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Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
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Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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2
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Martin-Solana E, Diaz-Lopez I, Mohamedi Y, Ventoso I, Fernandez JJ, Fernandez-Fernandez MR. Progressive alterations in polysomal architecture and activation of ribosome stalling relief factors in a mouse model of Huntington's disease. Neurobiol Dis 2024; 195:106488. [PMID: 38565397 PMCID: PMC7616275 DOI: 10.1016/j.nbd.2024.106488] [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: 02/02/2024] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
Given their highly polarized morphology and functional singularity, neurons require precise spatial and temporal control of protein synthesis. Alterations in protein translation have been implicated in the development and progression of a wide range of neurological and neurodegenerative disorders, including Huntington's disease (HD). In this study we examined the architecture of polysomes in their native brain context in striatal tissue from the zQ175 knock-in mouse model of HD. We performed 3D electron tomography of high-pressure frozen and freeze-substituted striatal tissue from HD models and corresponding controls at different ages. Electron tomography results revealed progressive remodelling towards a more compacted polysomal architecture in the mouse model, an effect that coincided with the emergence and progression of HD related symptoms. The aberrant polysomal architecture is compatible with ribosome stalling phenomena. In fact, we also detected in the zQ175 model an increase in the striatal expression of the stalling relief factor EIF5A2 and an increase in the accumulation of eIF5A1, eIF5A2 and hypusinated eIF5A1, the active form of eIF5A1. Polysomal sedimentation gradients showed differences in the relative accumulation of 40S ribosomal subunits and in polysomal distribution in striatal samples of the zQ175 model. These findings indicate that changes in the architecture of the protein synthesis machinery may underlie translational alterations associated with HD, opening new avenues for understanding the progression of the disease.
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Affiliation(s)
- Eva Martin-Solana
- Centro Nacional de Biotecnología (CNB-CSIC). Campus UAM, Darwin 3, 28049 Madrid, Spain
| | - Irene Diaz-Lopez
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Yamina Mohamedi
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA). Av. Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain
| | - Ivan Ventoso
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Jose-Jesus Fernandez
- Centro Nacional de Biotecnología (CNB-CSIC). Campus UAM, Darwin 3, 28049 Madrid, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA). Av. Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain; Centro de Investigación en Nanomateriales y Nanotecnología (CINN-CSIC). Av. Vega 4-6, 33940 El Entrego, Asturias, Spain.
| | - Maria Rosario Fernandez-Fernandez
- Centro Nacional de Biotecnología (CNB-CSIC). Campus UAM, Darwin 3, 28049 Madrid, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA). Av. Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain; Centro de Investigación en Nanomateriales y Nanotecnología (CINN-CSIC). Av. Vega 4-6, 33940 El Entrego, Asturias, Spain.
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3
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Lee S, Jo K, Jeong SKC, Jeon H, Choi YS, Jung S. Characterization of peptides released from frozen-then-aged beef after digestion in an in vitro infant gastrointestinal model. Meat Sci 2024; 212:109468. [PMID: 38428150 DOI: 10.1016/j.meatsci.2024.109468] [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] [Received: 01/02/2024] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
This study investigated whether the freezing-then-aging treatment of beef affects protein digestibility and release of potentially bioactive peptides using an in vitro infant digestion model. After 28 days of storage, aged-only (AO) and frozen-then-aged (FA) beef exhibited higher α-amino group contents in the 10% trichloroacetic acid-soluble fraction compared to day 0 (P < 0.05). Following in vitro digestion in the infant model, FA showed higher contents of α-amino groups and smaller proteins (<3 and 1 kDa) than day 0 and AO (P < 0.05). Relative contributions of myofibrillar, sarcoplasmic, and stromal proteins to the bioactive peptides released from AO and FA differed from those of day 0. In addition, FA exhibited a higher proportion of potential bioactive peptide sequences. Overall, freezing-then-aging treatment can enhance the potential health benefits of beef to be used as a protein source for complementary foods.
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Affiliation(s)
- Seonmin Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kyung Jo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seul-Ki-Chan Jeong
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hayeon Jeon
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Yun-Sang Choi
- Research Group of Food Processing, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Samooel Jung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea.
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4
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Yu Y, Kass MA, Zhang M, Youssef N, Freije CA, Brock KP, Aguado LC, Seifert LL, Venkittu S, Hong X, Shlomai A, de Jong YP, Marks DS, Rice CM, Schneider WM. Deep mutational scanning of hepatitis B virus reveals a mechanism for cis-preferential reverse transcription. Cell 2024; 187:2735-2745.e12. [PMID: 38723628 PMCID: PMC11127778 DOI: 10.1016/j.cell.2024.04.008] [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: 08/02/2023] [Revised: 02/12/2024] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
Hepatitis B virus (HBV) is a small double-stranded DNA virus that chronically infects 296 million people. Over half of its compact genome encodes proteins in two overlapping reading frames, and during evolution, multiple selective pressures can act on shared nucleotides. This study combines an RNA-based HBV cell culture system with deep mutational scanning (DMS) to uncouple cis- and trans-acting sequence requirements in the HBV genome. The results support a leaky ribosome scanning model for polymerase translation, provide a fitness map of the HBV polymerase at single-nucleotide resolution, and identify conserved prolines adjacent to the HBV polymerase termination codon that stall ribosomes. Further experiments indicated that stalled ribosomes tether the nascent polymerase to its template RNA, ensuring cis-preferential RNA packaging and reverse transcription of the HBV genome.
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Affiliation(s)
- Yingpu Yu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Maximilian A Kass
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA; Department of Infectious Diseases, Molecular Virology, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Mengyin Zhang
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Noor Youssef
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Broad Institute of MIT and Harvard, Harvard University, Cambridge, MA 02138, USA
| | - Catherine A Freije
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Kelly P Brock
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Broad Institute of MIT and Harvard, Harvard University, Cambridge, MA 02138, USA
| | - Lauren C Aguado
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Leon L Seifert
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA; Center for Clinical and Translational Science, The Rockefeller University, New York, NY 10065, USA
| | - Sanjana Venkittu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Xupeng Hong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Amir Shlomai
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Ype P de Jong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Broad Institute of MIT and Harvard, Harvard University, Cambridge, MA 02138, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
| | - William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
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5
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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6
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Purohit R, Couch T, MacLean DM. Proline substitutions in the ASIC1 β11-12 linker slow desensitization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593312. [PMID: 38798386 PMCID: PMC11118455 DOI: 10.1101/2024.05.09.593312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Desensitization is a prominent feature of nearly all ligand gated ion channels. Acid-sensing ion channels (ASIC) undergo desensitization within hundreds of milliseconds to seconds upon continual extracellular acidification. The ASIC mechanism of desensitization is primarily due to the isomerization or "flipping" of a short linker joining the 11th and 12th beta sheets in the extracellular domain. In the resting and active states this β11-12 linker adopts an "upward" conformation while in the desensitized conformation the linker assumes a "downward" state. To accommodate this "downward" state, specific peptide bonds within the linker adopt either trans-like or cis-like conformations. Since proline-containing peptide bonds undergo cis-trans isomerization very slowly, we hypothesized that introducing proline residues in the linker may slow or even abolish ASIC desensitization, potentially providing a valuable research tools. Proline substitutions in the chicken ASIC1 β11-12 linker (L414P and Y416P) slowed desensitization decays approximately 100 to 1000-fold as measured in excised patches. Both L414P and Y416P shifted the steady state desensitization curves to more acidic pHs while activation curves and ion selectivity of these slow-desensitizing currents were largely unaffected. To investigate the functional stoichiometry of desensitization in the trimeric ASIC, we created families of L414P and Y416P concatemers with zero, one, two or three proline substitutions in all possible configurations. Introducing one or two L414P or Y416P mutations only slightly attenuated desensitization, suggesting that conformational changes in the remaining faster wild type subunits were sufficient to desensitize the channel. These data highlight the unusual cis-trans isomerization mechanism of ASIC desensitization and support a model where a single subunit is sufficient to desensitize the entire channel.
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Affiliation(s)
- Rutambhara Purohit
- Department of Pharmacology and Physiology, University of Rochester Medical Center
| | - Tyler Couch
- Department of Pharmacology and Physiology, University of Rochester Medical Center
| | - David M MacLean
- Department of Pharmacology and Physiology, University of Rochester Medical Center
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7
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Ma L, Ramasubramanian R, Mehta N, Cossette B, Morgan D, Sukaj I, Bergaggio E, Kadauke S, Myers R, Paruzzo L, Ghilardi G, Grzywa T, Cozzone A, Schuster S, Frey N, Zhang L, Yousefpour P, Abraham W, Suh H, Ruella M, Grupp S, Chiarle R, Wittrup KD, Irvine DJ. Directed evolution-based discovery of ligands for in vivo restimulation of CAR-T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589780. [PMID: 38659938 PMCID: PMC11042270 DOI: 10.1101/2024.04.16.589780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Chimeric antigen receptor (CAR) T cell therapy targeting CD19 elicits remarkable clinical efficacy in B-cell malignancies, but many patients relapse due to failed expansion and/or progressive loss of CAR-T cells. We recently reported a strategy to potently restimulate CAR-T cells in vivo, enhancing their functionality by administration of a vaccine-like stimulus comprised of surrogate peptide ligands for a CAR linked to a lymph node-targeting amphiphilic PEG-lipid (termed CAR-T-vax). Here, we demonstrate a general strategy to generate and optimize peptide mimotopes enabling CAR-T-vax generation for any CAR. Using the clinical CD19 CAR FMC63 as a test case, we employed yeast surface display to identify peptide binders to soluble IgG versions of FMC63, which were subsequently affinity matured by directed evolution. CAR-T vaccines using these optimized mimotopes triggered marked expansion of both murine CD19 CAR-T cells in a syngeneic model and human CAR-T cells in a humanized mouse model of B cell acute lymphoblastic leukemia (B-ALL), and enhanced control of leukemia progression. This approach thus enables vaccine boosting to be applied to any clinically-relevant CAR-T cell product.
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8
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Oliveira MM, Mohamed M, Elder MK, Banegas-Morales K, Mamcarz M, Lu EH, Golhan EAN, Navrange N, Chatterjee S, Abel T, Klann E. The integrated stress response effector GADD34 is repurposed by neurons to promote stimulus-induced translation. Cell Rep 2024; 43:113670. [PMID: 38219147 PMCID: PMC10964249 DOI: 10.1016/j.celrep.2023.113670] [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: 07/04/2023] [Revised: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 01/16/2024] Open
Abstract
Neuronal protein synthesis is required for long-lasting plasticity and long-term memory consolidation. Dephosphorylation of eukaryotic initiation factor 2α is one of the key translational control events that is required to increase de novo protein synthesis that underlies long-lasting plasticity and memory consolidation. Here, we interrogate the molecular pathways of translational control that are triggered by neuronal stimulation with brain-derived neurotrophic factor (BDNF), which results in eukaryotic initiation factor 2α (eIF2α) dephosphorylation and increases in de novo protein synthesis. Primary rodent neurons exposed to BDNF display elevated translation of GADD34, which facilitates eIF2α dephosphorylation and subsequent de novo protein synthesis. Furthermore, GADD34 requires G-actin generated by cofilin to dephosphorylate eIF2α and enhance protein synthesis. Finally, GADD34 is required for BDNF-induced translation of synaptic plasticity-related proteins. Overall, we provide evidence that neurons repurpose GADD34, an effector of the integrated stress response, as an orchestrator of rapid increases in eIF2-dependent translation in response to plasticity-inducing stimuli.
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Affiliation(s)
| | - Muhaned Mohamed
- Center for Neural Science, New York University, New York, NY, USA
| | - Megan K Elder
- Center for Neural Science, New York University, New York, NY, USA
| | | | - Maggie Mamcarz
- Center for Neural Science, New York University, New York, NY, USA
| | - Emily H Lu
- Center for Neural Science, New York University, New York, NY, USA
| | - Ela A N Golhan
- Center for Neural Science, New York University, New York, NY, USA
| | - Nishika Navrange
- Center for Neural Science, New York University, New York, NY, USA
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY, USA; NYU Neuroscience Institute, New York University School of Medicine, New York, NY, USA.
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9
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Brunnsåker D, Kronström F, Tiukova IA, King RD. Interpreting protein abundance in Saccharomyces cerevisiae through relational learning. Bioinformatics 2024; 40:btae050. [PMID: 38273672 PMCID: PMC10868306 DOI: 10.1093/bioinformatics/btae050] [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: 05/24/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 01/27/2024] Open
Abstract
MOTIVATION Proteomic profiles reflect the functional readout of the physiological state of an organism. An increased understanding of what controls and defines protein abundances is of high scientific interest. Saccharomyces cerevisiae is a well-studied model organism, and there is a large amount of structured knowledge on yeast systems biology in databases such as the Saccharomyces Genome Database, and highly curated genome-scale metabolic models like Yeast8. These datasets, the result of decades of experiments, are abundant in information, and adhere to semantically meaningful ontologies. RESULTS By representing this knowledge in an expressive Datalog database we generated data descriptors using relational learning that, when combined with supervised machine learning, enables us to predict protein abundances in an explainable manner. We learnt predictive relationships between protein abundances, function and phenotype; such as α-amino acid accumulations and deviations in chronological lifespan. We further demonstrate the power of this methodology on the proteins His4 and Ilv2, connecting qualitative biological concepts to quantified abundances. AVAILABILITY AND IMPLEMENTATION All data and processing scripts are available at the following Github repository: https://github.com/DanielBrunnsaker/ProtPredict.
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Affiliation(s)
- Daniel Brunnsåker
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Filip Kronström
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Ievgeniia A Tiukova
- Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Department of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm 106 91, Sweden
| | - Ross D King
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
- The Alan Turing Institute, London NW1 2DB, United Kingdom
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10
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Yang CC, Wang ZY, Cheng CM. Insights into Superinfection Immunity Regulation of Xanthomonas axonopodis Filamentous Bacteriophage cf. Curr Microbiol 2023; 81:42. [PMID: 38112972 DOI: 10.1007/s00284-023-03539-y] [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: 01/31/2023] [Accepted: 10/26/2023] [Indexed: 12/21/2023]
Abstract
Filamentous bacteriophage cf infects Xanthomonas axonopodis pv. citri, a serious plant pathogen which causes citrus canker. To understand the immunity regulation of bacteria infected with bacteriophage cf, we applied DNA shuffling to mutate the cf intergenic region. One of the immunity mutants, cf-m3 (NCBI Taxonomy ID: 3050368) expressed a 106-109 fold greater superinfection ability compared with wild type cf. Nine mutations were identified on the cf-m3 phage, four of which were located within the coding region of an open reading frame (ORF165) for a hypothetical repressor, PT, and five located upstream of the PT coding region. A set of phages with mutations to the predicted PT protein or the upstream coding region were generated. All showed similarly low superinfection efficiency to wild type cf and no superinfection ability on cf lysogens. The results indicate that rather than superinfection inhibition, the PT protein and the un-transcribed cis element function individually as positive regulators of cf superinfection immunity. Greater superinfection ability depends on the simultaneous presence of both elements. This work yields further insight into the possible control of citrus canker disease through phages that overcome host superinfection immunity.
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Affiliation(s)
- Chia-Chin Yang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Zih-Yun Wang
- Department of Biomedical Sciences and Engineering, Tzu-Chi University, 701 Chung Yang Road Section 3, Hualien, 970, Taiwan
| | - Ching-Ming Cheng
- Department of Biomedical Sciences and Engineering, Tzu-Chi University, 701 Chung Yang Road Section 3, Hualien, 970, Taiwan.
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11
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Shnaider TA, Khabarova AA, Morozova KN, Yunusova AM, Yakovleva SA, Chvileva AS, Wolf ER, Kiseleva EV, Grigor'eva EV, Voinova VY, Lagarkova MA, Pomerantseva EA, Musatova EV, Smirnov AV, Smirnova AV, Stoklitskaya DS, Arefieva TI, Larina DA, Nikitina TV, Pristyazhnyuk IE. Ultrastructural Abnormalities in Induced Pluripotent Stem Cell-Derived Neural Stem Cells and Neurons of Two Cohen Syndrome Patients. Cells 2023; 12:2702. [PMID: 38067130 PMCID: PMC10705360 DOI: 10.3390/cells12232702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/12/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Cohen syndrome is an autosomal recessive disorder caused by VPS13B (COH1) gene mutations. This syndrome is significantly underdiagnosed and is characterized by intellectual disability, microcephaly, autistic symptoms, hypotension, myopia, retinal dystrophy, neutropenia, and obesity. VPS13B regulates intracellular membrane transport and supports the Golgi apparatus structure, which is critical for neuron formation. We generated induced pluripotent stem cells from two patients with pronounced manifestations of Cohen syndrome and differentiated them into neural stem cells and neurons. Using transmission electron microscopy, we documented multiple new ultrastructural changes associated with Cohen syndrome in the neuronal cells. We discovered considerable disturbances in the structure of some organelles: Golgi apparatus fragmentation and swelling, endoplasmic reticulum structural reorganization, mitochondrial defects, and the accumulation of large autophagosomes with undigested contents. These abnormalities underline the ultrastructural similarity of Cohen syndrome to many neurodegenerative diseases. The cell models that we developed based on patient-specific induced pluripotent stem cells can serve to uncover not only neurodegenerative processes, but the causes of intellectual disability in general.
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Affiliation(s)
- Tatiana A Shnaider
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna A Khabarova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ksenia N Morozova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anastasia M Yunusova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sophia A Yakovleva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anastasia S Chvileva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina R Wolf
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena V Kiseleva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Grigor'eva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Viktori Y Voinova
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
- The Mental Health Research Center, Moscow 115522, Russia
| | - Maria A Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | | | | | - Alexander V Smirnov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna V Smirnova
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
| | | | - Tatiana I Arefieva
- National Medical Research Centre of Cardiology Named after Academician E. I. Chazov., Moscow 121552, Russia
| | - Daria A Larina
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
| | - Tatiana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk 634050, Russia
| | - Inna E Pristyazhnyuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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12
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Taton A, Gilderman TS, Ernst DC, Omaga CA, Cohen LA, Rey-Bedon C, Golden JW, Golden SS. Synechococcus elongatus Argonaute reduces natural transformation efficiency and provides immunity against exogenous plasmids. mBio 2023; 14:e0184323. [PMID: 37791787 PMCID: PMC10653904 DOI: 10.1128/mbio.01843-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE S. elongatus is an important cyanobacterial model organism for the study of its prokaryotic circadian clock, photosynthesis, and other biological processes. It is also widely used for genetic engineering to produce renewable biochemicals. Our findings reveal an SeAgo-based defense mechanism in S. elongatus against the horizontal transfer of genetic material. We demonstrate that deletion of the ago gene facilitates genetic studies and genetic engineering of S. elongatus.
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Affiliation(s)
- Arnaud Taton
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Tami S. Gilderman
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Dustin C. Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Carla A. Omaga
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Lucas A. Cohen
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Camilo Rey-Bedon
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - James W. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Susan S. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
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13
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Thaler J, Syroegin EA, Breuker K, Polikanov YS, Micura R. Practical Synthesis of N-Formylmethionylated Peptidyl-tRNA Mimics. ACS Chem Biol 2023; 18:2233-2239. [PMID: 37433044 PMCID: PMC10594587 DOI: 10.1021/acschembio.3c00237] [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: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023]
Abstract
Hydrolysis-resistant RNA-peptide conjugates that mimic peptidyl-tRNAs are frequently needed for structural and functional studies of protein synthesis in the ribosome. Such conjugates are accessible by chemical solid-phase synthesis, allowing for the utmost flexibility of both the peptide and the RNA sequence. Commonly used protection group strategies, however, have severe limitations with respect to generating the characteristic Nα-formylmethionyl terminus because the formyl group of the conjugate synthesized at the solid support is easily cleaved during the final basic deprotection/release step. In this study, we demonstrate a simple solution to the problem by coupling appropriately activated Nα-formyl methionine to the fully deprotected conjugate. The structural integrity of the obtained Nα-formylmethionyl conjugate─and hence the chemoselectivity of the reaction─were verified by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry sequence analysis. Additionally, we confirmed the applicability of our procedure for structural studies by obtaining two structures of the ribosome in complex with either fMAI-nh-ACCA or fMFI-nh-ACCA in the P site and ACC-PMN in the A site of the bacterial ribosome at 2.65 and 2.60 Å resolution, respectively. In summary, our approach for hydrolysis-resistant Nα-formylated RNA-peptide conjugates is synthetically straightforward and opens up new avenues to explore ribosomal translation with high-precision substrate mimics.
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Affiliation(s)
- Julia Thaler
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Egor A. Syroegin
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
| | - Kathrin Breuker
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Yury S. Polikanov
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
- Department
of Pharmaceutical Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
- Center
for Biomolecular Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ronald Micura
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
- Center
for Biomolecular Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
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14
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Subbaiah S P V, Uttamrao PP, Das U, Sundaresan S, Rathinavelan T. Concentration and time-dependent amyloidogenic characteristics of intrinsically disordered N-terminal region of Saccharomyces cerevisiae Stm1. Front Microbiol 2023; 14:1206945. [PMID: 37928673 PMCID: PMC10620681 DOI: 10.3389/fmicb.2023.1206945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Saccharomyces cerevisiae Stm1 protein is a ribosomal association factor, which plays an important role in preserving ribosomes in a nutrition-deprived environment. It is also shown to take part in apoptosis-like cell death. Stm1 N-terminal region (Stm1_N1-113) is shown to recognize purine motif DNA triplex and G-quadruplex. Circular dichroism (CD) spectra of Stm1_N1-113 (enriched in positively-charged Lysine and Arginine; negatively-charged Aspartate; polar-uncharged Threonine, Asparagine, Proline and Serine; hydrophobic Alanine, Valine, and Glycine) collected after 0 and 24 h indicate that the protein assumes beta-sheet conformation at the higher concentrations in contrast to intrinsically disordered conformation seen for its monomeric form found in the crystal structure. Thioflavin-T kinetics experiments indicate that the lag phase is influenced by the salt concentration. Atomic force microscopy (AFM) images collected for a variety of Stm1_N1-113 concentrations (in the range of 1-400 μM) in the presence of 150 mM NaCl at 0, 24, and 48 h indicate a threshold concentration requirement to observe the time-dependent amyloid formation. This is prominent seen at the physiological salt concentration of 150 mM NaCl with the fibrillation observed for 400 μM concentration at 48 h, whereas oligomerization or proto-fibrillation is seen for the other concentrations. Such concentration-dependent fibrillation of Stm1_N1-113 explains that amyloid fibrils formed during the overexpression of Stm1_N1-113 may act as a molecular device to trigger apoptosis-like cell death.
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Affiliation(s)
- Venkata Subbaiah S P
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Patil Pranita Uttamrao
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Uttam Das
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Sruthi Sundaresan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
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15
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Polikanov YS, Etheve-Quelquejeu M, Micura R. Synthesis of Peptidyl-tRNA Mimics for Structural Biology Applications. Acc Chem Res 2023; 56:2713-2725. [PMID: 37728742 PMCID: PMC10552525 DOI: 10.1021/acs.accounts.3c00412] [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: 07/19/2023] [Indexed: 09/21/2023]
Abstract
Protein biosynthesis is a central process in all living cells that is catalyzed by a complex molecular machine─the ribosome. This process is termed translation because the language of nucleotides in mRNAs is translated into the language of amino acids in proteins. Transfer RNA (tRNA) molecules charged with amino acids serve as adaptors and recognize codons of mRNA in the decoding center while simultaneously the individual amino acids are assembled into a peptide chain in the peptidyl transferase center (PTC). As the nascent peptide emerges from the ribosome, it is threaded through a long tunnel referred to as a nascent peptide exit tunnel (NPET). The PTC and NPET are the sites targeted by many antibiotics and are thus of tremendous importance from a biomedical perspective and for drug development in the pharmaceutical industry.Researchers have achieved much progress in characterizing ribosomal translation at the molecular level; an impressive number of high-resolution structures of different functional and inhibited states of the ribosome are now available. These structures have significantly contributed to our understanding of how the ribosome interacts with its key substrates, namely, mRNA, tRNAs, and translation factors. In contrast, much less is known about the mechanisms of how small molecules, especially antibiotics, affect ribosomal protein synthesis. This mainly concerns the structural basis of small molecule-NPET interference with cotranslational protein folding and the regulation of protein synthesis. Growing biochemical evidence suggests that NPET plays an active role in the regulation of protein synthesis.Much-needed progress in this field is hampered by the fact that during the preparation of ribosome complexes for structural studies (i.e., X-ray crystallography, cryoelectron microscopy, and NMR spectroscopy) the aminoacyl- or peptidyl-tRNAs are unstable and become hydrolyzed. A solution to this problem is the application of hydrolysis-resistant mimics of aminoacyl- or peptidyl-tRNAs.In this Account, we present an overview of synthetic methods for the generation of peptidyl-tRNA analogs. Modular approaches have been developed that combine (i) RNA and peptide solid-phase synthesis on 3'-aminoacylamino-adenosine resins, (ii) native chemical ligations and Staudinger ligations, (iii) tailoring of tRNAs by the selective cleavage of natural native tRNAs with DNAzymes followed by reassembly with enzymatic ligation to synthetic peptidyl-RNA fragments, and (iv) enzymatic tailing and cysteine charging of the tRNA to obtain modified CCA termini of a tRNA that are chemically ligated to the peptide moiety of interest. With this arsenal of tools, in principle, any desired sequence of a stably linked peptidyl-tRNA mimic is accessible. To underline the significance of the synthetic conjugates, we briefly point to the most critical applications that have shed new light on the molecular mechanisms underlying the context-specific activity of ribosome-targeting antibiotics, ribosome-dependent incorporation of multiple consecutive proline residues, the incorporation of d-amino acids, and tRNA mischarging.Furthermore, we discuss new types of stably charged tRNA analogs, relying on triazole- and squarate (instead of amide)-linked conjugates. Those have pushed forward our mechanistic understanding of nonribosomal peptide synthesis, where aminoacyl-tRNA-dependent enzymes are critically involved in various cellular processes in primary and secondary metabolism and in bacterial cell wall synthesis.
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Affiliation(s)
- Yury S. Polikanov
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
- Department
of Pharmaceutical Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
- Center for
Biomolecular Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
| | - Mélanie Etheve-Quelquejeu
- Université
Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques
et Toxicologiques, Paris F-75006, France
| | - Ronald Micura
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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16
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Joiret M, Kerff F, Rapino F, Close P, Geris L. A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics. Comput Struct Biotechnol J 2023; 21:3768-3795. [PMID: 37560126 PMCID: PMC10407619 DOI: 10.1016/j.csbj.2023.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
The central function of the large subunit of the ribosome is to catalyze peptide bond formation. This biochemical reaction is conducted at the peptidyl transferase center (PTC). Experimental evidence shows that the catalytic activity is affected by the electrostatic environment around the peptidyl transferase center. Here, we set up a minimal geometrical model fitting the available x-ray solved structures of the ribonucleic cavity around the catalytic center of the large subunit of the ribosome. The purpose of this phenomenological model is to estimate quantitatively the electrostatic potential and electric field that are experienced during the peptidyl transfer reaction. At least two reasons motivate the need for developing this quantification. First, we inquire whether the electric field in this particular catalytic environment, made only of nucleic acids, is of the same order of magnitude as the one prevailing in catalytic centers of the proteic enzymes counterparts. Second, the protein synthesis rate is dependent on the nature of the amino acid sequentially incorporated in the nascent chain. The activation energy of the catalytic reaction and its detailed kinetics are shown to be dependent on the mechanical work exerted on the amino acids by the electric field, especially when one of the four charged amino acid residues (R, K, E, D) has previously been incorporated at the carboxy-terminal end of the peptidyl-tRNA. Physical values of the electric field provide quantitative knowledge of mechanical work, activation energy and rate of the peptide bond formation catalyzed by the ribosome. We show that our theoretical calculations are consistent with two independent sets of previously published experimental results. Experimental results for E.coli in the minimal case of the dipeptide bond formation when puromycin is used as the final amino acid acceptor strongly support our theoretically derived reaction time courses. Experimental Ribo-Seq results on E. coli and S. cerevisiae comparing the residence time distribution of ribosomes upon specific codons are also well accounted for by our theoretical calculations. The statistical queueing time theory was used to model the ribosome residence time per codon during nascent protein elongation and applied for the interpretation of the Ribo-Seq data. The hypo-exponential distribution fits the residence time observed distribution of the ribosome on a codon. An educated deconvolution of this distribution is used to estimate the rates of each elongation step in a codon specific manner. Our interpretation of all these results sheds light on the functional role of the electrostatic profile around the PTC and its impact on the ribosome elongation cycle.
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Affiliation(s)
- Marc Joiret
- Biomechanics Research Unit, GIGA in silico medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
| | - Frederic Kerff
- UR InBios Centre d'Ingénierie des Protéines, Liège University, Bât B6a, Allèe du 6 Août, 19, B-4000 Liège, Belgium
| | - Francesca Rapino
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Pierre Close
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Liesbet Geris
- Biomechanics Research Unit, GIGA in silico medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
- Skeletal Biology & Engineering Research Center, KU Leuven, ON I Herestraat 49 - box 813, 3000 Leuven, Belgium
- Biomechanics Section, KU Leuven, Celestijnenlaan 300C box 2419, B-3001 Heverlee, Belgium
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17
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Majumdar C, Walker JA, Francis MB, Schepartz A, Cate JHD. Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome. ACS CENTRAL SCIENCE 2023; 9:1160-1169. [PMID: 37396857 PMCID: PMC10311655 DOI: 10.1021/acscentsci.3c00153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 07/04/2023]
Abstract
The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives-3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)-the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.
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Affiliation(s)
- Chandrima Majumdar
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - Joshua A. Walker
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Alanna Schepartz
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Jamie H. D. Cate
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Innovative
Genomics Institute, University of California, Berkeley, California 94720, United States
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18
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Obradović M, Malešević M, Di Luca M, Kekić D, Gajić I, McAuliffe O, Neve H, Stanisavljević N, Vukotić G, Kojić M. Isolation, Characterization, Genome Analysis and Host Resistance Development of Two Novel Lastavirus Phages Active against Pandrug-Resistant Klebsiella pneumoniae. Viruses 2023; 15:v15030628. [PMID: 36992337 PMCID: PMC10052179 DOI: 10.3390/v15030628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Klebsiella pneumoniae is a global health threat and bacteriophages are a potential solution in combating pandrug-resistant K. pneumoniae infections. Two lytic phages, LASTA and SJM3, active against several pandrug-resistant, nosocomial strains of K. pneumoniae were isolated and characterized. Their host range is narrow and latent period is particularly long; however, their lysogenic nature was refuted using both bioinformatic and experimental approaches. Genome sequence analysis clustered them with only two other phages into the new genus Lastavirus. Genomes of LASTA and SJM3 differ in only 13 base pairs, mainly located in tail fiber genes. Individual phages, as well as their cocktail, demonstrated significant bacterial reduction capacity in a time-dependent manner, yielding up to 4 log reduction against planktonic, and up to 2.59 log on biofilm-embedded, cells. Bacteria emerging from the contact with the phages developed resistance and achieved numbers comparable to the growth control after 24 h. The resistance to the phage seems to be of a transient nature and varies significantly between the two phages, as resistance to LASTA remained constant while resensitization to SJM3 was more prominent. Albeit with very few differences, SJM3 performed better than LASTA overall; however, more investigation is needed in order to consider them for therapeutic application.
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Affiliation(s)
- Mina Obradović
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
| | - Milka Malešević
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
| | | | - Dušan Kekić
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Ina Gajić
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Olivia McAuliffe
- Department of Food Biosciences, Teagasc Food Research Centre, P61 C996 Fermoy, Ireland
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany
| | - Nemanja Stanisavljević
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
| | - Goran Vukotić
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
- Correspondence: (G.V.); (M.K.)
| | - Milan Kojić
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
- Correspondence: (G.V.); (M.K.)
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19
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Cozma E, Rao M, Dusick M, Genereaux J, Rodriguez-Mias RA, Villén J, Brandl CJ, Berg MD. Anticodon sequence determines the impact of mistranslating tRNA Ala variants. RNA Biol 2023; 20:791-804. [PMID: 37776539 PMCID: PMC10543346 DOI: 10.1080/15476286.2023.2257471] [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] [Accepted: 08/31/2023] [Indexed: 10/02/2023] Open
Abstract
Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNAAla and the anticodon plays no role in charging, tRNAAla variants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNAAla anticodon variants on the growth of Saccharomyces cerevisiae. Overall, 36 tRNAAla anticodon variants decreased growth in single- or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C-rich anticodons resulted in larger growth deficits than A/U-rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNAAla variant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNAAla anticodon variants.
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Affiliation(s)
- Ecaterina Cozma
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Megha Rao
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Madison Dusick
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christopher J. Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Matthew D. Berg
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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20
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Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes. Nat Chem 2023; 15:143-153. [PMID: 36316410 PMCID: PMC9840698 DOI: 10.1038/s41557-022-01073-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 09/23/2022] [Indexed: 12/24/2022]
Abstract
During protein synthesis, the growing polypeptide threads through the ribosomal exit tunnel and modulates ribosomal activity by itself or by sensing various small molecules, such as metabolites or antibiotics, appearing in the tunnel. While arrested ribosome-nascent chain complexes (RNCCs) have been extensively studied structurally, the lack of a simple procedure for the large-scale preparation of peptidyl-tRNAs, intermediates in polypeptide synthesis that carry the growing chain, means that little attention has been given to RNCCs representing functionally active states of the ribosome. Here we report the facile synthesis of stably linked peptidyl-tRNAs through a chemoenzymatic approach based on native chemical ligation and use them to determine several structures of RNCCs in the functional pre-attack state of the peptidyl transferase centre. These structures reveal that C-terminal parts of the growing peptides adopt the same uniform β-strand conformation stabilized by an intricate network of hydrogen bonds with the universally conserved 23S rRNA nucleotides, and explain how the ribosome synthesizes growing peptides containing various sequences with comparable efficiencies.
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21
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Insights into Network of Hot Spots of Aggregation in Nucleophosmin 1. Int J Mol Sci 2022; 23:ijms232314704. [PMID: 36499032 PMCID: PMC9736328 DOI: 10.3390/ijms232314704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
In a protein, point mutations associated with diseases can alter the native structure and provide loss or alteration of functional levels, and an internal structural network defines the connectivity among domains, as well as aggregate/soluble states' equilibria. Nucleophosmin (NPM)1 is an abundant nucleolar protein, which becomes mutated in acute myeloid leukemia (AML) patients. NPM1-dependent leukemogenesis, which leads to its aggregation in the cytoplasm (NPMc+), is still obscure, but the investigations have outlined a direct link between AML mutations and amyloid aggregation. Protein aggregation can be due to the cooperation among several hot spots located within the aggregation-prone regions (APR), often predictable with bioinformatic tools. In the present study, we investigated potential APRs in the entire NPM1 not yet investigated. On the basis of bioinformatic predictions and experimental structures, we designed several protein fragments and analyzed them through typical aggrsegation experiments, such as Thioflavin T (ThT), fluorescence and scanning electron microscopy (SEM) experiments, carried out at different times; in addition, their biocompatibility in SHSY5 cells was also evaluated. The presented data clearly demonstrate the existence of hot spots of aggregation located in different regions, mostly in the N-terminal domain (NTD) of the entire NPM1 protein, and provide a more comprehensive view of the molecular details potentially at the basis of NPMc+-dependent AML.
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22
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Kwon HN, Kurtzeborn K, Iaroshenko V, Jin X, Loh A, Escande-Beillard N, Reversade B, Park S, Kuure S. Omics profiling identifies the regulatory functions of the MAPK/ERK pathway in nephron progenitor metabolism. Development 2022; 149:276992. [PMID: 36189831 PMCID: PMC9641663 DOI: 10.1242/dev.200986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/25/2022] [Indexed: 11/07/2022]
Abstract
Nephron endowment is defined by fetal kidney growth and crucially dictates renal health in adults. Defects in the molecular regulation of nephron progenitors contribute to only a fraction of reduced nephron mass cases, suggesting alternative causative mechanisms. The importance of MAPK/ERK activation in nephron progenitor maintenance has been previously demonstrated, and here, we characterized the metabolic consequences of MAPK/ERK deficiency. Liquid chromatography/mass spectrometry-based metabolomics profiling identified 42 reduced metabolites, of which 26 were supported by in vivo transcriptional changes in MAPK/ERK-deficient nephron progenitors. Among these, mitochondria, ribosome and amino acid metabolism, together with diminished pyruvate and proline metabolism, were the most affected pathways. In vitro cultures of mouse kidneys demonstrated a dosage-specific function for pyruvate in controlling the shape of the ureteric bud tip, a regulatory niche for nephron progenitors. In vivo disruption of proline metabolism caused premature nephron progenitor exhaustion through their accelerated differentiation in pyrroline-5-carboxylate reductases 1 (Pycr1) and 2 (Pycr2) double-knockout kidneys. Pycr1/Pycr2-deficient progenitors showed normal cell survival, indicating no changes in cellular stress. Our results suggest that MAPK/ERK-dependent metabolism functionally participates in nephron progenitor maintenance by monitoring pyruvate and proline biogenesis in developing kidneys.
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Affiliation(s)
- Hyuk Nam Kwon
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Kristen Kurtzeborn
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Vladislav Iaroshenko
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Xing Jin
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea
| | - Abigail Loh
- Institute of Molecular and Cellular Biology (IMCB), A*STAR, Singapore 138648, Singapore
| | - Nathalie Escande-Beillard
- Institute of Molecular and Cellular Biology (IMCB), A*STAR, Singapore 138648, Singapore,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Bruno Reversade
- Institute of Molecular and Cellular Biology (IMCB), A*STAR, Singapore 138648, Singapore,Medical Genetics Department, School of Medicine, Koç University, Istanbul 34010, Turkey
| | - Sunghyouk Park
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea
| | - Satu Kuure
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland,GM-unit, Laboratory Animal Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Author for correspondence ()
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23
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Dual contribution of the mTOR pathway and of the metabolism of amino acids in prostate cancer. Cell Oncol (Dordr) 2022; 45:831-859. [PMID: 36036882 DOI: 10.1007/s13402-022-00706-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Prostate cancer is the leading cause of cancer in men, and its incidence increases with age. Among other risk factors, pre-existing metabolic diseases have been recently linked with prostate cancer, and our current knowledge recognizes prostate cancer as a condition with important metabolic anomalies as well. In malignancies, metabolic disorders are commonly associated with aberrations in mTOR, which is the master regulator of protein synthesis and energetic homeostasis. Although there are reports demonstrating the high dependency of prostate cancer cells for lipid derivatives and even for carbohydrates, the understanding regarding amino acids, and the relationship with the mTOR pathway ultimately resulting in metabolic aberrations, is still scarce. CONCLUSIONS AND PERSPECTIVES In this review, we briefly provide evidence supporting prostate cancer as a metabolic disease, and discuss what is known about mTOR signaling and prostate cancer. Next, we emphasized on the amino acids glutamine, leucine, serine, glycine, sarcosine, proline and arginine, commonly related to prostate cancer, to explore the alterations in their regulatory pathways and to link them with the associated metabolic reprogramming events seen in prostate cancer. Finally, we display potential therapeutic strategies for targeting mTOR and the referred amino acids, as experimental approaches to selectively attack prostate cancer cells.
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24
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Choi UY, Lee JJ, Park A, Jung KL, Lee SA, Choi YJ, Lee HR, Lai CJ, Eoh H, Jung JU. Herpesvirus-induced spermidine synthesis and eIF5A hypusination for viral episomal maintenance. Cell Rep 2022; 40:111234. [PMID: 35977517 DOI: 10.1016/j.celrep.2022.111234] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 05/16/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022] Open
Abstract
Spermidine is essential for cellular growth and acts as a prerequisite of hypusination, a post-translational modification of eukaryotic initiation factor 5A (eIF5A), allowing the translation of polyproline-containing proteins. Here, we show that oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV) increases spermidine synthesis and eIF5A hypusination to enhance expression of polyproline-containing latency-associated nuclear antigen (LANA) for viral episomal maintenance. KSHV upregulates intracellular spermidine levels by dysregulating polyamine metabolic pathways in three-dimensional (3D) culture and 2D de novo infection conditions. Increased intracellular spermidine leads to increased eIF5A hypusination, ultimately enhancing LANA expression. In contrast, inhibition of spermidine synthesis or eIF5A hypusination alleviates LANA expression, decreasing viral episomal maintenance and KSHV-infected cell proliferation in vitro and in vivo, which is reversed by spermidine supplement. This demonstrates that KSHV hijacks spermidine synthesis and eIF5A hypusination pathways to enhance LANA expression for viral episomal maintenance, suggesting polyamine metabolism and eIF5A hypusination as therapeutic targets for KSHV-induced tumorigenesis.
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Affiliation(s)
- Un Yung Choi
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Jae Jin Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Angela Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kyle L Jung
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Shin-Ae Lee
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Youn Jung Choi
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong 30019, Republic of Korea
| | - Chih-Jen Lai
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Hyungjin Eoh
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jae U Jung
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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25
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Sur VP, Simonik O, Novotna M, Mazumdar A, Liska F, Vimberg V, Komrskova K. Dynamic study of small toxic hydrophobic proteins PepA1 and PepG1 of Staphylococcus aureus. Int J Biol Macromol 2022; 219:1360-1371. [PMID: 35932805 DOI: 10.1016/j.ijbiomac.2022.07.192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022]
Abstract
Toxin-antitoxin (TA) systems are small genetic elements which encode toxin proteins that interfere with vital cellular functions. PepA1 and PepG1 toxin proteins, known also as SprA1 and SprG1, are type I TA. In Staphylococcus aureus (S. aureus), their expression without the antitoxin counterparts (SprA1AS and SprF1), is lethal to the pathogen. Molecular Dynamics (MD) simulation was performed for PepA1 and PepG1 to understand their dynamic state, conformational changes, and their toxicity. The protein structures were constructed and used for MD simulation and the conformational changes, stability, flexibility, fluctuations, hydrophobicity, and role of their dynamic state on function prediction were studied extensively by GROMACS MD simulation analysis tools. In silico study indicated that the PepA1 and PepG1 proteins change their structural conformation from an open to closed state where PepA1 conformational changes were faster (10 ns) than PepG1 (20 ns) while PepG1 exerted more stability and flexibility than PepA1. According to SASA values, PepG1 is more hydrophobic than the PepA1 and forms fewer hydrogen bonds than PepA1. The in vivo study with PepA1 and PepG1 proteins provided evidence that both the conformation changes between the open and closed states and the amino acid sequence are crucial for peptide toxicity.
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Affiliation(s)
- Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Ondrej Simonik
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Michaela Novotna
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Aninda Mazumdar
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Frantisek Liska
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Vladimir Vimberg
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic.
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26
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Zhang S, Zhu J. Untargeted Metabolomics Sensitively Differentiates Gut Bacterial Species in Single Culture and Co-Culture Systems. ACS OMEGA 2022; 7:14643-14652. [PMID: 35557670 PMCID: PMC9088763 DOI: 10.1021/acsomega.1c07114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/15/2022] [Indexed: 05/28/2023]
Abstract
Gut microbiome plays a vital role in human health, and its characteristic has been widely identified through next-generation sequencing techniques. Although with great genomic insights into gut microbiome, its functional information is not clearly elaborated through metagenomic techniques. On the other hand, it is suggested that fecal metabolome can be used as a functional readout of the microbiome composition; therefore, we designed a proof-of-concept study to first characterize the metabolome of different gut microbes and then investigate the relationship between bacterial metabolomes and their compositions in co-culture systems. We selected eight representative bacteria species from Bifidobacterium (2), Bacteroides (1), Lactobacillus (4), and Akkermansia (1) genera as our model microbes. Liquid chromatography coupled mass spectrometry-based untargeted metabolomics was utilized to explore the microbial metabolome of bacteria single cultures and co-culture systems. Through spectral comparisons, our results showed that untargeted metabolomics could capture the similarity and differences in metabolic profiles from eight representative gut bacteria. Also, untargeted metabolomics could sensitively differentiate gut bacterial species based on our statistical analyses. For example, citrulline and histamine levels were significantly different among four Lactobacillus species. In addition, in the co-culture systems with different bacteria population ratios, gut bacterial metabolomes can be used to quantitatively reflect bacterial population in a mixed culture. For instance, the relative abundance of 2-hydroxybutyric acid changed proportionately with the changed population ratio of Lactobacillus reuteri in the co-culture system. In summary, we proposed a workflow that could demonstrate the capability of untargeted metabolomics in differentiating gut bacterial species and detecting their characteristic metabolites proportionally to the microbial population in co-culture systems.
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Affiliation(s)
- Shiqi Zhang
- Human
Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jiangjiang Zhu
- Human
Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, Ohio 43210, United States
- James
Comprehensive Cancer Center, The Ohio State
University, Columbus, Ohio 43210, United States
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27
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Fujita T, Yokoyama T, Shirouzu M, Taguchi H, Ito T, Iwasaki S. The landscape of translational stall sites in bacteria revealed by monosome and disome profiling. RNA (NEW YORK, N.Y.) 2022; 28:290-302. [PMID: 34906996 PMCID: PMC8848927 DOI: 10.1261/rna.078188.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/24/2021] [Indexed: 05/29/2023]
Abstract
Ribosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; however, the landscape of ribosome pauses in bacteria remains ambiguous. Here, we harness monosome and disome (or collided ribosome) profiling strategies to survey ribosome pause sites in Escherichia coli Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences: a low frequency of disomes at stop codons, collisions occurring immediately after 70S assembly on start codons, and shorter queues of ribosomes trailing upstream. The pause sites corresponded with the biochemical validation by integrated nascent chain profiling (iNP) to detect polypeptidyl-tRNA, an elongation intermediate. Moreover, the subset of those sites showed puromycin resistance, presenting slow peptidyl transfer. Among the identified sites, the ribosome pause at Asn586 of ycbZ was validated by biochemical reporter assay, tRNA sequencing (tRNA-seq), and cryo-electron microscopy (cryo-EM) experiments. Our results provide a useful resource for ribosome stalling sites in bacteria.
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Affiliation(s)
- Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Midori-ku, Yokohama 226-8503, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
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28
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Kaldmäe M, Vosselman T, Zhong X, Lama D, Chen G, Saluri M, Kronqvist N, Siau JW, Ng AS, Ghadessy FJ, Sabatier P, Vojtesek B, Sarr M, Sahin C, Österlund N, Ilag LL, Väänänen VA, Sedimbi S, Arsenian-Henriksson M, Zubarev RA, Nilsson L, Koeck PJ, Rising A, Abelein A, Fritz N, Johansson J, Lane DP, Landreh M. A “spindle and thread” mechanism unblocks p53 translation by modulating N-terminal disorder. Structure 2022; 30:733-742.e7. [DOI: 10.1016/j.str.2022.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 01/17/2022] [Accepted: 02/16/2022] [Indexed: 01/08/2023]
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29
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McDonnell CM, Ghanim M, Mike Southern J, Kelly VP, Connon SJ. De-novo designed β-lysine derivatives can both augment and diminish the proliferation rates of E. coli through the action of Elongation Factor P. Bioorg Med Chem Lett 2022; 59:128545. [PMID: 35032607 DOI: 10.1016/j.bmcl.2022.128545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
An investigation into the effect of modified β -lysines on the growth rates of eubacterial cells is reported. It is shown that the effects observed are due to the post translational modification of Elongation Factor P (EFP) with these compounds catalysed by PoxA. PoxA was found to be remarkably promiscuous, which allowed the activity of a wide range of exogenous β -lysines to be examined. Two chain-elongated β -lysine derivatives which differ in aminoalkyl chain length by only 2 carbon units exhibited opposing biological activities - one promoting growth and the other retarding it. Both compounds were shown to operate through modification of EFP.
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Affiliation(s)
- Ciara M McDonnell
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland
| | - Magda Ghanim
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland
| | - J Mike Southern
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland.
| | - Vincent P Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland.
| | - Stephen J Connon
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland.
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30
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Jia B, Wang T, Lehmann J. Peptidyl transferase center decompaction and structural constraints during early protein elongation on the ribosome. Sci Rep 2021; 11:24061. [PMID: 34911999 PMCID: PMC8674327 DOI: 10.1038/s41598-021-02985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022] Open
Abstract
Peptide bond formation on the ribosome requires that aminoacyl-tRNAs and peptidyl-tRNAs are properly positioned on the A site and the P site of the peptidyl transferase center (PTC) so that nucleophilic attack can occur. Here we analyse some constraints associated with the induced-fit mechanism of the PTC, that promotes this positioning through a compaction around the aminoacyl ester orchestrated by U2506. The physical basis of PTC decompaction, that allows the elongated peptidyl-tRNA to free itself from that state and move to the P site of the PTC, is still unclear. From thermodynamics considerations and an analysis of published ribosome structures, the present work highlights the rational of this mechanism, in which the free-energy released by the new peptide bond is used to kick U2506 away from the reaction center. Furthermore, we show the evidence that decompaction is impaired when the nascent peptide is not yet anchored inside the exit tunnel, which may contribute to explain why the first rounds of elongation are inefficient, an issue that has attracted much interest for about two decades. Results in this field are examined in the light of the present analysis and a physico-chemical correlation in the genetic code, which suggest that elementary constraints associated with the size of the side-chain of the amino acids penalize early elongation events.
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Affiliation(s)
- Bin Jia
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Tianlong Wang
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Jean Lehmann
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), University of Paris-Saclay, 91198, Gif-sur-Yvette, France.
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31
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Sanjaya RE, Putri KDA, Kurniati A, Rohman A, Puspaningsih NNT. In silico characterization of the GH5-cellulase family from uncultured microorganisms: physicochemical and structural studies. J Genet Eng Biotechnol 2021; 19:143. [PMID: 34591195 PMCID: PMC8484414 DOI: 10.1186/s43141-021-00236-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 08/29/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Hydrolysis of cellulose-based biomass by cellulases produce fermented sugar for making biofuels, such as bioethanol. Cellulases hydrolyze the β-1,4-glycosidic linkage of cellulose and can be obtained from cultured and uncultured microorganisms. Uncultured microorganisms are a source for exploring novel cellulase genes through the metagenomic approach. Metagenomics concerns the extraction, cloning, and analysis of the entire genetic complement of a habitat without cultivating microbes. The glycoside hydrolase 5 family (GH5) is a cellulase family, as the largest group of glycoside hydrolases. Numerous variants of GH5-cellulase family have been identified through the metagenomic approach, including CelGH5 in this study. University-CoE-Research Center for Biomolecule Engineering, Universitas Airlangga successfully isolated CelGH5 from waste decomposition of oil palm empty fruit bunches (OPEFB) soil by metagenomics approach. The properties and structural characteristics of GH5-cellulases from uncultured microorganisms can be studied using computational tools and software. RESULTS The GH5-cellulase family from uncultured microorganisms was characterized using standard computational-based tools. The amino acid sequences and 3D-protein structures were retrieved from the GenBank Database and Protein Data Bank. The physicochemical analysis revealed the sequence length was roughly 332-751 amino acids, with the molecular weight range around 37-83 kDa, dominantly negative charges with pI values below 7. Alanine was the most abundant amino acid making up the GH5-cellulase family and the percentage of hydrophobic amino acids was more than hydrophilic. Interestingly, ten endopeptidases with the highest average number of cleavage sites were found. Another uniqueness demonstrated that there was also a difference in stability between in silico and wet lab. The II values indicated CelGH5 and ACA61162.1 as unstable enzymes, while the wet lab showed they were stable at broad pH range. The program of SOPMA, PDBsum, ProSA, and SAVES provided the secondary and tertiary structure analysis. The predominant secondary structure was the random coil, and tertiary structure has fulfilled the structure quality of QMEAN4, ERRAT, Ramachandran plot, and Z score. CONCLUSION This study can afford the new insights about the physicochemical and structural properties of the GH5-cellulase family from uncultured microorganisms. Furthermore, in silico analysis could be valuable in selecting a highly efficient cellulases for enhanced enzyme production.
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Affiliation(s)
- Rahmat Eko Sanjaya
- Mathematics and Natural Science Study Program, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Chemistry Education Study Program, Faculty of Teacher Training and Education, Universitas Lambung Mangkurat, Jl. Brigjend. H. Hasan Basry, Banjarmasin, Kalimantan, 70123, Indonesia
| | - Kartika Dwi Asni Putri
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
| | - Anita Kurniati
- Mathematics and Natural Science Study Program, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Department of Health, Faculty of Vocational Studies, Kampus B Universitas Airlangga, Surabaya, East Java, 60286, Indonesia
| | - Ali Rohman
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Department of Chemistry, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
| | - Ni Nyoman Tri Puspaningsih
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia.
- Department of Chemistry, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia.
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32
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Zou J, Li Z, Liu S, Peng C, Fang D, Wan X, Lin Z, Lee TS, Raleigh DP, Yang M, Simmerling C. Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies. J Chem Theory Comput 2021; 17:3710-3726. [PMID: 34029468 PMCID: PMC8215533 DOI: 10.1021/acs.jctc.1c00214] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In silico screening of drug-target interactions is a key part of the drug discovery process. Changes in the drug scaffold via contraction or expansion of rings, the breaking of rings, and the introduction of cyclic structures from acyclic structures are commonly applied by medicinal chemists to improve binding affinity and enhance favorable properties of candidate compounds. These processes, commonly referred to as scaffold hopping, are challenging to model computationally. Although relative binding free energy (RBFE) calculations have shown success in predicting binding affinity changes caused by perturbing R-groups attached to a common scaffold, applications of RBFE calculations to modeling scaffold hopping are relatively limited. Scaffold hopping inevitably involves breaking and forming bond interactions of quadratic functional forms, which is highly challenging. A novel method for handling ring opening/closure/contraction/expansion and linker contraction/expansion is presented here. To the best of our knowledge, RBFE calculations on linker contraction/expansion have not been previously reported. The method uses auxiliary restraints to hold the atoms at the ends of a bond in place during the breaking and forming of the bonds. The broad applicability of the method was demonstrated by examining perturbations involving small-molecule macrocycles and mutations of proline in proteins. High accuracy was obtained using the method for most of the perturbations studied. The rigor of the method was isolated from the force field by validating the method using relative and absolute hydration free energy calculations compared to standard simulation results. Unlike other methods that rely on λ-dependent functional forms for bond interactions, the method presented here can be employed using modern molecular dynamics software without modification of codes or force field functions.
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Affiliation(s)
- Junjie Zou
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Zhipeng Li
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Shuai Liu
- XtalPi Inc., 245 Main St, 11th Floor, Cambridge, MA 02142, United States
| | - Chunwang Peng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Dong Fang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Xiao Wan
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Zhixiong Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, Rutgers University, Piscataway, New Jersey, 08854-8076, United States
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Mingjun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
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33
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Han P, Shichino Y, Schneider-Poetsch T, Mito M, Hashimoto S, Udagawa T, Kohno K, Yoshida M, Mishima Y, Inada T, Iwasaki S. Genome-wide Survey of Ribosome Collision. Cell Rep 2021; 31:107610. [PMID: 32375038 DOI: 10.1016/j.celrep.2020.107610] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 12/31/2022] Open
Abstract
Ribosome movement is not always smooth and is rather often impeded. For ribosome pauses, fundamental issues remain to be addressed, including where ribosomes pause on mRNAs, what kind of RNA/amino acid sequence causes this pause, and the physiological significance of this attenuation of protein synthesis. Here, we survey the positions of ribosome collisions caused by ribosome pauses in humans and zebrafish using modified ribosome profiling. Collided ribosomes, i.e., disomes, emerge at various sites: Pro-Pro/Gly/Asp motifs; Arg-X-Lys motifs; stop codons; and 3' untranslated regions. The electrostatic interaction between the charged nascent chain and the ribosome exit tunnel determines the eIF5A-mediated disome rescue at the Pro-Pro sites. In particular, XBP1u, a precursor of endoplasmic reticulum (ER)-stress-responsive transcription factor, shows striking queues of collided ribosomes and thus acts as a degradation substrate by ribosome-associated quality control. Our results provide insight into the causes and consequences of ribosome pause by dissecting collided ribosomes.
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Affiliation(s)
- Peixun Han
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Satoshi Hashimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Tsuyoshi Udagawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Kenji Kohno
- Institute for Research Initiatives, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuichiro Mishima
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
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34
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Pereira KD, Tamborlin L, de Lima TI, Consonni SR, Silveira LR, Luchessi AD. Alternative human eIF5A protein isoform plays a critical role in mitochondria. J Cell Biochem 2021; 122:549-561. [PMID: 33459432 DOI: 10.1002/jcb.29884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/24/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023]
Abstract
The eukaryotic translation initiation factor 5A (eIF5A) is the only known protein containing the amino acid residue hypusine, essential for its activity. Hypusine residue is produced by a posttranslational modification involving deoxyhypusine synthetase and deoxyhypusine hydroxylase. Herein, we aimed to describe the role of the alternative human isoform A on mitochondrial processes. Isoform A depletion modulates oxidative metabolism in association with the downregulation of mitochondrial biogenesis-related genes. Through positive feedback, it increases cell respiration leading to highly reactive oxygen species production, which impacts mitochondrial bioenergetics. These metabolic changes compromise mitochondrial morphology, increasing its electron density and fission, observed by transmission electron microscopy. This set of changes leads the cells to apoptosis, evidenced by increased DNA fragmentation and proapoptotic BAK protein content increase. Thus, we show that the alternative eIF5A isoform A is crucial for energy metabolism controlled by mitochondria and cellular survival.
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Affiliation(s)
- Karina D Pereira
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, São Paulo, Brazil
- Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Letícia Tamborlin
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, São Paulo, Brazil
- Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Tanes I de Lima
- Department of Structural and Functional Biology, Obesity and Comorbidities Research Center, University of Campinas (UNICAMP), Limeira, São Paulo, Brazil
| | - Silvio R Consonni
- Laboratory of Cytochemistry and Immunocytochemistry, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Leonardo R Silveira
- Department of Structural and Functional Biology, Obesity and Comorbidities Research Center, University of Campinas (UNICAMP), Limeira, São Paulo, Brazil
| | - Augusto D Luchessi
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, São Paulo, Brazil
- Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
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35
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Krasheninina OA, Thaler J, Erlacher MD, Micura R. Amine-to-Azide Conversion on Native RNA via Metal-Free Diazotransfer Opens New Avenues for RNA Manipulations. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:7046-7050. [PMID: 38504956 PMCID: PMC10947191 DOI: 10.1002/ange.202015034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/19/2020] [Indexed: 03/21/2024]
Abstract
A major challenge in the field of RNA chemistry is the identification of selective and quantitative conversion reactions on RNA that can be used for tagging and any other RNA tool development. Here, we introduce metal-free diazotransfer on native RNA containing an aliphatic primary amino group using the diazotizing reagent fluorosulfuryl azide (FSO2N3). The reaction provides the corresponding azide-modified RNA in nearly quantitatively yields without affecting the nucleobase amino groups. The obtained azido-RNA can then be further processed utilizing well-established bioortho-gonal reactions, such as azide-alkyne cycloadditions (Click) or Staudinger ligations. We exemplify the robustness of this approach for the synthesis of peptidyl-tRNA mimics and for the pull-down of 3-(3-amino-3-carboxypropyl)uridine (acp3U)- and lysidine (k2C)-containing tRNAs of an Escherichia coli tRNA pool isolated from cellular extracts. Our approach therefore adds a new dimension to the targeted chemical manipulation of diverse RNA species.
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Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Julia Thaler
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Matthias D. Erlacher
- Institute of Genomics and RNomicsBiocenterMedical University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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36
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Krasheninina OA, Thaler J, Erlacher MD, Micura R. Amine-to-Azide Conversion on Native RNA via Metal-Free Diazotransfer Opens New Avenues for RNA Manipulations. Angew Chem Int Ed Engl 2021; 60:6970-6974. [PMID: 33400347 PMCID: PMC8048507 DOI: 10.1002/anie.202015034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/19/2020] [Indexed: 12/12/2022]
Abstract
A major challenge in the field of RNA chemistry is the identification of selective and quantitative conversion reactions on RNA that can be used for tagging and any other RNA tool development. Here, we introduce metal-free diazotransfer on native RNA containing an aliphatic primary amino group using the diazotizing reagent fluorosulfuryl azide (FSO2 N3 ). The reaction provides the corresponding azide-modified RNA in nearly quantitatively yields without affecting the nucleobase amino groups. The obtained azido-RNA can then be further processed utilizing well-established bioortho-gonal reactions, such as azide-alkyne cycloadditions (Click) or Staudinger ligations. We exemplify the robustness of this approach for the synthesis of peptidyl-tRNA mimics and for the pull-down of 3-(3-amino-3-carboxypropyl)uridine (acp3 U)- and lysidine (k2 C)-containing tRNAs of an Escherichia coli tRNA pool isolated from cellular extracts. Our approach therefore adds a new dimension to the targeted chemical manipulation of diverse RNA species.
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Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Julia Thaler
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Matthias D. Erlacher
- Institute of Genomics and RNomicsBiocenterMedical University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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37
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Faundes V, Jennings MD, Crilly S, Legraie S, Withers SE, Cuvertino S, Davies SJ, Douglas AGL, Fry AE, Harrison V, Amiel J, Lehalle D, Newman WG, Newkirk P, Ranells J, Splitt M, Cross LA, Saunders CJ, Sullivan BR, Granadillo JL, Gordon CT, Kasher PR, Pavitt GD, Banka S. Impaired eIF5A function causes a Mendelian disorder that is partially rescued in model systems by spermidine. Nat Commun 2021; 12:833. [PMID: 33547280 PMCID: PMC7864902 DOI: 10.1038/s41467-021-21053-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
The structure of proline prevents it from adopting an optimal position for rapid protein synthesis. Poly-proline-tract (PPT) associated ribosomal stalling is resolved by highly conserved eIF5A, the only protein to contain the amino acid hypusine. We show that de novo heterozygous EIF5A variants cause a disorder characterized by variable combinations of developmental delay, microcephaly, micrognathia and dysmorphism. Yeast growth assays, polysome profiling, total/hypusinated eIF5A levels and PPT-reporters studies reveal that the variants impair eIF5A function, reduce eIF5A-ribosome interactions and impair the synthesis of PPT-containing proteins. Supplementation with 1 mM spermidine partially corrects the yeast growth defects, improves the polysome profiles and restores expression of PPT reporters. In zebrafish, knockdown eif5a partly recapitulates the human phenotype that can be rescued with 1 µM spermidine supplementation. In summary, we uncover the role of eIF5A in human development and disease, demonstrate the mechanistic complexity of EIF5A-related disorder and raise possibilities for its treatment.
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Affiliation(s)
- Víctor Faundes
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Martin D Jennings
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Siobhan Crilly
- Division of Neuroscience & Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sarah Legraie
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sarah E Withers
- Division of Neuroscience & Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sara Cuvertino
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sally J Davies
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Andrew G L Douglas
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Andrew E Fry
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Victoria Harrison
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Jeanne Amiel
- Department of Genetics, AP-HP, Hôpital Necker Enfants Malades, Paris, France
- 1Laboratory of Embryology and Genetics of Human Malformations, INSERM UMR 1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Daphné Lehalle
- Department of Genetics, AP-HP, Hôpital Necker Enfants Malades, Paris, France
| | - William G Newman
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Patricia Newkirk
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, UK
| | - Judith Ranells
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, UK
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle upon Tyne, UK
| | - Laura A Cross
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO, USA
- Department of Pediatrics, University of Missour-Kansas City, Kansas City, MO, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine Children's Mercy, Kansas City, MO, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO, USA
- Department of Pediatrics, University of Missour-Kansas City, Kansas City, MO, USA
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher T Gordon
- 1Laboratory of Embryology and Genetics of Human Malformations, INSERM UMR 1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Paul R Kasher
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
- Division of Neuroscience & Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.
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38
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DuPai CD, Davies BW, Wilke CO. A systematic analysis of the beta hairpin motif in the Protein Data Bank. Protein Sci 2021; 30:613-623. [PMID: 33389765 DOI: 10.1002/pro.4020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 12/31/2022]
Abstract
The beta hairpin motif is a ubiquitous protein structural motif that can be found in molecules across the tree of life. This motif, which is also popular in synthetically designed proteins and peptides, is known for its stability and adaptability to broad functions. Here, we systematically probe all 49,000 unique beta hairpin substructures contained within the Protein Data Bank (PDB) to uncover key characteristics correlated with stable beta hairpin structure, including amino acid biases and enriched interstrand contacts. We find that position specific amino acid preferences, while seen throughout the beta hairpin structure, are most evident within the turn region, where they depend on subtle turn dynamics associated with turn length and secondary structure. We also establish a set of broad design principles, such as the inclusion of aspartic acid residues at a specific position and the careful consideration of desired secondary structure when selecting residues for the turn region, that can be applied to the generation of libraries encoding proteins or peptides containing beta hairpin structures.
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Affiliation(s)
- Cory D DuPai
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.,Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Bryan W Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, John Ring LaMontagne Center for Infectious Diseases, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Claus O Wilke
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
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39
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Shah FA, Ni J, Yao Y, Hu H, Wei R, Wu L. Overexpression of Karrikins Receptor Gene Sapium sebiferum KAI2 Promotes the Cold Stress Tolerance via Regulating the Redox Homeostasis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:657960. [PMID: 34335642 PMCID: PMC8320022 DOI: 10.3389/fpls.2021.657960] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/07/2021] [Indexed: 05/04/2023]
Abstract
KARRIKINS INSENSITIVE2 (KAI2) is the receptor gene for karrikins, recently found to be involved in seed germination, hypocotyl development, and the alleviation of salinity and osmotic stresses. Nevertheless, whether KAI2 could regulate cold tolerance remains elusive. In the present study, we identified that Arabidopsis mutants of KAI2 had a high mortality rate, while overexpression of, a bioenergy plant, Sapium sebiferum KAI2 (SsKAI2) significantly recovered the plants after cold stress. The results showed that the SsKAI2 overexpression lines (OEs) had significantly increased levels of proline, total soluble sugars, and total soluble protein. Meanwhile, SsKAI2 OEs had a much higher expression of cold-stress-acclimation-relate genes, such as Cold Shock Proteins and C-REPEAT BINDING FACTORS under cold stress. Moreover, the results showed that SsKAI2 OEs were hypersensitive to abscisic acid (ABA), and ABA signaling genes were w significantly affected in SsKAI2 OEs under cold stress, suggesting a potential interaction between SsKAI2 and ABA downstream signaling. In SsKAI2 OEs, the electrolyte leakage, hydrogen peroxide, and malondialdehyde contents were reduced under cold stress in Arabidopsis. SsKAI2 OEs enhanced the anti-oxidants like ascorbate peroxidase, catalase, peroxidase, superoxide dismutase, and total glutathione level under cold stress. Conclusively, these results provide novel insights into the understanding of karrikins role in the regulation of cold stress adaptation.
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Affiliation(s)
- Faheem Afzal Shah
- Key Laboratory of the High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Jun Ni
- Key Laboratory of the High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Yuanyuan Yao
- Key Laboratory of the High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hao Hu
- Key Laboratory of the High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Ruyue Wei
- Key Laboratory of the High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Lifang Wu
- Key Laboratory of the High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Taihe Experimental Station, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Taihe, China
- *Correspondence: Lifang Wu,
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40
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Kawaguchi D, Kodama A, Abe N, Takebuchi K, Hashiya F, Tomoike F, Nakamoto K, Kimura Y, Shimizu Y, Abe H. Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Daisuke Kawaguchi
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Ayumi Kodama
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Naoko Abe
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kei Takebuchi
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kosuke Nakamoto
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yasuaki Kimura
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yoshihiro Shimizu
- Biodynamics Research Center (BDR) RIKEN 6-2-3, Furuedai Suita Osaka 565-0874 Japan
| | - Hiroshi Abe
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- CREST (Japan) Science and Technology Agency 7, Gobancho, Chiyoda-ku Tokyo 102-0076 Japan
- Institute for Glyco-core Research Tokai National Higher Education and Research System Furo-cho, Chikusa-ku Nagoya Aichi 464-8601 Japan
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41
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Chang A, Ting JP, Espada A, Broughton H, Molina-Martin M, Afshar S. A novel phage display vector for selection of target-specific peptides. Protein Eng Des Sel 2020; 33:5917485. [PMID: 33009572 DOI: 10.1093/protein/gzaa023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 11/14/2022] Open
Abstract
Intrinsic low display level of polypeptides on phage is a fundamental and limiting hurdle in successful isolation of target-specific binders by phage display technology. To circumvent this challenge, we optimized the copy number of peptides displayed on the phage surface using type 33 phage vector. We randomized the first 67 amino acids of the wild type PIII to identify mutants that would result in its reduced expression. Consequently, the display level was improved by 30-fold due to higher incorporation of the synthetic PIII-peptide fusion protein on the phage surface. Utilization of this novel phage vector should provide a solid basis for the discovery of therapeutic peptides.
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Affiliation(s)
- Alex Chang
- Department of Pharmacy, Santa Clara Valley Medical Center, San Jose CA 95128, USA
| | - Joey P Ting
- Protein Engineering, Eli Lilly Biotechnology Center, San Diego, CA 92121, USA
| | - Alfonso Espada
- Department of Discovery Chemistry Research & Technology, Centro de Investigacion Lilly, Av. de la Industria, 30, 28108 Alcobendas, Madrid, Spain
| | - Howard Broughton
- Department of Discovery Chemistry Research & Technology, Centro de Investigacion Lilly, Av. de la Industria, 30, 28108 Alcobendas, Madrid, Spain
| | - Manuel Molina-Martin
- Department of Discovery Chemistry Research & Technology, Centro de Investigacion Lilly, Av. de la Industria, 30, 28108 Alcobendas, Madrid, Spain
| | - Sepideh Afshar
- Protein Engineering, Eli Lilly Biotechnology Center, San Diego, CA 92121, USA
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42
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Kawaguchi D, Kodama A, Abe N, Takebuchi K, Hashiya F, Tomoike F, Nakamoto K, Kimura Y, Shimizu Y, Abe H. Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. Angew Chem Int Ed Engl 2020; 59:17403-17407. [PMID: 32627275 DOI: 10.1002/anie.202007111] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Indexed: 01/19/2023]
Abstract
Messenger RNAs (mRNAs) with phosphorothioate modification (PS-mRNA) to the phosphate site of A, G, C, and U with all 16 possible combinations were prepared, and the translation reaction was evaluated using an E. coli cell-free translation system. Protein synthesis from PS-mRNA increased in 12 of 15 patterns when compared with that of unmodified mRNA. The protein yield increased 22-fold when the phosphorothioate modification at A/C sites was introduced into the region from the 5'-end to the initiation codon. Single-turnover analysis of PS-mRNA translation showed that phosphorothioate modification increases the number of translating ribosomes, thus suggesting that the rate of translation initiation (rate of ribosome complex formation) is positively affected by the modification. The method provides a new strategy for improving translation by using non-natural mRNA.
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Affiliation(s)
- Daisuke Kawaguchi
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ayumi Kodama
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kei Takebuchi
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kosuke Nakamoto
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yoshihiro Shimizu
- Biodynamics Research Center (BDR), RIKEN, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hiroshi Abe
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST (Japan) Science and Technology Agency, 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.,Institute for Glyco-core Research, Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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43
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Abe T, Nagai R, Shimazaki S, Kondo S, Nishimura S, Sakaguchi Y, Suzuki T, Imataka H, Tomita K, Takeuchi-Tomita N. In vitro yeast reconstituted translation system reveals function of eIF5A for synthesis of long polypeptide. J Biochem 2020; 167:451-462. [PMID: 32053170 DOI: 10.1093/jb/mvaa022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
We have recently developed an in vitro yeast reconstituted translation system, which is capable of synthesizing long polypeptides. Utilizing the system, we examined the role of eIF5A and its hypusine modification in translating polyproline sequence within long open reading frames. We found that polyproline motif inserted at the internal position of the protein arrests translation exclusively at low Mg2+ concentrations, and peptidylpolyproline-tRNA intrinsically destabilizes 80S ribosomes. We demonstrate that unmodified eIF5A essentially resolves such ribosome stalling; however, the hypusine modification drastically stimulates ability of eIF5A to rescue polyproline-mediated ribosome stalling and is particularly important for the efficient translation of the N-terminal or long internal polyproline motifs.
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Affiliation(s)
- Taisho Abe
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Riku Nagai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Shunta Shimazaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Shunta Kondo
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Satoshi Nishimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Imataka
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Nono Takeuchi-Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
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44
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Collart MA, Weiss B. Ribosome pausing, a dangerous necessity for co-translational events. Nucleic Acids Res 2020; 48:1043-1055. [PMID: 31598688 PMCID: PMC7026645 DOI: 10.1093/nar/gkz763] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/13/2019] [Accepted: 08/21/2019] [Indexed: 12/31/2022] Open
Abstract
In recent years translation elongation has emerged as an important contributor to the regulation of gene expression. There are multiple quality control checkpoints along the way of producing mature proteins and targeting them to the right cellular compartment, or associating them correctly with their partners. Ribosomes pause to allow co-translational protein folding, protein targeting or protein interactions, and the pausing is dictated by a combination of the mRNA sequence and structure, the tRNA availability and the nascent peptide. However, ribosome pausing can also lead to ribosome collisions and co-translational degradation of both mRNA and nascent chain. Understanding how the translating ribosome tunes the different maturation steps that nascent proteins must undergo, what the timing of these maturation events is, and how degradation can be avoided when pausing is needed, is now possible by the emergence of methods to follow ribosome dynamics in vivo. This review summarizes some of the recent studies that have advanced our knowledge about co-translational events using the power of ribosome profiling, and some of the questions that have emerged from these studies.
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Affiliation(s)
- Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics, Geneva, 1 rue Michel Servet, 1211 Genève 4, Switzerland
| | - Benjamin Weiss
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics, Geneva, 1 rue Michel Servet, 1211 Genève 4, Switzerland
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45
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Jash B, Richert C. Templates direct the sequence-specific anchoring of the C-terminus of peptido RNAs. Chem Sci 2020; 11:3487-3494. [PMID: 34109020 PMCID: PMC8152794 DOI: 10.1039/c9sc05958j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 02/28/2020] [Indexed: 02/02/2023] Open
Abstract
When amino acids and ribonucleotides react in aqueous condensation buffer, they form peptido RNA with a phosphoramidate bond between the N-terminus of the peptide and the 5'-terminal phosphate of a ribonucleotide. If peptido RNA was the product of spontaneous reactions of amino acids and nucleotides, there must have been a transition to peptidyl tRNAs, where the C-terminus of the peptide is ester-linked to the 2',3'-terminus of an oligonucleotide. Here we report how short peptido RNAs react with the 3'-terminus of oligodeoxynucleotides, templated by RNA strands. In our model system, the rate and yield of the anchoring of the C-terminus of the dipeptido dinucleotides to an amino group was found to depend on the sequence of the peptide, the 5'-terminal nucleotide of the dinucleotide and the RNA template. In all cases tested, highest yields were found for dinucleotides hybridizing next to the primer terminus. For the most reactive species, GlyPro-AA, anchoring yields ranged from 8-99%, depending on the template. When LeuLeu-AA, PhePhe-AA and GlyGly-AA were allowed to compete for anchoring on 3'-UUC-5' as templating sequence, they gave a product ratio of 1 : 2 : 6, and this selectivity was almost independent of the terminal base of the primer. Our results show the control that a simple duplex context has over the covalent anchoring of peptido RNAs at a position known from peptidyl tRNAs. Processes of this type may have bridged the gap between untemplated condensation reactions and the highly specific processes of ribosomal protein synthesis.
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Affiliation(s)
- Biswarup Jash
- Institute of Organic Chemistry, University of Stuttgart 70569 Stuttgart Germany +49 711 608 64321 +49 711 608 64311
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart 70569 Stuttgart Germany +49 711 608 64321 +49 711 608 64311
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46
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Hammerling MJ, Krüger A, Jewett MC. Strategies for in vitro engineering of the translation machinery. Nucleic Acids Res 2020; 48:1068-1083. [PMID: 31777928 PMCID: PMC7026604 DOI: 10.1093/nar/gkz1011] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023] Open
Abstract
Engineering the process of molecular translation, or protein biosynthesis, has emerged as a major opportunity in synthetic and chemical biology to generate novel biological insights and enable new applications (e.g. designer protein therapeutics). Here, we review methods for engineering the process of translation in vitro. We discuss the advantages and drawbacks of the two major strategies-purified and extract-based systems-and how they may be used to manipulate and study translation. Techniques to engineer each component of the translation machinery are covered in turn, including transfer RNAs, translation factors, and the ribosome. Finally, future directions and enabling technological advances for the field are discussed.
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Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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47
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Dynamics of transcription–translation coordination tune bacterial indole signaling. Nat Chem Biol 2019; 16:440-449. [DOI: 10.1038/s41589-019-0430-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 11/08/2019] [Indexed: 12/31/2022]
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48
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Verma M, Choi J, Cottrell KA, Lavagnino Z, Thomas EN, Pavlovic-Djuranovic S, Szczesny P, Piston DW, Zaher HS, Puglisi JD, Djuranovic S. A short translational ramp determines the efficiency of protein synthesis. Nat Commun 2019; 10:5774. [PMID: 31852903 PMCID: PMC6920384 DOI: 10.1038/s41467-019-13810-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/25/2019] [Indexed: 01/26/2023] Open
Abstract
Translation initiation is a major rate-limiting step for protein synthesis. However, recent studies strongly suggest that the efficiency of protein synthesis is additionally regulated by multiple factors that impact the elongation phase. To assess the influence of early elongation on protein synthesis, we employed a library of more than 250,000 reporters combined with in vitro and in vivo protein expression assays. Here we report that the identity of the amino acids encoded by codons 3 to 5 impact protein yield. This effect is independent of tRNA abundance, translation initiation efficiency, or overall mRNA structure. Single-molecule measurements of translation kinetics revealed pausing of the ribosome and aborted protein synthesis on codons 4 and 5 of distinct amino acid and nucleotide compositions. Finally, introduction of preferred sequence motifs only at specific codon positions improves protein synthesis efficiency for recombinant proteins. Collectively, our data underscore the critical role of early elongation events in translational control of gene expression. Several factors contribute to the efficiency of protein expression. Here the authors show that the identity of amino acids encoded by codons at position 3–5 significantly impact translation efficiency and protein expression levels.
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Affiliation(s)
- Manasvi Verma
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305-5126, USA.,Department of Applied Physics, Stanford University, Stanford, CA, 94305-5126, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kyle A Cottrell
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Zeno Lavagnino
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA.,Experimental Imaging Center, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Erica N Thomas
- Department of Biology, Washington University, St Louis, MO, 63105, USA
| | - Slavica Pavlovic-Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Pawel Szczesny
- Department of Bioinformatics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - David W Piston
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Hani S Zaher
- Department of Biology, Washington University, St Louis, MO, 63105, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305-5126, USA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA.
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49
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Katoh T, Suga H. Flexizyme-catalyzed synthesis of 3'-aminoacyl-NH-tRNAs. Nucleic Acids Res 2019; 47:e54. [PMID: 30843032 PMCID: PMC6511858 DOI: 10.1093/nar/gkz143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/08/2019] [Accepted: 03/02/2019] [Indexed: 11/15/2022] Open
Abstract
Structural analysis of ribosomes in complex with aminoacyl- and/or peptidyl-transfer RNA (tRNA) often suffers from rapid hydrolysis of the ester bond of aminoacyl-tRNAs. To avoid this issue, several methods to introduce an unhydrolyzable amide bond instead of the canonical ester bond have been developed to date. However, the existing methodologies require rather complex steps of synthesis and are often inapplicable to a variety of amino acids including those with noncanonical structures. Here, we report a new method to synthesize 3'-aminoacyl-NH-tRNAs by means of flexizymes-ribozymes capable of charging amino acids onto tRNAs. We show that two types of flexizymes, dFx and eFx, are able to charge various amino acids, including nonproteinogenic ones, onto tRNA or microhelix RNA bearing the 3'-deoxy-3'-amino-adenosine. Due to the versatility of the flexizymes toward any pair of nonproteinogenic amino acids and full-length or fragment tRNAs, this method provides researchers an opportunity to use a wide array of hydrolytically stable 3'-aminoacyl-NH-tRNAs and analogs for various studies.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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50
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Sharma IM, Rappé MC, Addepalli B, Grabow WW, Zhuang Z, Abeysirigunawardena SC, Limbach PA, Jaeger L, Woodson SA. A metastable rRNA junction essential for bacterial 30S biogenesis. Nucleic Acids Res 2019; 46:5182-5194. [PMID: 29850893 PMCID: PMC6007441 DOI: 10.1093/nar/gky120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/13/2018] [Indexed: 12/26/2022] Open
Abstract
Tertiary sequence motifs encode interactions between RNA helices that create the three-dimensional structures of ribosomal subunits. A Right Angle motif at the junction between 16S helices 5 and 6 (J5/6) is universally conserved amongst small subunit rRNAs and forms a stable right angle in minimal RNAs. J5/6 does not form a right angle in the mature ribosome, suggesting that this motif encodes a metastable structure needed for ribosome biogenesis. In this study, J5/6 mutations block 30S ribosome assembly and 16S maturation in Escherichia coli. Folding assays and in-cell X-ray footprinting showed that J5/6 mutations favor an assembly intermediate of the 16S 5' domain and prevent formation of the central pseudoknot. Quantitative mass spectrometry revealed that mutant pre-30S ribosomes lack protein uS12 and are depleted in proteins uS5 and uS2. Together, these results show that impaired folding of the J5/6 right angle prevents the establishment of inter-domain interactions, resulting in global collapse of the 30S structure observed in electron micrographs of mutant pre-30S ribosomes. We propose that the J5/6 motif is part of a spine of RNA helices that switch conformation at distinct stages of assembly, linking peripheral domains with the 30S active site to ensure the integrity of 30S biogenesis.
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Affiliation(s)
- Indra Mani Sharma
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Mollie C Rappé
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Balasubrahmanyam Addepalli
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Wade W Grabow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | - Zhuoyun Zhuang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | | | - Patrick A Limbach
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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