1
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Ziegelhoffer T, Verma AK, Delewski W, Schilke BA, Hill PM, Pitek M, Marszalek J, Craig EA. NAC and Zuotin/Hsp70 chaperone systems coexist at the ribosome tunnel exit in vivo. Nucleic Acids Res 2024; 52:3346-3357. [PMID: 38224454 PMCID: PMC11014269 DOI: 10.1093/nar/gkae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
The area surrounding the tunnel exit of the 60S ribosomal subunit is a hub for proteins involved in maturation and folding of emerging nascent polypeptide chains. How different factors vie for positioning at the tunnel exit in the complex cellular environment is not well understood. We used in vivo site-specific cross-linking to approach this question, focusing on two abundant factors-the nascent chain-associated complex (NAC) and the Hsp70 chaperone system that includes the J-domain protein co-chaperone Zuotin. We found that NAC and Zuotin can cross-link to each other at the ribosome, even when translation initiation is inhibited. Positions yielding NAC-Zuotin cross-links indicate that when both are present the central globular domain of NAC is modestly shifted from the mutually exclusive position observed in cryogenic electron microscopy analysis. Cross-linking results also suggest that, even in NAC's presence, Hsp70 can situate in a manner conducive for productive nascent chain interaction-with the peptide binding site at the tunnel exit and the J-domain of Zuotin appropriately positioned to drive stabilization of nascent chain binding. Overall, our results are consistent with the idea that, in vivo, the NAC and Hsp70 systems can productively position on the ribosome simultaneously.
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Affiliation(s)
- Thomas Ziegelhoffer
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Amit K Verma
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Wojciech Delewski
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Brenda A Schilke
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Paige M Hill
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Marcin Pitek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk 80-307, Poland
| | - Jaroslaw Marszalek
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk 80-307, Poland
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
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2
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Cacioppo R, Lindon C. Immunoprecipitation of Reporter Nascent Chains from Active Ribosomes to Study Translation Efficiency. Bio Protoc 2023; 13:e4821. [PMID: 37753466 PMCID: PMC10518778 DOI: 10.21769/bioprotoc.4821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 09/28/2023] Open
Abstract
The study of translation is important to the understanding of gene expression. While genome-wide measurements of translation efficiency (TE) rely upon ribosome profiling, classical approaches to address translation of individual genes of interest rely on biochemical methods, such as polysome fractionation and immunoprecipitation (IP) of ribosomal components, or on reporter constructs, such as luciferase reporters. Methods to investigate translation have been developed that, however, require considerable research effort, including addition of numerous features to mRNA regions, genomic integration of reporters, and complex data analysis. Here, we describe a simple biochemical reporter assay to study TE of mRNAs expressed from a transiently transfected plasmid, which we term Nascent Chain Immunoprecipitation (NC IP). The assay is based on a plasmid expressing an N-terminally Flag-tagged protein and relies on the IP of Flag-tagged nascent chains from elongating ribosomes, followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR) quantification of eluted mRNA. We report that elution of mRNA following IP can be achieved by treatment with puromycin, which releases ribosome-mRNA complexes, or with purified Flag peptide, which instead releases nascent chain-ribosome-mRNA complexes. In the example described in this protocol, untranslated regions (UTRs) of a gene of interest were used to flank a FlagVenus coding sequence, with the method allowing to infer UTR-dependent regulation of TE. Importantly, our method enables discrimination of translating from non-translating mRNAs. Additionally, it requires simple procedures and standard laboratory equipment. Our method can be used to test the effect of regulators, such as microRNAs or therapeutic drugs or of various genetic backgrounds, on translation of any user-selected mRNA. Key features • The novel NC IP protocol builds upon a previously published method for detection of mRNA-binding proteins (Williams et al., 2022). • The NC IP protocol is adapted for detecting mRNA actively undergoing translation. • The method uses mammalian cell culture but could be adapted to multiple organisms, including budding yeast (S. cerevisiae).
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Affiliation(s)
- Roberta Cacioppo
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, UK
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3
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Bailey AD, Talkish J, Ding H, Igel H, Duran A, Mantripragada S, Paten B, Ares M. Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling. eLife 2022; 11:e76562. [PMID: 35384842 PMCID: PMC9045821 DOI: 10.7554/elife.76562] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/05/2022] [Indexed: 12/02/2022] Open
Abstract
Nucleotides in RNA and DNA are chemically modified by numerous enzymes that alter their function. Eukaryotic ribosomal RNA (rRNA) is modified at more than 100 locations, particularly at highly conserved and functionally important nucleotides. During ribosome biogenesis, modifications are added at various stages of assembly. The existence of differently modified classes of ribosomes in normal cells is unknown because no method exists to simultaneously evaluate the modification status at all sites within a single rRNA molecule. Using a combination of yeast genetics and nanopore direct RNA sequencing, we developed a reliable method to track the modification status of single rRNA molecules at 37 sites in 18 S rRNA and 73 sites in 25 S rRNA. We use our method to characterize patterns of modification heterogeneity and identify concerted modification of nucleotides found near functional centers of the ribosome. Distinct, undermodified subpopulations of rRNAs accumulate upon loss of Dbp3 or Prp43 RNA helicases, suggesting overlapping roles in ribosome biogenesis. Modification profiles are surprisingly resistant to change in response to many genetic and acute environmental conditions that affect translation, ribosome biogenesis, and pre-mRNA splicing. The ability to capture single-molecule RNA modification profiles provides new insights into the roles of nucleotide modifications in RNA function.
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Affiliation(s)
- Andrew D Bailey
- Department of Biomolecular Engineering and Santa Cruz Genomics Institute, University of California, Santa CruzSanta CruzUnited States
| | - Jason Talkish
- RNA Center and Department of Molecular, Cell & Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Hongxu Ding
- Department of Biomolecular Engineering and Santa Cruz Genomics Institute, University of California, Santa CruzSanta CruzUnited States
- Department of Pharmacy Practice & Science, College of Pharmacy, University of ArizonaTucsonUnited States
| | - Haller Igel
- RNA Center and Department of Molecular, Cell & Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | | | | | - Benedict Paten
- Department of Biomolecular Engineering and Santa Cruz Genomics Institute, University of California, Santa CruzSanta CruzUnited States
| | - Manuel Ares
- RNA Center and Department of Molecular, Cell & Developmental Biology, University of California, Santa CruzSanta CruzUnited States
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4
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Shi L, Wen Z, Li H, Song Y. Identification of Hub Genes Associated With Tuberculous Pleurisy by Integrated Bioinformatics Analysis. Front Genet 2021; 12:730491. [PMID: 34925441 PMCID: PMC8678451 DOI: 10.3389/fgene.2021.730491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/26/2021] [Indexed: 12/29/2022] Open
Abstract
Improving the understanding of the molecular mechanism of tuberculous pleurisy is required to develop diagnosis and new therapy strategies of targeted genes. The purpose of this study is to identify important genes related to tuberculous pleurisy. In this study, the expression profile obtained by sequencing the surgically resected pleural tissue was used to explore the differentially co-expressed genes between tuberculous pleurisy tissue and normal tissue. 29 differentially co-expressed genes were screened by weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis methods. According to the functional annotation analysis of R clusterProfiler software package, these genes are mainly enriched in nucleotide−sugar biosynthetic process (biological process), ficolin−1−rich granule lumen (cell component), and electron transfer activity (molecular function). In addition, in the protein-protein interaction (PPI) network, 20 hub genes of DEGs and WCGNA genes were identified using the CytoHubba plug-in of Cytoscape. In the end, RPL17 was identified as a gene that can be the biomarker of tuberculous pleurisy. At the same time, there are seven genes that may have relationship with the disease (UBA7, NDUFB8, UQCRFS1, JUNB, PSMC4, PHPT1, and MAPK11).
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Affiliation(s)
- Lei Shi
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zilu Wen
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hongwei Li
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yanzheng Song
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,TB Center, Shanghai Emerging and Re-emerging Infectious Diseases Institute, Shanghai, China
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5
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Zou Q, Yang L, Shi R, Qi Y, Zhang X, Qi H. Proteostasis regulated by testis-specific ribosomal protein RPL39L maintains mouse spermatogenesis. iScience 2021; 24:103396. [PMID: 34825148 PMCID: PMC8605100 DOI: 10.1016/j.isci.2021.103396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 01/03/2023] Open
Abstract
Maintaining proteostasis is important for animal development. How proteostasis influences spermatogenesis that generates male gametes, spermatozoa, is not clear. We show that testis-specific paralog of ribosomal large subunit protein RPL39, RPL39L, is required for mouse spermatogenesis. Deletion of Rpl39l in mouse caused reduced proliferation of spermatogonial stem cells, malformed sperm mitochondria and flagella, leading to sub-fertility in males. Biochemical analyses revealed that lack of RPL39L deteriorated protein synthesis and protein quality control in spermatogenic cells, partly due to reduced biogenesis of ribosomal subunits and ribosome homeostasis. RPL39/RPL39L is likely assembled into ribosomes via H/ACA domain containing NOP10 complex early in ribosome biogenesis pathway. Furthermore, Rpl39l null mice exhibited compromised regenerative spermatogenesis after chemical insult and early degenerative spermatogenesis in aging mice. These data demonstrate that maintaining proteostasis is important for spermatogenesis, of which ribosome homeostasis maintained by ribosomal proteins coordinates translation machinery to the regulation of cellular growth. Rpl39l deletion causes reduced spermatogenesis and subfertility in male mice SSC proliferation, mitochondria and sperm flagella compromised in Rpl39l–/– mice Rpl39l deletion affects ribosomal LSU formation and protein quality control Aberrant proteostasis affects spermatogenesis and regeneration
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Affiliation(s)
- Qianxing Zou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lele Yang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China
| | - Ruona Shi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Yuling Qi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou 510630, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou 510630, China
| | - Huayu Qi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Lee K, Ziegelhoffer T, Delewski W, Berger SE, Sabat G, Craig EA. Pathway of Hsp70 interactions at the ribosome. Nat Commun 2021; 12:5666. [PMID: 34580293 PMCID: PMC8476630 DOI: 10.1038/s41467-021-25930-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
In eukaryotes, an Hsp70 molecular chaperone triad assists folding of nascent chains emerging from the ribosome tunnel. In fungi, the triad consists of canonical Hsp70 Ssb, atypical Hsp70 Ssz1 and J-domain protein cochaperone Zuo1. Zuo1 binds the ribosome at the tunnel exit. Zuo1 also binds Ssz1, tethering it to the ribosome, while its J-domain stimulates Ssb’s ATPase activity to drive efficient nascent chain interaction. But the function of Ssz1 and how Ssb engages at the ribosome are not well understood. Employing in vivo site-specific crosslinking, we found that Ssb(ATP) heterodimerizes with Ssz1. Ssb, in a manner consistent with the ADP conformation, also crosslinks to ribosomal proteins across the tunnel exit from Zuo1. These two modes of Hsp70 Ssb interaction at the ribosome suggest a functionally efficient interaction pathway: first, Ssb(ATP) with Ssz1, allowing optimal J-domain and nascent chain engagement; then, after ATP hydrolysis, Ssb(ADP) directly with the ribosome. Here, the authors use in vivo site-specific crosslinking to provide molecular-level insight into how the fungal Hsp70 chaperone system — the Ssb:Ssz1:Zuo1 triad — assists the folding process for the nascent peptide chain emerging from the ribosome tunnel.
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Affiliation(s)
- Kanghyun Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94158, USA
| | - Thomas Ziegelhoffer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Wojciech Delewski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Scott E Berger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Chemistry, Lafayette College, Easton, PA, 18042, USA.,Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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7
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Norris K, Hopes T, Aspden JL. Ribosome heterogeneity and specialization in development. Wiley Interdiscip Rev RNA 2021; 12:e1644. [PMID: 33565275 PMCID: PMC8647923 DOI: 10.1002/wrna.1644] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Regulation of protein synthesis is a vital step in controlling gene expression, especially during development. Over the last 10 years, it has become clear that rather than being homogeneous machines responsible for mRNA translation, ribosomes are highly heterogeneous and can play an active part in translational regulation. These "specialized ribosomes" comprise of specific protein and/or rRNA components, which are required for the translation of particular mRNAs. However, while there is extensive evidence for ribosome heterogeneity, support for specialized functions is limited. Recent work in a variety of developmental model organisms has shed some light on the biological relevance of ribosome heterogeneity. Tissue-specific expression of ribosomal components along with phenotypic analysis of ribosomal gene mutations indicate that ribosome heterogeneity and potentially specialization are common in key development processes like embryogenesis, spermatogenesis, oogenesis, body patterning, and neurogenesis. Several examples of ribosome specialization have now been proposed but strong links between ribosome heterogeneity, translation of specific mRNAs by defined mechanisms, and role of these translation events remain elusive. Furthermore, several studies have indicated that heterogeneous ribosome populations are a product of tissue-specific expression rather than specialized function and that ribosomal protein phenotypes are the result of extra-ribosomal function or overall reduced ribosome levels. Many important questions still need to be addressed in order to determine the functional importance of ribosome heterogeneity to development and disease, which is likely to vary across systems. It will be essential to dissect these issues to fully understand diseases caused by disruptions to ribosomal composition, such as ribosomopathies. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Structure/Function RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Karl Norris
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Julie Louise Aspden
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
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8
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Hirayama C, Machida K, Noi K, Murakawa T, Okumura M, Ogura T, Imataka H, Inaba K. Distinct roles and actions of protein disulfide isomerase family enzymes in catalysis of nascent-chain disulfide bond formation. iScience 2021; 24:102296. [PMID: 33855279 PMCID: PMC8024706 DOI: 10.1016/j.isci.2021.102296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/13/2021] [Accepted: 03/05/2021] [Indexed: 12/04/2022] Open
Abstract
The mammalian endoplasmic reticulum (ER) harbors more than 20 members of the protein disulfide isomerase (PDI) family that act to maintain proteostasis. Herein, we developed an in vitro system for directly monitoring PDI- or ERp46-catalyzed disulfide bond formation in ribosome-associated nascent chains of human serum albumin. The results indicated that ERp46 more efficiently introduced disulfide bonds into nascent chains with a short segment exposed outside the ribosome exit site than PDI. Single-molecule analysis by high-speed atomic force microscopy further revealed that PDI binds nascent chains persistently, forming a stable face-to-face homodimer, whereas ERp46 binds for a shorter time in monomeric form, indicating their different mechanisms for substrate recognition and disulfide bond introduction. Thus, ERp46 serves as a more potent disulfide introducer especially during the early stages of translation, whereas PDI can catalyze disulfide formation when longer nascent chains emerge out from ribosome. We developed an in vitro system for monitoring nascent-chain disulfide formation High-speed AFM visualized PDI and ERp46 molecules acting on nascent chains PDI persistently holds nascent chains via dimerization for disulfide introduction ERp46 rapidly introduces disulfide bonds to nascent chains via short-time binding
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Affiliation(s)
- Chihiro Hirayama
- Institute of Multidisciplinary Research for Advanced Materials, Katahira 2-1-1, Aoba-ku, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Kodai Machida
- Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280, Japan
| | - Kentaro Noi
- Institute for NanoScience Design, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tadayoshi Murakawa
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
| | - Masaki Okumura
- Institute of Multidisciplinary Research for Advanced Materials, Katahira 2-1-1, Aoba-ku, Tohoku University, Sendai, Miyagi 980-8577, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Teru Ogura
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Kumamoto 860-0811, Japan.,Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto 862-0973, Japan
| | - Hiroaki Imataka
- Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Katahira 2-1-1, Aoba-ku, Tohoku University, Sendai, Miyagi 980-8577, Japan
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9
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Zhang Y, De Laurentiis E, Bohnsack KE, Wahlig M, Ranjan N, Gruseck S, Hackert P, Wölfle T, Rodnina MV, Schwappach B, Rospert S. Ribosome-bound Get4/5 facilitates the capture of tail-anchored proteins by Sgt2 in yeast. Nat Commun 2021; 12:782. [PMID: 33542241 PMCID: PMC7862611 DOI: 10.1038/s41467-021-20981-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/05/2021] [Indexed: 02/03/2023] Open
Abstract
The guided entry of tail-anchored proteins (GET) pathway assists in the posttranslational delivery of tail-anchored proteins, containing a single C-terminal transmembrane domain, to the ER. Here we uncover how the yeast GET pathway component Get4/5 facilitates capture of tail-anchored proteins by Sgt2, which interacts with tail-anchors and hands them over to the targeting component Get3. Get4/5 binds directly and with high affinity to ribosomes, positions Sgt2 close to the ribosomal tunnel exit, and facilitates the capture of tail-anchored proteins by Sgt2. The contact sites of Get4/5 on the ribosome overlap with those of SRP, the factor mediating cotranslational ER-targeting. Exposure of internal transmembrane domains at the tunnel exit induces high-affinity ribosome binding of SRP, which in turn prevents ribosome binding of Get4/5. In this way, the position of a transmembrane domain within nascent ER-targeted proteins mediates partitioning into either the GET or SRP pathway directly at the ribosomal tunnel exit. The guided entry of tail-anchored proteins (GET) pathway assists in the delivery of such proteins to the ER. Here, the authors reveal that the pathway components Get4/5 probe a region near the ribosomal exit tunnel. Upon emergence of a client protein, Get4/5 recruits Sgt2 and initiates the targeting phase of the pathway.
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Affiliation(s)
- Ying Zhang
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Evelina De Laurentiis
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Mascha Wahlig
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Namit Ranjan
- Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Simon Gruseck
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Tina Wölfle
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Marina V Rodnina
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany.,Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany. .,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany.
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
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10
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Abe T, Nagai R, Shimazaki S, Kondo S, Nishimura S, Sakaguchi Y, Suzuki T, Imataka H, Tomita K, Takeuchi-Tomita N. In vitro yeast reconstituted translation system reveals function of eIF5A for synthesis of long polypeptide. J Biochem 2020; 167:451-462. [PMID: 32053170 DOI: 10.1093/jb/mvaa022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
We have recently developed an in vitro yeast reconstituted translation system, which is capable of synthesizing long polypeptides. Utilizing the system, we examined the role of eIF5A and its hypusine modification in translating polyproline sequence within long open reading frames. We found that polyproline motif inserted at the internal position of the protein arrests translation exclusively at low Mg2+ concentrations, and peptidylpolyproline-tRNA intrinsically destabilizes 80S ribosomes. We demonstrate that unmodified eIF5A essentially resolves such ribosome stalling; however, the hypusine modification drastically stimulates ability of eIF5A to rescue polyproline-mediated ribosome stalling and is particularly important for the efficient translation of the N-terminal or long internal polyproline motifs.
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Affiliation(s)
- Taisho Abe
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Riku Nagai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Shunta Shimazaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Shunta Kondo
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Satoshi Nishimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Imataka
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Nono Takeuchi-Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
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11
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Zhang Y, Valentín Gesé G, Conz C, Lapouge K, Kopp J, Wölfle T, Rospert S, Sinning I. The ribosome-associated complex RAC serves in a relay that directs nascent chains to Ssb. Nat Commun 2020; 11:1504. [PMID: 32198371 DOI: 10.1038/s41467-020-15313-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/03/2020] [Indexed: 11/21/2022] Open
Abstract
The conserved ribosome-associated complex (RAC) consisting of Zuo1 (Hsp40) and Ssz1 (non-canonical Hsp70) acts together with the ribosome-bound Hsp70 chaperone Ssb in de novo protein folding at the ribosomal tunnel exit. Current models suggest that the function of Ssz1 is confined to the support of Zuo1, however, it is not known whether RAC by itself serves as a chaperone for nascent chains. Here we show that, via its rudimentary substrate binding domain (SBD), Ssz1 directly binds to emerging nascent chains prior to Ssb. Structural and biochemical analyses identify a conserved LP-motif at the Zuo1 N-terminus forming a polyproline-II helix, which binds to the Ssz1-SBD as a pseudo-substrate. The LP-motif competes with nascent chain binding to the Ssz1-SBD and modulates nascent chain transfer. The combined data indicate that Ssz1 is an active chaperone optimized for transient, low-affinity substrate binding, which ensures the flux of nascent chains through RAC/Ssb. The ribosome-associated complex (RAC), which contains the Hsp40 protein Zuo1 and the non-canonical Hsp70 protein Ssz1 forms a chaperone triad with the fungal-specific Hsp70 protein Ssb. Here the authors combine X-ray crystallography, crosslinking and biochemical experiments and present the structure of the Zuo1 N-terminus bound to Ssz1 and demonstrate that Ssz1 is an active chaperone for nascent chains.
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12
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Collart MA, Weiss B. Ribosome pausing, a dangerous necessity for co-translational events. Nucleic Acids Res 2020; 48:1043-1055. [PMID: 31598688 PMCID: PMC7026645 DOI: 10.1093/nar/gkz763] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/13/2019] [Accepted: 08/21/2019] [Indexed: 12/31/2022] Open
Abstract
In recent years translation elongation has emerged as an important contributor to the regulation of gene expression. There are multiple quality control checkpoints along the way of producing mature proteins and targeting them to the right cellular compartment, or associating them correctly with their partners. Ribosomes pause to allow co-translational protein folding, protein targeting or protein interactions, and the pausing is dictated by a combination of the mRNA sequence and structure, the tRNA availability and the nascent peptide. However, ribosome pausing can also lead to ribosome collisions and co-translational degradation of both mRNA and nascent chain. Understanding how the translating ribosome tunes the different maturation steps that nascent proteins must undergo, what the timing of these maturation events is, and how degradation can be avoided when pausing is needed, is now possible by the emergence of methods to follow ribosome dynamics in vivo. This review summarizes some of the recent studies that have advanced our knowledge about co-translational events using the power of ribosome profiling, and some of the questions that have emerged from these studies.
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Affiliation(s)
- Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics, Geneva, 1 rue Michel Servet, 1211 Genève 4, Switzerland
| | - Benjamin Weiss
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics, Geneva, 1 rue Michel Servet, 1211 Genève 4, Switzerland
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13
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Hristou A, Gerlach I, Stolle DS, Neumann J, Bischoff A, Dünschede B, Nowaczyk MM, Zoschke R, Schünemann D. Ribosome-Associated Chloroplast SRP54 Enables Efficient Cotranslational Membrane Insertion of Key Photosynthetic Proteins. Plant Cell 2019; 31:2734-2750. [PMID: 31444312 PMCID: PMC6881123 DOI: 10.1105/tpc.19.00169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/12/2019] [Accepted: 08/22/2019] [Indexed: 05/20/2023]
Abstract
Key proteins of the photosynthetic complexes are encoded in the chloroplast genome and cotranslationally inserted into the thylakoid membrane. However, the molecular details of this process are largely unknown. Here, we demonstrate by ribosome profiling that the conserved chloroplast signal recognition particle subunit (cpSRP54) is required for efficient cotranslational targeting of several central photosynthetic proteins, such as the PSII PsbA (D1) subunit, in Arabidopsis (Arabidopsis thaliana). High-resolution analysis of membrane-associated and soluble ribosome footprints revealed that the SRP-dependent membrane targeting of PsbA is already initiated at an early translation step before exposure of the nascent chain from the ribosome. In contrast to cytosolic SRP, which contacts the ribosome close to the peptide tunnel exit site, analysis of the cpSRP54/ribosome binding interface revealed a direct interaction of cpSRP54 and the ribosomal subunit uL4, which is not located at the tunnel exit site but forms a part of the internal peptide tunnel wall by a loop domain. The plastid-specific C-terminal tail region of cpSRP54 plays a crucial role in uL4 binding. Our data indicate a novel mechanism of SRP-dependent membrane protein transport with the cpSRP54/uL4 interaction as a central element in early initiation of cotranslational membrane targeting.
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Affiliation(s)
- Athina Hristou
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Ines Gerlach
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Dominique S Stolle
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Jennifer Neumann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Annika Bischoff
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Marc M Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
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14
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Hoffman AM, Chen Q, Zheng T, Nicchitta CV. Heterogeneous translational landscape of the endoplasmic reticulum revealed by ribosome proximity labeling and transcriptome analysis. J Biol Chem 2019; 294:8942-8958. [PMID: 31004035 DOI: 10.1074/jbc.ra119.007996] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER) is a nexus for mRNA localization and translation, and recent studies have demonstrated that ER-bound ribosomes also play a transcriptome-wide role in regulating proteome composition. The Sec61 translocon (SEC61) serves as the receptor for ribosomes that translate secretory/integral membrane protein-encoding mRNAs, but whether SEC61 also serves as a translation site for cytosolic protein-encoding mRNAs remains unknown. Here, using a BioID proximity-labeling approach in HEK293T Flp-In cell lines, we examined interactions between ER-resident proteins and ribosomes in vivo Using in vitro analyses, we further focused on bona fide ribosome interactors (i.e. SEC61) and ER proteins (ribophorin I, leucine-rich repeat-containing 59 (LRRC59), and SEC62) previously implicated in associating with ribosomes. We observed labeling of ER-bound ribosomes with the SEC61β and LRRC59 BioID reporters, comparatively modest labeling with the ribophorin I reporter, and no labeling with the SEC62 reporter. A biotin pulse-chase/subcellular fractionation approach to examine ribosome exchange at the SEC61β and LRRC59 sites revealed that, at steady state, ribosomes at these sites comprise both rapid- and slow-exchanging pools. Global translational initiation arrest elicited by the inhibitor harringtonine accelerated SEC61β reporter-labeled ribosome exchange. RNA-Seq analyses of the mRNAs associated with SEC61β- and LRRC59-labeled ribosomes revealed both site-enriched and shared mRNAs and further established that the ER has a transcriptome-wide role in regulating proteome composition. These results provide evidence that ribosomes interact with the ER membrane via multiple modes and suggest regulatory mechanisms that control global proteome composition via ER membrane-bound ribosomes.
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Affiliation(s)
| | - Qiang Chen
- Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Tianli Zheng
- Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Christopher V Nicchitta
- From the Departments of Biochemistry and .,Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
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15
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Panasenko OO, Somasekharan SP, Villanyi Z, Zagatti M, Bezrukov F, Rashpa R, Cornut J, Iqbal J, Longis M, Carl SH, Peña C, Panse VG, Collart MA. Co-translational assembly of proteasome subunits in NOT1-containing assemblysomes. Nat Struct Mol Biol 2019; 26:110-20. [PMID: 30692646 DOI: 10.1038/s41594-018-0179-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 12/06/2018] [Indexed: 01/31/2023]
Abstract
The assembly of large multimeric complexes in the crowded cytoplasm is challenging. Here we reveal a mechanism that ensures accurate production of the yeast proteasome, involving ribosome pausing and co-translational assembly of Rpt1 and Rpt2. Interaction of nascent Rpt1 and Rpt2 then lifts ribosome pausing. We show that the N-terminal disordered domain of Rpt1 is required to ensure efficient ribosome pausing and association of nascent Rpt1 protein complexes into heavy particles, wherein the nascent protein complexes escape ribosome quality control. Immunofluorescence and in situ hybridization studies indicate that Rpt1- and Rpt2-encoding messenger RNAs co-localize in these particles that contain, and are dependent on, Not1, the scaffold of the Ccr4-Not complex. We refer to these particles as Not1-containing assemblysomes, as they are smaller than and distinct from other RNA granules such as stress granules and GW- or P-bodies. Synthesis of Rpt1 with ribosome pausing and Not1-containing assemblysome induction is conserved from yeast to human cells.
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16
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Zhang Y, Sinning I, Rospert S. Two chaperones locked in an embrace: structure and function of the ribosome-associated complex RAC. Nat Struct Mol Biol 2017; 24:611-9. [PMID: 28771464 DOI: 10.1038/nsmb.3435] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/14/2017] [Indexed: 12/26/2022]
Abstract
Chaperones, which assist protein folding are essential components of every living cell. The yeast ribosome-associated complex (RAC) is a chaperone that is highly conserved in eukaryotic cells. The RAC consists of the J protein Zuo1 and the unconventional Hsp70 homolog Ssz1. The RAC heterodimer stimulates the ATPase activity of the ribosome-bound Hsp70 homolog Ssb, which interacts with nascent polypeptide chains to facilitate de novo protein folding. In addition, the RAC-Ssb system is required to maintain the fidelity of protein translation. Recent work reveals important details of the unique structures of RAC and Ssb and identifies how the chaperones interact with the ribosome. The new findings start to uncover how the exceptional chaperone triad cooperates in protein folding and maintenance of translational fidelity and its connection to extraribosomal functions.
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17
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Abstract
The synthesis of cytoplasmic eukaryotic ribosomes is an extraordinarily energy-demanding cellular activity that occurs progressively from the nucleolus to the cytoplasm. In the nucleolus, precursor rRNAs associate with a myriad of trans-acting factors and some ribosomal proteins to form pre-ribosomal particles. These factors include snoRNPs, nucleases, ATPases, GTPases, RNA helicases, and a vast list of proteins with no predicted enzymatic activity. Their coordinate activity orchestrates in a spatiotemporal manner the modification and processing of precursor rRNAs, the rearrangement reactions required for the formation of productive RNA folding intermediates, the ordered assembly of the ribosomal proteins, and the export of pre-ribosomal particles to the cytoplasm; thus, providing speed, directionality and accuracy to the overall process of formation of translation-competent ribosomes. Here, we review a particular class of trans-acting factors known as "placeholders". Placeholder factors temporarily bind selected ribosomal sites until these have achieved a structural context that is appropriate for exchanging the placeholder with another site-specific binding factor. By this strategy, placeholders sterically prevent premature recruitment of subsequently binding factors, premature formation of structures, avoid possible folding traps, and act as molecular clocks that supervise the correct progression of pre-ribosomal particles into functional ribosomal subunits. We summarize the current understanding of those factors that delay the assembly of distinct ribosomal proteins or subsequently bind key sites in pre-ribosomal particles. We also discuss recurrent examples of RNA-protein and protein-protein mimicry between rRNAs and/or factors, which have clear functional implications for the ribosome biogenesis pathway.
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Affiliation(s)
- Francisco J Espinar-Marchena
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain
| | - Reyes Babiano
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain
| | - Jesús Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain
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18
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Huber FM, Hoelz A. Molecular basis for protection of ribosomal protein L4 from cellular degradation. Nat Commun 2017; 8:14354. [PMID: 28148929 DOI: 10.1038/ncomms14354] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/19/2016] [Indexed: 12/26/2022] Open
Abstract
Eukaryotic ribosome biogenesis requires the nuclear import of ∼80 nascent ribosomal proteins and the elimination of excess amounts by the cellular degradation machinery. Assembly chaperones recognize nascent unassembled ribosomal proteins and transport them together with karyopherins to their nuclear destination. We report the crystal structure of ribosomal protein L4 (RpL4) bound to its dedicated assembly chaperone of L4 (Acl4), revealing extensive interactions sequestering 70 exposed residues of the extended RpL4 loop. The observed molecular recognition fundamentally differs from canonical promiscuous chaperone–substrate interactions. We demonstrate that the eukaryote-specific RpL4 extension harbours overlapping binding sites for Acl4 and the nuclear transport factor Kap104, facilitating its continuous protection from the cellular degradation machinery. Thus, Acl4 serves a dual function to facilitate nuclear import and simultaneously protect unassembled RpL4 from the cellular degradation machinery. Acl4 is a dedicated assembly chaperone for ribosomal protein RpL4 that recognizes RpL4 in the cytoplasm to facilitate its nuclear import. Here the authors reveal the mechanism whereby Acl4 recognizes RpL4 and functions to protect it from Tom1-mediated degradation until RpL4 incorporation into the maturing 60S pre-ribosomal subunit.
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19
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Gumiero A, Conz C, Gesé GV, Zhang Y, Weyer FA, Lapouge K, Kappes J, von Plehwe U, Schermann G, Fitzke E, Wölfle T, Fischer T, Rospert S, Sinning I. Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain. Nat Commun 2016; 7:13563. [PMID: 27882919 PMCID: PMC5123055 DOI: 10.1038/ncomms13563] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/13/2016] [Indexed: 12/22/2022] Open
Abstract
Cotranslational chaperones assist in de novo folding of nascent polypeptides in all organisms. In yeast, the heterodimeric ribosome-associated complex (RAC) forms a unique chaperone triad with the Hsp70 homologue Ssb. We report the X-ray structure of full length Ssb in the ATP-bound open conformation at 2.6 Å resolution and identify a positively charged region in the α-helical lid domain (SBDα), which is present in all members of the Ssb-subfamily of Hsp70s. Mutational analysis demonstrates that this region is strictly required for ribosome binding. Crosslinking shows that Ssb binds close to the tunnel exit via contacts with both, ribosomal proteins and rRNA, and that specific contacts can be correlated with switching between the open (ATP-bound) and closed (ADP-bound) conformation. Taken together, our data reveal how Ssb dynamics on the ribosome allows for the efficient interaction with nascent chains upon RAC-mediated activation of ATP hydrolysis. In yeast, the heterodimeric ribosome-associated complex (RAC) acts in concert with the Hsp70 protein Ssb, forming a unique chaperone triad. Here the authors use structural and biochemical approaches to shed light on how translation and folding are coupled in eukaryotes.
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Affiliation(s)
- Andrea Gumiero
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Charlotte Conz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Genís Valentín Gesé
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Ying Zhang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Felix Alexander Weyer
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Julia Kappes
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Ulrike von Plehwe
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Géza Schermann
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Edith Fitzke
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Tina Wölfle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Tamás Fischer
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
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20
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Homma K, Noguchi T, Fukuchi S. Codon usage is less optimized in eukaryotic gene segments encoding intrinsically disordered regions than in those encoding structural domains. Nucleic Acids Res 2016; 44:10051-10061. [PMID: 27915289 PMCID: PMC5137448 DOI: 10.1093/nar/gkw899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/15/2016] [Accepted: 09/29/2016] [Indexed: 12/14/2022] Open
Abstract
Codon usage tends to be optimized in highly expressed genes. A plausible explanation for this phenomenon is that translational accuracy is increased in highly expressed genes with infrequent use of rare codons. Besides structural domains (SDs), eukaryotic proteins generally have intrinsically disordered regions (IDRs) that by themselves do not assume unique three-dimensional structures. As IDRs are free from structural constraint, they can probably accommodate more translational errors than SDs can. Thus, codon usage in IDRs is likely to be less optimized than that in SDs. Codon usage in all the genes of seven eukaryotes was examined in terms of both tRNA adaptation index and codon adaptation index. Different amino acid compositions in different protein regions were taken into account in calculating expected adaptation indices, to which observed indices were compared. Codon usage is less optimized in gene regions encoding IDRs than in those corresponding to SDs. The finding does not depend on whether IDRs are located at the N-terminus, in the middle, or at the C-terminus of proteins. Furthermore, the observation remains unchanged in two different algorithms used to predict IDRs in proteins. The result is consistent with the idea that IDRs tolerate more translational errors than SDs.
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Affiliation(s)
- Keiichi Homma
- Department of Life Science and Informatics, Maebashi Institute of Technology, 460-1 Kamisadori-machi, Maebashi-shi 371-0816, Japan
| | - Tamotsu Noguchi
- Pharmaceutical Education Research Center, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Satoshi Fukuchi
- Department of Life Science and Informatics, Maebashi Institute of Technology, 460-1 Kamisadori-machi, Maebashi-shi 371-0816, Japan
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21
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Lee K, Sharma R, Shrestha OK, Bingman CA, Craig EA. Dual interaction of the Hsp70 J-protein cochaperone Zuotin with the 40S and 60S ribosomal subunits. Nat Struct Mol Biol 2016; 23:1003-1010. [PMID: 27669034 PMCID: PMC5097012 DOI: 10.1038/nsmb.3299] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/31/2016] [Indexed: 12/30/2022]
Abstract
Ribosome-associated J protein-Hsp70 chaperones promote nascent polypeptide folding and normal translational fidelity. Though known to span the ribosome subunits, understanding of J protein Zuo1 function is limited. New structural and crosslinking data allow more precise positioning of Saccharomyces cerevisiae Zuo1 near the 60S polypeptide exit site, pointing to interactions with ribosomal protein eL31 and 25S rRNA helix 24. The junction between the 60S-interacting and subunit-spanning helices is a hinge, positioning Zuo1 on the 40S, yet accommodating subunit rotation. Interaction between C-terminus of Zuo1 and 40S occurs via 18S rRNA expansion segment 12 (ES12) of helix 44, which originates at the decoding site. Deletions in either ES12 or C-terminus of Zuo1 alter stop codon readthrough and −1 frameshifting. Our study offers insight into how this cotranslational chaperone system may monitor decoding site activity and nascent polypeptide transit, thereby coordinating protein translation and folding.
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Affiliation(s)
- Kanghyun Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ruchika Sharma
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Om Kumar Shrestha
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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22
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Zhang Y, Schäffer T, Wölfle T, Fitzke E, Thiel G, Rospert S. Cotranslational Intersection between the SRP and GET Targeting Pathways to the Endoplasmic Reticulum of Saccharomyces cerevisiae. Mol Cell Biol 2016; 36:2374-83. [PMID: 27354063 DOI: 10.1128/MCB.00131-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/17/2016] [Indexed: 01/21/2023] Open
Abstract
Targeting of transmembrane proteins to the endoplasmic reticulum (ER) proceeds via either the signal recognition particle (SRP) or the guided entry of tail-anchored proteins (GET) pathway, consisting of Get1 to -5 and Sgt2. While SRP cotranslationally targets membrane proteins containing one or multiple transmembrane domains, the GET pathway posttranslationally targets proteins containing a single C-terminal transmembrane domain termed the tail anchor. Here, we dissect the roles of the SRP and GET pathways in the sorting of homologous, two-membrane-spanning K(+) channel proteins termed Kcv, Kesv, and Kesv-VV. We show that Kcv is targeted to the ER cotranslationally via its N-terminal transmembrane domain, while Kesv-VV is targeted posttranslationally via its C-terminal transmembrane domain, which recruits Get4-5/Sgt2 and Get3. Unexpectedly, nascent Kcv recruited not only SRP but also the Get4-5 module of the GET pathway to ribosomes. Ribosome binding of Get4-5 was independent of Sgt2 and was strongly outcompeted by SRP. The combined data indicate a previously unrecognized cotranslational interplay between the SRP and GET pathways.
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23
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Suresh S, Ahn HW, Joshi K, Dakshinamurthy A, Kananganat A, Garfinkel DJ, Farabaugh PJ. Ribosomal protein and biogenesis factors affect multiple steps during movement of the Saccharomyces cerevisiae Ty1 retrotransposon. Mob DNA 2015; 6:22. [PMID: 26664557 PMCID: PMC4673737 DOI: 10.1186/s13100-015-0053-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/30/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A large number of Saccharomyces cerevisiae cellular factors modulate the movement of the retrovirus-like transposon Ty1. Surprisingly, a significant number of chromosomal genes required for Ty1 transposition encode components of the translational machinery, including ribosomal proteins, ribosomal biogenesis factors, protein trafficking proteins and protein or RNA modification enzymes. RESULTS To assess the mechanistic connection between Ty1 mobility and the translation machinery, we have determined the effect of these mutations on ribosome biogenesis and Ty1 transcriptional and post-transcriptional regulation. Lack of genes encoding ribosomal proteins or ribosome assembly factors causes reduced accumulation of the ribosomal subunit with which they are associated. In addition, these mutations cause decreased Ty1 + 1 programmed translational frameshifting, and reduced Gag protein accumulation despite at least normal levels of Ty1 mRNA. Several ribosome subunit mutations increase the level of both an internally initiated Ty1 transcript and its encoded truncated Gag-p22 protein, which inhibits transposition. CONCLUSIONS Together, our results suggest that this large class of cellular genes modulate Ty1 transposition through multiple pathways. The effects are largely post-transcriptional acting at a variety of levels that may include translation initiation, protein stability and subcellular protein localization.
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Affiliation(s)
- Susmitha Suresh
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
- />Present address: Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305 USA
| | - Hyo Won Ahn
- />Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Kartikeya Joshi
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
| | - Arun Dakshinamurthy
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
- />Present address: Department of Nanosciences and Technology, Karunya University, Karunya Nagar, Coimbatore, 641 114 Tamil Nadu India
| | - Arun Kananganat
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
| | - David J. Garfinkel
- />Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Philip J. Farabaugh
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
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Wang M, Parshin AV, Shcherbik N, Pestov DG. Reduced expression of the mouse ribosomal protein Rpl17 alters the diversity of mature ribosomes by enhancing production of shortened 5.8S rRNA. RNA 2015; 21:1240-1248. [PMID: 25995445 PMCID: PMC4478343 DOI: 10.1261/rna.051169.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/10/2015] [Indexed: 06/04/2023]
Abstract
Processing of rRNA during ribosome assembly can proceed through alternative pathways but it is unclear whether this could affect the structure of the ribosome. Here, we demonstrate that shortage of a ribosomal protein can change pre-rRNA processing in a way that over time alters ribosome diversity in the cell. Reducing the amount of Rpl17 in mouse cells led to stalled 60S subunit maturation, causing degradation of most of the synthesized precursors. A fraction of pre-60S subunits, however, were able to complete maturation, but with a 5'-truncated 5.8S rRNA, which we named 5.8SC. The 5' exoribonuclease Xrn2 is involved in the generation of both 5.8S(C) and the canonical long form of 5.8S rRNA. Ribosomes containing 5.8S(C) rRNA are present in various mouse and human cells and engage in translation. These findings uncover a previously undescribed form of mammalian 5.8S rRNA and demonstrate that perturbations in ribosome assembly can be a source of heterogeneity in mature ribosomes.
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Affiliation(s)
- Minshi Wang
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, USA
| | - Andrey V Parshin
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, USA
| | - Natalia Shcherbik
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, USA
| | - Dimitri G Pestov
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, USA
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25
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Stelter P, Huber FM, Kunze R, Flemming D, Hoelz A, Hurt E. Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension. Mol Cell 2015; 58:854-62. [PMID: 25936803 DOI: 10.1016/j.molcel.2015.03.029] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/06/2015] [Accepted: 03/23/2015] [Indexed: 02/06/2023]
Abstract
Eukaryotic ribosome biogenesis requires nuclear import and hierarchical incorporation of ∼80 ribosomal proteins (RPs) into the ribosomal RNA core. In contrast to prokaryotes, many eukaryotic RPs possess long extensions that interdigitate in the mature ribosome. RpL4 is a prime example, with an ∼80-residue-long surface extension of unknown function. Here, we identify assembly chaperone Acl4 that initially binds the universally conserved internal loop of newly synthesized RpL4 via its superhelical TPR domain, thereby restricting RpL4 loop insertion at its cognate nascent rRNA site. RpL4 release from Acl4 is orchestrated with pre-ribosome assembly, during which the eukaryote-specific RpL4 extension makes several distinct interactions with the 60S surface, including a co-evolved site on neighboring RpL18. Consequently, mutational inactivation of this contact site, on either RpL4 or RpL18, impairs RpL4-Acl4 disassembly and RpL4 pre-ribosome incorporation. We propose that hierarchical ribosome assembly can be achieved by eukaryotic RP extensions and dedicated assembly chaperones.
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Affiliation(s)
- Philipp Stelter
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Ferdinand M Huber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ruth Kunze
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Dirk Flemming
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
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Kim DH, Lee JE, Xu ZY, Geem KR, Kwon Y, Park JW, Hwang I. Cytosolic targeting factor AKR2A captures chloroplast outer membrane-localized client proteins at the ribosome during translation. Nat Commun 2015; 6:6843. [PMID: 25880450 DOI: 10.1038/ncomms7843] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 03/04/2015] [Indexed: 01/30/2023] Open
Abstract
In eukaryotic cells, organellar proteome biogenesis is pivotal for cellular function. Chloroplasts contain a complex proteome, the biogenesis of which includes post-translational import of nuclear-encoded proteins. However, the mechanisms determining when and how nascent chloroplast-targeted proteins are sorted in the cytosol are unknown. Here, we establish the timing and mode of interaction between ankyrin repeat-containing protein 2 (AKR2A), the cytosolic targeting factor of chloroplast outer membrane (COM) proteins, and its interacting partners during translation at the single-molecule level. The targeting signal of a nascent AKR2A client protein residing in the ribosomal exit tunnel induces AKR2A binding to ribosomal RPL23A. Subsequently, RPL23A-bound AKR2A binds to the targeting signal when it becomes exposed from ribosomes. Failure of AKR2A binding to RPL23A in planta severely disrupts protein targeting to the COM; thus, AKR2A-mediated targeting of COM proteins is coupled to their translation, which in turn is crucial for biogenesis of the entire chloroplast proteome.
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Affiliation(s)
- Dae Heon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Jae-Eun Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Zheng-Yi Xu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Kyoung Rok Geem
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Yun Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea
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Han Y, Gao X, Liu B, Wan J, Zhang X, Qian SB. Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation. Cell Res 2014; 24:842-51. [PMID: 24903108 DOI: 10.1038/cr.2014.74] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/30/2014] [Accepted: 04/24/2014] [Indexed: 02/07/2023] Open
Abstract
The journey of a newly synthesized polypeptide starts in the peptidyltransferase center of the ribosome, from where it traverses the exit tunnel. The interior of the ribosome exit tunnel is neither straight nor smooth. How the ribosome dynamics in vivo is influenced by the exit tunnel is poorly understood. Genome-wide ribosome profiling in mammalian cells reveals elevated ribosome density at the start codon and surprisingly the downstream 5th codon position as well. We found that the highly focused ribosomal pausing shortly after initiation is attributed to the geometry of the exit tunnel, as deletion of the loop region from ribosome protein L4 diminishes translational pausing at the 5th codon position. Unexpectedly, the ribosome variant undergoes translational abandonment shortly after initiation, suggesting that there exists an obligatory step between initiation and elongation commitment. We propose that the post-initiation pausing of ribosomes represents an inherent signature of the translation machinery to ensure productive translation.
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