1
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Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T. Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat Chem Biol 2024; 20:605-614. [PMID: 38267667 DOI: 10.1038/s41589-023-01513-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 11/24/2023] [Indexed: 01/26/2024]
Abstract
In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.
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Affiliation(s)
- Mayuki Tanaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeshi Yokoyama
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hironori Saito
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Madoka Nishimoto
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Kengo Tsuda
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Naoyuki Sotta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hideki Shigematsu
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Sayo, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Shintaro Iwasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- RIKEN Cluster for Pioneering Research, Wako, Japan.
| | - Takuhiro Ito
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan.
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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2
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Ferrara S, Bertoni G. Genome-Scale Analysis of the Structure and Function of RNA Pathways and Networks in Pseudomonas aeruginosa. Methods Mol Biol 2024; 2721:183-195. [PMID: 37819523 DOI: 10.1007/978-1-0716-3473-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
In recent years, several genome-wide approaches based on RNA sequencing (RNA-seq) have been developed. These methods allow a comprehensive and dynamic view of the structure and function of the multi-layered RNA pathways and networks. Many of these approaches, including the promising one of single-cell transcriptome analysis, have been successfully applied to Pseudomonas aeruginosa. However, we are only at the beginning because only a few surrounding conditions have been considered. Here, we aim to illustrate the different types of approaches based on RNA-seq that will lead us in the future to a better understanding of the dynamics of RNA biology in P. aeruginosa.
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Affiliation(s)
- Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy.
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3
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Richardson MO, Eddy SR. ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events. BMC Bioinformatics 2023; 24:471. [PMID: 38093195 PMCID: PMC10720069 DOI: 10.1186/s12859-023-05602-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND In canonical protein translation, ribosomes initiate translation at a specific start codon, maintain a single reading frame throughout elongation, and terminate at the first in-frame stop codon. However, ribosomal behavior can deviate at each of these steps, sometimes in a programmed manner. Certain mRNAs contain sequence and structural elements that cause ribosomes to begin translation at alternative start codons, shift reading frame, read through stop codons, or reinitiate on the same mRNA. These processes represent important translational control mechanisms that can allow an mRNA to encode multiple functional protein products or regulate protein expression. The prevalence of these events remains uncertain, due to the difficulty of systematic detection. RESULTS We have developed a computational model to infer non-canonical translation events from ribosome profiling data. CONCLUSION ORFeus identifies known examples of alternative open reading frames and recoding events across different organisms and enables transcriptome-wide searches for novel events.
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Affiliation(s)
- Mary O Richardson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Sean R Eddy
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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4
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Fuchs S, Engelmann S. Small proteins in bacteria - Big challenges in prediction and identification. Proteomics 2023; 23:e2200421. [PMID: 37609810 DOI: 10.1002/pmic.202200421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023]
Abstract
Proteins with up to 100 amino acids have been largely overlooked due to the challenges associated with predicting and identifying them using traditional methods. Recent advances in bioinformatics and machine learning, DNA sequencing, RNA and Ribo-seq technologies, and mass spectrometry (MS) have greatly facilitated the detection and characterisation of these elusive proteins in recent years. This has revealed their crucial role in various cellular processes including regulation, signalling and transport, as toxins and as folding helpers for protein complexes. Consequently, the systematic identification and characterisation of these proteins in bacteria have emerged as a prominent field of interest within the microbial research community. This review provides an overview of different strategies for predicting and identifying these proteins on a large scale, leveraging the power of these advanced technologies. Furthermore, the review offers insights into the future developments that may be expected in this field.
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Affiliation(s)
- Stephan Fuchs
- Genome Competence Center (MF1), Department MFI, Robert-Koch-Institut, Berlin, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung GmbH, Braunschweig, Germany
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5
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Weber M, Sogues A, Yus E, Burgos R, Gallo C, Martínez S, Lluch‐Senar M, Serrano L. Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium. Mol Syst Biol 2023; 19:e11301. [PMID: 37642167 PMCID: PMC10568206 DOI: 10.15252/msb.202211301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.
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Affiliation(s)
- Marc Weber
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Adrià Sogues
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Eva Yus
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Raul Burgos
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sira Martínez
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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6
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Zhang Y, Xiao F, Zhang L, Ding Z, Shi G, Li Y. A New Mechanism of Carbon Metabolism and Acetic Acid Balance Regulated by CcpA. Microorganisms 2023; 11:2303. [PMID: 37764147 PMCID: PMC10535407 DOI: 10.3390/microorganisms11092303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Catabolite control protein A (CcpA) is a critical regulator in Gram-positive bacteria that orchestrates carbon metabolism by coordinating the utilization of different carbon sources. Although it has been widely proved that CcpA helps prioritize the utilization of glucose over other carbon sources, this global regulator's precise mechanism of action remains unclear. In this study, a mutant Bacillus licheniformis deleted for CcpA was constructed. Cell growth, carbon utilization, metabolites and the transcription of key enzymes of the mutant strain were compared with that of the wild-type one. It was found that CcpA is involved in the regulation of glucose concentration metabolism in Bacillus. At the same time, CcpA regulates glucose metabolism by inhibiting acetic acid synthesis and pentose phosphate pathway key gene zwF. The conversion rate of acetic acid is increased by about 3.5 times after ccpA is deleted. The present study provides a new mechanism of carbon metabolism and acetic acid balance regulated by CcpA. On the one hand, this work deepens the understanding of the regulatory function of CcpA and provides a new view on the regulation of glucose metabolism. On the other hand, it is helpful to the transformation of B. licheniformis chassis microorganisms.
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Affiliation(s)
- Yupeng Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Fengxu Xiao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
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7
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Ferrara S, Brignoli T, Bertoni G. Little reason to call them small noncoding RNAs. Front Microbiol 2023; 14:1191166. [PMID: 37455713 PMCID: PMC10339803 DOI: 10.3389/fmicb.2023.1191166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Hundreds of different species of small RNAs can populate a bacterial cell. This small transcriptome contains important information for the adaptation of cellular physiology to environmental changes. Underlying cellular networks involving small RNAs are RNA-RNA and RNA-protein interactions, which are often intertwined. In addition, small RNAs can function as mRNAs. In general, small RNAs are referred to as noncoding because very few are known to contain translated open reading frames. In this article, we intend to highlight that the number of small RNAs that fall within the set of translated RNAs is bound to increase. In addition, we aim to emphasize that the dynamics of the small transcriptome involve different functional codes, not just the genetic code. Therefore, since the role of small RNAs is always code-driven, we believe that there is little reason to continue calling them small noncoding RNAs.
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8
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Choi W, Maharjan A, Im HG, Park JY, Park JT, Park JH. Identification and Characterization of HEPN-MNT Type II TA System from Methanothermobacter thermautotrophicus ΔH. J Microbiol 2023; 61:411-421. [PMID: 37071293 DOI: 10.1007/s12275-023-00041-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 04/19/2023]
Abstract
Toxin-antitoxin (TA) systems are widespread in bacteria and archaea plasmids and genomes to regulate DNA replication, gene transcription, or protein translation. Higher eukaryotic and prokaryotic nucleotide-binding (HEPN) and minimal nucleotidyltransferase (MNT) domains are prevalent in prokaryotic genomes and constitute TA pairs. However, three gene pairs (MTH304/305, 408/409, and 463/464) of Methanothermobacter thermautotropicus ΔH HEPN-MNT family have not been studied as TA systems. Among these candidates, our study characterizes the MTH463/MTH464 TA system. MTH463 expression inhibited Escherichia coli growth, whereas MTH464 did not and blocked MTH463 instead. Using site-directed MTH463 mutagenesis, we determined that amino acids R99G, H104A, and Y106A from the R[ɸX]4-6H motif are involved with MTH463 cell toxicity. Furthermore, we established that purified MTH463 could degrade MS2 phage RNA, whereas purified MTH464 neutralized MTH463 activity in vitro. Our results indicate that the endonuclease toxin MTH463 (encoding a HEPN domain) and its cognate antitoxin MTH464 (encoding the MNT domain) may act as a type II TA system in M. thermautotropicus ΔH. This study provides initial and essential information studying TA system functions, primarily archaea HEPN-MNT family.
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Affiliation(s)
- Wonho Choi
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
- 4D Convergence Technology Institute (National Key Technology Institute in University), Korea National University of Transportation, Jungpyeong, 27909, Republic of Korea
| | - Anoth Maharjan
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Hae Gang Im
- BIORCHESTRA Co., LTD., Daejeon, 34013, Republic of Korea
| | - Ji-Young Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Jong-Tae Park
- Department of Food Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.
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9
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Ebihara S, Yen H, Tobe T. A novel toxin-antitoxin system swpAB alters gene expression patterns and reduces virulence expression in enterohemorrhagic Escherichia coli. Microbiol Immunol 2023; 67:171-184. [PMID: 36636756 DOI: 10.1111/1348-0421.13054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 01/14/2023]
Abstract
Toxin-antitoxin (TA) systems are found widely among many bacteria, including enterohemorrhagic Escherichia coli (EHEC), but their functions are still poorly understood. In this study, we identified and characterized a novel TA system belonging to the relBE family, classified as a type II TA system, found in EHEC. The protein encoded by the toxin gene is homologous to RelE ribonuclease. Using various conditions for increasing the toxin activity, high-level induction of a toxin gene, and repression of an antitoxin gene in wild-type EHEC, we showed that the TA system, named swpAB (switching of gene expression profile), is involved in selective repression of a set of genes, including some virulence genes, and in the reduction of adherence capacity, rather than in suppression of bacterial growth. A detailed analysis of the profiles of RNA levels along sequences at 15 min after high expression of swpA revealed that two virulence genes, espA and tir, were direct targets of the SwpA toxin. These results suggested that the swpAB system can alter gene expression patterns and change bacterial physiological activity without affecting bacterial growth.
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Affiliation(s)
- Shinya Ebihara
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hilo Yen
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Toru Tobe
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
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10
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Sawyer EB, Cortes T. Ribosome profiling enhances understanding of mycobacterial translation. Front Microbiol 2022; 13:976550. [PMID: 35992675 PMCID: PMC9386245 DOI: 10.3389/fmicb.2022.976550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/22/2022] [Indexed: 11/21/2022] Open
Abstract
A recent addition to the -omics toolkit, ribosome profiling, enables researchers to gain insight into the process and regulation of translation by mapping fragments of mRNA protected from nuclease digestion by ribosome binding. In this review, we discuss how ribosome profiling applied to mycobacteria has led to discoveries about translational regulation. Using case studies, we show that the traditional view of “canonical” translation mechanisms needs expanding to encompass features of mycobacterial translation that are more widespread than previously recognized. We also discuss the limitations of the method and potential future developments that could yield further insight into the fundamental biology of this important human pathogen.
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Affiliation(s)
- Elizabeth B. Sawyer
- School of Life Sciences, University of Westminster, London, United Kingdom
- *Correspondence: Elizabeth B. Sawyer,
| | - Teresa Cortes
- Pathogen Gene Regulation Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
- Teresa Cortes,
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11
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Focht CM, Strobel SA. Efficient quantitative monitoring of translational initiation by RelE cleavage. Nucleic Acids Res 2022; 50:e105. [PMID: 35871288 PMCID: PMC9561414 DOI: 10.1093/nar/gkac614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/23/2022] [Accepted: 07/19/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
The sequences of the 5′ untranslated regions (5′-UTRs) of mRNA alter gene expression across domains of life. Transcriptional modulators can be easily assayed through transcription termination, but translational regulators often require indirect, laborious methods. We have leveraged RelE’s ribosome-dependent endonuclease activity to develop a quantitative assay to monitor translation initiation of cis-regulatory mRNAs. RelE cleavage accurately reports ligand-dependent changes in ribosome association for two translational riboswitches and provides quantitative information about each switch's sensitivity and range of response. RelE accurately reads out sequence-driven changes in riboswitch specificity and function and is quantitatively dependent upon ligand concentration. RelE cleavage similarly captures differences in translation initiation between yeast 5′-UTR isoforms. RelE cleavage can thus reveal a plethora of information about translation initiation in different domains of life.
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Affiliation(s)
- Caroline M Focht
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven , CT 06510 , USA
- Institute of Biomolecular Design and Discovery , West Haven , CT 06516 , USA
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven , CT 06510 , USA
- Institute of Biomolecular Design and Discovery , West Haven , CT 06516 , USA
- Department of Chemistry, Yale University , New Haven , CT 06511 , USA
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12
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Herzel L, Stanley JA, Yao CC, Li GW. Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome. Nucleic Acids Res 2022; 50:5029-5046. [PMID: 35524564 PMCID: PMC9122600 DOI: 10.1093/nar/gkac295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 01/01/2023] Open
Abstract
Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.
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Affiliation(s)
- Lydia Herzel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Julian A Stanley
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Chun-Chen Yao
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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13
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Vazquez-Laslop N, Sharma CM, Mankin A, Buskirk AR. Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling. J Bacteriol 2022; 204:e0029421. [PMID: 34339296 PMCID: PMC8765392 DOI: 10.1128/jb.00294-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small proteins encoded by open reading frames (ORFs) shorter than 50 codons (small ORFs [sORFs]) are often overlooked by annotation engines and are difficult to characterize using traditional biochemical techniques. Ribosome profiling has tremendous potential to empirically improve the annotations of prokaryotic genomes. Recent improvements in ribosome profiling methods for bacterial model organisms have revealed many new sORFs in well-characterized genomes. Antibiotics that trap ribosomes just after initiation have played a key role in these developments by allowing the unambiguous identification of the start codons (and, hence, the reading frame) for novel ORFs. Here, we describe these new methods and highlight critical controls and considerations for adapting ribosome profiling to different prokaryotic species.
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Affiliation(s)
- Nora Vazquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Cynthia M. Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alexander Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Allen R. Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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14
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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15
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Global Analysis of the Specificities and Targets of Endoribonucleases from Escherichia coli Toxin-Antitoxin Systems. mBio 2021; 12:e0201221. [PMID: 34544284 PMCID: PMC8546651 DOI: 10.1128/mbio.02012-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Toxin-antitoxin systems are widely distributed genetic modules typically featuring toxins that can inhibit bacterial growth and antitoxins that can reverse inhibition. Although Escherichia coli encodes 11 toxins with known or putative endoribonuclease activity, the targets of most of these toxins remain poorly characterized. Using a new RNA sequencing (RNA-seq) pipeline that enables the mapping and quantification of RNA cleavage with single-nucleotide resolution, we characterized the targets and specificities of 9 endoribonuclease toxins from E. coli. We found that these toxins use low-information cleavage motifs to cut a significant proportion of mRNAs in E. coli, but not tRNAs or the rRNAs from mature ribosomes. However, all the toxins, including those that are ribosome dependent and cleave only translated RNA, inhibit ribosome biogenesis. This inhibition likely results from the cleavage of ribosomal protein transcripts, which disrupts the stoichiometry and biogenesis of new ribosomes and causes the accumulation of aberrant ribosome precursors. Collectively, our results provide a comprehensive, global analysis of endoribonuclease-based toxin-antitoxin systems in E. coli and support the conclusion that, despite their diversity, each disrupts translation and ribosome biogenesis.
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16
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Fremin BJ, Nicolaou C, Bhatt AS. Simultaneous ribosome profiling of hundreds of microbes from the human microbiome. Nat Protoc 2021; 16:4676-4691. [PMID: 34381207 PMCID: PMC8750612 DOI: 10.1038/s41596-021-00592-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023]
Abstract
Ribosome profiling enables sequencing of ribosome-bound fragments of RNA, revealing which transcripts are being translated as well as the position of ribosomes along mRNAs. Although ribosome profiling has been applied to cultured bacterial isolates, its application to uncultured, mixed communities has been challenging. We present MetaRibo-Seq, a protocol that enables the application of ribosome profiling directly to the human fecal microbiome. MetaRibo-Seq is a benchmarked method that includes several modifications to existing ribosome profiling protocols, specifically addressing challenges involving fecal sample storage, purity and input requirements. We also provide a computational workflow to quality control and trim reads, de novo assemble a reference metagenome with metagenomic reads, align MetaRibo-Seq reads to the reference, and assess MetaRibo-Seq library quality ( https://github.com/bhattlab/bhattlab_workflows/tree/master/metariboseq ). This MetaRibo-Seq protocol enables researchers in standard molecular biology laboratories to study translation in the fecal microbiome in ~5 d.
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Affiliation(s)
| | - Cosmos Nicolaou
- Divisions of Hematology and Blood & Marrow Transplantation, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ami S. Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.,Divisions of Hematology and Blood & Marrow Transplantation, Department of Medicine, Stanford University, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to A.S.B.
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17
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Abstract
Narnaviruses are RNA viruses detected in diverse fungi, plants, protists, arthropods, and nematodes. Though initially described as simple single-gene nonsegmented viruses encoding RNA-dependent RNA polymerase (RdRp), a subset of narnaviruses referred to as "ambigrammatic" harbor a unique genomic configuration consisting of overlapping open reading frames (ORFs) encoded on opposite strands. Phylogenetic analysis supports selection to maintain this unusual genome organization, but functional investigations are lacking. Here, we establish the mosquito-infecting Culex narnavirus 1 (CxNV1) as a model to investigate the functional role of overlapping ORFs in narnavirus replication. In CxNV1, a reverse ORF without homology to known proteins covers nearly the entire 3.2-kb segment encoding the RdRp. Additionally, two opposing and nearly completely overlapping novel ORFs are found on the second putative CxNV1 segment, the 0.8-kb "Robin" RNA. We developed a system to launch CxNV1 in a naive mosquito cell line and then showed that functional RdRp is required for persistence of both segments, and an intact reverse ORF is required on the RdRp segment for persistence. Mass spectrometry of persistently CxNV1-infected cells provided evidence for translation of this reverse ORF. Finally, ribosome profiling yielded a striking pattern of footprints for all four CxNV1 RNA strands that was distinct from actively translating ribosomes on host mRNA or coinfecting RNA viruses. Taken together, these data raise the possibility that the process of translation itself is important for persistence of ambigrammatic narnaviruses, potentially by protecting viral RNA with ribosomes, thus suggesting a heretofore undescribed viral tactic for replication and transmission. IMPORTANCE Fundamental to our understanding of RNA viruses is a description of which strand(s) of RNA are transmitted as the viral genome relative to which encode the viral proteins. Ambigrammatic narnaviruses break the mold. These viruses, found broadly in fungi, plants, and insects, have the unique feature of two overlapping genes encoded on opposite strands, comprising nearly the full length of the viral genome. Such extensive overlap is not seen in other RNA viruses and comes at the cost of reduced evolutionary flexibility in the sequence. The present study is motivated by investigating the benefits which balance that cost. We show for the first time a functional requirement for the ambigrammatic genome configuration in Culex narnavirus 1, which suggests a model for how translation of both strands might benefit this virus. Our work highlights a new blueprint for viral persistence, distinct from strategies defined by canonical definitions of the coding strand.
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18
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Li SHJ, Nofal M, Parsons LR, Rabinowitz JD, Gitai Z. Monitoring mammalian mitochondrial translation with MitoRiboSeq. Nat Protoc 2021; 16:2802-2825. [PMID: 33953394 PMCID: PMC8610098 DOI: 10.1038/s41596-021-00517-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/05/2021] [Indexed: 02/03/2023]
Abstract
Several essential components of the electron transport chain, the major producer of ATP in mammalian cells, are encoded in the mitochondrial genome. These 13 proteins are translated within mitochondria by 'mitoribosomes'. Defective mitochondrial translation underlies multiple inborn errors of metabolism and has been implicated in pathologies such as aging, metabolic syndrome and cancer. Here, we provide a detailed ribosome profiling protocol optimized to interrogate mitochondrial translation in mammalian cells (MitoRiboSeq), wherein mitoribosome footprints are generated with micrococcal nuclease and mitoribosomes are separated from cytosolic ribosomes and other RNAs by ultracentrifugation in a single straightforward step. We highlight critical steps during library preparation and provide a step-by-step guide to data analysis accompanied by open-source bioinformatic code. Our method outputs mitoribosome footprints at single-codon resolution. Codons with high footprint densities are sites of mitoribosome stalling. We recently applied this approach to demonstrate that defects in mitochondrial serine catabolism or in mitochondrial tRNA methylation cause stalling of mitoribosomes at specific codons. Our method can be applied to study basic mitochondrial biology or to characterize abnormalities in mitochondrial translation in patients with mitochondrial disorders.
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Affiliation(s)
| | - Michel Nofal
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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19
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Oh E. Monitoring Bacterial Translation Rates Genome-Wide. Methods Mol Biol 2021; 2252:3-26. [PMID: 33765269 DOI: 10.1007/978-1-0716-1150-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Modern DNA sequencing technologies have allowed for the sequencing of tens of thousands of bacterial genomes. While this explosion of information has brought about new insights into the diversity of the prokaryotic world, much less is known of the identity of proteins encoded within these genomes, as well as their rates of production. The advent of ribosome profiling, or the deep sequencing of ribosome-protected footprints, has recently enabled the systematic evaluation of every protein-coding region in a given experimental condition, the rates of protein production for each gene, and the variability in translation rates across each message. Here, I provide an update to the bacterial ribosome profiling approach, with a particular emphasis on a simplified strategy to reduce cloning time.
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Affiliation(s)
- Eugene Oh
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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20
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Abstract
Bacterial endoribonuclease toxins belong to a protein family that inhibits bacterial growth by degrading mRNA or rRNA sequences. The toxin genes are organized in pairs with its cognate antitoxins in the chromosome and thus the activities of the toxins are antagonized by antitoxin proteins or RNAs during active translation. In response to a variety of cellular stresses, the endoribonuclease toxins appear to be released from antitoxin molecules via proteolytic cleavage of antitoxin proteins or preferential degradation of antitoxin RNAs and cleave a diverse range of mRNA or rRNA sequences in a sequence-specific or codon-specific manner, resulting in various biological phenomena such as antibiotic tolerance and persister cell formation. Given that substrate specificity of each endoribonuclease toxin is determined by its structure and the composition of active site residues, we summarize the biology, structure, and substrate specificity of the updated bacterial endoribonuclease toxins.
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Affiliation(s)
- Yoontak Han
- Department of Life Sciences, Korea University, Seoul 02481, Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul 02481, Korea
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21
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Ovchinnikov SV, Bikmetov D, Livenskyi A, Serebryakova M, Wilcox B, Mangano K, Shiriaev DI, Osterman IA, Sergiev PV, Borukhov S, Vazquez-Laslop N, Mankin AS, Severinov K, Dubiley S. Mechanism of translation inhibition by type II GNAT toxin AtaT2. Nucleic Acids Res 2020; 48:8617-8625. [PMID: 32597957 PMCID: PMC7470980 DOI: 10.1093/nar/gkaa551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Type II toxin–antitoxins systems are widespread in prokaryotic genomes. Typically, they comprise two proteins, a toxin, and an antitoxin, encoded by adjacent genes and forming a complex in which the enzymatic activity of the toxin is inhibited. Under stress conditions, the antitoxin is degraded liberating the active toxin. Though thousands of various toxin–antitoxins pairs have been predicted bioinformatically, only a handful has been thoroughly characterized. Here, we describe the AtaT2 toxin from a toxin–antitoxin system from Escherichia coli O157:H7. We show that AtaT2 is the first GNAT (Gcn5-related N-acetyltransferase) toxin that specifically targets charged glycyl tRNA. In vivo, the AtaT2 activity induces ribosome stalling at all four glycyl codons but does not evoke a stringent response. In vitro, AtaT2 acetylates the aminoacyl moiety of isoaccepting glycyl tRNAs, thus precluding their participation in translation. Our study broadens the known target specificity of GNAT toxins beyond the earlier described isoleucine and formyl methionine tRNAs, and suggest that various GNAT toxins may have evolved to specificaly target other if not all individual aminoacyl tRNAs.
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Affiliation(s)
- Stepan V Ovchinnikov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Dmitry Bikmetov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.,Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia
| | - Alexei Livenskyi
- Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Marina Serebryakova
- Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Brendan Wilcox
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Dmitrii I Shiriaev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ilya A Osterman
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Petr V Sergiev
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1489, USA
| | - Nora Vazquez-Laslop
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.,Waksman Institute for Microbiology, Piscataway, NJ 08854-8020, USA
| | - Svetlana Dubiley
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia
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22
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Glaub A, Huptas C, Neuhaus K, Ardern Z. Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data. J Biol Chem 2020; 295:8999-9011. [PMID: 32385111 PMCID: PMC7335797 DOI: 10.1074/jbc.ra119.012161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/05/2020] [Indexed: 02/03/2023] Open
Abstract
Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a "one-size-fits-all" ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.
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Affiliation(s)
- Alina Glaub
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Christopher Huptas
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany; Core Facility Microbiome, ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Zachary Ardern
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany.
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23
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Zehentner B, Ardern Z, Kreitmeier M, Scherer S, Neuhaus K. A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC). Front Microbiol 2020; 11:377. [PMID: 32265854 PMCID: PMC7103648 DOI: 10.3389/fmicb.2020.00377] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 02/20/2020] [Indexed: 12/23/2022] Open
Abstract
Antisense transcription is well known in bacteria. However, translation of antisense RNAs is typically not considered, as the implied overlapping coding at a DNA locus is assumed to be highly improbable. Therefore, such overlapping genes are systematically excluded in prokaryotic genome annotation. Here we report an exceptional 603 bp long open reading frame completely embedded in antisense to the gene of the outer membrane protein ompA. An active σ70 promoter, transcription start site (TSS), Shine-Dalgarno motif and rho-independent terminator were experimentally validated, providing evidence that this open reading frame has all the structural features of a functional gene. Furthermore, ribosomal profiling revealed translation of the mRNA, the protein was detected in Western blots and a pH-dependent phenotype conferred by the protein was shown in competitive overexpression growth experiments of a translationally arrested mutant versus wild type. We designate this novel gene pop (pH-regulated overlapping protein-coding gene), thus adding another example to the growing list of overlapping, protein coding genes in bacteria.
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Affiliation(s)
- Barbara Zehentner
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Zachary Ardern
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Michaela Kreitmeier
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
- ZIEL – Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- ZIEL – Institute for Food & Health, Technical University of Munich, Freising, Germany
- Core Facility Microbiome, ZIEL – Institute for Food & Health, Technical University of Munich, Freising, Germany
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24
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Michel AM, Kiniry SJ, O'Connor PBF, Mullan JP, Baranov PV. GWIPS-viz: 2018 update. Nucleic Acids Res 2019; 46:D823-D830. [PMID: 28977460 PMCID: PMC5753223 DOI: 10.1093/nar/gkx790] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/29/2017] [Indexed: 12/15/2022] Open
Abstract
The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold increase in the last three years. The increase is particularly substantial for data derived from human sources. Following user requests, we added the functionality to download these tracks in bigWig format. We also incorporated new types of data (e.g. TCP-seq) as well as auxiliary tracks from other sources that help with the interpretation of Ribo-seq data. Improvements in the visualization of the data have been carried out particularly for bacterial genomes where the Ribo-seq data are now shown in a strand specific manner. For higher eukaryotic datasets, we provide characteristics of individual datasets using the RUST program which includes the triplet periodicity, sequencing biases and relative inferred A-site dwell times. This information can be used for assessing the quality of Ribo-seq datasets. To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome.
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Affiliation(s)
- Audrey M Michel
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | | | - James P Mullan
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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25
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Sawyer EB, Grabowska AD, Cortes T. Translational regulation in mycobacteria and its implications for pathogenicity. Nucleic Acids Res 2019; 46:6950-6961. [PMID: 29947784 PMCID: PMC6101614 DOI: 10.1093/nar/gky574] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/14/2018] [Indexed: 01/13/2023] Open
Abstract
Protein synthesis is a fundamental requirement of all cells for survival and replication. To date, vast numbers of genetic and biochemical studies have been performed to address the mechanisms of translation and its regulation in Escherichia coli, but only a limited number of studies have investigated these processes in other bacteria, particularly in slow growing bacteria like Mycobacterium tuberculosis, the causative agent of human tuberculosis. In this Review, we highlight important differences in the translational machinery of M. tuberculosis compared with E. coli, specifically the presence of two additional proteins and subunit stabilizing elements such as the B9 bridge. We also consider the role of leaderless translation in the ability of M. tuberculosis to establish latent infection and look at the experimental evidence that translational regulatory mechanisms operate in mycobacteria during stress adaptation, particularly focussing on differences in toxin-antitoxin systems between E. coli and M. tuberculosis and on the role of tuneable translational fidelity in conferring phenotypic antibiotic resistance. Finally, we consider the implications of these differences in the context of the biological adaptation of M. tuberculosis and discuss how these regulatory mechanisms could aid in the development of novel therapeutics for tuberculosis.
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Affiliation(s)
- Elizabeth B Sawyer
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.,TB Centre, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Anna D Grabowska
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.,TB Centre, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Teresa Cortes
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.,TB Centre, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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26
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Liu B, Molinaro G, Shu H, Stackpole EE, Huber KM, Richter JD. Optimization of ribosome profiling using low-input brain tissue from fragile X syndrome model mice. Nucleic Acids Res 2019; 47:e25. [PMID: 30590705 PMCID: PMC6411937 DOI: 10.1093/nar/gky1292] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/23/2018] [Accepted: 12/15/2018] [Indexed: 01/23/2023] Open
Abstract
Dysregulated protein synthesis is a major underlying cause of many neurodevelopmental diseases including fragile X syndrome. In order to capture subtle but biologically significant differences in translation in these disorders, a robust technique is required. One powerful tool to study translational control is ribosome profiling, which is based on deep sequencing of mRNA fragments protected from ribonuclease (RNase) digestion by ribosomes. However, this approach has been mainly applied to rapidly dividing cells where translation is active and large amounts of starting material are readily available. The application of ribosome profiling to low-input brain tissue where translation is modest and gene expression changes between genotypes are expected to be small has not been carefully evaluated. Using hippocampal tissue from wide type and fragile X mental retardation 1 (Fmr1) knockout mice, we show that variable RNase digestion can lead to significant sample batch effects. We also establish GC content and ribosome footprint length as quality control metrics for RNase digestion. We performed RNase titration experiments for low-input samples to identify optimal conditions for this critical step that is often improperly conducted. Our data reveal that optimal RNase digestion is essential to ensure high quality and reproducibility of ribosome profiling for low-input brain tissue.
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Affiliation(s)
- Botao Liu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gemma Molinaro
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Huan Shu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Emily E Stackpole
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kimberly M Huber
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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27
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Mohammad F, Green R, Buskirk AR. A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution. eLife 2019; 8:e42591. [PMID: 30724162 PMCID: PMC6377232 DOI: 10.7554/elife.42591] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/05/2019] [Indexed: 12/17/2022] Open
Abstract
In eukaryotes, ribosome profiling provides insight into the mechanism of protein synthesis at the codon level. In bacteria, however, the method has been more problematic and no consensus has emerged for how to best prepare profiling samples. Here, we identify the sources of these problems and describe new solutions for arresting translation and harvesting cells in order to overcome them. These improvements remove confounding artifacts and improve the resolution to allow analyses of ribosome behavior at the codon level. With a clearer view of the translational landscape in vivo, we observe that filtering cultures leads to translational pauses at serine and glycine codons through the reduction of tRNA aminoacylation levels. This observation illustrates how bacterial ribosome profiling studies can yield insight into the mechanism of protein synthesis at the codon level and how these mechanisms are regulated in response to changes in the physiology of the cell.
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Affiliation(s)
- Fuad Mohammad
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
| | - Rachel Green
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
- Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Allen R Buskirk
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
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28
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The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase. Sci Rep 2018; 8:17875. [PMID: 30552341 PMCID: PMC6294744 DOI: 10.1038/s41598-018-35756-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/08/2018] [Indexed: 12/02/2022] Open
Abstract
Only a few overlapping gene pairs are known in the best-analyzed bacterial model organism Escherichia coli. Automatic annotation programs usually annotate only one out of six reading frames at a locus, allowing only small overlaps between protein-coding sequences. However, both RNAseq and RIBOseq show signals corresponding to non-trivially overlapping reading frames in antisense to annotated genes, which may constitute protein-coding genes. The transcription and translation of the novel 264 nt gene asa, which overlaps in antisense to a putative TEGT (Testis-Enhanced Gene Transfer) transporter gene is detected in pathogenic E. coli, but not in two apathogenic E. coli strains. The gene in E. coli O157:H7 (EHEC) was further analyzed. An overexpression phenotype was identified in two stress conditions, i.e. excess in salt or arginine. For this, EHEC overexpressing asa was grown competitively against EHEC with a translationally arrested asa mutant gene. RT-qPCR revealed conditional expression dependent on growth phase, sodium chloride, and arginine. Two potential promoters were computationally identified and experimentally verified by reporter gene expression and determination of the transcription start site. The protein Asa was verified by Western blot. Close homologues of asa have not been found in protein databases, but bioinformatic analyses showed that it may be membrane associated, having a largely disordered structure.
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29
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Condon C, Piton J, Braun F. Distribution of the ribosome associated endonuclease Rae1 and the potential role of conserved amino acids in codon recognition. RNA Biol 2018; 15:683-688. [PMID: 29557713 DOI: 10.1080/15476286.2018.1454250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We recently identified a novel ribonuclease in Bacillus subtilis called Rae1 that cleaves mRNAs in a translation-dependent manner. Rae1 is a member of the NYN/PIN family of ribonucleases and is highly conserved in the Firmicutes, the Cyanobacteria and the chloroplasts of photosynthetic algae and plants. We have proposed a model in which Rae1 enters the A-site of ribosomes that are paused following translation of certain sequences that are still ill-defined. In the only case identified thus far, Rae1 cleaves between a conserved glutamate and lysine codon during translation of a short peptide called S1025. Certain other codons are also tolerated on either side of the cleavage site, but these are recognized less efficiently. The model of Rae1 docked in the A-site allows us to make predictions about which conserved residues may be important for recognition of mRNA, the tRNA in the adjacent P-site and binding to the 50S ribosome subunit.
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Affiliation(s)
- Ciarán Condon
- a UMR 8261 (CNRS - Univ. Paris Diderot), Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, Paris , France
| | | | - Frédérique Braun
- a UMR 8261 (CNRS - Univ. Paris Diderot), Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, Paris , France
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30
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Buskirk AR. Toxins that Trash Translation. Mol Cell 2018; 70:759-760. [PMID: 29883601 DOI: 10.1016/j.molcel.2018.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Culviner and Laub (2018) use RNA-seq and ribosome profiling to determine how MazF inhibits translation in E. coli. Challenging an earlier model, they argue that MazF cleaves mRNA and blocks ribosome biogenesis but does not generate specialized ribosomes that preferentially translate leaderless transcripts.
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Affiliation(s)
- Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA.
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31
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Culviner PH, Laub MT. Global Analysis of the E. coli Toxin MazF Reveals Widespread Cleavage of mRNA and the Inhibition of rRNA Maturation and Ribosome Biogenesis. Mol Cell 2018; 70:868-880.e10. [PMID: 29861158 DOI: 10.1016/j.molcel.2018.04.026] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/03/2018] [Accepted: 04/27/2018] [Indexed: 10/14/2022]
Abstract
Toxin-antitoxin systems are widely distributed genetic modules that regulate growth and persistence in bacteria. Many systems, including E. coli MazEF, include toxins that are endoribonucleases, but the full set of targets for these toxins remains poorly defined. Previous studies on a limited set of transcripts suggested that MazF creates a pool of leaderless mRNAs that are preferentially translated by specialized ribosomes created through MazF cleavage of mature 16S rRNA. Here, using paired-end RNA sequencing (RNA-seq) and ribosome profiling, we provide a comprehensive, global analysis of MazF cleavage specificity and its targets. We find that MazF cleaves most transcripts at multiple sites within their coding regions, with very few full-length, leaderless mRNAs created. Additionally, our results demonstrate that MazF does not create a large pool of specialized ribosomes but instead rapidly disrupts ribosome biogenesis by targeting both ribosomal protein transcripts and rRNA precursors, helping to inhibit cell growth.
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Affiliation(s)
- Peter H Culviner
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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32
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Eastman G, Smircich P, Sotelo-Silveira JR. Following Ribosome Footprints to Understand Translation at a Genome Wide Level. Comput Struct Biotechnol J 2018; 16:167-176. [PMID: 30069283 PMCID: PMC6066590 DOI: 10.1016/j.csbj.2018.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 12/11/2022] Open
Abstract
Protein translation is a key step in gene expression. The development of Ribosome Profiling has allowed the global analysis of this process at sub-codon resolution. In the last years the method has been applied to several models ranging from bacteria to mammalian cells yielding a surprising amount of insight on the mechanism and the regulation of translation. In this review we describe the key aspects of the experimental protocol and comment on the main conclusions raised in different models.
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Affiliation(s)
- Guillermo Eastman
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo, CP 11600, Uruguay
| | - Pablo Smircich
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo, CP 11600, Uruguay
- Laboratory of Molecular Interactions, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
| | - José R. Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo, CP 11600, Uruguay
- Department of Cell and Molecular Biology, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
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33
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Andrade JM, Dos Santos RF, Chelysheva I, Ignatova Z, Arraiano CM. The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity. EMBO J 2018; 37:embj.201797631. [PMID: 29669858 DOI: 10.15252/embj.201797631] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 02/28/2018] [Accepted: 03/13/2018] [Indexed: 11/09/2022] Open
Abstract
Ribosome biogenesis is a complex process involving multiple factors. Here, we show that the widely conserved RNA chaperone Hfq, which can regulate sRNA-mRNA basepairing, plays a critical role in rRNA processing and ribosome assembly in Escherichia coli Hfq binds the 17S rRNA precursor and facilitates its correct processing and folding to mature 16S rRNA Hfq assists ribosome assembly and associates with pre-30S particles but not with mature 30S subunits. Inactivation of Hfq strikingly decreases the pool of mature 70S ribosomes. The reduction in ribosome levels depends on residues located in the distal face of Hfq but not on residues found in the proximal and rim surfaces which govern interactions with the sRNAs. Our results indicate that Hfq-mediated regulation of ribosomes is independent of its function as sRNA-regulator. Furthermore, we observed that inactivation of Hfq compromises translation efficiency and fidelity, both features of aberrantly assembled ribosomes. Our work expands the functions of the Sm-like protein Hfq beyond its function in small RNA-mediated regulation and unveils a novel role of Hfq as crucial in ribosome biogenesis and translation.
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Affiliation(s)
- José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Irina Chelysheva
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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34
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Gawroński P, Jensen PE, Karpiński S, Leister D, Scharff LB. Pausing of Chloroplast Ribosomes Is Induced by Multiple Features and Is Linked to the Assembly of Photosynthetic Complexes. PLANT PHYSIOLOGY 2018; 176:2557-2569. [PMID: 29298822 PMCID: PMC5841727 DOI: 10.1104/pp.17.01564] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/02/2018] [Indexed: 05/11/2023]
Abstract
Many mRNAs contain pause sites that briefly interrupt the progress of translation. Specific features that induce ribosome pausing have been described; however, their individual contributions to pause-site formation, and the overall biological significance of ribosome pausing, remain largely unclear. We have taken advantage of the compact genome of chloroplasts to carry out a plastid genome-wide survey of pause sites, as a basis for studying the impact of pausing on posttranslational processes. Based on ribosomal profiling of Arabidopsis (Arabidopsis thaliana) chloroplast mRNAs, we demonstrate that a combination of factors-mRNA secondary structure, internal Shine-Dalgarno sequences, and positively charged amino acids in the nascent peptide chain-explains 95% of the major pause sites on plastid mRNAs, whereas codon usage has little impact. The distribution of the pause sites is nonrandom and conforms to distinct patterns in the vicinity of sequences coding for transmembrane domains, which depend on their orientation within the membrane as well as being next to sequences coding for cofactor binding sites. We found strong indications that the mechanisms causing ribosomal pausing and at least some of the ribosomes pause sites are conserved between distantly related plant species. In addition, the positions of features that cause pausing are well conserved in photoautotrophic plants, but less so in their nonphotosynthetic, parasitic relatives, implying that the synthesis and assembly of photosynthetic multiprotein complexes requires localized ribosome pausing.
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Affiliation(s)
- Piotr Gawroński
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Poul Erik Jensen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Dario Leister
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Plant Molecular Biology, Department Biology I, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Lars B Scharff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
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Fang H, Huang YF, Radhakrishnan A, Siepel A, Lyon GJ, Schatz MC. Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Syst 2018; 6:180-191.e4. [PMID: 29361467 PMCID: PMC5832574 DOI: 10.1016/j.cels.2017.12.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/24/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
Ribosome profiling (Ribo-seq) is a powerful technique for measuring protein translation; however, sampling errors and biological biases are prevalent and poorly understood. Addressing these issues, we present Scikit-ribo (https://github.com/schatzlab/scikit-ribo), an open-source analysis package for accurate genome-wide A-site prediction and translation efficiency (TE) estimation from Ribo-seq and RNA sequencing data. Scikit-ribo accurately identifies A-site locations and reproduces codon elongation rates using several digestion protocols (r = 0.99). Next, we show that the commonly used reads per kilobase of transcript per million mapped reads-derived TE estimation is prone to biases, especially for low-abundance genes. Scikit-ribo introduces a codon-level generalized linear model with ridge penalty that correctly estimates TE, while accommodating variable codon elongation rates and mRNA secondary structure. This corrects the TE errors for over 2,000 genes in S. cerevisiae, which we validate using mass spectrometry of protein abundances (r = 0.81), and allows us to determine the Kozak-like sequence directly from Ribo-seq. We conclude with an analysis of coverage requirements needed for robust codon-level analysis and quantify the artifacts that can occur from cycloheximide treatment.
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Affiliation(s)
- Han Fang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yi-Fei Huang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Aditya Radhakrishnan
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD 21211, USA.
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36
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Hör J, Gorski SA, Vogel J. Bacterial RNA Biology on a Genome Scale. Mol Cell 2018; 70:785-799. [PMID: 29358079 DOI: 10.1016/j.molcel.2017.12.023] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/11/2017] [Accepted: 12/22/2017] [Indexed: 12/16/2022]
Abstract
Bacteria are an exceedingly diverse group of organisms whose molecular exploration is experiencing a renaissance. While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. Moreover, increasing interest in members of the human microbiota and environmental microbial communities has highlighted the importance of understudied bacterial species with largely unknown transcriptome structures and RNA-based control mechanisms. Collectively, this creates a need for global RNA biology approaches that can rapidly and comprehensively analyze the RNA composition of a bacterium of interest. We review such approaches with a focus on RNA-seq as a versatile tool to investigate the different layers of gene expression in which RNA is made, processed, regulated, modified, translated, and turned over.
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Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Stanislaw A Gorski
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany.
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37
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Hücker SM, Ardern Z, Goldberg T, Schafferhans A, Bernhofer M, Vestergaard G, Nelson CW, Schloter M, Rost B, Scherer S, Neuhaus K. Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome. PLoS One 2017; 12:e0184119. [PMID: 28902868 PMCID: PMC5597208 DOI: 10.1371/journal.pone.0184119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/20/2017] [Indexed: 12/29/2022] Open
Abstract
In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value. This led to discovery of 465 unique, putative novel genes not yet annotated in this E. coli strain, which are evenly distributed over both DNA strands of the genome. For 255 of the novel genes, annotated homologs in other bacteria were found, and a machine-learning algorithm, trained on small protein-coding E. coli genes, predicted that 89% of these translated open reading frames represent bona fide genes. The remaining 210 putative novel genes without annotated homologs were compared to the 255 novel genes with homologs and to 250 short annotated genes of this E. coli strain. All three groups turned out to be similar with respect to their translatability distribution, fractions of differentially regulated genes, secondary structure composition, and the distribution of evolutionary constraint, suggesting that both novel groups represent legitimate genes. However, the machine-learning algorithm only recognized a small fraction of the 210 genes without annotated homologs. It is possible that these genes represent a novel group of genes, which have unusual features dissimilar to the genes of the machine-learning algorithm training set.
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Affiliation(s)
- Sarah M. Hücker
- Chair for Microbial Ecology, Technische Universität München, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Zachary Ardern
- Chair for Microbial Ecology, Technische Universität München, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Tatyana Goldberg
- Department of Informatics—Bioinformatics & TUM-IAS, Technische Universität München, Garching, Germany
| | - Andrea Schafferhans
- Department of Informatics—Bioinformatics & TUM-IAS, Technische Universität München, Garching, Germany
| | - Michael Bernhofer
- Department of Informatics—Bioinformatics & TUM-IAS, Technische Universität München, Garching, Germany
| | - Gisle Vestergaard
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Chase W. Nelson
- Sackler Institute for Comparative Genomics, American Museum of Natural History New York, New York, United States of America
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Burkhard Rost
- Department of Informatics—Bioinformatics & TUM-IAS, Technische Universität München, Garching, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Technische Universität München, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technische Universität München, Freising, Germany
- Core Facility Microbiome/NGS, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
- * E-mail:
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38
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Giess A, Jonckheere V, Ndah E, Chyżyńska K, Van Damme P, Valen E. Ribosome signatures aid bacterial translation initiation site identification. BMC Biol 2017; 15:76. [PMID: 28854918 PMCID: PMC5576327 DOI: 10.1186/s12915-017-0416-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information, developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated. RESULTS Utilising these signatures in combination with nucleotide sequence information, we build a model capable of predicting translation initiation sites and demonstrate its high accuracy using N-terminal proteomics. Applying this to prokaryotic translatomes, we re-annotate translation initiation sites and provide evidence of N-terminal truncations and extensions of previously annotated coding sequences. These re-annotations are supported by the presence of structural and sequence-based features next to N-terminal peptide evidence. Finally, our model identifies 61 novel genes previously undiscovered in the Salmonella enterica genome. CONCLUSIONS Signatures within ribosome profiling read length distributions can be used in combination with nucleotide sequence information to provide accurate genome-wide identification of translation initiation sites.
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Affiliation(s)
- Adam Giess
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, 5020, Norway
| | - Veronique Jonckheere
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Elvis Ndah
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium.,Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, B-9000, Ghent, Belgium
| | - Katarzyna Chyżyńska
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, 5020, Norway
| | - Petra Van Damme
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium. .,Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium.
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, 5020, Norway. .,Sars International Centre for Marine Molecular Biology, University of Bergen, 5008, Bergen, Norway.
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