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Sanders C, Dzelamonyuy A, Ntemafack A, Alatoom N, Nchinda G, Georgiadis MM, Bopda Waffo A. Mapping immunological and host receptor binding determinants of SARS-CoV spike protein utilizing the Qubevirus platform. J Biol Chem 2023; 299:105460. [PMID: 37977224 PMCID: PMC10750099 DOI: 10.1016/j.jbc.2023.105460] [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: 08/03/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
The motifs involved in tropism and immunological interactions of SARS-CoV spike (S) protein were investigated utilizing the Qubevirus platform. We showed that separately, 14 overlapping peptide fragments representing the S protein (F1-14 of 100 residues each) could be inserted into the C terminus of A1 on recombinant Qubevirus without affecting its viability. Additionally, recombinant phage expression resulted in the surface exposure of different engineered fragments in an accessible manner. The F6 from S425-525 was found to contain the binding determinant of the recombinant human angiotensin-converting enzyme 2, with the shortest active binding motif situated between residues S437-492. Upstream, another fragment, F7, containing an overlapping portion of F6 would not bind to recombinant human angiotensin-converting enzyme 2, confirming that a contiguous stretch of residues could adopt the appropriate structural orientation of F6 as an insertion within the Qubevirus. The F6 (S441-460) and other inserts, including F7/F8 (S601-620) and F10 (S781-800), were demonstrated to contain important immunological determinants through recognition and binding of S protein specific (anti-S) antibodies. An engineered chimeric insert bearing the fusion of all three anti-S reactive epitopes improved substantially the recognition and binding to their cognate antibodies. These results provide insights into humoral immune relevant epitopes and tropism characteristics of the S protein with implications for the development of subunit vaccines or other biologics against SARS-CoV.
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Affiliation(s)
- Carrie Sanders
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Disease, Center for Disease Control, Atlanta, Georgia, USA
| | - Aristide Dzelamonyuy
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Augustin Ntemafack
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nadia Alatoom
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Godwin Nchinda
- Department of Immunology, Laboratory of Vaccinology and Biobanking, Yaoundé, Cameroon
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Alain Bopda Waffo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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Su-Tobon Q, Fan J, Feeney K, Ren H, Autissier P, Wang P, Huang Y, Niu J. CRISPR-Hybrid: A CRISPR-Mediated Intracellular Directed Evolution Platform for RNA Aptamers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555185. [PMID: 37693461 PMCID: PMC10491168 DOI: 10.1101/2023.08.29.555185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Recent advances in gene editing and precise regulation of gene expression based on CRISPR technologies have provided powerful tools for the understanding and manipulation of gene functions. Fusing RNA aptamers to the sgRNA of CRISPR can recruit cognate RNA-binding protein (RBP) effectors to target genomic sites, and the expression of sgRNA containing different RNA aptamers permit simultaneous multiplexed and multifunctional gene regulations. Here, we report an intracellular directed evolution platform for RNA aptamers against intracellularly expressed RBPs. We optimized a bacterial CRISPR-hybrid system coupled with FACS, and identified novel high affinity RNA aptamers orthogonal to existing aptamer-RBP pairs. Application of orthogonal aptamer-RBP pairs in multiplexed CRISPR allowed effective simultaneous transcriptional activation and repression of endogenous genes in mammalian cells.
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3
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Sanders C, Dzelamonyuy A, Ntemafack A, Alatoom N, Nchinda G, Georgiadis M, Waffo AB. Mapping immunological and host receptor binding determinants of SARS-CoV spike protein utilizing the Qubevirus platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550841. [PMID: 37546816 PMCID: PMC10402108 DOI: 10.1101/2023.07.27.550841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The motifs involved in tropism and immunological interactions of SARS-CoV spike (S) protein were investigated utilizing the Qubevirus platform. We showed that separately, 14 overlapping peptide fragments representing the S protein (F1-14 of 100 residues each) could be inserted into the C-terminus of A1 on recombinant Qubevirus without affecting its viability. Additionally, recombinant phage expression resulted in the surface exposure of different engineered fragments in an accessible manner. The F6 from S 425-525 , was found to contain the binding determinant of the recombinant human angiotensin converting enzyme 2 (rhACE2), with the shortest active binding motif situated between residues S 437-492 . Upstream, another fragment, F7, containing an overlapping portion of F6 would not bind to rhACE2, confirming not just only that residues were linear but equally also the appropriate structural orientation of F6 upon the Qubevirus. The F6 (S 441-460 ) and other inserts, including F7/F8 (S 601-620 ) and F10 (S 781-800 ), were demonstrated to contain important immunological determinants through recognition and binding of S protein specific (anti-S) antibodies. An engineered chimeric insert bearing the fusion of all three anti-S reactive epitopes, improved substantially the recognition and binding to their cognate antibodies. These results provide insights into humoral immune relevant epitopes and tropism characteristics of the S protein with implications for the development of subunit vaccines or other biologics against SARS-CoV. Significance Mapping epitopes within the receptor binding domains of viruses which are essential for viral tropism is critical for developing antiviral agents and subunit vaccines. In this study we have engineered the surface of Qubevirus to display a peptide library derived from the SARS-CoV S protein. In biopanning with S protein antibodies, we have identified three peptide fragments (EP1, EP2 and EP3) which reacted selectively with antibodies specific to the S protein. We demonstrated that all recombinant phage displayed peptide fragments both individually and as chimera exposed important immunological epitopes to their cognate antibodies. A peptide fragment F6 situated at S 425-525 , was found containing the binding determinant of the recombinant human angiotensin converting enzyme 2 (rhACE2), with the shortest active binding motif situated between residues S 437-492 . The platform is rapidly to identify epitopes and receptor binding sites within viral receptors found in target host cell. Thus, this platform holds great significance.
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Trashi I, Durbacz MZ, Trashi O, Wijesundara YH, Ehrman RN, Chiev AC, Darwin CB, Herbert FC, Gadhvi J, De Nisco NJ, Nielsen SO, Gassensmith JJ. Self-assembly of a fluorescent virus-like particle for imaging in tissues with high autofluorescence. J Mater Chem B 2023; 11:4445-4452. [PMID: 37144595 DOI: 10.1039/d3tb00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Virus-like particles (VLPs) are engineered nanoparticles that mimic the properties of viruses-like high tolerance to heat and proteases-but lack a viral genome, making them non-infectious. They are easily modified chemically and genetically, making them useful in drug delivery, enhancing vaccine efficacy, gene delivery, and cancer immunotherapy. One such VLP is Qβ, which has an affinity towards an RNA hairpin structure found in its viral RNA that drives the self-assembly of the capsid. It is possible to usurp the native way infectious Qβ self-assembles to encapsidate its RNA to place enzymes inside the VLP's lumen as a protease-resistant cage. Further, using RNA templates that mimic the natural self-assembly of the native capsid, fluorescent proteins (FPs) have been placed inside VLPs in a "one pot" expression system. Autofluorescence in tissues can lead to misinterpretation of results and unreliable science, so we created a single-pot expression system that uses the fluorescent protein smURFP, which avoids autofluorescence and has spectral properties compatible with standard commercial filter sets on confocal microscopes. In this work, we were able to simplify the existing "one-pot" expression system while creating high-yielding fluorescent VLP nanoparticles that could easily be imaged inside lung epithelial tissue.
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Affiliation(s)
- Ikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Mateusz Z Durbacz
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Orikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Yalini H Wijesundara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Ryanne N Ehrman
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Alyssa C Chiev
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Cary B Darwin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Fabian C Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Jashkaran Gadhvi
- Department of Biological Science, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Nicole J De Nisco
- Department of Biological Science, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Steven O Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
- Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas 75080, USA
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Alam MM, Jarvis CM, Hincapie R, McKay CS, Schimer J, Sanhueza-Chavez CA, Xu K, Diehl RC, Finn MG, Kiessling LL. Glycan-Modified Virus-like Particles Evoke T Helper Type 1-like Immune Responses. ACS NANO 2021; 15:309-321. [PMID: 32790346 PMCID: PMC8249087 DOI: 10.1021/acsnano.0c03023] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Dendritic cells (DCs) are highly effective antigen-presenting cells that shape immune responses. Vaccines that deliver antigen to the DCs can harness their power. DC surface lectins recognize glycans not typically present on host tissue to facilitate antigen uptake and presentation. Vaccines that target these surface lectins should offer improved antigen delivery, but their efficacy will depend on how lectin targeting influences the T cell subtypes that result. We examined how antigen structure influences uptake and signaling from the C-type lectin DC-SIGN (dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin or CD209). Virus-like particles (VLPs) were engineered from bacteriophage Qβ to present an array of mannoside ligands. The VLPs were taken up by DCs and efficiently trafficked to endosomes. The signaling that ensued depended on the ligand displayed on the VLP: only those particles densely functionalized with an aryl mannoside, Qβ-Man540, elicited DC maturation and induced the expression of the proinflammatory cytokines characteristic of a T helper type 1 (TH1)-like immune response. This effect was traced to differential binding to DC-SIGN at the acidic pH of the endosome. Mice immunized with a VLP bearing the aryl mannoside, and a peptide antigen (Qβ-Ova-Man540) had antigen-specific responses, including the production of CD4+ T cells producing the activating cytokines interferon-γ and tumor necrosis factor-α. A TH1 response is critical for intracellular pathogens (e.g., viruses) and cancer; thus, our data highlight the value of targeting DC lectins for antigen delivery and validate the utility of DC-targeted VLPs as vaccine vehicles that induce cellular immunity.
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Affiliation(s)
- Mohammad Murshid Alam
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
| | - Cassie M. Jarvis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
| | - Robert Hincapie
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Craig S. McKay
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Jiri Schimer
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Carlos A Sanhueza-Chavez
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
- Current address: Department of Pharmaceutical Sciences, St. John’s University, 8000 Utopia Pkwy. Queens, NY 11439, USA
| | - Ke Xu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Roger C Diehl
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
| | - M. G. Finn
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
- Corresponding Author: Laura L. Kiessling,
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Abstract
Much of virus fate, both in the environment and in physical/chemical treatment, is dependent on electrostatic interactions. Developing an accurate means of predicting virion isoelectric point (pI) would help to understand and anticipate virus fate and transport, especially for viruses that are not readily propagated in the lab. One simple approach to predicting pI estimates the pH at which the sum of charges from ionizable amino acids in capsid proteins approaches zero. However, predicted pIs based on capsid charges frequently deviate by several pH units from empirically measured pIs. Recently, the discrepancy between empirical and predicted pI was attributed to the electrostatic neutralization of predictable polynucleotide-binding regions (PBRs) of the capsid interior. In this paper, we review models presupposing (i) the influence of the viral polynucleotide on surface charge or (ii) the contribution of only exterior residues to surface charge. We then compare these models to the approach of excluding only PBRs and hypothesize a conceptual electrostatic model that aligns with this approach. The PBR exclusion method outperformed methods based on three-dimensional (3D) structure and accounted for major discrepancies in predicted pIs without adversely affecting pI prediction for a diverse range of viruses. In addition, the PBR exclusion method was determined to be the best available method for predicting virus pI, since (i) PBRs are predicted independently of the impact on pI, (ii) PBR prediction relies on proteome sequences rather than detailed structural models, and (iii) PBR exclusion was successfully demonstrated on a diverse set of viruses. These models apply to nonenveloped viruses only. A similar model for enveloped viruses is complicated by a lack of data on enveloped virus pI, as well as uncertainties regarding the influence of the phospholipid envelope on charge and ion gradients.
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Affiliation(s)
- Joe Heffron
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
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Heffron J, Mayer BK. Improved Virus Isoelectric Point Estimation by Exclusion of Known and Predicted Genome-Binding Regions. Appl Environ Microbiol 2020; 86:e01674-20. [PMID: 32978129 PMCID: PMC7657617 DOI: 10.1128/aem.01674-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/18/2020] [Indexed: 01/16/2023] Open
Abstract
Knowledge of the isoelectric points (pIs) of viruses is beneficial for predicting virus behavior in environmental transport and physical/chemical treatment applications. However, the empirically measured pIs of many viruses have thus far defied simple explanation, let alone prediction, based on the ionizable amino acid composition of the virus capsid. Here, we suggest an approach for predicting the pI of nonenveloped viruses by excluding capsid regions that stabilize the virus polynucleotide via electrostatic interactions. This method was applied first to viruses with known polynucleotide-binding regions (PBRs) and/or three-dimensional (3D) structures. Then, PBRs were predicted in a group of 32 unique viral capsid proteome sequences via conserved structures and sequence motifs. Removing predicted PBRs resulted in a significantly better fit to empirical pI values. After modification, mean differences between theoretical and empirical pI values were reduced from 2.1 ± 2.4 to 0.1 ± 1.7 pH units.IMPORTANCE This model fits predicted pIs to empirical values for a diverse set of viruses. The results suggest that many previously reported discrepancies between theoretical and empirical virus pIs can be explained by coulombic neutralization of PBRs of the inner capsid. Given the diversity of virus capsid structures, this nonarbitrary, heuristic approach to predicting virus pI offers an effective alternative to a simplistic, one-size-fits-all charge model of the virion. The accurate, structure-based prediction of PBRs of the virus capsid employed here may also be of general interest to structural virologists.
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Affiliation(s)
- Joe Heffron
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
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Rūmnieks J, Liekniņa I, Kalniņš G, Šišovs M, Akopjana I, Bogans J, Tārs K. Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes. SCIENCE ADVANCES 2020; 6:6/36/eabc0023. [PMID: 32917600 PMCID: PMC7467689 DOI: 10.1126/sciadv.abc0023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins (CPs) in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome-derived ssRNA phage CPs to produce virus-like particles and determined the three-dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage-based vaccine design.
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Affiliation(s)
- Jānis Rūmnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Ilva Liekniņa
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Mihails Šišovs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Ināra Akopjana
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Jānis Bogans
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia.
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Gorzelnik KV, Zhang J. Cryo-EM reveals infection steps of single-stranded RNA bacteriophages. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:79-86. [PMID: 32841651 DOI: 10.1016/j.pbiomolbio.2020.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/23/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
Abstract
Single-stranded RNA bacteriophages (ssRNA phages) are small spherical RNA viruses that infect bacteria with retractile pili. The single positive-sense genomic RNA of ssRNA phages, which is protected by a capsid shell, is delivered into the host via the retraction of the host pili. Structures involved in ssRNA phage infection cycle are essential for understanding the underlying mechanisms that can be used to engineer them for therapeutic applications. This review summarizes the recent breakthroughs in high-resolution structural studies of two ssRNA phages, MS2 and Qβ, and their interaction with the host, E. coli, by cryo-electron microscopy (cryo-EM). These studies revealed new cryo-EM structures, which provide insights into how MS2 and Qβ package the RNA, lyse E. coli, and adsorb to the receptor F-pili, responsible for conjugation. Methodologies described here can be expanded to study other ssRNA phages that target pathogenic bacteria.
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Affiliation(s)
- Karl Victor Gorzelnik
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA.
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Hossain MT, Yokono T, Kashiwagi A. The Single-Stranded RNA Bacteriophage Qβ Adapts Rapidly to High Temperatures: An Evolution Experiment. Viruses 2020; 12:v12060638. [PMID: 32545482 PMCID: PMC7354602 DOI: 10.3390/v12060638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 11/22/2022] Open
Abstract
Single-stranded (ss)RNA viruses are thought to evolve rapidly due to an inherently high mutation rate. However, it remains unclear how ssRNA viruses adapt to novel environments and/or how many and what types of substitutions are needed to facilitate this evolution. In this study, we followed the adaptation of the ssRNA bacteriophage Qβ using thermally adapted Escherichia coli as a host, which can efficiently grow at temperatures between 37.2 and 45.3 °C. This made it possible to evaluate Qβ adaptation to the highest known temperature that supports growth, 45.3 °C. We found that Qβ was capable of replication at this temperature; within 114 days (~1260 generations), we detected more than 34 novel point mutations in the genome of the thermally adapted Qβ population, representing 0.8% of the total Qβ genome. In addition, we returned the 45.3 °C-adapted Qβ populations to 37.2 °C and passaged them for 8 days (~124 generations). We found that the reverse-adapted Qβ population showed little to no decrease in fitness. These results indicate that Qβ can evolve in response to increasing temperatures in a short period of time with the accumulation of point mutations.
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Affiliation(s)
- Md. Tanvir Hossain
- The United Graduate School of Agricultural Science, Iwate University, Morioka 020-8550, Japan;
| | - Toma Yokono
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan;
| | - Akiko Kashiwagi
- The United Graduate School of Agricultural Science, Iwate University, Morioka 020-8550, Japan;
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan;
- Correspondence: ; Tel.: +81-172-39-3789
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11
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Fu J, Woycechowsky KJ. Guest Sequence Can Influence RNA Encapsulation by an Engineered Cationic Protein Capsid. Biochemistry 2020; 59:1517-1526. [DOI: 10.1021/acs.biochem.0c00077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiannan Fu
- School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China
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12
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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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13
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Somovilla P, Manrubia S, Lázaro E. Evolutionary Dynamics in the RNA Bacteriophage Qβ Depends on the Pattern of Change in Selective Pressures. Pathogens 2019; 8:pathogens8020080. [PMID: 31216651 PMCID: PMC6631425 DOI: 10.3390/pathogens8020080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 12/14/2022] Open
Abstract
The rate of change in selective pressures is one of the main factors that determines the likelihood that populations can adapt to stress conditions. Generally, the reduction in the population size that accompanies abrupt environmental changes makes it difficult to generate and select adaptive mutations. However, in systems with high genetic diversity, as happens in RNA viruses, mutations with beneficial effects under new conditions can already be present in the population, facilitating adaptation. In this work, we have propagated an RNA bacteriophage (Qβ) at temperatures higher than the optimum, following different patterns of change. We have determined the fitness values and the consensus sequences of all lineages throughout the evolutionary process in order to establish correspondences between fitness variations and adaptive pathways. Our results show that populations subjected to a sudden temperature change gain fitness and fix mutations faster than those subjected to gradual changes, differing also in the particular selected mutations. The life-history of populations prior to the environmental change has great importance in the dynamics of adaptation. The conclusion is that in the bacteriophage Qβ, the standing genetic diversity together with the rate of temperature change determine both the rapidity of adaptation and the followed evolutionary pathways.
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Affiliation(s)
- Pilar Somovilla
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain.
- Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain.
| | - Susanna Manrubia
- Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain.
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - Ester Lázaro
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain.
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14
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Liekniņa I, Kalniņš G, Akopjana I, Bogans J, Šišovs M, Jansons J, Rūmnieks J, Tārs K. Production and characterization of novel ssRNA bacteriophage virus-like particles from metagenomic sequencing data. J Nanobiotechnology 2019; 17:61. [PMID: 31084612 PMCID: PMC6513524 DOI: 10.1186/s12951-019-0497-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/04/2019] [Indexed: 12/30/2022] Open
Abstract
Background Protein shells assembled from viral coat proteins are an attractive platform for development of new vaccines and other tools such as targeted bioimaging and drug delivery agents. Virus-like particles (VLPs) derived from the single-stranded RNA (ssRNA) bacteriophage coat proteins (CPs) have been important and successful contenders in the area due to their simplicity and robustness. However, only a few different VLP types are available that put certain limitations on continued developments and expanded adaptation of ssRNA phage VLP technology. Metagenomic studies have been a rich source for discovering novel viral sequences, and in recent years have unraveled numerous ssRNA phage genomes significantly different from those known before. Here, we describe the use of ssRNA CP sequences found in metagenomic data to experimentally produce and characterize novel VLPs. Results Approximately 150 ssRNA phage CP sequences were sourced from metagenomic sequence data and grouped into 14 different clusters based on CP sequence similarity analysis. 110 CP-encoding sequences were obtained by gene synthesis and expressed in bacteria which in 80 cases resulted in VLP assembly. Production and purification of the VLPs was straightforward and compatible with established protocols, with the only exception that a considerable proportion of the CPs had to be produced at a lower temperature to ensure VLP assembly. The VLP morphology was similar to that of the previously studied phages, although a few deviations such as elongated or smaller particles were noted in certain cases. In addition, stabilizing inter-subunit disulfide bonds were detected in six VLPs and several possible candidate RNA structures in the phage genomes were identified that might bind to the coat protein and ensure specific RNA packaging. Conclusions Compared to the few types of ssRNA phage VLPs that were used before, several dozens of new particles representing ten distinct similarity groups are now available with a notable potential for biotechnological applications. It is believed that the novel VLPs described in this paper will provide the groundwork for future development of new vaccines and other applications based on ssRNA bacteriophage VLPs. Electronic supplementary material The online version of this article (10.1186/s12951-019-0497-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ilva Liekniņa
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Ināra Akopjana
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Jānis Bogans
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Mihails Šišovs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Jānis Rūmnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia.
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15
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Abstract
Bacteriophages of the Leviviridae family are small viruses with short single-stranded RNA (ssRNA) genomes. Protein-RNA interactions play a key role throughout the phage life cycle, and all of the conserved phage proteins - the maturation protein, the coat protein and the replicase - are able to recognize specific structures in the RNA genome. The phage-coded replicase subunit associates with several host proteins to form a catalytically active complex. Recognition of the genomic RNA by the replicase complex is achieved in a remarkably complex manner that exploits the RNA-binding properties of host proteins and the particular three-dimensional structure of the phage genome. The coat protein recognizes a hairpin structure at the beginning of the replicase gene. The binding interaction serves to regulate the expression of the replicase gene and can be remarkably different in various ssRNA phages. The maturation protein is a minor structural component of the virion that binds to the genome, mediates attachment to the host and guides the genome into the cell. The maturation protein has two distinct RNA-binding surfaces that are in contact with different regions of the genome. The maturation and coat proteins also work together to ensure the encapsidation of the phage genome in new virus particles. In this chapter, the different ssRNA phage protein-RNA interactions, as well as some of their practical applications, are discussed in detail.
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Affiliation(s)
| | - Kaspars Tārs
- Biomedical Research and Study Center, Riga, Latvia.
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16
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Fang PY, Bowman JC, Gómez Ramos L, Hsiao C, Williams LD. RNA: packaged and protected by VLPs. RSC Adv 2018; 8:21399-21406. [PMID: 35539947 PMCID: PMC9080931 DOI: 10.1039/c8ra02084a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023] Open
Abstract
VLP packaging is most efficient for compact RNA, and protects RNA against assault by small diffusible damaging agents.
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Affiliation(s)
- Po-Yu Fang
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Lizzette M. Gómez Ramos
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemical and Biomolecular Engineering
| | - Chiaolong Hsiao
- Institute of Biochemical Sciences
- National Taiwan University
- Taipei 10617
- Republic of China
| | - Loren Dean Williams
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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17
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Structures of Qβ virions, virus-like particles, and the Qβ-MurA complex reveal internal coat proteins and the mechanism of host lysis. Proc Natl Acad Sci U S A 2017; 114:11697-11702. [PMID: 29078304 DOI: 10.1073/pnas.1707102114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Allolevivirus Qβ the maturation protein, A2, has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis. Here, we determined structures of Qβ virions, virus-like particles, and the Qβ-MurA complex using single-particle cryoelectron microscopy, at 4.7-Å, 3.3-Å, and 6.1-Å resolutions, respectively. We identified the outer surface of the β-region in A2 as the MurA-binding interface. Moreover, the pattern of MurA mutations that block Qβ lysis and the conformational changes of MurA that facilitate A2 binding were found to be due to the intimate fit between A2 and the region encompassing the closed catalytic cleft of substrate-liganded MurA. Additionally, by comparing the Qβ virion with Qβ virus-like particles that lack a maturation protein, we observed a structural rearrangement in the capsid coat proteins that is required to package the viral gRNA in its dominant conformation. Unexpectedly, we found a coat protein dimer sequestered in the interior of the virion. This coat protein dimer binds to the gRNA and interacts with the buried α-region of A2, suggesting that it is sequestered during the early stage of capsid formation to promote the gRNA condensation required for genome packaging. These internalized coat proteins are the most asymmetrically arranged major capsid proteins yet observed in virus structures.
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18
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Czapiński J, Kiełbus M, Kałafut J, Kos M, Stepulak A, Rivero-Müller A. How to Train a Cell-Cutting-Edge Molecular Tools. Front Chem 2017; 5:12. [PMID: 28344971 PMCID: PMC5344921 DOI: 10.3389/fchem.2017.00012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/20/2017] [Indexed: 12/28/2022] Open
Abstract
In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for in vivo spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications.
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Affiliation(s)
- Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Postgraduate School of Molecular Medicine, Medical University of WarsawWarsaw, Poland
| | - Michał Kiełbus
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Michał Kos
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi UniversityTurku, Finland
- Department of Biosciences, Åbo Akademi UniversityTurku, Finland
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19
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Pumpens P, Renhofa R, Dishlers A, Kozlovska T, Ose V, Pushko P, Tars K, Grens E, Bachmann MF. The True Story and Advantages of RNA Phage Capsids as Nanotools. Intervirology 2016; 59:74-110. [DOI: 10.1159/000449503] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/30/2016] [Indexed: 11/19/2022] Open
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20
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Gorzelnik KV, Cui Z, Reed CA, Jakana J, Young R, Zhang J. Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ. Proc Natl Acad Sci U S A 2016; 113:11519-11524. [PMID: 27671640 PMCID: PMC5068298 DOI: 10.1073/pnas.1609482113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A2, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A2 and the gRNA. A2 contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.
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Affiliation(s)
- Karl V Gorzelnik
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Zhicheng Cui
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Catrina A Reed
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Ry Young
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843;
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21
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Shishovs M, Rumnieks J, Diebolder C, Jaudzems K, Andreas LB, Stanek J, Kazaks A, Kotelovica S, Akopjana I, Pintacuda G, Koning RI, Tars K. Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages. J Mol Biol 2016; 428:4267-4279. [PMID: 27591890 DOI: 10.1016/j.jmb.2016.08.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/18/2016] [Accepted: 08/27/2016] [Indexed: 12/18/2022]
Abstract
AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruction of the assembled particle, together with secondary structure information from site-specific solid-state NMR data. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions.
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Affiliation(s)
- Mihails Shishovs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Christoph Diebolder
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kristaps Jaudzems
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Loren B Andreas
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Jan Stanek
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Andris Kazaks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Svetlana Kotelovica
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Inara Akopjana
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Roman I Koning
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands; Department of Cell Biology, Leiden University Medical Center, Postal Zone S1-P, P.O.Box 9600, 2300 RC Leiden, The Netherlands
| | - Kaspars Tars
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia; Faculty of Biology, Department of Molecular Biology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia.
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22
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Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:61-88. [PMID: 27256382 DOI: 10.1007/978-3-319-29073-7_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, and cellular localization. Most RBPs have distinct mRNA-binding and functional domains; thus, the function of an RBP can be studied independently of RNA-binding by artificially recruiting the RBP to a reporter RNA and then measuring the effect of RBP recruitment on reporter splicing, stability, translational efficiency, or intracellular trafficking. These tethered function assays therefore do not require prior knowledge of the RBP's endogenous RNA targets or its binding sites within these RNAs. Here, we provide an overview of the experimental strategy and the strengths and limitations of common tethering systems. We illustrate specific examples of the application of the assay in elucidating the function of various classes of RBPs. We also discuss how classic tethering assay approaches and insights gained from them have been empowered by more recent technological advances, including efficient genome editing and high-throughput RNA-sequencing.
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23
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Clare DK, Pechnikova EV, Skurat EV, Makarov VV, Sokolova OS, Solovyev AG, Orlova EV. Novel Inter-Subunit Contacts in Barley Stripe Mosaic Virus Revealed by Cryo-Electron Microscopy. Structure 2015; 23:1815-1826. [PMID: 26278173 PMCID: PMC4597109 DOI: 10.1016/j.str.2015.06.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/27/2015] [Accepted: 06/21/2015] [Indexed: 11/30/2022]
Abstract
Barley stripe mosaic virus (BSMV, genus Hordeivirus) is a rod-shaped single-stranded RNA virus similar to viruses of the structurally characterized and well-studied genus Tobamovirus. Here we report the first high-resolution structure of BSMV at 4.1 Å obtained by cryo-electron microscopy. We discovered that BSMV forms two types of virion that differ in the number of coat protein (CP) subunits per turn and interactions between the CP subunits. While BSMV and tobacco mosaic virus CP subunits have a similar fold and interact with RNA using conserved residues, the axial contacts between the CP of these two viral groups are considerably different. BSMV CP subunits lack substantial axial contacts and are held together by a previously unobserved lateral contact formed at the virion surface via an interacting loop, which protrudes from the CP hydrophobic core to the adjacent CP subunit. These data provide an insight into diversity in structural organization of helical viruses.
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Affiliation(s)
- Daniel Kofi Clare
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London WC1E 7HX, UK
| | - Eugenia V Pechnikova
- A.V. Shubnikov Institute of Crystallography RAS, 59 Leninsky Avenue, 119333 Moscow, Russia
| | - Eugene V Skurat
- Department of Biology, Moscow State University, 1 Leninskie Gory, Building 12, 119991 Moscow, Russia
| | - Valentin V Makarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - Olga S Sokolova
- A.V. Shubnikov Institute of Crystallography RAS, 59 Leninsky Avenue, 119333 Moscow, Russia; Department of Biology, Moscow State University, 1 Leninskie Gory, Building 12, 119991 Moscow, Russia
| | - Andrey G Solovyev
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - Elena V Orlova
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London WC1E 7HX, UK.
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24
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Duss O, Michel E, Diarra dit Konté N, Schubert M, Allain FHT. Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition. Nucleic Acids Res 2014; 42:5332-46. [PMID: 24561806 PMCID: PMC4005645 DOI: 10.1093/nar/gku141] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude (∼10 nM to ∼3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein-RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein.
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Affiliation(s)
- Olivier Duss
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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