta Bantia
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA.
| | - Debra Kellogg-Yelder
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA
| | - Pooran Chand
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA.
| | - Y S Babu
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA
| | - Pravin L Kotian
- BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center, Building 200, Suite 200, Birmingham, Alabama 35244, USA.
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11
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Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS. Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase. bioRxiv 2024:2024.01.11.575193. [PMID: 38260627 PMCID: PMC10802570 DOI: 10.1101/2024.01.11.575193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β'1 and β'2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spans approximately half of the β'2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding at the active site results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms.
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Affiliation(s)
- M. Zuhaib Qayyum
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Current address: Protein Technologies Center, Inspiration4 Advanced Research Center, Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Masahiko Imashimizu
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8565 Japan
| | - Miron Leanca
- The Centre for Bacterial Cell Biology, Newcastle University, UK
| | - Rishi K. Vishwakarma
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Yulia Yuzenkova
- The Centre for Bacterial Cell Biology, Newcastle University, UK
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
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12
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Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X. Structural basis of σ 54 displacement and promoter escape in bacterial transcription. Proc Natl Acad Sci U S A 2024; 121:e2309670120. [PMID: 38170755 PMCID: PMC10786286 DOI: 10.1073/pnas.2309670120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated, and in bacteria, transcription initiation is mediated by sigma (σ) factors. σ recruits RNAP to the promoter DNA region, located upstream of the transcription start site (TSS) and facilitates open complex formation, where double-stranded DNA is opened up into a transcription bubble and template strand DNA is positioned inside RNAP for initial RNA synthesis. During initial transcription, RNAP remains bound to σ and upstream DNA, presumably with an enlarging transcription bubble. The release of RNAP from upstream DNA is required for promoter escape and processive transcription elongation. Bacteria sigma factors can be broadly separated into two classes with the majority belonging to the σ70 class, represented by the σ70 that regulates housekeeping genes. σ54 forms a class on its own and regulates stress response genes. Extensive studies on σ70 have revealed the molecular mechanisms of the σ70 dependent process while how σ54 transitions from initial transcription to elongation is currently unknown. Here, we present a series of cryo-electron microscopy structures of the RNAP-σ54 initial transcribing complexes with progressively longer RNA, which reveal structural changes that lead to promoter escape. Our data show that initially, the transcription bubble enlarges, DNA strands scrunch, reducing the interactions between σ54 and DNA strands in the transcription bubble. RNA extension and further DNA scrunching help to release RNAP from σ54 and upstream DNA, enabling the transition to elongation.
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Affiliation(s)
- Forson Gao
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, LondonSW7 2AZ, United Kingdom
| | - Fuzhou Ye
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, LondonSW7 2AZ, United Kingdom
| | - Bowen Zhang
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, LondonSW7 2AZ, United Kingdom
| | - Nora Cronin
- London Consortium for High Resolution cryoEM, the Francis Crick Institute, LondonNW1 1AT, United Kingdom
| | - Martin Buck
- Department of Life Sciences, Imperial College London, LondonSW7 2AZ, United Kingdom
| | - Xiaodong Zhang
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, LondonSW7 2AZ, United Kingdom
- DNA processing machines laboratory, the Francis Crick Institute, LondonNW1 1AT, United Kingdom
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13
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Anwar AF, Cain CF, Garza MJ, Degen D, Ebright RH, Del Valle JR. Stabilizing Pseudouridimycin: Synthesis, RNA Polymerase Inhibitory Activity, and Antibacterial Activity of Dipeptide-Modified Analogues. ChemMedChem 2024; 19:e202300474. [PMID: 37751316 PMCID: PMC10843019 DOI: 10.1002/cmdc.202300474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 09/28/2023]
Abstract
Pseudouridimycin (PUM) is a microbially produced C-nucleoside dipeptide that selectively targets the nucleotide addition site of bacterial RNA polymerase (RNAP) and that has a lower rate of spontaneous resistance emergence relative to current drugs that target RNAP. Despite its promising biological profile, PUM undergoes relatively rapid decomposition in buffered aqueous solutions. Here, we describe the synthesis, RNAP-inhibitory activity, and antibacterial activity of chemically stabilized analogues of PUM. These analogues feature targeted modifications that mitigate guanidine-mediated hydroxamate bond scission. A subset of analogues in which the central hydroxamate is replaced with amide or hydrazide isosteres retain the antibacterial activity of the natural product.
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Affiliation(s)
- Avraz F Anwar
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Christopher F Cain
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Michael J Garza
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - David Degen
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ, 08854, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ, 08854, USA
| | - Juan R Del Valle
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
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14
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Kumar C, Remus D. Looping out of control: R-loops in transcription-replication conflict. Chromosoma 2024; 133:37-56. [PMID: 37419963 PMCID: PMC10771546 DOI: 10.1007/s00412-023-00804-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Transcription-replication conflict is a major cause of replication stress that arises when replication forks collide with the transcription machinery. Replication fork stalling at sites of transcription compromises chromosome replication fidelity and can induce DNA damage with potentially deleterious consequences for genome stability and organismal health. The block to DNA replication by the transcription machinery is complex and can involve stalled or elongating RNA polymerases, promoter-bound transcription factor complexes, or DNA topology constraints. In addition, studies over the past two decades have identified co-transcriptional R-loops as a major source for impairment of DNA replication forks at active genes. However, how R-loops impede DNA replication at the molecular level is incompletely understood. Current evidence suggests that RNA:DNA hybrids, DNA secondary structures, stalled RNA polymerases, and condensed chromatin states associated with R-loops contribute to the of fork progression. Moreover, since both R-loops and replication forks are intrinsically asymmetric structures, the outcome of R-loop-replisome collisions is influenced by collision orientation. Collectively, the data suggest that the impact of R-loops on DNA replication is highly dependent on their specific structural composition. Here, we will summarize our current understanding of the molecular basis for R-loop-induced replication fork progression defects.
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Affiliation(s)
- Charanya Kumar
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA.
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15
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Francis C, Frida J P, Thanh-Huong B, Alicja M, Artem K, Jérémie P, Sven Even B. Urea supplementation improves mRNA in vitro transcription by decreasing both shorter and longer RNA byproducts. RNA Biol 2024; 21:1-6. [PMID: 38411163 PMCID: PMC10900265 DOI: 10.1080/15476286.2024.2321764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
The current letter to the editor describes the presence of RNA byproducts in small-scale in vitro transcription (IVT) reactions as evaluated by capillary gel electrophoresis, asymmetric flow field flow fractionation, immunoblotting, cell-free translation assays, and in IFN reporter cells. We compare standard T7 RNA polymerase (RNAP) based IVT reactions to two recently described protocols employing either urea supplementation or using the VSW3 RNAP. Our results indicate that urea supplementation yields considerably less RNA byproducts and positively affects the overall number of full-length transcripts. In contrast, VSW3 IVT reactions demonstrated a low yield and generated a higher fraction of truncated transcripts. Lastly, both urea mRNA and VSW3 mRNA elicited considerably less IFN responses after transfection in mouse macrophages.
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Affiliation(s)
- Combes Francis
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
| | | | - Bui Thanh-Huong
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
| | - Molska Alicja
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
| | - Komissarov Artem
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
| | - Parot Jérémie
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
| | - Borgos Sven Even
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
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16
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Zhou XJ, Good SS, Pietropaolo K, Huang Q, Moussa A, Hammond JM, Sommadossi JP. Bemnifosbuvir (BEM, AT-527), a novel nucleotide analogue inhibitor of the hepatitis C virus NS5B polymerase. Expert Opin Investig Drugs 2024; 33:9-17. [PMID: 38265202 DOI: 10.1080/13543784.2024.2305137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Chronic hepatitis C virus (HCV) persists as a public health concern worldwide. Consequently, optimizing HCV therapy remains an important objective. While current therapies are generally highly effective, advanced antiviral agents are needed to maximize cure rates with potentially shorter treatment durations in a broader patient population, particularly those patients with advanced diseases who remain difficult to treat. AREAS COVERED This review summarizes the in vitro anti-HCV activity, preclinical pharmacological properties of bemnifosbuvir (BEM, AT-527), a novel prodrug that is metabolically converted to AT-9010, the active guanosine triphosphate analogue that potently and selectively inhibits several viral RNA polymerases, including the HCV NS5B polymerase. Results from clinical proof-of-concept and phase 2 combination studies are also discussed. EXPERT OPINION BEM exhibits potent pan-genotype activity against HCV, and has favorable safety, and drug interaction profiles. BEM is approximately 10-fold more potent than sofosbuvir against HCV genotypes (GT) tested in vitro. When combined with a potent NS5A inhibitor, BEM is expected to be a promising once-daily oral antiviral for chronic HCV infection of all genotypes and fibrosis stages with potentially short treatment durations.
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Affiliation(s)
- Xiao-Jian Zhou
- Departments of Preclinical and Clinical Development, Atea Pharmaceuticals, Boston, MA, USA
| | - Steven S Good
- Departments of Preclinical and Clinical Development, Atea Pharmaceuticals, Boston, MA, USA
| | - Keith Pietropaolo
- Departments of Preclinical and Clinical Development, Atea Pharmaceuticals, Boston, MA, USA
| | - Qi Huang
- Departments of Preclinical and Clinical Development, Atea Pharmaceuticals, Boston, MA, USA
| | - Adel Moussa
- Departments of Preclinical and Clinical Development, Atea Pharmaceuticals, Boston, MA, USA
| | - Janet Mj Hammond
- Departments of Preclinical and Clinical Development, Atea Pharmaceuticals, Boston, MA, USA
| | - Jean-Pierre Sommadossi
- Departments of Preclinical and Clinical Development, Atea Pharmaceuticals, Boston, MA, USA
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17
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Feklistov A. Dynamics and logic of promoter melting. Trends Biochem Sci 2024; 49:8-11. [PMID: 37863673 DOI: 10.1016/j.tibs.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/22/2023]
Abstract
Despite significant progress in our understanding of promoter melting dynamics, underlying principles of the process remain elusive, with opposing views on key aspects held by many in the field. Here, I discuss the mechanistic logic behind the interplay of thermal and deterministic forces acting to create transcriptionally competent promoter complexes.
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Affiliation(s)
- Andrey Feklistov
- Department of Structural Biology, Stanford School of Medicine, Stanford, CA 94305, USA.
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18
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Sabsay KR, te Velthuis AJW. Negative and ambisense RNA virus ribonucleocapsids: more than protective armor. Microbiol Mol Biol Rev 2023; 87:e0008223. [PMID: 37750733 PMCID: PMC10732063 DOI: 10.1128/mmbr.00082-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
SUMMARYNegative and ambisense RNA viruses are the causative agents of important human diseases such as influenza, measles, Lassa fever, and Ebola hemorrhagic fever. The viral genome of these RNA viruses consists of one or more single-stranded RNA molecules that are encapsidated by viral nucleocapsid proteins to form a ribonucleoprotein complex (RNP). This RNP acts as protection, as a scaffold for RNA folding, and as the context for viral replication and transcription by a viral RNA polymerase. However, the roles of the viral nucleoproteins extend beyond these functions during the viral infection cycle. Recent advances in structural biology techniques and analysis methods have provided new insights into the formation, function, dynamics, and evolution of negative sense virus nucleocapsid proteins, as well as the role that they play in host innate immune responses against viral infection. In this review, we discuss the various roles of nucleocapsid proteins, both in the context of RNPs and in RNA-free states, as well as the open questions that remain.
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Affiliation(s)
- Kimberly R. Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Aartjan J. W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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19
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Tewary A, Prajapati RK, Mukhopadhyay J. Mechanism of δ Mediated Transcription Activation in Bacillus subtilis: Interaction with α CTD of RNA Polymerase Stabilizes δ and Successively Facilitates the Open Complex Formation. J Mol Biol 2023; 435:168366. [PMID: 37972688 DOI: 10.1016/j.jmb.2023.168366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The α CTD (C-terminal domain of the α subunit) of RNA polymerase (RNAP) is a target for transcriptional regulators. In the transcription activation at Class I, Class II, and Class III promoters of bacteria, the transcriptional regulator, binds to DNA at different sites and interacts with the α CTD to stabilize the RNAP at the promoter or it binds to the α CTD to form a prerecruitment complex that searches for its cognate binding site. This 'simple recruitment mechanism' of the transcriptional machinery at the promoter is responsible for the activation of transcription. Strikingly, in B. subtilis the binding of RNAP at the promoter stabilizes the transcriptional regulator, δ at the -41 site of the promoter DNA through an interaction with its α CTD and successively facilitates the open complex formation. Two residues R293 and K294 of α CTD (equivalent to K297 and K298 of E. coli) are involved in the interactions with δ and essential for the activation of transcription. R293 is responsible for the stabilization of δ, while K294 is responsible for facilitating the open complex formation. Based on our data we propose a new model of transcription activation by δ of B. subtilis that is similar to (its binding location and interaction with α CTD), but distinct from (the recruitment of transcription factor by RNAP at the DNA, and enhancement of the open complex formation) the model Class II promoters in bacteria.
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Affiliation(s)
- Aniruddha Tewary
- Department of Chemical Science, Bose Institute, EN80 Sector V, Kolkata 700091, India.
| | | | - Jayanta Mukhopadhyay
- Department of Chemical Science, Bose Institute, EN80 Sector V, Kolkata 700091, India.
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20
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Ho CH, Chen CJ, Hsieh CY, Su PY. Amino acid substitutions in the region between RpoB clusters II and III on rifampin susceptibility in Haemophilus influenzae. Eur J Clin Microbiol Infect Dis 2023; 42:1499-1509. [PMID: 37906391 DOI: 10.1007/s10096-023-04689-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Rifampin is a potent chemoprophylactic antibiotic for Haemophilus influenzae infection, and the resistance rate in H. influenzae is low. In this study, we assessed rifampin resistance-related genetic variations in H. influenzae. METHODS Rifampin susceptibility testing and whole-genome sequencing were performed in 51 H. influenzae isolates. Variations associated with rifampin resistance were identified using Fisher's exact tests. Functional assays were performed to evaluate the effect of RpoB substitutions on rifampin susceptibility. RESULTS Using the genome of the Rd KW20 H. influenzae strain as the reference, we detected 40 genetic variations in rpoB, which resulted in 39 deduced amino acid substitutions among the isolates. Isolate A0586 was resistant to rifampin, with a minimum inhibitory concentration (MIC) = 8 μg/mL. Phylogenetic analyses revealed that the RpoB sequence of isolate A0586 was distinct from other isolates. Five substitutions, including H526N located in cluster I and L623F, R628C, L645F, and L672F in the region between clusters II and III, were unique to isolate A0586. In two rifampin-susceptible H. influenzae isolates, RpoB-H526N alone and in combination with RpoB-L672F increased the MICs of rifampin to 4 and 8 μg/mL, respectively. RpoB-L672F did not affect cell growth and transcription in H. influenzae isolates. No amino acid substitutions in the AcrAB-TolC efflux pump or outer membrane proteins were found to be associated with rifampin resistance in H. influenzae. CONCLUSIONS Our findings indicate that L672F substitution in the region between RpoB clusters II and III has an aggravating effect on rifampin resistance in H. influenzae.
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Affiliation(s)
- Cheng-Hsun Ho
- Department of Medical Laboratory Science, College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan.
| | - Chuan-Jung Chen
- Department of Medical Laboratory Science, College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
| | - Chia-Yun Hsieh
- Department of Medical Laboratory Science, College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
| | - Pei-Yi Su
- Department of Laboratory Medicine, E-DA Hospital, Kaohsiung, Taiwan
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21
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Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H. Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. J Biol Chem 2023; 299:105477. [PMID: 37981206 PMCID: PMC10703601 DOI: 10.1016/j.jbc.2023.105477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/30/2023] [Accepted: 11/11/2023] [Indexed: 11/21/2023] Open
Abstract
RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome.
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Affiliation(s)
- Munetaka Akatsu
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Haruhiko Ehara
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, Japan; Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Risa Fujita
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tomoko Ito
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Ken Osumi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Mitsuo Ogasawara
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shun-Ichi Sekine
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan.
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan.
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22
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Faisal S, Badshah SL, Sharaf M, Abdalla M. Insight into the Hantaan virus RNA-dependent RNA polymerase inhibition using in-silico approaches. Mol Divers 2023; 27:2505-2522. [PMID: 36376718 PMCID: PMC9663193 DOI: 10.1007/s11030-022-10567-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022]
Abstract
The Hantaan virus (HTN) is a member of the hantaviridae family. It is a segmented type, negative-strand virus (sNSVs). It causes hemorrhagic fever with renal syndrome, which includes fever, vascular hemorrhage, and renal failure. This illness is one of the most serious hemorrhagic diseases in the world, and it is a major public health concern due to its high mortality rate. The Hantaan virus RNA-dependent RNA polymerase complex (RdRp) is involved in viral RNA transcription and replication for the survival and transmission of this virus. Therefore, it is a primary target for antiviral drug development. Interference with the endonucleolytic "cap-snatching" reaction by the HTN virus RdRp endonuclease domain is a particularly appealing approach for drug discovery against this virus. This RdRp endonuclease domain of the HTN virus has a metal-dependent catalytic activity. We targeted this metal-dependent enzymatic activity to identify inhibitors that can bind and disrupt this endonuclease enzyme activity using in-silico approaches i.e., molecular docking, molecular dynamics simulation, predicted absorption, distribution, metabolism, excretion, toxicity (ADMET) and drug-likeness studies. The docking studies showed that peramivir, and ingavirin compounds can effectively bind with the manganese ions and engage with other active site residues of this protein. Molecular simulations also showed stable binding of these ligands with the active site of HTN RdRp. Simulation analysis showed that they were in constant contact with the active site manganese ions and amino acid residues of the HTN virus endonuclease domain. This study will help in better understanding the HTN and related viruses.
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Affiliation(s)
- Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar, 25120, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, 25120, Pakistan.
| | - Mohamed Sharaf
- Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo, 11751, Egypt
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, 250022, China.
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23
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Abstract
Transcription and replication both require large macromolecular complexes to act on a DNA template, yet these machineries cannot simultaneously act on the same DNA sequence. Conflicts between the replication and transcription machineries (transcription-replication conflicts, or TRCs) are widespread in both prokaryotes and eukaryotes and have the capacity to both cause DNA damage and compromise complete, faithful replication of the genome. This review will highlight recent studies investigating the genomic locations of TRCs and the mechanisms by which they may be prevented, mitigated, or resolved. We address work from both model organisms and mammalian systems but predominantly focus on multicellular eukaryotes owing to the additional complexities inherent in the coordination of replication and transcription in the context of cell type-specific gene expression and higher-order chromatin organization.
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Affiliation(s)
- Liana Goehring
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Duncan J Smith
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA;
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Mehnath S, Sathish Kumar M, Chitra K, Jeyaraj M. Bone-Adhesive Hydrogel for Effective Inhibition of M. tuberculosis and Osteoblast Regeneration. ACS Infect Dis 2023; 9:2269-2281. [PMID: 37904258 DOI: 10.1021/acsinfecdis.3c00328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Currently, bone tuberculosis (TB) treatment largely involves lifelong drug prescriptions and surgical intervention, resulting in poor quality of life for patients. Therefore, the fabrication of injectable scaffolds to form a solid framework around the defective bone region is gaining importance over the extensive use of antimicrobial inhibitors. Herein, we synthesized a novel bone-adhesive and thermoresponsive hydrogel via conjugation of poly(N-isopropylacrylamide-co-glycidyl methacrylate) (PNIPAM-co-GMA) and cysteine (CYS). Thiolation of the polymer enables chemical cross-linking with the bone glycoprotein, enhancing bone adhesion and permitting control of scaffold retention time. The PNIPAM-co-GMA-CYS hydrogel shows higher cross-linking behavior at 37 °C, forms a strong gel in 260 s, and has 151 kPa adhesion strength on cortical bone. The lead compounds 5-methyl-5H-[1,2,4]triazino[5,6-b]indole-3-thiol (MTIT) and N-tert-butyl-4-methyl-6-(5-methyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)pyrimidin-2-amine (TMTIPA) were identified by a high-throughput screening method. Effective MTIT and TMTIPA are encapsulated in bone-adhesive hydrogel separately, and both have a high release rate above >70% in 180 h. The MTIT- and TMTIPA-loaded PNIPAM-co-GMA-CYS showed an excellent bactericidal effect, reducing the relative intracellular bacterial survival in macrophages. Furthermore, the as-synthesized hydrogel has outstanding mechanical and biocompatibility properties to become a bone-replacing material and provide support to promote bone repair. This work presents a novel bone-adhesive PNIPAM-co-GMA-CYS for the sustained release of lead compounds toward promising alternative bone TB treatment.
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Affiliation(s)
- Sivaraj Mehnath
- National Centre for Nanoscience and Nanotechnology, University of Madras, Guindy Campus, Chennai , Tamil Nadu 600 025, India
| | - Marimuthu Sathish Kumar
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu 613 401, India
| | - Karuppannan Chitra
- Translational Research Platform for Veterinary Biologicals, Madhavaram Milk Colony, Chennai, Tamil Nadu 600 051, India
| | - Murugaraj Jeyaraj
- National Centre for Nanoscience and Nanotechnology, University of Madras, Guindy Campus, Chennai , Tamil Nadu 600 025, India
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25
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Silver BD, Willett CG, Maher KA, Wang D, Deal RB. Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements. bioRxiv 2023:2023.11.03.565513. [PMID: 37961418 PMCID: PMC10635121 DOI: 10.1101/2023.11.03.565513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Transcriptional initiation is among the first regulated steps controlling eukaryotic gene expression. High-throughput profiling of fungal and animal genomes has revealed that RNA Polymerase II (Pol II) often initiates transcription in both directions at the promoter transcription start site (TSS), but generally only elongates productively into the gene body. Additionally, Pol II can initiate transcription in both directions at cis-regulatory elements (CREs) such as enhancers. These bidirectional Pol II initiation events can be observed directly with methods that capture nascent transcripts, and they are also revealed indirectly by the presence of transcription-associated histone modifications on both sides of the TSS or CRE. Previous studies have shown that nascent RNAs and transcription-associated histone modifications in the model plant Arabidopsis thaliana accumulate mainly in the gene body, suggesting that transcription does not initiate widely in the upstream direction from genes in this plant. We compared transcription-associated histone modifications and nascent transcripts at both TSSs and CREs in Arabidopsis thaliana, Drosophila melanogaster, and Homo sapiens. Our results provide evidence for mostly unidirectional Pol II initiation at both promoters and gene-proximal CREs of Arabidopsis thaliana, whereas bidirectional transcription initiation is observed widely at promoters in both Drosophila melanogaster and Homo sapiens, as well as CREs in Drosophila. Furthermore, the distribution of transcription-associated histone modifications around TSSs in the Oryza sativa (rice) and Glycine max (soybean) genomes suggests that unidirectional transcription initiation is the norm in these genomes as well. These results suggest that there are fundamental differences in transcriptional initiation directionality between flowering plant and metazoan genomes, which are manifested as distinct patterns of chromatin modifications around RNA polymerase initiation sites.
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Affiliation(s)
- Brianna D. Silver
- Department of Biology, Emory University, Atlanta, GA 30322 USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322 USA
| | - Courtney G. Willett
- Department of Biology, Emory University, Atlanta, GA 30322 USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322 USA
| | - Kelsey A. Maher
- Department of Biology, Emory University, Atlanta, GA 30322 USA
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322 USA
| | - Dongxue Wang
- Department of Biology, Emory University, Atlanta, GA 30322 USA
| | - Roger B. Deal
- Department of Biology, Emory University, Atlanta, GA 30322 USA
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26
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Lamb CH, Pitré EM, Elshina E, Rigby CV, Bisht K, Jalal H, Myhrvold C, te Velthuis AJ. Cas13-based amplification-free quantification of aberrant RNAs during influenza virus infection. bioRxiv 2023:2023.11.03.565460. [PMID: 37961440 PMCID: PMC10635118 DOI: 10.1101/2023.11.03.565460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Influenza A virus RNA synthesis produces full-length and aberrant RNA molecules, which include defective viral genomes (DVG) and mini viral RNAs (mvRNA). Sequencing approaches have shown that several hundred unique aberrant RNA species may be present during infection, and that they can vary in size, segment origin, and sequence. Moreover, a subset of aberrant RNA molecules can bind and activate host pathogen receptor retinoic acid-inducible gene I (RIG-I), leading to innate immune signaling and the expression of type I and III interferons. Understanding the kinetics and distribution of these immunostimulatory aberrant RNA sequences is important for modeling the outcomes of IAV infection. We here first show that reverse transcription and PCR steps can yield imperfect aberrant RNA quantification data in a sequence-dependent manner. Next, we developed an amplification-free LbuCas13a-based detection method to quantify mvRNA amplification kinetics and subcellular distributions. We show that our assay can quantify the copy numbers of 10 specific mvRNA sequences in total RNA from cell culture, animal tissue or clinical nasopharyngeal swab extracts. In addition, we find kinetic and distribution differences between immunostimulatory and non-immunostimulatory mvRNAs, as well as mvRNAs derived from different segments, during infection. Overall, our results reveal a hitherto hidden diversity in the behavior of IAV mvRNAs and they suggest that their production is linked to replication of the individual viral segments. Cas13 is therefore a valuable new tool in our repertoire for investigating the impact of aberrant RNAs on RNA virus infection.
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Affiliation(s)
- Caitlin H. Lamb
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Emmanuelle M. Pitré
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- University of Cambridge, Department of Pathology, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
| | - Elizaveta Elshina
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Charlotte V. Rigby
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- University of Cambridge, Department of Pathology, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
- Public Health England, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
| | - Karishma Bisht
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Hamid Jalal
- Public Health England, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544
- Department of Chemistry, Princeton University, Princeton, NJ 08544
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27
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Sudzinová P, Šanderová H, Koval' T, Skálová T, Borah N, Hnilicová J, Kouba T, Dohnálek J, Krásný L. What the Hel: recent advances in understanding rifampicin resistance in bacteria. FEMS Microbiol Rev 2023; 47:fuac051. [PMID: 36549665 PMCID: PMC10719064 DOI: 10.1093/femsre/fuac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
Rifampicin is a clinically important antibiotic that binds to, and blocks the DNA/RNA channel of bacterial RNA polymerase (RNAP). Stalled, nonfunctional RNAPs can be removed from DNA by HelD proteins; this is important for maintenance of genome integrity. Recently, it was reported that HelD proteins from high G+C Actinobacteria, called HelR, are able to dissociate rifampicin-stalled RNAPs from DNA and provide rifampicin resistance. This is achieved by the ability of HelR proteins to dissociate rifampicin from RNAP. The HelR-mediated mechanism of rifampicin resistance is discussed here, and the roles of HelD/HelR in the transcriptional cycle are outlined. Moreover, the possibility that the structurally similar HelD proteins from low G+C Firmicutes may be also involved in rifampicin resistance is explored. Finally, the discovery of the involvement of HelR in rifampicin resistance provides a blueprint for analogous studies to reveal novel mechanisms of bacterial antibiotic resistance.
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Affiliation(s)
- Petra Sudzinová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Tomáš Koval'
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Tereza Skálová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Nabajyoti Borah
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Tomáš Kouba
- Cryogenic Electron Microscopy Research-Service Group, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16000 Prague, Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
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Kompaniiets D, Wang D, Yang Y, Hu Y, Liu B. Structure and molecular mechanism of bacterial transcription activation. Trends Microbiol 2023:S0966-842X(23)00290-1. [PMID: 37903670 DOI: 10.1016/j.tim.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 11/01/2023]
Abstract
Transcription activation is an important checkpoint of regulation of gene expression which occurs in response to different intracellular and extracellular signals. The key elements in this signal transduction process are transcription activators, which determine when and how gene expression is activated. Recent structural studies on a considerable number of new transcription activation complexes (TACs) revealed the remarkable mechanistic diversity of transcription activation mediated by different factors, necessitating a review and re-evaluation of the transcription activation mechanisms. In this review, we present a comprehensive summary of transcription activation mechanisms and propose a new, elaborate, and systematic classification of transcription activation mechanisms, primarily based on the structural features of diverse TAC components.
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Affiliation(s)
- Dmytro Kompaniiets
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Dong Wang
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Bin Liu
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
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29
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Reichelt R, Rothmeier T, Grünberger F, Willkomm S, Bruckmann A, Hausner W, Grohmann D. The archaeal Lsm protein from Pyrococcus furiosus binds co-transcriptionally to poly(U)-rich target RNAs. Biol Chem 2023; 404:1085-1100. [PMID: 37709673 DOI: 10.1515/hsz-2023-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Posttranscriptional processes in Bacteria include the association of small regulatory RNAs (sRNA) with a target mRNA. The sRNA/mRNA annealing process is often mediated by an RNA chaperone called Hfq. The functional role of bacterial and eukaryotic Lsm proteins is partially understood, whereas knowledge about archaeal Lsm proteins is scarce. Here, we used the genetically tractable archaeal hyperthermophile Pyrococcus furiosus to identify the protein interaction partners of the archaeal Sm-like proteins (PfuSmAP1) using mass spectrometry and performed a transcriptome-wide binding site analysis of PfuSmAP1. Most of the protein interaction partners we found are part of the RNA homoeostasis network in Archaea including ribosomal proteins, the exosome, RNA-modifying enzymes, but also RNA polymerase subunits, and transcription factors. We show that PfuSmAP1 preferentially binds messenger RNAs and antisense RNAs recognizing a gapped poly(U) sequence with high affinity. Furthermore, we found that SmAP1 co-transcriptionally associates with target RNAs. Our study reveals that in contrast to bacterial Hfq, PfuSmAP1 does not affect the transcriptional activity or the pausing behaviour of archaeal RNA polymerases. We propose that PfuSmAP1 recruits antisense RNAs to target mRNAs and thereby executes its putative regulatory function on the posttranscriptional level.
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Affiliation(s)
- Robert Reichelt
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Tamara Rothmeier
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Sarah Willkomm
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology (Biochemistry I), Protein Mass Spectrometry Laboratory, University of Regensburg, D-93053 Regensburg, Germany
| | - Winfried Hausner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, D-93053 Regensburg, Germany
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30
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Camp AH, Ellermeier CD. From regulation to ruin: a rogue sigma factor causes cell death in Bacillus subtilis. J Bacteriol 2023; 205:e0020323. [PMID: 37795990 PMCID: PMC10601719 DOI: 10.1128/jb.00203-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
A rogue, plasmid-encoded sigma factor that kills Bacillus subtilis is the focus of a new study by A. T. Burton, D. Pospíšilová, P. Sudzinová, E. V. Snider, A. M. Burrage, L. Krásný, and D. B. Kearns (J Bacteriol 205:e00112-23, 2023, https://doi.org/10.1128/jb.00112-23). The authors demonstrate that SigN is toxic in its own right, causing cell death by potently outcompeting the housekeeping sigma factor for access to RNA polymerase.
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Affiliation(s)
- Amy H. Camp
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts, USA
| | - Craig D. Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
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31
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Trouillon J, Doubleday PF, Sauer U. Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli. Cell Syst 2023; 14:860-871.e4. [PMID: 37820729 DOI: 10.1016/j.cels.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/01/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Our knowledge of transcriptional responses to changes in nutrient availability comes primarily from few well-studied transcription factors (TFs), often lacking an unbiased genome-wide perspective. Leveraging recent advances allowing bacterial genomic footprinting, we comprehensively mapped the genome-wide regulatory responses of Escherichia coli to exogenous leucine, methionine, alanine, and lysine. The global TF Lrp was found to individually sense three amino acids and mount three different target gene responses. Overall, 531 genes had altered RNA polymerase occupancy, and 32 TFs responded directly or indirectly to the presence of amino acids, including regulators of membrane and osmotic pressure homeostasis. About 70% of the detected TF-DNA interactions had not been reported before. We thus identified 682 previously unknown TF-binding locations, for a subset of which the involved TFs were identified by affinity purification. This comprehensive map of amino acid regulation illustrates the incompleteness of the known transcriptional regulation network, even in E. coli.
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Affiliation(s)
- Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Peter F Doubleday
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland.
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Peralta-Castro A, Cordoba-Andrade F, Díaz-Quezada C, Sotelo-Mundo R, Winkler R, Brieba LG. The plant organellar primase-helicase directs template recognition and primosome assembly via its zinc finger domain. BMC Plant Biol 2023; 23:467. [PMID: 37803262 PMCID: PMC10557236 DOI: 10.1186/s12870-023-04477-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND The mechanisms and regulation for DNA replication in plant organelles are largely unknown, as few proteins involved in replisome assembly have been biochemically studied. A primase-helicase dubbed Twinkle (T7 gp4-like protein with intramitochondrial nucleoid localization) unwinds double-stranded DNA in metazoan mitochondria and plant organelles. Twinkle in plants is a bifunctional enzyme with an active primase module. This contrast with animal Twinkle in which the primase module is inactive. The organellar primase-helicase of Arabidopsis thaliana (AtTwinkle) harbors a primase module (AtPrimase) that consists of an RNA polymerase domain (RPD) and a Zn + + finger domain (ZFD). RESULTS Herein, we investigate the mechanisms by which AtTwinkle recognizes its templating sequence and how primer synthesis and coupling to the organellar DNA polymerases occurs. Biochemical data show that the ZFD of the AtPrimase module is responsible for template recognition, and this recognition is achieved by residues N163, R166, and K168. The role of the ZFD in template recognition was also corroborated by swapping the RPDs of bacteriophage T7 primase and AtPrimase with their respective ZFDs. A chimeric primase harboring the ZFD of T7 primase and the RPD of AtPrimase synthesizes ribonucleotides from the T7 primase recognition sequence and conversely, a chimeric primase harboring the ZFD of AtPrimase and the RPD of T7 primase synthesizes ribonucleotides from the AtPrimase recognition sequence. A chimera harboring the RPDs of bacteriophage T7 and the ZBD of AtTwinkle efficiently synthesizes primers for the plant organellar DNA polymerase. CONCLUSIONS We conclude that the ZFD is responsible for recognizing a single-stranded sequence and for primer hand-off into the organellar DNA polymerases active site. The primase activity of plant Twinkle is consistent with phylogeny-based reconstructions that concluded that Twinkle´s last eukaryotic common ancestor (LECA) was an enzyme with primase and helicase activities. In plants, the primase domain is active, whereas the primase activity was lost in metazoans. Our data supports the notion that AtTwinkle synthesizes primers at the lagging-strand of the organellar replication fork.
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Affiliation(s)
- Antolin Peralta-Castro
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico
| | - Francisco Cordoba-Andrade
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico
| | - Corina Díaz-Quezada
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico
| | - Rogerio Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. Carretera Gustavo Enrique Astiazarán Rosas Núm. 46, Ejido a La Victoria, 83304, Hermosillo, Sonora, Mexico
| | - Robert Winkler
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico
| | - Luis G Brieba
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821, Irapuato Guanajuato, Mexico.
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Kędzierska-Mieszkowska S. Sigma factors of RNA polymerase in the pathogenic spirochaete Leptospira interrogans, the causative agent of leptospirosis. FASEB J 2023; 37:e23163. [PMID: 37688587 DOI: 10.1096/fj.202300252rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/13/2023] [Accepted: 08/14/2023] [Indexed: 09/11/2023]
Abstract
The aim of this review is to summarize the current knowledge on the role of σ factors in a highly invasive spirochaete Leptospira interrogans responsible for leptospirosis that affects many mammals, including humans. This disease has a significant impact on public health and the economy worldwide. In bacteria, σ factors are the key regulators of gene expression at the transcriptional level and therefore play an important role in bacterial adaptative response to different environmental stimuli. These factors form a holoenzyme with the RNA polymerase core enzyme and then direct it to specific promoters, which results in turning on selected genes. Most bacteria possess several different σ factors that enable them to maintain basal gene expression, as well as to regulate gene expression in response to specific environmental signals. Recent comparative genomics and in silico genome-wide analyses have revealed that the L. interrogans genome, consisting of two circular chromosomes, encodes a total of 14 σ factors. Among them, there is one putative housekeeping σ70 -like factor, and three types of alternative σ factors, i.e., one σ54 , one σ28 and 11 putative ECF (extracytoplasmic function) σE -type factors. Here, characteristics of these putative σ factors and their possible role in the L. interrogans gene regulation (especially in this pathogen's adaptive response to various environmental conditions, an important determinant of leptospiral virulence), are presented.
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Papadopoulos D, Uhl L, Ha SA, Eilers M. Beyond gene expression: how MYC relieves transcription stress. Trends Cancer 2023; 9:805-816. [PMID: 37422352 DOI: 10.1016/j.trecan.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023]
Abstract
MYC oncoproteins are key drivers of tumorigenesis. As transcription factors, MYC proteins regulate transcription by all three nuclear polymerases and gene expression. Accumulating evidence shows that MYC proteins are also crucial for enhancing the stress resilience of transcription. MYC proteins relieve torsional stress caused by active transcription, prevent collisions between the transcription and replication machineries, resolve R-loops, and repair DNA damage by participating in a range of protein complexes and forming multimeric structures at sites of genomic instability. We review the key complexes and multimerization properties of MYC proteins that allow them to mitigate transcription-associated DNA damage, and propose that the oncogenic functions of MYC extend beyond the modulation of gene expression.
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Affiliation(s)
- Dimitrios Papadopoulos
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University Hospital Würzburg, Würzburg, Germany
| | - Leonie Uhl
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stefanie Anh Ha
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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35
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Murase LS, Lima DDS, Souza JVPD, Palomo CT, Caleffi-Ferracioli KR, Scodro RBDL, Siqueira VLD, Seixas FAV, Cardoso RF. Binding of piperine to mycobacterial RNA polymerase improves the efficacy of rifampicin activity against Mycobacterium leprae and nontuberculous mycobacteria. J Biomol Struct Dyn 2023; 41:8671-8681. [PMID: 36255291 DOI: 10.1080/07391102.2022.2135602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/08/2022] [Indexed: 10/24/2022]
Abstract
Piperine (PPN) is a known inhibitor of efflux pumps in Mycobacterium tuberculosis and in vitro synergism with rifampicin (RIF) has been proven. The current study evaluates the activity of PPN and synergism with RIF in rapidly and slowly growing nontuberculous mycobacteria (NTM). Also, to propose a possible mechanism of interaction of PPN with M. leprae (Mlp) RNA polymerase (RNAp). Minimal inhibitory concentration and drug combination assay was determined by resazurin microtiter assay and resazurin drug combination assay, respectively. In silico evaluation of PPN binding was performed by molecular docking and molecular dynamics (MD). PPN showed higher antimicrobial activity against rapidly growing NTM (32-128 mg/L) rather than for slowly growing NTM (≥ 256 mg/L). Further, 77.8% of NTM tested exhibited FICI ≤ 0.5 when exposed to PPN and RIF combination, regardless of growth speed. Docking and MD simulations showed a possible PPN binding site at the interface between β and β' subunits of RNAp, in close proximity to the trigger-helix and bridge-helix elements. MD results indicated that PPN binding hindered the mobility of these elements, which are essential for RNA transcription. We hypothesize that PPN binding might affect mycobacterial RNAp activity, and, possibly, RIF activity and that this mechanism is partially responsible for synergic behaviors with RIF reported in vitro. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Letícia Sayuri Murase
- Postgraduate Program in Health Sciences, State University of Maringa, Maringa, Brazil
| | - Diego de Souza Lima
- Postgraduate Program in Biological Sciences, State University of Maringa, Maringa, Brazil
| | - João Vítor Perez de Souza
- Postgraduate Program in Biosciences and Physiopathology, State University of Maringa, Maringa, Brazil
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Thompson VF, Wieland DR, Mendoza-Leon V, Janis HI, Lay MA, Harrell LM, Schwartz JC. Binding of the nuclear ribonucleoprotein family member FUS to RNA prevents R-loop RNA:DNA hybrid structures. J Biol Chem 2023; 299:105237. [PMID: 37690693 PMCID: PMC10556777 DOI: 10.1016/j.jbc.2023.105237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
The protein FUS (FUSed in sarcoma) is a metazoan RNA-binding protein that influences RNA production by all three nuclear polymerases. FUS also binds nascent transcripts, RNA processing factors, RNA polymerases, and transcription machinery. Here, we explored the role of FUS binding interactions for activity during transcription. In vitro run-off transcription assays revealed FUS-enhanced RNA produced by a non-eukaryote polymerase. The activity also reduced the formation of R-loops between RNA products and their DNA template. Analysis by domain mutation and deletion indicated RNA-binding was required for activity. We interpret that FUS binds and sequesters nascent transcripts to prevent R-loops from forming with nearby DNA. DRIP-seq analysis showed that a knockdown of FUS increased R-loop enrichment near expressed genes. Prevention of R-loops by FUS binding to nascent transcripts has the potential to affect transcription by any RNA polymerase, highlighting the broad impact FUS can have on RNA metabolism in cells and disease.
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Affiliation(s)
- Valery F Thompson
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, Tucson, Arizona, USA
| | - Daniel R Wieland
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Vivian Mendoza-Leon
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Helen I Janis
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Michelle A Lay
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, Tucson, Arizona, USA; Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Lucas M Harrell
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Jacob C Schwartz
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, Tucson, Arizona, USA.
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37
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Dubrovin EV. Atomic force microscopy-based approaches for single-molecule investigation of nucleic acid- protein complexes. Biophys Rev 2023; 15:1015-1033. [PMID: 37974971 PMCID: PMC10643717 DOI: 10.1007/s12551-023-01111-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/07/2023] [Indexed: 11/19/2023] Open
Abstract
The interaction of nucleic acids with proteins plays an important role in many fundamental biological processes in living cells, including replication, transcription, and translation. Therefore, understanding nucleic acid-protein interaction is of high relevance in many areas of biology, medicine and technology. During almost four decades of its existence atomic force microscopy (AFM) accumulated a significant experience in investigation of biological molecules at a single-molecule level. AFM has become a powerful tool of molecular biology and biophysics providing unique information about properties, structure, and functioning of biomolecules. Despite a great variety of nucleic acid-protein systems under AFM investigations, there are a number of typical approaches for such studies. This review is devoted to the analysis of the typical AFM-based approaches of investigation of DNA (RNA)-protein complexes with a major focus on transcription studies. The basic strategies of AFM analysis of nucleic acid-protein complexes including investigation of the products of DNA-protein reactions and real-time dynamics of DNA-protein interaction are categorized and described by the example of the most relevant research studies. The described approaches and protocols have many universal features and, therefore, are applicable for future AFM studies of various nucleic acid-protein systems.
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Affiliation(s)
- Evgeniy V. Dubrovin
- Lomonosov Moscow State University, Leninskie Gory 1 Bld. 2, 119991 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny, 141700 Russian Federation
- Sirius University of Science and Technology, Olimpiyskiy Ave 1, Township Sirius, Krasnodar Region, 354349 Russia
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Romeo R, Legnani L, Chiacchio MA, Giofrè SV, Iannazzo D. Antiviral Compounds to Address Influenza Pandemics: An Update from 2016-2022. Curr Med Chem 2023; 31:CMC-EPUB-134322. [PMID: 37691217 DOI: 10.2174/0929867331666230907093501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/11/2023] [Accepted: 07/24/2023] [Indexed: 09/12/2023]
Abstract
In recent decades, the world has gained experience of the dangerous effects of pandemic events caused by emerging respiratory viruses. In particular, annual epidemics of influenza are responsible for severe illness and deaths. Even if conventional influenza vaccines represent the most effective tool for preventing virus infections, they are not completely effective in patients with severe chronic disease and immunocompromised and new small molecules have emerged to prevent and control the influenza viruses. Thus, the attention of chemists is continuously focused on the synthesis of new antiviral drugs able to interact with the different molecular targets involved in the virus replication cycle. To date, different classes of influenza viruses inhibitors able to target neuraminidase enzyme, hemagglutinin protein, Matrix-2 (M2) protein ion channel, nucleoprotein or RNA-dependent RNA polymerase have been synthesized using several synthetic strategies comprising the chemical modification of currently used drugs. The best results, in terms of inhibitory activity, are in the nanomolar range and have been obtained from the chemical modification of clinically used drugs such as Peramivir, Zanamivir, Oseltamir, Rimantadine, as well as sialylated molecules, and hydroxypyridinone derivatives. The aim of this review is to report, covering the period 2016-2022, the most recent routes related to the synthesis of effective influenza virus inhibitors.
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Affiliation(s)
- Roberto Romeo
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno D'Alcontres, 98166 Messina, Italy
| | - Laura Legnani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Maria Assunta Chiacchio
- Dipartimento di Scienze del Farmaco e della Salute, Università di Catania,Viale A. Doria 6, 95125 Catania, Italy
| | - Salvatore V Giofrè
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno D'Alcontres, 98166 Messina, Italy
| | - Daniela Iannazzo
- Dipartimento di Ingegneria, Università di Messina, Contrada di Dio, 98166 Messina, Italy
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Aleebrahim-Dehkordi E, Ghoshouni H, Koochaki P, Esmaili-Dehkordi M, Aleebrahim E, Chichagi F, Jafari A, Hanaei S, Heidari-Soureshjani E, Rezaei N. Targeting the vital non-structural proteins (NSP12, NSP7, NSP8 and NSP3) from SARS-CoV-2 and inhibition of RNA polymerase by natural bioactive compound naringenin as a promising drug candidate against COVID-19. J Mol Struct 2023; 1287:135642. [PMID: 37131962 PMCID: PMC10131750 DOI: 10.1016/j.molstruc.2023.135642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/04/2023]
Abstract
The prevalence of SARS-CoV-2-induced respiratory infections is now a major challenge worldwide. There is currently no specific antiviral drug to prevent or treat this disease. Infection with COVID-19 seriously needs to find effective therapeutic agents. In the present study, naringenin, as a potential inhibitor candidate for RNA Polymerase SARS-CoV-2 was compared with remdesivir (FDA-approved drug) and GS-441,524 (Derivative of the drug remdesivir) by screening with wild-type and mutant SARS-CoV-2 NSP12 (NSP7-NSP8) and NSP3 interfaces, then complexes were simulated by molecular dynamics (MD) simulations to gain their stabilities. The docking results displayed scores of -3.45 kcal/mol and -4.32 kcal/mol against NSP12 and NSP3, respectively. Our results showed that naringenin had ΔG values more negative than the ΔG values of Remdesivir (RDV) and GS-441,524. Hence, naringenin was considered to be a potential inhibitor. Also, the number of hydrogen bonds of naringenin with NSP3 and later NSP12 are more than Remdesivir and its derivative. In this research, Mean root mean square deviation (RMSD) values of NSP3 and NSP12with naringenin ligand (5.55±1.58 nm to 3.45±0.56 nm and 0.238±0.01 to 0.242±0.021 nm, respectively showed stability in the presence of ligand. The root mean square fluctuations (RMSF) values of NSP3 and NSP12 amino acid units in the presence of naringenin in were 1.5 ± 0.31 nm and 0.118±0.058, respectively. Pharmacokinetic properties and prediction of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of naringenin and RDV showed that these two compounds had no potential cytotoxicity.
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Affiliation(s)
- Elahe Aleebrahim-Dehkordi
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hamed Ghoshouni
- Medical student, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Pooneh Koochaki
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Elham Aleebrahim
- PhD Student in Food Sciences and Engineering, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Fatemeh Chichagi
- Research Development Center, Sina Hospital, Tehran University of Medical Science, Tehran, Iran
| | - Ali Jafari
- Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Student Research Committee, Department of Nutrition, School of Health, Golestan University of Medical Sciences, Gorgan, Iran
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Sara Hanaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ehsan Heidari-Soureshjani
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box. 115, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Nima Rezaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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40
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Tužinčin D, Padrta P, Šanderová H, Rabatinová A, Bendová K, Krásný L, Žídek L, Kadeřávek P. Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of σ A factor of RNA polymerase from Bacillus subtilis. Proteins 2023; 91:1276-1287. [PMID: 37350110 DOI: 10.1002/prot.26531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 06/24/2023]
Abstract
σ factors are essential parts of bacterial RNA polymerase (RNAP) as they allow to recognize promotor sequences and initiate transcription. Domain 1.1 of vegetative σ factors occupies the primary channel of RNAP and also prevents binding of the σ factor to promoter DNA alone. Here, we show that domain 1.1 of Bacillus subtilisσ A exists in more structurally distinct variants in dynamic equilibrium. The major conformation at room temperature is represented by a previously reported well-folded structure solved by nuclear magnetic resonance (NMR), but 4% of the protein molecules are present in a less thermodynamically favorable state. We show that this population increases with temperature and we predict its significant elevation at higher but still biologically relevant temperatures. We characterized the minor state of the domain 1.1 using specialized methods of NMR. We found that, in contrast to the major state, the detected minor state is partially unfolded. Its propensity to form secondary structure elements is especially decreased for the first and third α helices, while the second α helix and β strand close to the C-terminus are more stable. We also analyzed thermal unfolding of the domain 1.1 and performed functional experiments with full lengthσ A and its shortened version lacking domain 1.1 (σ A _ Δ 1.1 ). The results revealed that while full lengthσ A increases transcription activity of RNAP with increasing temperature, transcription withσ A _ Δ 1.1 remains constant. In summary, this study reveals conformational dynamics of domain 1.1 and provides a basis for studies of its interaction with RNAP and effects on transcription regulation.
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Affiliation(s)
- Dávid Tužinčin
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Petr Padrta
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Rabatinová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Kateřina Bendová
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Lukáš Žídek
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Pavel Kadeřávek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
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41
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Bhandari N, Acharya D, Chatterjee A, Mandve L, Kumar P, Pratap S, Malakar P, Shukla SK. Pan-cancer integrated bioinformatic analysis of RNA polymerase subunits reveal RNA Pol I member CD3EAP regulates cell growth by modulating autophagy. Cell Cycle 2023; 22:1986-2002. [PMID: 37795959 PMCID: PMC10761113 DOI: 10.1080/15384101.2023.2265676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
Transcription is a crucial stage in gene expression. An integrated study of 34 RNA polymerase subunits (RNAPS) in the six most frequent cancer types identified several genetic and epigenetic modification. We discovered nine mutant RNAPS with a mutation frequency of more than 1% in at least one tumor type. POLR2K and POLR2H were found to be amplified and overexpressed, whereas POLR3D was deleted and downregulated. Multiple RNAPS were also observed to be regulated by variations in promoter methylation. 5-Aza-2-deoxycytidine mediated re-expression in cell lines verified methylation-driven inhibition of POLR2F and POLR2L expression in BRCA and NSCLC, respectively. Next, we showed that CD3EAP, a Pol I subunit, was overexpressed in all cancer types and was associated with worst survival in breast, liver, lung, and prostate cancers. The knockdown studies showed that CD3EAP is required for cell proliferation and induces autophagy but not apoptosis. Furthermore, autophagy inhibition rescued the cell proliferation in CD3EAP knockdown cells. CD3EAP expression correlated with S and G2 phase cell cycle regulators, and CD3EAP knockdown inhibited the expression of S and G2 CDK/cyclins. We also identified POLR2D, an RNA pol II subunit, as a commonly overexpressed and prognostic gene in multiple cancers. POLR2D knockdown also decreased cell proliferation. POLR2D is related to the transcription of just a subset of RNA POL II transcribe genes, indicating a distinct role. Taken together, we have shown the genetic and epigenetic regulation of RNAPS genes in most common tumors. We have also demonstrated the cancer-specific function of CD3EAP and POLR2D genes.
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Affiliation(s)
- Nikita Bhandari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Disha Acharya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Annesha Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Lakshana Mandve
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Pranjal Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Shreesh Pratap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sudhanshu K. Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
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42
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O'Brien MJ, Gurdziel K, Ansari A. Global Run-On sequencing to measure nascent transcription in Saccharomyces cerevisiae. Methods 2023; 217:18-26. [PMID: 37356780 PMCID: PMC10529987 DOI: 10.1016/j.ymeth.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023] Open
Abstract
Global Run-On sequencing is a reliable and widely used approach for monitoring nascent transcription on a genomewide scale. The assay has been successfully used for studying global transcription in humans, plants, worms, flies, and fission yeast. Here we describe a GRO-seq protocol for studying transcription in budding yeast, Saccharomyces cerevisiae. Briefly, the technique involves permeabilization of actively growing yeast cells, allowing transcription to proceed in permeabilized cells in the presence of brominated UTP, affinity purification of bromo-UMP incorporated nascent transcripts followed by cDNA library construction, deep sequencing, and mapping against the reference genome. The approach maps the position of transcriptionally active RNA polymerase on a genomewide basis. In addition to identifying the complete set of transcriptionally active genes in a cell under a given set of conditions, the method can be used to determine elongation rate, termination defect and promoter directionality at the genomewide level. The approach is especially useful in identifying short-lived unstable transcripts that are rapidly degraded even before they leave the nucleus.
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Affiliation(s)
- Michael J O'Brien
- Department of Biological Science, Wayne State University, Detroit, MI 48202, USA
| | | | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI 48202, USA.
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Rigby CV, Sabsay KR, Bisht K, Eggink D, Jalal H, te Velthuis AJW. Evolution of transient RNA structure- RNA polymerase interactions in respiratory RNA virus genomes. Virus Evol 2023; 9:vead056. [PMID: 37692892 PMCID: PMC10492445 DOI: 10.1093/ve/vead056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/02/2023] [Accepted: 08/24/2023] [Indexed: 09/12/2023] Open
Abstract
RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and optimize their replication and spread in human cells. In IAV, adaptation occurs in all viral proteins, including the viral ribonucleoprotein (RNP) complex. RNPs consist of a copy of the viral RNA polymerase, a double-helical coil of nucleoprotein, and one of the eight segments of the IAV RNA genome. The RNA segments and their transcripts are partially structured to coordinate the packaging of the viral genome and modulate viral mRNA translation. In addition, RNA structures can affect the efficiency of viral RNA synthesis and the activation of host innate immune response. Here, we investigated if RNA structures that modulate IAV replication processivity, so-called template loops (t-loops), vary during the adaptation of pandemic and emerging IAV to humans. Using cell culture-based replication assays and in silico sequence analyses, we find that the sensitivity of the IAV H3N2 RNA polymerase to t-loops increased between isolates from 1968 and 2017, whereas the total free energy of t-loops in the IAV H3N2 genome was reduced. This reduction is particularly prominent in the PB1 gene. In H1N1 IAV, we find two separate reductions in t-loop free energy, one following the 1918 pandemic and one following the 2009 pandemic. No destabilization of t-loops is observed in the influenza B virus genome, whereas analysis of SARS-CoV-2 isolates reveals destabilization of viral RNA structures. Overall, we propose that a loss of free energy in the RNA genome of emerging respiratory RNA viruses may contribute to the adaption of these viruses to the human population.
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Affiliation(s)
- Charlotte V Rigby
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
- Addenbrooke’s Hospital, Public Health England, Hills Road, Cambridge CB2 2QQ, UK
| | - Kimberly R Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Carl Icahn Laboratory, Lewis-Sigler Institute, Princeton University, South Drive, Princeton, NJ 08544, USA
| | - Karishma Bisht
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
| | - Hamid Jalal
- Addenbrooke’s Hospital, Public Health England, Hills Road, Cambridge CB2 2QQ, UK
| | - Aartjan J W te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands
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44
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Zhao M, Gao B, Wen A, Feng Y, Lu YQ. Structural basis of λCII-dependent transcription activation. Structure 2023; 31:968-974.e3. [PMID: 37269829 DOI: 10.1016/j.str.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 06/05/2023]
Abstract
The CII protein of bacteriophage λ activates transcription from the phage promoters PRE, PI, and PAQ by binding to two direct repeats that straddle the promoter -35 element. Although genetic, biochemical, and structural studies have elucidated many aspects of λCII-mediated transcription activation, no precise structure of the transcription machinery in the process is available. Here, we report a 3.1-Å cryo-electron microscopy (cryo-EM) structure of an intact λCII-dependent transcription activation complex (TAC-λCII), which comprises λCII, E. coli RNAP-σ70 holoenzyme, and the phage promoter PRE. The structure reveals the interactions between λCII and the direct repeats responsible for promoter specificity and the interactions between λCII and RNAP α subunit C-terminal domain responsible for transcription activation. We also determined a 3.4-Å cryo-EM structure of an RNAP-promoter open complex (RPo-PRE) from the same dataset. Structural comparison between TAC-λCII and RPo-PRE provides new insights into λCII-dependent transcription activation.
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Affiliation(s)
- Minxing Zhao
- Department of Emergency Medicine of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Bo Gao
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Aijia Wen
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Immunity and Inflammatory Diseases, Hangzhou 310058, China.
| | - Yuan-Qiang Lu
- Department of Emergency Medicine of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
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Morozov SY, Lezzhov AA, Solovyev AG. Predicted Membrane-Associated Domains in Proteins Encoded by Novel Monopartite Plant RNA Viruses Related to Members of the Family Benyviridae. Int J Mol Sci 2023; 24:12161. [PMID: 37569537 PMCID: PMC10418960 DOI: 10.3390/ijms241512161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
As a continuation of our previous work, in this paper, we examine in greater detail the genome organization and some protein properties of the members of a potential group named Reclovirids and belonging to Benyviridae-related viruses. It can be proposed that the single-component Reclovirid genomes encode previously undiscovered transport genes. Indeed, analysis of the coding potential of these novel viral genomes reveals one or more cistrons ranging in size from 40 to 80 to about 600 codons, located in the 3'-terminal region of the genomic RNA, encoding proteins with predicted hydrophobic segments that are structurally diverse among Reclovirids and have no analogues in other plant RNA viruses. Additionally, in many cases, the possible methyltransferase domain of Reclovirid replicases is preceded by membrane-embedded protein segments that are not present in annotated members of the Benyviridae family. These observations suggest a general association of most Reclovirid proteins with cell membranes.
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Affiliation(s)
- Sergey Y. Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia; (A.A.L.); (A.G.S.)
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - Alexander A. Lezzhov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia; (A.A.L.); (A.G.S.)
| | - Andrey G. Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia; (A.A.L.); (A.G.S.)
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
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Malagoda Pathiranage K, Martin CT. A simple approach to improving RNA synthesis: Salt inhibition of RNA rebinding coupled with strengthening promoter binding by a targeted gap in the DNA. Methods Enzymol 2023; 691:209-222. [PMID: 37914447 DOI: 10.1016/bs.mie.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
T7 RNA polymerase is widely used to synthesize RNA of any length, and long-standing protocols exist to efficiently generate large amounts of RNA. Such synthesis, however, is often plagued by so-called "nontemplated additions" at the 3' end, which are in fact templated by the RNA itself and give rise to double-stranded RNA impurities in RNA therapeutics. These additions are generated by RNA polymerase rebinding to the product RNA (independent of DNA) and this rebinding is in competition with promoter binding. This chapter reports on a general approach that simultaneously weakens RNA rebinding by increasing salt, while at the same time increases promoter binding through manipulating the promoter DNA structure, shifting the balance away from self-primed extension. We present two approaches for use in different regimes. For (short) RNAs using synthetic oligonucleotides as DNA, promoter binding is strengthened by using a partially single stranded promoter construct already in wide use in the field. For the synthesis of RNA (of any length), one can replicate the behavior of the first approach by introducing a targeted gap in the promoter, using a PCR primer containing an engineered deoxyuracil that is then excised by a commercially available enzyme system, to leave a promoter-strengthening gap. Both approaches are simple to implement, with only slight variations on standard synthesis approaches, making them valuable tools for a wide range of applications, from basic science to mRNA, CRISPR, lncRNA, and other therapeutics.
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Affiliation(s)
| | - Craig T Martin
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, United States.
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Scull CE, Twa G, Zhang Y, Yang NJ, Hunter RN, Augelli-Szafran CE, Schneider DA. Small Molecule RBI2 Disrupts Ribosome Biogenesis through Pre-rRNA Depletion. Cancers (Basel) 2023; 15:3303. [PMID: 37444413 PMCID: PMC10340317 DOI: 10.3390/cancers15133303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Cancer cells are especially sensitive to perturbations in ribosome biogenesis as they rely on finely tuned protein homeostasis to facilitate their rapid growth and proliferation. While ribosome synthesis and cancer have a well-established relationship, ribosome biogenesis has only recently drawn interest as a cancer therapeutic target. In this study, we exploited the relationship between ribosome biogenesis and cancer cell proliferation by using a potent ribosome biogenesis inhibitor, RBI2 (Ribosome Biogenesis Inhibitor 2), to perturb cancer cell growth and viability. We demonstrate herein that RBI2 significantly decreases cell viability in malignant melanoma cells and breast cancer cell lines. Treatment with RBI2 dramatically and rapidly decreased ribosomal RNA (rRNA) synthesis, without affecting the occupancy of RNA polymerase I (Pol I) on the ribosomal DNA template. Next-generation RNA sequencing (RNA-seq) revealed that RBI2 and previously described ribosome biogenesis inhibitor CX-5461 induce distinct changes in the transcriptome. An investigation of the content of the pre-rRNAs through RT-qPCR revealed an increase in the polyadenylation of cellular rRNA after treatment with RBI2, constituting a known pathway by which rRNA degradation occurs. Northern blotting revealed that RBI2 does not appear to impair or alter rRNA processing. Collectively, these data suggest that RBI2 inhibits rRNA synthesis differently from other previously described ribosome biogenesis inhibitors, potentially acting through a novel pathway that upregulates the turnover of premature rRNAs.
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Affiliation(s)
- Catherine E. Scull
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy Twa
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Naiheng J. Yang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | | | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Neves RPD, Chagoyen M, Martinez-Lorente A, Iñiguez C, Calatrava A, Calabuig J, Iborra FJ. Each Cellular Compartment Has a Characteristic Protein Reactive Cysteine Ratio Determining Its Sensitivity to Oxidation. Antioxidants (Basel) 2023; 12:1274. [PMID: 37372004 DOI: 10.3390/antiox12061274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Signaling and detoxification of Reactive Oxygen Species (ROS) are important patho-physiologcal processes. Despite this, we lack comprehensive information on individual cells and cellular structures and functions affected by ROS, which is essential to build quantitative models of the effects of ROS. The thiol groups from cysteines (Cys) in proteins play a major role in redox defense, signaling, and protein function. In this study, we show that the proteins in each subcellular compartment contain a characteristic Cys amount. Using a fluorescent assay for -SH in thiolate form and amino groups in proteins, we show that the thiolate content correlates with ROS sensitivity and signaling properties of each compartment. The highest absolute thiolate concentration was found in the nucleolus, followed by the nucleoplasm and cytoplasm whereas protein thiolate groups per protein showed an inverse pattern. In the nucleoplasm, protein reactive thiols concentrated in SC35 speckles, SMN, and the IBODY that accumulated oxidized RNA. Our findings have important functional consequences, and explain differential sensitivity to ROS.
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Affiliation(s)
- Ricardo Pires das Neves
- Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
- IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mónica Chagoyen
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | - Antonio Martinez-Lorente
- Unidad de Investigación, Innovación y Docencia Médica, Hospital Universitario Vinalopó, 03293 Elx, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 Valencia, Spain
- Department of Biotecnology, University of Alicante, 03690 Alicante, Spain
| | - Carlos Iñiguez
- Department of Biotecnology, University of Alicante, 03690 Alicante, Spain
| | - Ana Calatrava
- Department of Pathology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain
| | | | - Francisco J Iborra
- Instituto de Biomedicina de Valencia, CSIC, Jaime Roig 11, 46010 Valencia, Spain
- Centro de Investigación Príncipe Felipe (CIPF), Primo Yufera 3, 46012 Valencia, Spain
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Calil Brondani J, Afful D, Nune H, Hart J, Cook S, Momany C. Overproduction, purification, and transcriptional activity of recombinant Acinetobacter baylyi ADP1 RNA polymerase holoenzyme. Protein Expr Purif 2023; 206:106254. [PMID: 36804950 DOI: 10.1016/j.pep.2023.106254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Acinetobacter baylyi is an interesting model organism to investigate bacterial metabolism due to its vast repertoire of metabolic enzymes and ease of genetic manipulation. However, the study of gene expression in vitro is dependent on the availability of its RNA polymerase (RNAp), an essential enzyme in transcription. In this work, we developed a convenient method of producing the recombinant A. baylyi ADP1 RNA polymerase holoenzyme (RNApholo) in E. coli that yields 22 mg of a >96% purity protein from a 1-liter shake flask culture. We further characterized the A. baylyi ADP1 RNApholo kinetic profile using T7 Phage DNA as template and demonstrated that it is a highly transcriptionally active enzyme with an elongation rate of 24 nt/s and a termination efficiency of 94%. Moreover, the A. baylyi ADP1 RNApholo has a substantial sequence identity (∼95%) with the RNApholo from the human pathogen Acinetobacter baumannii. This protein can serve as a source of material for structural and biological studies towards advancing our understanding of genome expression and regulation in Acinetobacter species.
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Affiliation(s)
- Juliana Calil Brondani
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Derrick Afful
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Hanna Nune
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Jesse Hart
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Shelby Cook
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Cory Momany
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA.
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50
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Hao N, Donnelly AJ, Dodd IB, Shearwin KE. When push comes to shove - RNA polymerase and DNA-bound protein roadblocks. Biophys Rev 2023; 15:355-366. [PMID: 37396453 PMCID: PMC10310618 DOI: 10.1007/s12551-023-01064-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 07/04/2023] Open
Abstract
In recent years, transcriptional roadblocking has emerged as a crucial regulatory mechanism in gene expression, whereby other DNA-bound obstacles can block the progression of transcribing RNA polymerase (RNAP), leading to RNAP pausing and ultimately dissociation from the DNA template. In this review, we discuss the mechanisms by which transcriptional roadblocks can impede RNAP progression, as well as how RNAP can overcome these obstacles to continue transcription. We examine different DNA-binding proteins involved in transcriptional roadblocking and their biophysical properties that determine their effectiveness in blocking RNAP progression. The catalytically dead CRISPR-Cas (dCas) protein is used as an example of an engineered programmable roadblock, and the current literature in understanding the polarity of dCas roadblocking is also discussed. Finally, we delve into a stochastic model of transcriptional roadblocking and highlight the importance of transcription factor binding kinetics and its resistance to dislodgement by an elongating RNAP in determining the strength of a roadblock.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Alana J. Donnelly
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Ian B. Dodd
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Keith E. Shearwin
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
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