101
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Guzel P, Yildirim HZ, Yuce M, Kurkcuoglu O. Exploring Allosteric Signaling in the Exit Tunnel of the Bacterial Ribosome by Molecular Dynamics Simulations and Residue Network Model. Front Mol Biosci 2020; 7:586075. [PMID: 33102529 PMCID: PMC7545307 DOI: 10.3389/fmolb.2020.586075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/08/2020] [Indexed: 11/25/2022] Open
Abstract
The bacterial ribosomal tunnel is equipped with numerous sites highly sensitive to the course of the translation process. This study investigates allosteric pathways linking distant functional sites that collaboratively play a role either in translation regulation or recruitment of chaperones. We apply perturbation response scanning (PRS) analysis to 700 ns long and 500 ns long coarse-grained molecular dynamics simulations of E. coli and T. thermophilus large subunits, respectively, to reveal nucleotides/residues with the ability to transmit perturbations by dynamic rationale. We also use the residue network model with the k-shortest pathways method to calculate suboptimal pathways based on the contact topology of the ribosomal tunnel of E. coli crystal structure and 101 ClustENM generated conformers of T. thermophilus large subunit. In the upper part of the tunnel, results suggest that A2062 and A2451 can communicate in both directions for translation stalling, mostly through dynamically coupled C2063, C2064, and A2450. For a similar purpose, U2585 and U2586 are coupled with A2062, while they are also sensitive to uL4 and uL22 at the constriction region through two different pathways at the opposite sides of the tunnel wall. In addition, the constriction region communicates with the chaperone binding site on uL23 at the solvent side but through few nucleotides. Potential allosteric communication pathways between the lower part of the tunnel and chaperone binding site mostly use the flexible loop of uL23, while A1336–G1339 provide a suboptimal pathway. Both species seem to employ similar mechanisms in the long tunnel, where a non-conserved cavity at the bacterial uL23 and 23S rRNA interface is proposed as a novel drug target.
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Affiliation(s)
- Pelin Guzel
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey.,Science and Advanced Technology Research and Application Center, Istanbul Medeniyet University, Istanbul, Turkey
| | - Hatice Zeynep Yildirim
- Polymer Research Center and Graduate Program in Computational Science and Engineering, Bogazici University, Istanbul, Turkey
| | - Merve Yuce
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
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102
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Polymenis M. Ribosomal proteins: mutant phenotypes by the numbers and associated gene expression changes. Open Biol 2020; 10:200114. [PMID: 32810425 PMCID: PMC7479938 DOI: 10.1098/rsob.200114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosomal proteins are highly conserved, many universally so among organisms. All ribosomal proteins are structural parts of the same molecular machine, the ribosome. However, when ribosomal proteins are mutated individually, they often lead to distinct and intriguing phenotypes, including specific human pathologies. This review is an attempt to collect and analyse all the reported phenotypes of each ribosomal protein mutant in several eukaryotes (Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, Homo sapiens). These phenotypes were processed with unbiased computational approaches to reveal associations between different phenotypes and the contributions of individual ribosomal protein genes. An overview of gene expression changes in ribosomal protein mutants, with emphasis on ribosome profiling studies, is also presented. The available data point to patterns that may account for most of the observed phenotypes. The information presented here may also inform future studies about the molecular basis of the phenotypes that arise from mutations in ribosomal proteins.
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Affiliation(s)
- Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
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103
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Huang HJ, Cui JR, Hong XY. Comparative analysis of diet-associated responses in two rice planthopper species. BMC Genomics 2020; 21:565. [PMID: 32807078 PMCID: PMC7437935 DOI: 10.1186/s12864-020-06976-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 08/10/2020] [Indexed: 11/21/2022] Open
Abstract
Background Host adaptation is the primary determinant of insect diversification. However, knowledge of different host ranges in closely related species remains scarce. The brown planthopper (Nilaparvata lugens, BPH) and the small brown planthopper (Laodelphax striatellus, SBPH) are the most destructive insect pests within the family Delphacidae. These two species differ in their host range (SBPH can well colonize rice and wheat plants, whereas BPH survives on only rice plants), but the underlying mechanism of this difference remains unknown. High-throughput sequencing provides a powerful approach for analyzing the association between changes in gene expression and the physiological responses of insects. Therefore, gut transcriptomes were performed to elucidate the genes associated with host adaptation in planthoppers. The comparative analysis of planthopper responses to different diets will improve our knowledge of host adaptation regarding herbivorous insects. Results In the present study, we analyzed the change in gene expression of SBPHs that were transferred from rice plants to wheat plants over the short term (rSBPH vs tSBPH) or were colonized on wheat plants over the long term (rSBPH vs wSBPH). The results showed that the majority of differentially expressed genes in SBPH showed similar changes in expression for short-term transfer and long-term colonization. Based on a comparative analysis of BPH and SBPH after transfer, the genes associated with sugar transporters and heat-shock proteins showed similar variation. However, most of the genes were differentially regulated between the two species. The detoxification-related genes were upregulated in SBPH after transfer from the rice plants to the wheat plants, but these genes were downregulated in BPH under the same conditions. In contrast, ribosomal-related genes were downregulated in SBPH after transfer, but these genes were upregulated in BPH under the same conditions. Conclusions The results of this study provide evidence that host plants played a dominant role in shaping gene expression and that the low fitness of BPH on wheat plants might be determined within 24 h after transfer. This study deepens our understanding of different host ranges for the two planthopper species, which may provide a potential strategy for pest management.
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Affiliation(s)
- Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.,Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jia-Rong Cui
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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104
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Venkataram S, Monasky R, Sikaroodi SH, Kryazhimskiy S, Kacar B. Evolutionary stalling and a limit on the power of natural selection to improve a cellular module. Proc Natl Acad Sci U S A 2020; 117:18582-18590. [PMID: 32680961 PMCID: PMC7414050 DOI: 10.1073/pnas.1921881117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cells consist of molecular modules which perform vital biological functions. Cellular modules are key units of adaptive evolution because organismal fitness depends on their performance. Theory shows that in rapidly evolving populations, such as those of many microbes, adaptation is driven primarily by common beneficial mutations with large effects, while other mutations behave as if they are effectively neutral. As a consequence, if a module can be improved only by rare and/or weak beneficial mutations, its adaptive evolution would stall. However, such evolutionary stalling has not been empirically demonstrated, and it is unclear to what extent stalling may limit the power of natural selection to improve modules. Here we empirically characterize how natural selection improves the translation machinery (TM), an essential cellular module. We experimentally evolved populations of Escherichia coli with genetically perturbed TMs for 1,000 generations. Populations with severe TM defects initially adapted via mutations in the TM, but TM adaptation stalled within about 300 generations. We estimate that the genetic load in our populations incurred by residual TM defects ranges from 0.5 to 19%. Finally, we found evidence that both epistasis and the depletion of the pool of beneficial mutations contributed to evolutionary stalling. Our results suggest that cellular modules may not be fully optimized by natural selection despite the availability of adaptive mutations.
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Affiliation(s)
- Sandeep Venkataram
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Ross Monasky
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | - Shohreh H Sikaroodi
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Sergey Kryazhimskiy
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093;
| | - Betul Kacar
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721;
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ 85721
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105
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Kuncha SK, Venkadasamy VL, Amudhan G, Dahate P, Kola SR, Pottabathini S, Kruparani SP, Shekar PC, Sankaranarayanan R. Genomic innovation of ATD alleviates mistranslation associated with multicellularity in Animalia. eLife 2020; 9:58118. [PMID: 32463355 PMCID: PMC7302879 DOI: 10.7554/elife.58118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
The emergence of multicellularity in Animalia is associated with increase in ROS and expansion of tRNA-isodecoders. tRNA expansion leads to misselection resulting in a critical error of L-Ala mischarged onto tRNAThr, which is proofread by Animalia-specific-tRNA Deacylase (ATD) in vitro. Here we show that in addition to ATD, threonyl-tRNA synthetase (ThrRS) can clear the error in cellular scenario. This two-tier functional redundancy for translation quality control breaks down during oxidative stress, wherein ThrRS is rendered inactive. Therefore, ATD knockout cells display pronounced sensitivity through increased mistranslation of threonine codons leading to cell death. Strikingly, we identify the emergence of ATD along with the error inducing tRNA species starting from Choanoflagellates thus uncovering an important genomic innovation required for multicellularity that occurred in unicellular ancestors of animals. The study further provides a plausible regulatory mechanism wherein the cellular fate of tRNAs can be switched from protein biosynthesis to non-canonical functions. The first animals evolved around 750 million years ago from single-celled ancestors that were most similar to modern-day organisms called the Choanoflagellates. As animals evolved they developed more complex body plans consisting of multiple cells organized into larger structures known as tissues and organs. Over time cells also evolved increased levels of molecules called reactive oxygen species, which are involved in many essential cell processes but are toxic at high levels. Animal cells also contain more types of molecules known as transfer ribonucleic acids, or tRNAs for short, than Choanoflagellate cells and other single-celled organisms. These molecules deliver building blocks known as amino acids to the machinery that produces new proteins. To ensure the proteins are made correctly, it is important that tRNAs deliver specific amino acids to the protein-building machinery in the right order. Each type of tRNA usually only pairs with a specific type of amino acid, but sometimes the enzymes involved in this process can make mistakes. Therefore, cells contain proofreading enzymes that help remove incorrect amino acids on tRNAs. One such enzyme – called ATD – is only found in animals. Experiments in test tubes reported that ATD removes an amino acid called alanine from tRNAs that are supposed to carry threonine, but its precise role in living cells remained unclear. To address this question, Kuncha et al. studied proofreading enzymes in human kidney cells. The experiments showed that, in addition to ATD, a second enzyme known as ThrRS was also able to correct alanine substitutions for threonines on tRNAs. However, reactive oxygen species inactivated the proofreading ability of ThrRS, suggesting ATD plays an essential role in correcting errors in cells containing high levels of reactive oxygen species. These findings suggest that as organisms evolved multiple cells and the levels of tRNA and oxidative stress increased, this led to the appearance of a new proofreading enzyme. Further studies found that ATD originated around 900 million years ago, before Choanoflagellates and animals diverged, indicating these enzymes might have helped to shape the evolution of animals. The next step following on from this work will be to understand the role of ATD in the cells of organs that are known to have particularly high levels of reactive oxygen species, such as testis and ovaries.
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Affiliation(s)
- Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | | | - Priyanka Dahate
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sankara Rao Kola
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - P Chandra Shekar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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106
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Ethylicin Prevents Potato Late Blight by Disrupting Protein Biosynthesis of Phytophthora infestans. Pathogens 2020; 9:pathogens9040299. [PMID: 32325810 PMCID: PMC7238019 DOI: 10.3390/pathogens9040299] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
Phytophthora infestans, the causal agent of potato late blight, triggered the devastating Great Irish Famine that lasted from 1845 to 1852. Today, it is still the greatest threat to the potato yield. Ethylicin is a broad-spectrum biomimetic-fungicide. However, its application in the control of Phytophthora infestans is still unknown. In this study, we investigated the effects of ethylicin on Phytophthora infestans. We found that ethylicin inhibited the mycelial growth, sporulation capacity, spore germination and virulence of Phytophthora infestans. Furthermore, the integrated analysis of proteomics and metabolomics indicates that ethylicin may inhibit peptide or protein biosynthesis by suppressing both the ribosomal function and amino acid metabolism, causing an inhibitory effect on Phytophthora infestans. These observations indicate that ethylicin may be an anti-oomycete agent that can be used to control Phytophthora infestans.
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107
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New codons for efficient production of unnatural proteins in a semisynthetic organism. Nat Chem Biol 2020; 16:570-576. [PMID: 32251411 PMCID: PMC7263176 DOI: 10.1038/s41589-020-0507-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/20/2020] [Accepted: 02/25/2020] [Indexed: 12/02/2022]
Abstract
Natural organisms use a four-letter genetic alphabet that makes available
64 triplet codons, of which 61 are sense codons used to encode proteins with the
20 canonical amino acids. We have shown that the unnatural nucleotides dNaM and
dTPT3 pair to form an unnatural base pair (UBP) and allow for the creation of
semi-synthetic organisms (SSOs) with additional sense codons. Here we report a
systematic analysis of the unnatural codons. We identify nine unnatural codons
that can produce unnatural protein with nearly complete incorporation of an
encoded non-canonical amino acid (ncAA). We also show that at least three of the
codons are orthogonal and can be simultaneously decoded in the SSO, affording
the first 67-codon organism. The ability to site-specifically incorporate
multiple, different ncAAs into a protein should now allow for the development of
proteins with novel activities and possibly even SSOs with new forms and
functions.
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108
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Komar AA, Merrick WC. A Retrospective on eIF2A-and Not the Alpha Subunit of eIF2. Int J Mol Sci 2020; 21:E2054. [PMID: 32192132 PMCID: PMC7139343 DOI: 10.3390/ijms21062054] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/29/2020] [Accepted: 03/13/2020] [Indexed: 12/31/2022] Open
Abstract
Initiation of protein synthesis in eukaryotes is a complex process requiring more than 12 different initiation factors, comprising over 30 polypeptide chains. The functions of many of these factors have been established in great detail; however, the precise role of some of them and their mechanism of action is still not well understood. Eukaryotic initiation factor 2A (eIF2A) is a single chain 65 kDa protein that was initially believed to serve as the functional homologue of prokaryotic IF2, since eIF2A and IF2 catalyze biochemically similar reactions, i.e., they stimulate initiator Met-tRNAi binding to the small ribosomal subunit. However, subsequent identification of a heterotrimeric 126 kDa factor, eIF2 (α,β,γ) showed that this factor, and not eIF2A, was primarily responsible for the binding of Met-tRNAi to 40S subunit in eukaryotes. It was found however, that eIF2A can promote recruitment of Met-tRNAi to 40S/mRNA complexes under conditions of inhibition of eIF2 activity (eIF2α-phosphorylation), or its absence. eIF2A does not function in major steps in the initiation process, but is suggested to act at some minor/alternative initiation events such as re-initiation, internal initiation, or non-AUG initiation, important for translational control of specific mRNAs. This review summarizes our current understanding of the eIF2A structure and function.
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Affiliation(s)
- Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - William C. Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
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109
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Li X, Liang QX, Lin JR, Peng J, Yang JH, Yi C, Yu Y, Zhang QC, Zhou KR. Epitranscriptomic technologies and analyses. SCIENCE CHINA-LIFE SCIENCES 2020; 63:501-515. [DOI: 10.1007/s11427-019-1658-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/12/2020] [Indexed: 01/28/2023]
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110
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Chan CW, Badong D, Rajan R, Mondragón A. Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs. RNA (NEW YORK, N.Y.) 2020; 26:278-289. [PMID: 31848215 PMCID: PMC7025506 DOI: 10.1261/rna.073478.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
Ubiquitous across all domains of life, tRNAs constitute an essential component of cellular physiology, carry out an indispensable role in protein synthesis, and have been historically the subject of a wide range of biochemical and biophysical studies as prototypical folded RNA molecules. Although conformational flexibility is a well-established characteristic of tRNA structure, it is typically regarded as an adaptive property exhibited in response to an inducing event, such as the binding of a tRNA synthetase or the accommodation of an aminoacyl-tRNA into the ribosome. In this study, we present crystallographic data of a tRNA molecule to expand on this paradigm by showing that structural flexibility and plasticity are intrinsic properties of tRNAs, apparent even in the absence of other factors. Based on two closely related conformations observed within the same crystal, we posit that unbound tRNAs by themselves are flexible and dynamic molecules. Furthermore, we demonstrate that the formation of the T-loop conformation by the tRNA TΨC stem-loop, a well-characterized and classic RNA structural motif, is possible even in the absence of important interactions observed in fully folded tRNAs.
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Affiliation(s)
- Clarence W Chan
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA
| | - Deanna Badong
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA
| | - Rakhi Rajan
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA
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111
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Janzen E, Blanco C, Peng H, Kenchel J, Chen IA. Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution. Chem Rev 2020; 120:4879-4897. [PMID: 32011135 PMCID: PMC7291351 DOI: 10.1021/acs.chemrev.9b00620] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
The ability of enzymes,
including ribozymes, to catalyze side reactions
is believed to be essential to the evolution of novel biochemical
activities. It has been speculated that the earliest ribozymes, whose
emergence marked the origin of life, were low in activity but high
in promiscuity, and that these early ribozymes gave rise to specialized
descendants with higher activity and specificity. Here, we review
the concepts related to promiscuity and examine several cases of highly
promiscuous ribozymes. We consider the evidence bearing on the question
of whether de novo ribozymes would be quantitatively
more promiscuous than later evolved ribozymes or protein enzymes.
We suggest that while de novo ribozymes appear to
be promiscuous in general, they are not obviously more promiscuous
than more highly evolved or active sequences. Promiscuity is a trait
whose value would depend on selective pressures, even during prebiotic
evolution.
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Affiliation(s)
- Evan Janzen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Celia Blanco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Huan Peng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Josh Kenchel
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Irene A Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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112
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Morgan CE, Huang W, Rudin SD, Taylor DJ, Kirby JE, Bonomo RA, Yu EW. Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development. mBio 2020; 11:e03117-19. [PMID: 31964740 PMCID: PMC6974574 DOI: 10.1128/mbio.03117-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 01/11/2023] Open
Abstract
Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is Acinetobacter baumannii, a Gram-negative opportunistic pathogen that exhibits the remarkable ability to resist antibiotics through multiple mechanisms. As bacterial ribosomes represent a target for multiple distinct classes of existing antimicrobial agents, we here use single-particle cryo-electron microscopy (cryo-EM) to elucidate five different structural states of the A. baumannii ribosome, including the 70S, 50S, and 30S forms. We also determined interparticle motions of the 70S ribosome in different tRNA bound states using three-dimensional (3D) variability analysis. Together, our structural data further our understanding of the ribosome from A. baumannii and other Gram-negative pathogens and will enable structure-based drug discovery to combat antibiotic-resistant bacterial infections.IMPORTANCEAcinetobacter baumannii is a severe nosocomial threat largely due to its intrinsic antibiotic resistance and remarkable ability to acquire new resistance determinants. The bacterial ribosome serves as a major target for modern antibiotics and the design of new therapeutics. Here, we present cryo-EM structures of the A. baumannii 70S ribosome, revealing several unique species-specific structural features that may facilitate future drug development to combat this recalcitrant bacterial pathogen.
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Affiliation(s)
- Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Susan D Rudin
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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113
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A putative mechanism underlying secondary metabolite overproduction by Streptomyces strains with a 23S rRNA mutation conferring erythromycin resistance. Appl Microbiol Biotechnol 2020; 104:2193-2203. [PMID: 31925486 DOI: 10.1007/s00253-019-10288-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 02/07/2023]
Abstract
Mutations in rrn encoding ribosomal RNA (rRNA) and rRNA modification often confer resistance to ribosome-targeting antibiotics by altering the site of their interaction with the small (30S) and large (50S) subunits of the bacterial ribosome. The highly conserved central loop of domain V of 23S rRNA (nucleotides 2042-2628 in Escherichia coli; the exact position varies by species) of the 50S subunit, which is implicated in peptidyl transferase activity, is known to be important in macrolide interactions and resistance. In this study, we identified an A2302T mutation in the rrnA-23S rRNA gene and an A2281G mutation in the rrnC-23S rRNA gene that were responsible for resistance to erythromycin in the model actinomycete Streptomyces coelicolor A3(2) and its close relative Streptomyces lividans 66, respectively. Interestingly, genetic and phenotypic characterization of the erythromycin-resistant mutants indicated a possibility that under coexistence of the 23S rRNA mutation and mutations in other genes, S. coelicolor A3(2) and S. lividans 66 can produce abundant amounts of the pigmented antibiotics actinorhodin and undecylprodigiosin depending on the combinations of mutations. Herein, we report the unique phenomenon occurring by unexpected characteristics of the 23S rRNA mutations that can affect the emergence of additional mutations probably with an upswing in spontaneous mutations and enrichment in their variations in Streptomyces strains. Further, we discuss a putative mechanism underlying secondary metabolite overproduction by Streptomyces strains with a 23S rRNA mutation conferring erythromycin resistance.
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114
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Dos Santos RF, Bárria C, Arraiano CM, Andrade JM. Isolation and Analysis of Bacterial Ribosomes Through Sucrose Gradient Ultracentrifugation. Methods Mol Biol 2020; 2106:299-310. [PMID: 31889266 DOI: 10.1007/978-1-0716-0231-7_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ribosomes are large macromolecular complexes responsible for the translation process. During the course of ribosome biogenesis and protein synthesis, extra-ribosomal factors interact with the ribosome or its subunits to assist in these vital processes. Here we describe a method to isolate and analyze not only bacterial ribosomes but also their associated factors, providing insights into translation regulation. This detailed protocol allows the separation and monitoring of the ribosomal species and their interacting partners along a sucrose density gradient. Simultaneously, fractionation of the gradient allows for the recovery of 70S ribosomes and its subunits enabling a wide range of downstream applications. This protocol can be easily adapted to ribosome-related studies in other species or for separating other macromolecular complexes.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cátia Bárria
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Cui H, Hu H, Zeng J, Chen T. DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data. BMC Bioinformatics 2019; 20:678. [PMID: 31861979 PMCID: PMC6923924 DOI: 10.1186/s12859-019-3244-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Ribosome profiling brings insight to the process of translation. A basic step in profile construction at transcript level is to map Ribo-seq data to transcripts, and then assign a huge number of multiple-mapped reads to similar isoforms. Existing methods either discard the multiple mapped-reads, or allocate them randomly, or assign them proportionally according to transcript abundance estimated from RNA-seq data. Results Here we present DeepShape, an RNA-seq free computational method to estimate ribosome abundance of isoforms, and simultaneously compute their ribosome profiles using a deep learning model. Our simulation results demonstrate that DeepShape can provide more accurate estimations on both ribosome abundance and profiles when compared to state-of-the-art methods. We applied DeepShape to a set of Ribo-seq data from PC3 human prostate cancer cells with and without PP242 treatment. In the four cell invasion/metastasis genes that are translationally regulated by PP242 treatment, different isoforms show very different characteristics of translational efficiency and regulation patterns. Transcript level ribosome distributions were analyzed by “Codon Residence Index (CRI)” proposed in this study to investigate the relative speed that a ribosome moves on a codon compared to its synonymous codons. We observe consistent CRI patterns in PC3 cells. We found that the translation of several codons could be regulated by PP242 treatment. Conclusion In summary, we demonstrate that DeepShape can serve as a powerful tool for Ribo-seq data analysis.
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Affiliation(s)
- Hongfei Cui
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing, China.,DonLinks School of Economics and Management, University of Science and Technology Beijing, Beijing, China
| | - Hailin Hu
- School of Medicine, Tsinghua University, Beijing, China
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.
| | - Ting Chen
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing, China.
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116
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Wang J, Yang D, Guo X, Song Q, Tan L, Dong L. A novel RNA aptamer-modified riboswitch as chemical sensor. Anal Chim Acta 2019; 1100:240-249. [PMID: 31987147 DOI: 10.1016/j.aca.2019.11.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/20/2019] [Accepted: 11/30/2019] [Indexed: 12/19/2022]
Abstract
In this study, a novel label- and immobilization-free RNA aptamer-modified riboswitch-based biosensor was developed by using RNA aptamer modified secondary-structural scaffolds to control the identity of the ribosomal binding sequence (RBS). In the developed sensor, the duplex RNA aptamers-modified cis-repressor sequence is introduced upstream to the RBS of the indicating gene (gfp gene), leading to formatting an RNA bubble due to the none-complementary state of the RNA aptamers in the hairpin structure of the cis-repressor sequence. Without the presence of the target molecule, the ribosome cannot identify the RBS of the indicating gene as the RBS is hidden by the introduced cis-repressor, consequently, the indicating gene in the sensor would not be expressed, demonstrating the absence of the target. On the contrary, with the presence of the target molecule, the binding of aptamer with the target would induce the enlargement of the RNA bubble, leading to the separation of the cis-repressor sequence and RBS. Hence, the indicating gene would be expressed, manifesting the existence of the target. In addition, the developed sensor can quantitatively report the target concentrations by measuring the gfp gene-encoded GFP (green fluorescent protein) concentration. The approach proposed in this study can be used to construct sensors for detecting various chemicals by introducing the corresponding aptamers, therefore, this strategy can potentially provide a new set of analytical tools in the field of analytical chemistry.
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Affiliation(s)
- Jing Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China; College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education, Chongqing University, Chongqing, 40004, PR China
| | - Dongmei Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China
| | - Xiaogang Guo
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing, 408100, China
| | - Qitao Song
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Luxi Tan
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China; Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education, Chongqing University, Chongqing, 40004, PR China.
| | - Lichun Dong
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China; Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education, Chongqing University, Chongqing, 40004, PR China.
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117
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Rudler DL, Hughes LA, Perks KL, Richman TR, Kuznetsova I, Ermer JA, Abudulai LN, Shearwood AMJ, Viola HM, Hool LC, Siira SJ, Rackham O, Filipovska A. Fidelity of translation initiation is required for coordinated respiratory complex assembly. SCIENCE ADVANCES 2019; 5:eaay2118. [PMID: 31903419 PMCID: PMC6924987 DOI: 10.1126/sciadv.aay2118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/30/2019] [Indexed: 05/22/2023]
Abstract
Mammalian mitochondrial ribosomes are unique molecular machines that translate 11 leaderless mRNAs; however, it is not clear how mitoribosomes initiate translation, since mitochondrial mRNAs lack untranslated regions. Mitochondrial translation initiation shares similarities with prokaryotes, such as the formation of a ternary complex of fMet-tRNAMet, mRNA and the 28S subunit, but differs in the requirements for initiation factors. Mitochondria have two initiation factors: MTIF2, which closes the decoding center and stabilizes the binding of the fMet-tRNAMet to the leaderless mRNAs, and MTIF3, whose role is not clear. We show that MTIF3 is essential for survival and that heart- and skeletal muscle-specific loss of MTIF3 causes cardiomyopathy. We identify increased but uncoordinated mitochondrial protein synthesis in mice lacking MTIF3, resulting in loss of specific respiratory complexes. Ribosome profiling shows that MTIF3 is required for recognition and regulation of translation initiation of mitochondrial mRNAs and for coordinated assembly of OXPHOS complexes in vivo.
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Affiliation(s)
- Danielle L. Rudler
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Laetitia A. Hughes
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Kara L. Perks
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Tara R. Richman
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Irina Kuznetsova
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Judith A. Ermer
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Laila N. Abudulai
- Centre for Microscopy, Characterisation and Analysis and School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Anne-Marie J. Shearwood
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Helena M. Viola
- School of Human Sciences (Physiology), The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Livia C. Hool
- School of Human Sciences (Physiology), The University of Western Australia, Crawley, Western Australia 6009, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Stefan J. Siira
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Corresponding author.
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118
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Basak S, Sengupta S, Chattopadhyay K. Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells. Biophys Rev 2019; 11:851-872. [PMID: 31444739 PMCID: PMC6957588 DOI: 10.1007/s12551-019-00580-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 01/24/2023] Open
Abstract
In order to maintain cellular function, biomolecules like protein, DNA, and RNAs have to diffuse to the target spaces within the cell. Changes in the cytosolic microenvironment or in the nucleus during the fulfillment of these cellular processes affect their mobility, folding, and stability thereby impacting the transient or stable interactions with their adjacent neighbors in the organized and dynamic cellular interior. Using classical Brownian motion to elucidate the diffusion behavior of these biomolecules is hard considering their complex nature. The understanding of biomolecular diffusion inside cells still remains elusive due to the lack of a proper model that can be extrapolated to these cases. In this review, we have comprehensively addressed the progresses in this field, laying emphasis on the different aspects of anomalous diffusion in the different biochemical reactions in cell interior. These experiment-based models help to explain the diffusion behavior of biomolecules in the cytosolic and nuclear microenvironment. Moreover, since understanding of biochemical reactions within living cellular system is our main focus, we coupled the experimental observations with the concept of sub-diffusion from in vitro to in vivo condition. We believe that the pairing between the understanding of complex behavior and structure-function paradigm of biological molecules would take us forward by one step in order to solve the puzzle around diseases caused by cellular dysfunction.
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Affiliation(s)
- Sujit Basak
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.
| | - Sombuddha Sengupta
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
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119
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Waduge P, Sati GC, Crich D, Chow CS. Use of a fluorescence assay to determine relative affinities of semisynthetic aminoglycosides to small RNAs representing bacterial and mitochondrial A sites. Bioorg Med Chem 2019; 27:115121. [PMID: 31610941 PMCID: PMC6961810 DOI: 10.1016/j.bmc.2019.115121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/02/2019] [Accepted: 09/12/2019] [Indexed: 10/26/2022]
Abstract
The off-target binding of aminoglycosides (AGs) to the A site of human mitochondrial ribosomes in addition to bacterial ribosomes causes ototoxicity and limits their potential as antibiotics. A fluorescence assay was employed to determine relative binding affinities of classical and improved AG compounds to synthetic RNA constructs representing the bacterial and mitochondrial A sites. Results compared well with previously reported in vitro translation assays with engineered ribosomes. Therefore, the minimal RNA motifs and fluorescence assay are shown here to be useful for assessing the selectivity of new compounds.
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Affiliation(s)
- Prabuddha Waduge
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Girish C Sati
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - David Crich
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Christine S Chow
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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120
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Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K. Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell Rep 2019; 29:1351-1368.e5. [PMID: 31665645 PMCID: PMC6873818 DOI: 10.1016/j.celrep.2019.09.060] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/30/2019] [Accepted: 09/18/2019] [Indexed: 12/16/2022] Open
Abstract
RNA-binding proteins (RBPs) play essential roles in biology and are frequently associated with human disease. Although recent studies have systematically identified individual RNA-binding proteins, their higher-order assembly into ribonucleoprotein (RNP) complexes has not been systematically investigated. Here, we describe a proteomics method for systematic identification of RNP complexes in human cells. We identify 1,428 protein complexes that associate with RNA, indicating that more than 20% of known human protein complexes contain RNA. To explore the role of RNA in the assembly of each complex, we identify complexes that dissociate, change composition, or form stable protein-only complexes in the absence of RNA. We use our method to systematically identify cell-type-specific RNA-associated proteins in mouse embryonic stem cells and finally, distribute our resource, rna.MAP, in an easy-to-use online interface (rna.proteincomplexes.org). Our system thus provides a methodology for explorations across human tissues, disease states, and throughout all domains of life.
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Affiliation(s)
- Anna L Mallam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Wisath Sae-Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Fan Tu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Anna Battenhouse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Kevin Drew
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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121
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Kuncha SK, Kruparani SP, Sankaranarayanan R. Chiral checkpoints during protein biosynthesis. J Biol Chem 2019; 294:16535-16548. [PMID: 31591268 DOI: 10.1074/jbc.rev119.008166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Protein chains contain only l-amino acids, with the exception of the achiral glycine, making the chains homochiral. This homochirality is a prerequisite for proper protein folding and, hence, normal cellular function. The importance of d-amino acids as a component of the bacterial cell wall and their roles in neurotransmission in higher eukaryotes are well-established. However, the wider presence and the corresponding physiological roles of these specific amino acid stereoisomers have been appreciated only recently. Therefore, it is expected that enantiomeric fidelity has to be a key component of all of the steps in translation. Cells employ various molecular mechanisms for keeping d-amino acids away from the synthesis of nascent polypeptide chains. The major factors involved in this exclusion are aminoacyl-tRNA synthetases (aaRSs), elongation factor thermo-unstable (EF-Tu), the ribosome, and d-aminoacyl-tRNA deacylase (DTD). aaRS, EF-Tu, and the ribosome act as "chiral checkpoints" by preferentially binding to l-amino acids or l-aminoacyl-tRNAs, thereby excluding d-amino acids. Interestingly, DTD, which is conserved across all life forms, performs "chiral proofreading," as it removes d-amino acids erroneously added to tRNA. Here, we comprehensively review d-amino acids with respect to their occurrence and physiological roles, implications for chiral checkpoints required for translation fidelity, and potential use in synthetic biology.
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Affiliation(s)
- Santosh Kumar Kuncha
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India.,Academy of Scientific and Innovative Research, CSIR-CCMB Campus, Hyderabad, Telangana 500007, India
| | - Shobha P Kruparani
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India
| | - Rajan Sankaranarayanan
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India
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122
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Engineered ribosomes with tethered subunits for expanding biological function. Nat Commun 2019; 10:3920. [PMID: 31477696 PMCID: PMC6718428 DOI: 10.1038/s41467-019-11427-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/10/2019] [Indexed: 01/01/2023] Open
Abstract
Ribo-T is a ribosome with covalently tethered subunits where core 16S and 23S ribosomal RNAs form a single chimeric molecule. Ribo-T makes possible a functionally orthogonal ribosome-mRNA system in cells. Unfortunately, use of Ribo-T has been limited because of low activity of its original version. Here, to overcome this limitation, we use an evolutionary approach to select new tether designs that are capable of supporting faster cell growth and increased protein expression. Further, we evolve new orthogonal Ribo-T/mRNA pairs that function in parallel with, but independent of, natural ribosomes and mRNAs, increasing the efficiency of orthogonal protein expression. The Ribo-T with optimized designs is able to synthesize a diverse set of proteins, and can also incorporate multiple non-canonical amino acids into synthesized polypeptides. The enhanced Ribo-T designs should be useful for exploring poorly understood functions of the ribosome and engineering ribosomes with altered catalytic properties.
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124
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Janapala Y, Preiss T, Shirokikh NE. Control of Translation at the Initiation Phase During Glucose Starvation in Yeast. Int J Mol Sci 2019; 20:E4043. [PMID: 31430885 PMCID: PMC6720308 DOI: 10.3390/ijms20164043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/10/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Glucose is one of the most important sources of carbon across all life. Glucose starvation is a key stress relevant to all eukaryotic cells. Glucose starvation responses have important implications in diseases, such as diabetes and cancer. In yeast, glucose starvation causes rapid and dramatic effects on the synthesis of proteins (mRNA translation). Response to glucose deficiency targets the initiation phase of translation by different mechanisms and with diverse dynamics. Concomitantly, translationally repressed mRNAs and components of the protein synthesis machinery may enter a variety of cytoplasmic foci, which also form with variable kinetics and may store or degrade mRNA. Much progress has been made in understanding these processes in the last decade, including with the use of high-throughput/omics methods of RNA and RNA:protein detection. This review dissects the current knowledge of yeast reactions to glucose starvation systematized by the stage of translation initiation, with the focus on rapid responses. We provide parallels to mechanisms found in higher eukaryotes, such as metazoans, for the most critical responses, and point out major remaining gaps in knowledge and possible future directions of research on translational responses to glucose starvation.
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Affiliation(s)
- Yoshika Janapala
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.
| | - Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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125
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Abstract
Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they face a distinct set of challenges compared with more familiar human-engineered macroscopic machines. Here we review central questions in their performance as free energy transducers, outline theoretical and modeling approaches to understand these questions, identify both physical limits on their operational characteristics and design principles for improving performance, and discuss emerging areas of research.
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Affiliation(s)
- Aidan I Brown
- Department of Physics , University of California, San Diego , La Jolla , California 92093 , United States
| | - David A Sivak
- Department of Physics , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
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126
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Bervoets I, Charlier D. Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. FEMS Microbiol Rev 2019; 43:304-339. [PMID: 30721976 PMCID: PMC6524683 DOI: 10.1093/femsre/fuz001] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Gene expression occurs in two essential steps: transcription and translation. In bacteria, the two processes are tightly coupled in time and space, and highly regulated. Tight regulation of gene expression is crucial. It limits wasteful consumption of resources and energy, prevents accumulation of potentially growth inhibiting reaction intermediates, and sustains the fitness and potential virulence of the organism in a fluctuating, competitive and frequently stressful environment. Since the onset of studies on regulation of enzyme synthesis, numerous distinct regulatory mechanisms modulating transcription and/or translation have been discovered. Mostly, various regulatory mechanisms operating at different levels in the flow of genetic information are used in combination to control and modulate the expression of a single gene or operon. Here, we provide an extensive overview of the very diverse and versatile bacterial gene regulatory mechanisms with major emphasis on their combined occurrence, intricate intertwinement and versatility. Furthermore, we discuss the potential of well-characterized basal expression and regulatory elements in synthetic biology applications, where they may ensure orthogonal, predictable and tunable expression of (heterologous) target genes and pathways, aiming at a minimal burden for the host.
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Affiliation(s)
- Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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127
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Scull CE, Schneider DA. Coordinated Control of rRNA Processing by RNA Polymerase I. Trends Genet 2019; 35:724-733. [PMID: 31358304 DOI: 10.1016/j.tig.2019.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 11/19/2022]
Abstract
Ribosomal RNA (rRNA) is co- and post-transcriptionally processed into active ribosomes. This process is dynamically regulated by direct covalent modifications of the polymerase that synthesizes the rRNA, RNA polymerase I (Pol I), and by interactions with cofactors that influence initiation, elongation, and termination activities of Pol I. The rate of transcription elongation by Pol I directly influences processing of nascent rRNA, and changes in Pol I transcription rate result in alternative rRNA processing events that lead to cellular signaling alterations and stress. It is clear that in divergent species, there exists robust organization of nascent rRNA processing events during transcription elongation. This review evaluates the current state of our understanding of the complex relationship between transcription elongation and rRNA processing.
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Affiliation(s)
- Catherine E Scull
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Abstract
Protein synthesis consumes a large fraction of available resources in the cell. When bacteria encounter unfavorable conditions and cease to grow, specialized mechanisms are in place to ensure the overall reduction of costly protein synthesis while maintaining a basal level of translation. A number of ribosome-associated factors are involved in this regulation; some confer an inactive, hibernating state of the ribosome in the form of 70S monomers (RaiA; this and the following are based on Escherichia coli nomenclature) or 100S dimers (RMF and HPF homologs), and others inhibit translation at different stages in the translation cycle (RsfS, YqjD and paralogs, SRA, and EttA). Stationary phase cells therefore exhibit a complex array of different ribosome subpopulations that adjusts the translational capacity of the cell to the encountered conditions and ensures efficient reactivation of translation when conditions improve. Here, we review the current state of research regarding stationary phase-specific translation factors, in particular ribosome hibernation factors and other forms of translational regulation in response to stress conditions.
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Affiliation(s)
- Thomas Prossliner
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | | | | | - Kenn Gerdes
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
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129
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Künzle M, Lach M, Budiarta M, Beck T. Higher-Order Structures Based on Molecular Interactions for the Formation of Natural and Artificial Biomaterials. Chembiochem 2019; 20:1637-1641. [PMID: 30734442 DOI: 10.1002/cbic.201800824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/06/2019] [Indexed: 11/09/2022]
Abstract
The assembly of molecular building blocks into highly ordered structures is crucial, both in nature and for the development of novel functional materials. In nature, noncovalent interactions, such as hydrogen bonds or hydrophobic interactions, enable the reversible assembly of biopolymers, such as DNA or proteins. Inspired by these design principles, scientists have created biohybrid materials that employ natural building blocks and their assembly properties. Thus, structures and materials are attainable that cannot be made through other synthetic procedures. Herein, we review current concepts and highlight recent advances.
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Affiliation(s)
- Matthias Künzle
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1a, 52074, Aachen, Germany
| | - Marcel Lach
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1a, 52074, Aachen, Germany
| | - Made Budiarta
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1a, 52074, Aachen, Germany
| | - Tobias Beck
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1a, 52074, Aachen, Germany.,I3TM, RWTH Aachen University, Landoltweg 1a, 52074, Aachen, Germany.,JARA SOFT and JARA FIT, RWTH Aachen University, Landoltweg 1a, 52074, Aachen, Germany
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130
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Pilla SP, Thomas A, Bahadur RP. Dissecting macromolecular recognition sites in ribosome: implication to its self-assembly. RNA Biol 2019; 16:1300-1312. [PMID: 31179876 DOI: 10.1080/15476286.2019.1629767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Interactions between macromolecules play a crucial role in ribosome assembly that follows a highly coordinated process involving RNA folding and binding of ribosomal proteins (r-proteins). Although extensive studies have been carried out to understand macromolecular interactions in ribosomes, most of them are confined to either large or small ribosomal-subunit of few species. A comparative analysis of macromolecular interactions across different domains is still missing. We have analyzed the structural and physicochemical properties of protein-protein (PP), protein-RNA (PR) and RNA-RNA (RR) interfaces in small and large subunits of ribosomes, as well as in between the two subunits. Additionally, we have also developed Random Forest (RF) classifier to catalog the r-proteins. We find significant differences as well as similarities in macromolecular recognition sites between ribosomal assemblies of prokaryotes and eukaryotes. PR interfaces are substantially larger and have more ionic interactions than PP and RR interfaces in both prokaryotes and eukaryotes. PP, PR and RR interfaces in eukaryotes are well packed compared to those in prokaryotes. However, the packing density between the large and the small subunit interfaces in the entire assembly is strikingly low in both prokaryotes and eukaryotes, indicating the periodic association and dissociation of the two subunits during the translation. The structural and physicochemical properties of PR interfaces are used to predict the r-proteins in the assembly pathway into early, intermediate and late binders using RF classifier with an accuracy of 80%. The results provide new insights into the classification of r-proteins in the assembly pathway.
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Affiliation(s)
- Smita P Pilla
- a Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Amal Thomas
- a Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Ranjit Prasad Bahadur
- a Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur , Kharagpur , India
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131
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Topf U, Uszczynska-Ratajczak B, Chacinska A. Mitochondrial stress-dependent regulation of cellular protein synthesis. J Cell Sci 2019; 132:132/8/jcs226258. [DOI: 10.1242/jcs.226258] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
ABSTRACT
The production of newly synthesized proteins is vital for all cellular functions and is a determinant of cell growth and proliferation. The synthesis of polypeptide chains from mRNA molecules requires sophisticated machineries and mechanisms that need to be tightly regulated, and adjustable to current needs of the cell. Failures in the regulation of translation contribute to the loss of protein homeostasis, which can have deleterious effects on cellular function and organismal health. Unsurprisingly, the regulation of translation appears to be a crucial element in stress response mechanisms. This review provides an overview of mechanisms that modulate cytosolic protein synthesis upon cellular stress, with a focus on the attenuation of translation in response to mitochondrial stress. We then highlight links between mitochondrion-derived reactive oxygen species and the attenuation of reversible cytosolic translation through the oxidation of ribosomal proteins at their cysteine residues. We also discuss emerging concepts of how cellular mechanisms to stress are adapted, including the existence of alternative ribosomes and stress granules, and the regulation of co-translational import upon organelle stress.
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Affiliation(s)
- Ulrike Topf
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw 02-106, Poland
| | | | - Agnieszka Chacinska
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
- ReMedy International Research Agenda Unit, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
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132
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Ognjenović J, Grisshammer R, Subramaniam S. Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies. Annu Rev Biomed Eng 2019; 21:395-415. [PMID: 30892930 DOI: 10.1146/annurev-bioeng-060418-052453] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In recent years, cryo electron microscopy (cryo-EM) technology has been transformed with the development of better instrumentation, direct electron detectors, improved methods for specimen preparation, and improved software for data analysis. Analyses using single-particle cryo-EM methods have enabled determination of structures of proteins with sizes smaller than 100 kDa and resolutions of ∼2 Å in some cases. The use of electron tomography combined with subvolume averaging is beginning to allow the visualization of macromolecular complexes in their native environment in unprecedented detail. As a result of these advances, solutions to many intractable challenges in structural and cell biology, such as analysis of highly dynamic soluble and membrane-embedded protein complexes or partially ordered protein aggregates, are now within reach. Recent reports of structural studies of G protein-coupled receptors, spliceosomes, and fibrillar specimens illustrate the progress that has been made using cryo-EM methods, and are the main focus of this review.
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Affiliation(s)
- Jana Ognjenović
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20814, USA; ,
| | - Reinhard Grisshammer
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20814, USA; ,
| | - Sriram Subramaniam
- University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada;
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133
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RNA structure maps across mammalian cellular compartments. Nat Struct Mol Biol 2019; 26:322-330. [PMID: 30886404 PMCID: PMC6640855 DOI: 10.1038/s41594-019-0200-7] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/07/2019] [Indexed: 11/15/2022]
Abstract
RNA structure is intimately connected to each step of gene expression. Recent advances have enabled transcriptome-wide maps of RNA secondary structure, termed RNA structuromes. However, previous whole-cell analyses lacked the resolution to unravel the landscape and also the regulatory mechanisms of RNA structural changes across subcellular compartments. Here we reveal the RNA structuromes in three compartments — chromatin, nucleoplasm and cytoplasm in human and mouse cells. The cytotopic structuromes substantially expand RNA structural information, and enable detailed investigation of the central role of RNA structure in linking transcription, translation, and RNA decay. We develop a resource to visualize the interplay of RNA-protein interactions, RNA modifications, and RNA structure, and predict both direct and indirect reader proteins of RNA modifications. We also validate a novel role of the RNA binding protein LIN28A as an N6-methyladenosine modification “anti-reader”. Our results highlight the dynamic nature of RNA structures and its functional significance in gene regulation.
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134
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Waduge P, Sakakibara Y, Chow CS. Chemical probing for examining the structure of modified RNAs and ligand binding to RNA. Methods 2019; 156:110-120. [DOI: 10.1016/j.ymeth.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/04/2018] [Accepted: 10/22/2018] [Indexed: 12/15/2022] Open
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135
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Wu J, Zhan M, Chang Y, Su Q, Yu R. Adaption and recovery of Nitrosomonas europaea to chronic TiO 2 nanoparticle exposure. WATER RESEARCH 2018; 147:429-439. [PMID: 30342338 DOI: 10.1016/j.watres.2018.09.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 06/08/2023]
Abstract
Although the adverse impacts of emerging nanoparticles (NPs) on the biological nitrogen removal (BNR) process have been broadly reported, the adaptive responses of NP-impaired nitrifiers and the related mechanisms have seldom been addressed to date. Here, we systematically explored the adaption and recovery capacities of the ammonia oxidizer Nitrosomonas europaea under chronic TiO2 NP exposure and different dissolved oxygen (DO) conditions at the physiological and transcriptional levels in a chemostat reactor. N. europaea cells adapted to 50 mg/L TiO2 NP exposure after 40-d incubation and the inhibited cell growth, membrane integrity, nitritation rate, and ammonia monooxygenase activity all recovered regardless of the DO concentrations. Transmission electron microscope imaging indicated the remission of the membrane distortion after the cells' 40-d adaption to the NP exposure. The microarray results further suggested that the metabolic processes associated with the membrane repair were pivotal for cellular adaption/recovery, such as the membrane efflux for toxicant exclusion, the structural preservation or stabilization, and the osmotic equilibrium adjustment. In addition, diverse metabolic and stress-defense pathways, including aminoacyl-tRNA biosynthesis, respiratory chain, ATP production, toxin-antitoxin 'stress-fighting', and DNA repair were activated for the cellular adaption coupled with the metabolic activity recovery, probably via recovering the energy production/conversion efficiency and mediating the non-photooxidative stress. Finally, low DO (0.5 mg/L) incubated cells were more susceptible to TiO2 NP exposure and required more time to adapt to and recover from the stress, which was probably due to the stimulation limitation of the oxygen-dependent energy metabolism with a lower oxygen supply. The findings of this study provide new insights into NP contamination control and management adjustments during the BNR process.
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Affiliation(s)
- Junkang Wu
- Department of Environmental Science and Engineering, School of Energy and Environment, Wuxi Engineering Research Center of Taihu Lake Water Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China; Department of Environmental Engineering, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Manjun Zhan
- Nanjing Research Institute of Environmental Protection, Nanjing Environmental Protection Bureau, Nanjing, Jiangsu, 210013, China
| | - Yan Chang
- Department of Environmental Science and Engineering, School of Energy and Environment, Wuxi Engineering Research Center of Taihu Lake Water Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Qingxian Su
- Department of Environmental Engineering, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Ran Yu
- Department of Environmental Science and Engineering, School of Energy and Environment, Wuxi Engineering Research Center of Taihu Lake Water Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China.
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136
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Pizzolato S, Štacko P, Kistemaker JCM, van Leeuwen T, Otten E, Feringa BL. Central-to-Helical-to-Axial-to-Central Transfer of Chirality with a Photoresponsive Catalyst. J Am Chem Soc 2018; 140:17278-17289. [PMID: 30458108 PMCID: PMC6326533 DOI: 10.1021/jacs.8b10816] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 12/26/2022]
Abstract
Recent advances in molecular design have displayed striking examples of dynamic chirality transfer between various elements of chirality, e.g., from central to either helical or axial chirality and vice versa. While considerable progress in atroposelective synthesis has been made, it is intriguing to design chiral molecular switches able to provide selective and dynamic control of axial chirality with an external stimulus to modulate stereochemical functions. Here, we report the synthesis and characterization of a photoresponsive bis(2-phenol)-substituted molecular switch 1. The unique design exhibits a dynamic hybrid central-helical-axial transfer of chirality. The change of preferential axial chirality in the biaryl motif is coupled to the reversible switching of helicity of the overcrowded alkene core, dictated by the fixed stereogenic center. The potential for dynamic control of axial chirality was demonstrated by using ( R)-1 as switchable catalyst to direct the stereochemical outcome of the catalytic enantioselective addition of diethylzinc to aromatic aldehydes, with successful reversal of enantioselectivity for several substrates.
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Affiliation(s)
- Stefano
F. Pizzolato
- Center for Systems Chemistry, Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials,
Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Peter Štacko
- Center for Systems Chemistry, Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials,
Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jos C. M. Kistemaker
- Center for Systems Chemistry, Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials,
Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas van Leeuwen
- Center for Systems Chemistry, Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials,
Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Edwin Otten
- Center for Systems Chemistry, Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials,
Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ben L. Feringa
- Center for Systems Chemistry, Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials,
Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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137
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Bray MS, Lenz TK, Haynes JW, Bowman JC, Petrov AS, Reddi AR, Hud NV, Williams LD, Glass JB. Multiple prebiotic metals mediate translation. Proc Natl Acad Sci U S A 2018; 115:12164-12169. [PMID: 30413624 PMCID: PMC6275528 DOI: 10.1073/pnas.1803636115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Today, Mg2+ is an essential cofactor with diverse structural and functional roles in life's oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O2, high Fe2+, and high Mn2+) can revert the ribosome to a functional ancestral state. First, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) was used to compare the effect of Mg2+, Fe2+, and Mn2+ on the tertiary structure of rRNA. Then, we used in vitro translation reactions to test whether Fe2+ or Mn2+ could mediate protein production, and quantified ribosomal metal content. We found that (i) Mg2+, Fe2+, and Mn2+ had strikingly similar effects on rRNA folding; (ii) Fe2+ and Mn2+ can replace Mg2+ as the dominant divalent cation during translation of mRNA to functional protein; and (iii) Fe and Mn associate extensively with the ribosome. Given that the translation system originated and matured when Fe2+ and Mn2+ were abundant, these findings suggest that Fe2+ and Mn2+ played a role in early ribosomal evolution.
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Affiliation(s)
- Marcus S Bray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Timothy K Lenz
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Jay William Haynes
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Jessica C Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332;
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332
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138
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Song Y, Shin J, Jin S, Lee JK, Kim DR, Kim SC, Cho S, Cho BK. Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth. BMC Genomics 2018; 19:837. [PMID: 30470174 PMCID: PMC6260860 DOI: 10.1186/s12864-018-5238-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/09/2018] [Indexed: 11/11/2022] Open
Abstract
Background Acetogenic bacteria constitute promising biocatalysts for the conversion of CO2/H2 or synthesis gas (H2/CO/CO2) into biofuels and value-added biochemicals. These microorganisms are naturally capable of autotrophic growth via unique acetogenesis metabolism. Despite their biosynthetic potential for commercial applications, a systemic understanding of the transcriptional and translational regulation of the acetogenesis metabolism remains unclear. Results By integrating genome-scale transcriptomic and translatomic data, we explored the regulatory logic of the acetogenesis to convert CO2 into biomass and metabolites in Eubacterium limosum. The results indicate that majority of genes associated with autotrophic growth including the Wood-Ljungdahl pathway, the reduction of electron carriers, the energy conservation system, and gluconeogenesis were transcriptionally upregulated. The translation efficiency of genes in cellular respiration and electron bifurcation was also highly enhanced. In contrast, the transcriptionally abundant genes involved in the carbonyl branch of the Wood-Ljungdahl pathway, as well as the ion-translocating complex and ATP synthase complex in the energy conservation system, showed decreased translation efficiency. The translation efficiencies of genes were regulated by 5′UTR secondary structure under the autotrophic growth condition. Conclusions The results illustrated that the acetogenic bacteria reallocate protein synthesis, focusing more on the translation of genes for the generation of reduced electron carriers via electron bifurcation, rather than on those for carbon metabolism under autotrophic growth. Electronic supplementary material The online version of this article (10.1186/s12864-018-5238-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoseb Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Jongoh Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dong Rip Kim
- Department of Mechanical Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Intelligent Synthetic Biology Center, Daejeon, 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,Intelligent Synthetic Biology Center, Daejeon, 34141, Republic of Korea.
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139
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Structural modules of the stress-induced protein HflX: an outlook on its evolution and biological role. Curr Genet 2018; 65:363-370. [PMID: 30448945 DOI: 10.1007/s00294-018-0905-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 12/23/2022]
Abstract
Multifunctional proteins often show modular structures. A functional domain and the structural modules within the domain show evolutionary conservation of their spatial arrangement since that gives the protein its functionality. However, the question remains as to how members of different domains of life (Archaea, Bacteria, Eukarya), polish and perfect these modules within conserved multidomain proteins, to tailor functional proteins according to their specific requirements. In the quest for plausible answers to this question, we studied the bacterial protein HflX. HflX is a universally conserved member of the Obg-GTPase superfamily but its functional role in Archaea and Eukarya is barely known. It is a multidomain protein and possesses, in addition to its conserved GTPase domain, an ATP-binding N-terminal domain. It is involved in heat stress response in Escherichia coli and our laboratory recently identified an ATP-dependent RNA helicase activity of E. coli HflX, which is likely instrumental in rescuing ribosomes during heat stress. Because perception and response to stress is expected to be different in different life forms, the question is whether this activity is preserved in higher organisms or not. Thus, we explored the evolution pattern of different structural modules of HflX, with particular emphasis on the ATP-binding domain, to understand plausible biological role of HflX in other forms of life. Our analyses indicate that, while the evolutionary pattern of the GTPase domain follows a conserved phylogeny, conservation of the ATP-binding domain shows a complicated pattern. The limited analysis described here hints towards possible evolutionary adaptations and modifications of the domain, something which needs to be investigated in more depth in homologs from other life forms. Deciphering how nature 'tweaks' such modules, both structurally and functionally, may help in understanding the evolution of such proteins, and, on a large-scale, of stress-related proteins in general as well.
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140
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Tamaru D, Amikura K, Shimizu Y, Nierhaus KH, Ueda T. Reconstitution of 30S ribosomal subunits in vitro using ribosome biogenesis factors. RNA (NEW YORK, N.Y.) 2018; 24:1512-1519. [PMID: 30076205 PMCID: PMC6191716 DOI: 10.1261/rna.065615.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/25/2018] [Indexed: 05/20/2023]
Abstract
Reconstitution of ribosomes in vitro from individual ribosomal proteins provides a powerful tool for understanding the ribosome assembly process including the sequential incorporation of ribosomal proteins. However, conventional assembly methods require high-salt conditions for efficient ribosome assembly. In this study, we reconstituted 30S ribosomal subunits from individually purified ribosomal proteins in the presence of ribosome biogenesis factors. In this system, two GTPases (Era and YjeQ) facilitated assembly of a 30S subunit exhibiting poly(U)-directed polyphenylalanine synthesis and native protein synthesis under physiological conditions. This in vitro system permits a study of the assembly process and function of ribosome biogenesis factors, and it will facilitate the generation of ribosomes from DNA without using cells.
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Affiliation(s)
- Daichi Tamaru
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Kazuaki Amikura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center, Suita, Osaka 565-0874, Japan
| | - Knud H Nierhaus
- Institute for Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
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141
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A single N 1-methyladenosine on the large ribosomal subunit rRNA impacts locally its structure and the translation of key metabolic enzymes. Sci Rep 2018; 8:11904. [PMID: 30093689 PMCID: PMC6085284 DOI: 10.1038/s41598-018-30383-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/29/2018] [Indexed: 12/18/2022] Open
Abstract
The entire chemical modification repertoire of yeast ribosomal RNAs and the enzymes responsible for it have recently been identified. Nonetheless, in most cases the precise roles played by these chemical modifications in ribosome structure, function and regulation remain totally unclear. Previously, we demonstrated that yeast Rrp8 methylates m1A645 of 25S rRNA in yeast. Here, using mung bean nuclease protection assays in combination with quantitative RP-HPLC and primer extension, we report that 25S/28S rRNA of S. pombe, C. albicans and humans also contain a single m1A methylation in the helix 25.1. We characterized nucleomethylin (NML) as a human homolog of yeast Rrp8 and demonstrate that NML catalyzes the m1A1322 methylation of 28S rRNA in humans. Our in vivo structural probing of 25S rRNA, using both DMS and SHAPE, revealed that the loss of the Rrp8-catalyzed m1A modification alters the conformation of domain I of yeast 25S rRNA causing translation initiation defects detectable as halfmers formation, likely because of incompetent loading of 60S on the 43S-preinitiation complex. Quantitative proteomic analysis of the yeast Δrrp8 mutant strain using 2D-DIGE, revealed that loss of m1A645 impacts production of specific set of proteins involved in carbohydrate metabolism, translation and ribosome synthesis. In mouse, NML has been characterized as a metabolic disease-associated gene linked to obesity. Our findings in yeast also point to a role of Rrp8 in primary metabolism. In conclusion, the m1A modification is crucial for maintaining an optimal 60S conformation, which in turn is important for regulating the production of key metabolic enzymes.
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142
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Cao M, Wang Y, Zhao W, Qi R, Han Y, Wu R, Wang Y, Xu H. Peptide-Induced DNA Condensation into Virus-Mimicking Nanostructures. ACS APPLIED MATERIALS & INTERFACES 2018; 10:24349-24360. [PMID: 29979028 DOI: 10.1021/acsami.8b00246] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A series of surfactant-like peptides have been designed for inducing DNA condensation, which are all comprised of the same set of amino acids in different sequences. Results from experiments and molecular dynamics simulations show that the peptide's self-assembly and DNA-interaction behaviors can be well manipulated through sequence variation. With optimized pairing modes between the β-sheets, the peptide of I3V3A3G3K3 can induce efficient DNA condensation into virus-mimicking structures. The condensation involves two steps; the peptide molecules first bind onto the DNA chain through electrostatic interactions and then self-associate into β-sheets under hydrophobic interactions and hydrogen bonding. In such condensates, the peptide β-sheets act as scaffolds to assist the ordered arrangement of DNA, mimicking the very nature of the virus capsid in helping DNA packaging. Such a hierarchy affords an extremely stable structure to attain the highly condensed state and protect DNA against enzymatic degradation. Moreover, the condensate size can be well tuned by the DNA length. The condensates with smaller sizes and narrow size distribution can deliver DNA efficiently into cells. The study helps not only for probing into the DNA packaging mechanism in virus but also delineating the role of peptide self-assembly in DNA condensation, which may lead to development of peptide-based gene vectors for therapeutic applications.
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Affiliation(s)
- Meiwen Cao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Yu Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Wenjing Zhao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Ruilian Qi
- Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Yuchun Han
- Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Rongliang Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering , Donghua University , Shanghai 201620 , China
| | - Yilin Wang
- Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
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143
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Nürenberg-Goloub E, Heinemann H, Gerovac M, Tampé R. Ribosome recycling is coordinated by processive events in two asymmetric ATP sites of ABCE1. Life Sci Alliance 2018; 1. [PMID: 30198020 PMCID: PMC6124641 DOI: 10.26508/lsa.201800095] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The stepwise ribosome disassembly in the translation cycle of eukaryotes and archaea is scheduled by discrete molecular events within the asymmetric ribosome recycling factor ABCE1. Ribosome recycling orchestrated by ABCE1 is a fundamental process in protein translation and mRNA surveillance, connecting termination with initiation. Beyond the plenitude of well-studied translational GTPases, ABCE1 is the only essential factor energized by ATP, delivering the energy for ribosome splitting via two nucleotide-binding sites by a yet unknown mechanism. Here, we define how allosterically coupled ATP binding and hydrolysis events in ABCE1 empower ribosome recycling. ATP occlusion in the low-turnover control site II promotes formation of the pre-splitting complex and facilitates ATP engagement in the high-turnover site I, which in turn drives the structural reorganization required for ribosome splitting. ATP hydrolysis and ensuing release of ABCE1 from the small subunit terminate the post-splitting complex. Thus, ABCE1 runs through an allosterically coupled cycle of closure and opening at both sites, consistent with a processive clamp model. This study delineates the inner mechanics of ABCE1 and reveals why various ABCE1 mutants lead to defects in cell homeostasis, growth, and differentiation.
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Affiliation(s)
- Elina Nürenberg-Goloub
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany
| | - Holger Heinemann
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany
| | - Milan Gerovac
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany
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144
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SUN LL, SU YY, GAO YJ, Li W, LYU H, LI B, LI D. Progresses of Single Molecular Fluorescence Resonance Energy Transfer in Studying Biomacromolecule Dynamic Process. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61088-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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145
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Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chem Rev 2018; 118:4120-4155. [PMID: 29363314 PMCID: PMC5918467 DOI: 10.1021/acs.chemrev.7b00519] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.
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Affiliation(s)
| | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
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146
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Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Annu Rev Biochem 2018; 87:451-478. [PMID: 29570352 DOI: 10.1146/annurev-biochem-062917-011942] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic information is translated into proteins by the ribosome. Structural studies of the ribosome and of its complexes with factors and inhibitors have provided invaluable information on the mechanism of protein synthesis. Ribosome inhibitors are among the most successful antimicrobial drugs and constitute more than half of all medicines used to treat infections. However, bacterial infections are becoming increasingly difficult to treat because the microbes have developed resistance to the most effective antibiotics, creating a major public health care threat. This has spurred a renewed interest in structure-function studies of protein synthesis inhibitors, and in few cases, compounds have been developed into potent therapeutic agents against drug-resistant pathogens. In this review, we describe the modes of action of many ribosome-targeting antibiotics, highlight the major resistance mechanisms developed by pathogenic bacteria, and discuss recent advances in structure-assisted design of new molecules.
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Affiliation(s)
- Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Dejian Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
| | - Yury S Polikanov
- Department of Biological Sciences, and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
| | - Matthieu G Gagnon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA.,Current affiliation: Department of Microbiology and Immunology, and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA;
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147
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El-Naggar AM, Sorensen PH. Translational control of aberrant stress responses as a hallmark of cancer. J Pathol 2018; 244:650-666. [PMID: 29293271 DOI: 10.1002/path.5030] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022]
Abstract
Altered mRNA translational control is emerging as a critical factor in cancer development and progression. Targeting specific elements of the translational machinery, such as mTORC1 or eIF4E, is emerging as a new strategy for innovative cancer therapy. While translation of most mRNAs takes place through cap-dependent mechanisms, a sub-population of cellular mRNA species, particularly stress-inducible mRNAs with highly structured 5'-UTR regions, are primarily translated through cap-independent mechanisms. Intriguingly, many of these mRNAs encode proteins that are involved in tumour cell adaptation to microenvironmental stress, and thus linked to aggressive behaviour including tumour invasion and metastasis. This necessitates a rigorous search for links between microenvironmental stress and aggressive tumour phenotypes. Under stress, cells block global protein synthesis to preserve energy while maintaining selective synthesis of proteins that support cell survival. One highly conserved mechanism to regulate protein synthesis under cell stress is to sequester mRNAs into cytosolic aggregates called stress granules (SGs), where their translation is silenced. SGs confer survival advantages and chemotherapeutic resistance to tumour cells under stress. Recently, it has been shown that genetically blocking SG formation dramatically reduces tumour invasive and metastatic capacity in vivo. Therefore, targeting SG formation might represent a potential treatment strategy to block cancer metastasis. Here, we present the critical link between selective mRNA translation, stress adaptation, SGs, and tumour progression. Further, we also explain how deciphering mechanisms of selective mRNA translation occurs under cell stress holds great promise for the identification of new targets in the treatment of cancer. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Egypt
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
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148
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Flores JK, Ataide SF. Structural Changes of RNA in Complex with Proteins in the SRP. Front Mol Biosci 2018; 5:7. [PMID: 29459899 PMCID: PMC5807370 DOI: 10.3389/fmolb.2018.00007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/17/2018] [Indexed: 12/18/2022] Open
Abstract
The structural flexibility of RNA allows it to exist in several shapes and sizes. Thus, RNA is functionally diverse and is known to be involved in processes such as catalysis, ligand binding, and most importantly, protein recognition. RNA can adopt different structures, which can often dictate its functionality. When RNA binds onto protein to form a ribonucleoprotein complex (RNP), multiple interactions and conformational changes occur with the RNA and protein. However, there is the question of whether there is a specific pattern for these changes to occur upon recognition. In particular when RNP complexity increases with the addition of multiple proteins/RNA, it becomes difficult to structurally characterize the overall changes using the current structural determination techniques. Hence, there is a need to use a combination of biochemical, structural and computational modeling to achieve a better understanding of the processes that RNPs are involved. Nevertheless, there are well-characterized systems that are evolutionarily conserved [such as the signal recognition particle (SRP)] that give us important information on the structural changes of RNA and protein upon complex formation.
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Affiliation(s)
- Janine K Flores
- Ataide Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Sandro F Ataide
- Ataide Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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149
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Pavlov MY, Liljas A, Ehrenberg M. A recent intermezzo at the Ribosome Club. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0185. [PMID: 28138071 PMCID: PMC5311929 DOI: 10.1098/rstb.2016.0185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/01/2022] Open
Abstract
Two sets of ribosome structures have recently led to two different interpretations of what limits the accuracy of codon translation by transfer RNAs. In this review, inspired by this intermezzo at the Ribosome Club, we briefly discuss accuracy amplification by energy driven proofreading and its implementation in genetic code translation. We further discuss general ways by which the monitoring bases of 16S rRNA may enhance the ultimate accuracy (d-values) and how the codon translation accuracy is reduced by the actions of Mg2+ ions and the presence of error inducing aminoglycoside antibiotics. We demonstrate that complete freezing-in of cognate-like tautomeric states of ribosome-bound nucleotide bases in transfer RNA or messenger RNA is not compatible with recent experiments on initial codon selection by transfer RNA in ternary complex with elongation factor Tu and GTP. From these considerations, we suggest that the sets of 30S subunit structures from the Ramakrishnan group and 70S structures from the Yusupov/Yusupova group may, after all, reflect two sides of the same coin and how the structurally based intermezzo at the Ribosome Club may be resolved simply by taking the dynamic aspects of ribosome function into account. This article is part of the themed issue ‘Perspectives on the ribosome’.
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Affiliation(s)
- Michael Y Pavlov
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala 75124, Sweden
| | - Anders Liljas
- Department of Biochemistry and Structural Biology, Lund University, Box 124, 22100 Lund, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala 75124, Sweden
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150
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Rangel-Chavez C, Galan-Vasquez E, Martinez-Antonio A. Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology. MOLECULAR BIOSYSTEMS 2017; 13:665-676. [PMID: 28256660 DOI: 10.1039/c6mb00789a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genetic information in genomes is ordered, arranged in such a way that it constitutes a code, the so-called cis regulatory code. The regulatory machinery of the cell, termed trans-factors, decodes and expresses this information. In this way, genomes maintain a potential repertoire of genetic programs, parts of which are executed depending on the presence of active regulators in each condition. These genetic programs, executed by the regulatory machinery, have functional units in the genome delimited by punctuation-like marks. In genetic terms, these informational phrases correspond to transcription units, which are the minimal genetic information expressed consistently from initiation to termination marks. Between the start and final punctuation marks, additional marks are present that are read by the transcriptional and translational machineries. In this work, we look at all the experimentally described and predicted genetic elements in the bacterium Escherichia coli K-12 MG1655 and define a comprehensive architectural organization of transcription units to reveal the natural genome-design and to guide the construction of synthetic genetic programs.
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Affiliation(s)
- Cynthia Rangel-Chavez
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico.
| | - Edgardo Galan-Vasquez
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico.
| | - Agustino Martinez-Antonio
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico.
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