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Tipo J, Gottipati K, Slaton M, Gonzalez-Gutierrez G, Choi KH. Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site. Nat Commun 2024; 15:4198. [PMID: 38760344 PMCID: PMC11101469 DOI: 10.1038/s41467-024-48162-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/22/2024] [Indexed: 05/19/2024] Open
Abstract
During HIV infection, specific RNA-protein interaction between the Rev response element (RRE) and viral Rev protein is required for nuclear export of intron-containing viral mRNA transcripts. Rev initially binds the high-affinity site in stem-loop II, which promotes oligomerization of additional Rev proteins on RRE. Here, we present the crystal structure of RRE stem-loop II in distinct closed and open conformations. The high-affinity Rev-binding site is located within the three-way junction rather than the predicted stem IIB. The closed and open conformers differ in their non-canonical interactions within the three-way junction, and only the open conformation has the widened major groove conducive to initial Rev interaction. Rev binding assays show that RRE stem-loop II has high- and low-affinity binding sites, each of which binds a Rev dimer. We propose a binding model, wherein Rev-binding sites on RRE are sequentially created through structural rearrangements induced by Rev-RRE interactions.
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Affiliation(s)
- Jerricho Tipo
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX, 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Keerthi Gottipati
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Michael Slaton
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | | | - Kyung H Choi
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, TX, 77555, USA.
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2
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Kretsch RC, Xu L, Zheludev IN, Zhou X, Huang R, Nye G, Li S, Zhang K, Chiu W, Das R. Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. Proc Natl Acad Sci U S A 2024; 121:e2320493121. [PMID: 38427602 DOI: 10.1073/pnas.2320493121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/05/2024] [Indexed: 03/03/2024] Open
Abstract
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T's "arms." Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.
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Affiliation(s)
| | - Lily Xu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Ivan N Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Xueting Zhou
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305
| | - Rui Huang
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Grace Nye
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Shanshan Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kaiming Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Wah Chiu
- Biophysics Program, Stanford University, Stanford, CA 94305
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
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3
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Zhang J. Recognition of the tRNA structure: Everything everywhere but not all at once. Cell Chem Biol 2024; 31:36-52. [PMID: 38159570 PMCID: PMC10843564 DOI: 10.1016/j.chembiol.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/02/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
tRNAs are among the most abundant and essential biomolecules in cells. These spontaneously folding, extensively structured yet conformationally flexible anionic polymers literally bridge the worlds of RNAs and proteins, and serve as Rosetta stones that decipher and interpret the genetic code. Their ubiquitous presence, functional irreplaceability, and privileged access to cellular compartments and ribosomes render them prime targets for both endogenous regulation and exogenous manipulation. There is essentially no part of the tRNA that is not touched by another interaction partner, either as programmed or imposed by an external adversary. Recent progresses in genetic, biochemical, and structural analyses of the tRNA interactome produced a wealth of new knowledge into their interaction networks, regulatory functions, and molecular interfaces. In this review, I describe and illustrate the general principles of tRNA recognition by proteins and other RNAs, and discuss the underlying molecular mechanisms that deliver affinity, specificity, and functional competency.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
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4
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Abram QH, Landry BN, Wang AB, Kothe RF, Hauch HC, Sagan SM. The myriad roles of RNA structure in the flavivirus life cycle. RNA Biol 2024; 21:14-30. [PMID: 38797925 PMCID: PMC11135854 DOI: 10.1080/15476286.2024.2357857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
As positive-sense RNA viruses, the genomes of flaviviruses serve as the template for all stages of the viral life cycle, including translation, replication, and infectious particle production. Yet, they encode just 10 proteins, suggesting that the structure and dynamics of the viral RNA itself helps shepherd the viral genome through these stages. Herein, we highlight advances in our understanding of flavivirus RNA structural elements through the lens of their impact on the viral life cycle. We highlight how RNA structures impact translation, the switch from translation to replication, negative- and positive-strand RNA synthesis, and virion assembly. Consequently, we describe three major themes regarding the roles of RNA structure in flavivirus infections: 1) providing a layer of specificity; 2) increasing the functional capacity; and 3) providing a mechanism to support genome compaction. While the interactions described herein are specific to flaviviruses, these themes appear to extend more broadly across RNA viruses.
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Affiliation(s)
- Quinn H. Abram
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Breanna N. Landry
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B. Wang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ronja F. Kothe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Hannah C.H. Hauch
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M. Sagan
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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5
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Chen K, Zhou Y, Wang S, Xiong P. RNA tertiary structure modeling with BRiQ potential in CASP15. Proteins 2023; 91:1771-1778. [PMID: 37638558 DOI: 10.1002/prot.26574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/22/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023]
Abstract
We describe the modeling method for RNA tertiary structures employed by team AIchemy_RNA2 in the 15th Critical Assessment of Structure Prediction (CASP15). The method consists of the following steps. Firstly, secondary structure information was derived from various manually-verified sources. With this information, the full length RNA was fragmented into structural modules. The structures of each module were predicted and then assembled into the full structure. To reduce the searching conformational space, an RNA structure was organized into an optimal base folding tree. And to further improve the sampling efficiency, the energy surface was smoothed at high temperatures during the Monte Carlo sampling to make it easier to move across the energy barrier. The statistical potential energy function BRiQ was employed during Monte Carlo energy optimization.
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Affiliation(s)
- Ke Chen
- University of Science and Technology of China, Hefei, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China
| | - Yaoqi Zhou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Co. Ltd, Shanghai, China
| | - Peng Xiong
- University of Science and Technology of China, Hefei, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China
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6
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Kretsch RC, Xu L, Zheludev IN, Zhou X, Huang R, Nye G, Li S, Zhang K, Chiu W, Das R. Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.567964. [PMID: 38076883 PMCID: PMC10705266 DOI: 10.1101/2023.11.22.567964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically-determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus SARS-CoV-2, resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T's "arms." Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4-6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across the studied human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9-8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4-9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities, with implications for potential protein-binding modes and therapeutic targets.
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Affiliation(s)
| | - Lily Xu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Ivan N. Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Xueting Zhou
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Rui Huang
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Grace Nye
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Shanshan Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kaiming Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Wah Chiu
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
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