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Thongchol J, Yu Z, Harb L, Lin Y, Koch M, Theodore M, Narsaria U, Shaevitz J, Gitai Z, Wu Y, Zhang J, Zeng L. Removal of Pseudomonas type IV pili by a small RNA virus. Science 2024; 384:eadl0635. [PMID: 38574145 PMCID: PMC11126211 DOI: 10.1126/science.adl0635] [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: 09/29/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen Pseudomonas aeruginosa. The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics.
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Affiliation(s)
- Jirapat Thongchol
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Zihao Yu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Laith Harb
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Yiruo Lin
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Matthias Koch
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew Theodore
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Utkarsh Narsaria
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Joshua Shaevitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, NY 10461, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
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Thongchol J, Lill Z, Hoover Z, Zhang J. Recent Advances in Structural Studies of Single-Stranded RNA Bacteriophages. Viruses 2023; 15:1985. [PMID: 37896763 PMCID: PMC10610835 DOI: 10.3390/v15101985] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Positive-sense single-stranded RNA (ssRNA) bacteriophages (phages) were first isolated six decades ago. Since then, extensive research has been conducted on these ssRNA phages, particularly those infecting E. coli. With small genomes of typically 3-4 kb that usually encode four essential proteins, ssRNA phages employ a straightforward infectious cycle involving host adsorption, genome entry, genome replication, phage assembly, and host lysis. Recent advancements in metagenomics and transcriptomics have led to the identification of ~65,000 sequences from ssRNA phages, expanding our understanding of their prevalence and potential hosts. This review article illuminates significant investigations into ssRNA phages, with a focal point on their structural aspects, providing insights into the various stages of their infectious cycle.
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Affiliation(s)
| | | | | | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; (J.T.); (Z.L.); (Z.H.)
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Wang J, Yashiro Y, Sakaguchi Y, Suzuki T, Tomita K. Mechanistic insights into tRNA cleavage by a contact-dependent growth inhibitor protein and translation factors. Nucleic Acids Res 2022; 50:4713-4731. [PMID: 35411396 PMCID: PMC9071432 DOI: 10.1093/nar/gkac228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
Contact-dependent growth inhibition is a mechanism of interbacterial competition mediated by delivery of the C-terminal toxin domain of CdiA protein (CdiA–CT) into neighboring bacteria. The CdiA–CT of enterohemorrhagic Escherichia coli EC869 (CdiA–CTEC869) cleaves the 3′-acceptor regions of specific tRNAs in a reaction that requires the translation factors Tu/Ts and GTP. Here, we show that CdiA–CTEC869 has an intrinsic ability to recognize a specific sequence in substrate tRNAs, and Tu:Ts complex promotes tRNA cleavage by CdiA–CTEC869. Uncharged and aminoacylated tRNAs (aa-tRNAs) were cleaved by CdiA–CTEC869 to the same extent in the presence of Tu/Ts, and the CdiA–CTEC869:Tu:Ts:tRNA(aa-tRNA) complex formed in the presence of GTP. CdiA–CTEC869 interacts with domain II of Tu, thereby preventing the 3′-moiety of tRNA to bind to Tu as in canonical Tu:GTP:aa-tRNA complexes. Superimposition of the Tu:GTP:aa-tRNA structure onto the CdiA–CTEC869:Tu structure suggests that the 3′-portion of tRNA relocates into the CdiA–CTEC869 active site, located on the opposite side to the CdiA–CTEC869 :Tu interface, for tRNA cleavage. Thus, CdiA–CTEC869 is recruited to Tu:GTP:Ts, and CdiA–CT:Tu:GTP:Ts recognizes substrate tRNAs and cleaves them. Tu:GTP:Ts serves as a reaction scaffold that increases the affinity of CdiA–CTEC869 for substrate tRNAs and induces a structural change of tRNAs for efficient cleavage by CdiA–CTEC869.
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Affiliation(s)
- Jing Wang
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa,Chiba277-8562, Japan
| | - Yuka Yashiro
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa,Chiba277-8562, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa,Chiba277-8562, Japan
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Lund PE, Chatterjee S, Daher M, Walter NG. Protein unties the pseudoknot: S1-mediated unfolding of RNA higher order structure. Nucleic Acids Res 2020; 48:2107-2125. [PMID: 31832686 PMCID: PMC7038950 DOI: 10.1093/nar/gkz1166] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022] Open
Abstract
Ribosomal protein S1 plays important roles in the translation initiation step of many Escherichia coli mRNAs, particularly those with weak Shine-Dalgarno sequences or structured 5′ UTRs, in addition to a variety of cellular processes beyond the ribosome. In all cases, the RNA-binding activity of S1 is a central feature of its function. While sequence determinants of S1 affinity and many elements of the interactions of S1 with simple secondary structures are known, mechanistic details of the protein's interactions with RNAs of more complex secondary and tertiary structure are less understood. Here, we investigate the interaction of S1 with the well-characterized H-type pseudoknot of a class-I translational preQ1 riboswitch as a highly structured RNA model whose conformation and structural dynamics can be tuned by the addition of ligands of varying binding affinity, particularly preQ1, guanine, and 2,6-diaminopurine. Combining biochemical and single molecule fluorescence approaches, we show that S1 preferentially interacts with the less folded form of the pseudoknot and promotes a dynamic, partially unfolded conformation. The ability of S1 to unfold the RNA is inversely correlated with the structural stability of the pseudoknot. These mechanistic insights delineate the scope and limitations of S1-chaperoned unfolding of structured RNAs.
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Affiliation(s)
- Paul E Lund
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Surajit Chatterjee
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - May Daher
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
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Abstract
ssRNA phages belonging to the family Leviviridae are among the tiniest viruses, infecting various Gram-negative bacteria by adsorption to their pilus structures. Due to their simplicity, they have been intensively studied as models for understanding various problems in molecular biology and virology. Several of the studied ssRNA characteristics, such as coat protein–RNA interactions and the ability to readily form virus-like particles in recombinant expression systems, have fueled many practical applications such as RNA labeling and tracking systems and vaccine development. In this chapter, we review the life cycle, structure and applications of these small yet fascinating viruses.
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Attenuation of Live-Attenuated Yellow Fever 17D Vaccine Virus Is Localized to a High-Fidelity Replication Complex. mBio 2019; 10:mBio.02294-19. [PMID: 31641088 PMCID: PMC6805994 DOI: 10.1128/mbio.02294-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Live-attenuated viral vaccines are highly safe and efficacious but represent complex and often multigenic attenuation mechanisms. Most of these vaccines have been generated empirically by serial passaging of a wild-type (WT) virus in cell culture. One of the safest and most effective live-attenuated vaccines is yellow fever (YF) virus strain 17D, which has been used for over 80 years to control YF disease. The availability of the WT parental strain of 17D, Asibi virus, and large quantities of clinical data showing the effectiveness of the 17D vaccine make this WT parent/vaccine pair an excellent model for investigating RNA virus attenuation. Here, we investigate a mechanism of 17D attenuation and show that the vaccine virus is resistant to the antiviral compound ribavirin. The findings suggest that attenuation is in part due to a low probability of reversion or mutation of the vaccine virus genome to WT, thus maintaining a stable genotype despite external pressures. The molecular basis of attenuation for live-attenuated vaccines is poorly understood. The yellow fever (YF) 17D vaccine virus was derived from the wild-type, parental strain Asibi virus by serial passage in chicken tissue and has proven to be a very safe and efficacious vaccine. We have previously shown that wild-type Asibi is a typical RNA virus with high genetic diversity, while the 17D vaccine virus has very little genetic diversity. To investigate this further, we treated Asibi and 17D viruses with ribavirin, a GTP analog with strong antiviral activity that increases levels of mutations in the viral genome. As expected, ribavirin treatment introduced mutations into the Asibi virus genome at a very high frequency and decreased viral infectivity while, in contrast, the 17D vaccine virus was resistant to ribavirin, as treatment with the antiviral introduced very few mutations into the genome, and viral infectivity was not lost. The results were confirmed for another YF wild-type parental and vaccine pair, a wild-type French viscerotropic virus and French neurotropic vaccine. Using recombinant Asibi and 17D viruses, ribavirin sensitivity was located to viral nonstructural genes. Thus, two live-attenuated YF vaccine viruses are genetically stable even under intense mutagenic pressure, suggesting that attenuation of live-attenuated YF vaccines is due, at least in part, to fidelity of the replication complex resulting in high genetic stability.
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Kutlubaeva ZS, Chetverina HV, Chetverin AB. The Contribution of Ribosomal Protein S1 to the Structure and Function of Qβ Replicase. Acta Naturae 2017; 9:24-30. [PMID: 29340214 PMCID: PMC5762825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Indexed: 10/28/2022] Open
Abstract
The high resolution crystal structure of bacterial ribosome was determined more than 10 years ago; however, it contains no information on the structure of the largest ribosomal protein, S1. This unusual protein comprises six flexibly linked domains; therefore, it lacks a fixed structure and this prevents the formation of crystals. Besides being a component of the ribosome, protein S1 also serves as one of the four subunits of Qβ replicase, the RNA-directed RNA polymerase of bacteriophage Qβ. In each case, the role of this RNA-binding protein has been thought to consist in holding the template close to the active site of the enzyme. In recent years, a breakthrough was made in studies of protein S1 within Qβ replicase. This includes the discovery of its paradoxical ability to displace RNA from the replicase complex and determining the crystal structure of its fragment capable of performing this function. The new findings call for a re-examination of the contribution of protein S1 to the structure and function of the ribosome.
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Affiliation(s)
- Z. S. Kutlubaeva
- Institute of Protein Research, Institutskaya Str. 4, Pushchino, Moscow, 142290, Russia
| | - H. V. Chetverina
- Institute of Protein Research, Institutskaya Str. 4, Pushchino, Moscow, 142290, Russia
| | - A. B. Chetverin
- Institute of Protein Research, Institutskaya Str. 4, Pushchino, Moscow, 142290, Russia
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Usui K, Ichihashi N, Yomo T. A design principle for a single-stranded RNA genome that replicates with less double-strand formation. Nucleic Acids Res 2015. [PMID: 26202975 PMCID: PMC4652763 DOI: 10.1093/nar/gkv742] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Single-stranded RNA (ssRNA) is the simplest form of genetic molecule and constitutes the genome in some viruses and presumably in primitive life-forms. However, an innate and unsolved problem regarding the ssRNA genome is formation of inactive double-stranded RNA (dsRNA) during replication. Here, we addressed this problem by focusing on the secondary structure. We systematically designed RNAs with various structures and observed dsRNA formation during replication using an RNA replicase (Qβ replicase). From the results, we extracted a simple rule regarding ssRNA genome replication with less dsRNA formation (less GC number in loops) and then designed an artificial RNA that encodes a domain of the β-galactosidase gene based on this rule. We also obtained evidence that this rule governs the natural genomes of all bacterial and most fungal viruses presently known. This study revealed one of the structural design principles of an ssRNA genome that replicates continuously with less dsRNA formation.
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Affiliation(s)
- Kimihito Usui
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norikazu Ichihashi
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
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