1
|
Matsuura-Suzuki E, Toh H, Iwasaki S. Human-rabbit Hybrid Translation System to Explore the Function of Modified Ribosomes. Bio Protoc 2023; 13:e4714. [PMID: 37456340 PMCID: PMC10339341 DOI: 10.21769/bioprotoc.4714] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/15/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
In vitro translation systems are a useful biochemical tool to research translational regulation. Although the preparation of translation-competent cell extracts from mammals has often been a challenge, the commercially available rabbit reticulocyte lysate (RRL) is an exception. However, its valid use, investigating the mechanism of translation machinery such as ribosomes in RRL, presents an analytic hurdle. To overcome this issue, the hybrid translation system, which is based on the supplementation of purified human ribosomes into ribosome-depleted RRL, has been developed. Here, we describe the step-by-step protocol of this system to study translation driven by ribosomes lacking post-translational modifications of the ribosomal protein. Moreover, we combined this approach with a previously developed reporter mRNA to assess the processivity of translation elongation. This protocol could be used to study the potency of heterologous ribosomes.
Collapse
Affiliation(s)
- Eriko Matsuura-Suzuki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Hirotaka Toh
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| |
Collapse
|
2
|
Lee M, Takeuchi-Tomita N. Reconstitution of Mammalian Mitochondrial Translation System Capable of Long Polypeptide Synthesis. Methods Mol Biol 2023; 2661:233-255. [PMID: 37166641 DOI: 10.1007/978-1-0716-3171-3_14] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mammalian mitochondria have their own dedicated protein synthesis system, which produces 13 essential subunits of the oxidative phosphorylation complexes. Here, we describe the in vitro reconstitution of the mammalian mitochondrial translation system, utilizing purified recombinant mitochondrial translation factors, 55S ribosomes from pig liver mitochondria, and a heterologous yeast tRNA mixture. The system is capable of translating leaderless mRNAs encoding model proteins, such as nanoluciferase with a molecular weight of 19 kDa, and is readily applicable for in vitro evaluations of mRNAs and nascent peptide chain sequences, as well as factors and small molecules that affect mitochondrial translation.
Collapse
Affiliation(s)
- Muhoon Lee
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Nono Takeuchi-Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
| |
Collapse
|
3
|
Fieulaine S, Tubiana T, Bressanelli S. De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation. Virology 2023; 578:128-140. [PMID: 36527931 DOI: 10.1016/j.virol.2022.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 10/04/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
Hepatitis E virus (HEV), a major cause of acute viral hepatitis, is a single-stranded, positive-sense RNA virus. As such, it encodes a 1700-residue replication polyprotein pORF1 that directs synthesis of new viral RNA in infected cells. Here we report extensive modeling with AlphaFold2 of the full-length pORF1, and its production by in vitro translation. From this, we give a detailed update on the breakdown into domains of HEV pORF1. We also provide evidence that pORF1's N-terminal domain is likely to oligomerize to form a dodecameric pore, homologously to what has been described for Chikungunya virus. Beyond providing accurate folds for its five domains, our work highlights that there is no canonical protease encoded in pORF1 and that flexibility in several functionally important regions rather than proteolytic processing may serve to regulate HEV RNA synthesis.
Collapse
Affiliation(s)
- Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Thibault Tubiana
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| |
Collapse
|
4
|
Garcia VE, Dial R, DeRisi JL. Functional characterization of 5' UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans. Malar J 2022; 21:15. [PMID: 34991611 DOI: 10.1186/s12936-021-04024-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background The eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually while drug resistance to common anti-malarials is further confounding eradication efforts. Translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. As the rate limiting step of translation, initiation is a primary driver of translational efficiency. It is a complex process regulated by both cis and trans acting factors, providing numerous potential targets. Relative to model organisms and humans, P. falciparum mRNAs feature unusual 5′ untranslated regions suggesting cis-acting sequence complexity in this parasite may act to tune levels of protein synthesis through their effects on translational efficiency. Methods Here, in vitro translation is deployed to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream “AUG”s, in addition to the base composition of the 5′ untranslated regions, were characterized. Results The density of upstream “AUG”s differed significantly among the most and least efficiently translated genes in P. falciparum, as did the average “GC” content of the 5′ untranslated regions. Using exemplars from highly translated and poorly translated mRNAs, multiple putative upstream elements were interrogated for impact on translational efficiency. Upstream “AUG”s were found to repress translation to varying degrees, depending on their position and context, while combinations of upstream “AUG”s had non-additive effects. The base composition of the 5′ untranslated regions also impacted translation, but to a lesser degree. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans. Conclusions While translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discrete cis-acting features, acting alone or in context. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-04024-2.
Collapse
|
5
|
Gonskikh Y, Pecoraro V, Polacek N. Mammalian In Vitro Translation Systems. Methods Mol Biol 2022; 2428:101-111. [PMID: 35171476 DOI: 10.1007/978-1-0716-1975-9_7] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Under cellular stress, tight and coordinated regulation of the gene expression allows to minimize cellular damage, maintains cellular homeostasis, and ensures cell survival. Among stress-induced cellular responses, alteration of translation rates represents one of the most effective and rapid regulatory mechanisms available for cells. Here we report on detailed protocols of mammalian in vitro translation systems. While most of the available in vitro translation methods are based on bacterial or yeast components, tailor-made and robust mammalian systems are sparse. Our protocols allow measuring global translation of the total mRNA pool as well as translation of one specific reporter mRNA. Furthermore, it provides access to measuring translational activity of isolated ribosomes combined with non-ribosomal cytosolic fractions using reduced amounts of biological starting material. The herein described method can be applied to (1) investigate the effects of stress-dependent soluble factors regulating translation (such as tRNA fragments or ribosome-associated ncRNAs), (2) compare translational activity and translational fidelity of different ribosomes supplemented with the same non-ribosomal fractions, and (3) to investigate protein biosynthesis in various mammalian cell lines as well as tissue samples.
Collapse
Affiliation(s)
- Yulia Gonskikh
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Valentina Pecoraro
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| |
Collapse
|
6
|
Higashi H, Kato Y, Fujita T, Iwasaki S, Nakamura M, Nishimura Y, Takenaka M, Shikanai T. The Pentatricopeptide Repeat Protein PGR3 Is Required for the Translation of petL and ndhG by Binding Their 5' UTRs. Plant Cell Physiol 2021; 62:1146-1155. [PMID: 33439244 DOI: 10.1093/pcp/pcaa180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
PGR3 is a P-class pentatricopeptide repeat (PPR) protein required for the stabilization of petL operon RNA and the translation of the petL gene in plastids. Irrespective of its important roles in plastids, key questions have remained unanswered, including how PGR3 protein promotes translation and which plastid mRNA PGR3 activates the translation. Here, we show that PGR3 facilitates the translation from ndhG, in addition to petL, through binding to their 5' untranslated regions (UTRs). Ribosome profiling and RNA sequencing in pgr3 mutants revealed that translation from petL and ndhG was specifically suppressed. Harnessing small RNA fragments protected by PPR proteins in vivo, we probed the PGR3 recruitment to the 5' UTRs of petL and ndhG. The putative PGR3-bound RNA segments per se repress the translation possibly with a strong secondary structure and thereby block ribosomes' access. However, the PGR3 binding antagonizes the effects and facilitates the protein synthesis from petL and ndhG in vitro. The prediction of the 3-dimensional structure of PGR3 suggests that the 26th PPR motif plays important roles in target RNA binding. Our data show the specificity of a plastidic RNA-binding protein and provide a mechanistic insight into translational control.
Collapse
Affiliation(s)
- Haruka Higashi
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Yoshinobu Kato
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8503 Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198 Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561 Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Wako, Saitama 351-0198, Japan
| | - Masayuki Nakamura
- Center of Gene Research, Nagoya University, Nagoya, Aichi, 464-8602 Japan
| | - Yoshiki Nishimura
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Mizuki Takenaka
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Toshiharu Shikanai
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| |
Collapse
|
7
|
Masuda K, Kasahara K, Narumi R, Shimojo M, Shimizu Y. Versatile and multiplexed mass spectrometry-based absolute quantification with cell-free-synthesized internal standard peptides. J Proteomics 2021; 251:104393. [PMID: 34678518 DOI: 10.1016/j.jprot.2021.104393] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
Preparation of stable isotope-labeled internal standard peptides is crucial for mass spectrometry (MS)-based targeted proteomics. Herein, we developed versatile and multiplexed absolute protein quantification method using MS. A previously developed method based on the cell-free peptide synthesis system, termed MS-based quantification by isotope-labeled cell-free products (MS-QBiC), was improved for multiple peptide synthesis in one-pot reaction. We pluralized the quantification tags used for the quantification of synthesized peptides and thus, made it possible to use cell-free synthesized isotope-labeled peptides as mixtures for the absolute quantification. The improved multiplexed MS-QBiC method was proved to be applied to clarify ribosomal proteins stoichiometry in the ribosomal subunit, one of the largest cellular complexes. The study demonstrates that the developed method enables the preparation of several dozens and even several hundreds of internal standard peptides within a few days for quantification of multiple proteins with only a single-run of MS analysis. SIGNIFICANCE: The developed method can be applied for the preparation of internal standard peptides without limiting the number of peptides to be synthesized, which may result in more practical screening of quantitatively reliable peptides, one of the fundamental steps in the reliable absolute quantification using MS. Furthermore, the method is highly versatile for proteome analysis of any organisms or species without any cDNA or SIL peptide libraries. The quantification can be finished in a few days including design and preparation of appropriate SIL peptides using small-scale batch cell-free reactions, which has a potential to be a part of the standard methodology in a field of quantitative proteomics.
Collapse
Affiliation(s)
- Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Keiko Kasahara
- Department of Surgery, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan; Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Masaru Shimojo
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan.
| |
Collapse
|
8
|
Monroe JG, Smith TJ, Koutmou KS. Investigating the consequences of mRNA modifications on protein synthesis using in vitro translation assays. Methods Enzymol 2021; 658:379-406. [PMID: 34517955 DOI: 10.1016/bs.mie.2021.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ribosome translates the information stored in the genetic code into functional proteins. In this process messenger RNAs (mRNAs) serve as templates for the ribosome, ensuring that amino acids are linked together in the correct order. Chemical modifications to mRNA nucleosides have the potential to influence the rate and accuracy of protein synthesis. Here, we present an in vitro Escherichia coli translation system utilizing highly purified components to directly investigate the impact of mRNA modifications on the speed and accuracy of the ribosome. This system can be used to gain insights into how individual chemical modifications influence translation on the molecular level. While the fully reconstituted system described in this chapter requires a lengthy time investment to prepare experimental materials, it is highly verstaile and enables the systematic assessment of how single variables influence protein synthesis by the ribosome.
Collapse
Affiliation(s)
- Jeremy G Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Tyler J Smith
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States.
| |
Collapse
|
9
|
Mercier E, Wintermeyer W, Rodnina MV. Co-translational insertion and topogenesis of bacterial membrane proteins monitored in real time. EMBO J 2020; 39:e104054. [PMID: 32311161 PMCID: PMC7396858 DOI: 10.15252/embj.2019104054] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 11/19/2019] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 01/23/2023] Open
Abstract
Integral membrane proteins insert into the bacterial inner membrane co‐translationally via the translocon. Transmembrane (TM) segments of nascent proteins adopt their native topological arrangement with the N‐terminus of the first TM (TM1) oriented to the outside (type I) or the inside (type II) of the cell. Here, we study TM1 topogenesis during ongoing translation in a bacterial in vitro system, applying real‐time FRET and protease protection assays. We find that TM1 of the type I protein LepB reaches the translocon immediately upon emerging from the ribosome. In contrast, the type II protein EmrD requires a longer nascent chain before TM1 reaches the translocon and adopts its topology by looping inside the ribosomal peptide exit tunnel. Looping presumably is mediated by interactions between positive charges at the N‐terminus of TM1 and negative charges in the tunnel wall. Early TM1 inversion is abrogated by charge reversal at the N‐terminus. Kinetic analysis also shows that co‐translational membrane insertion of TM1 is intrinsically rapid and rate‐limited by translation. Thus, the ribosome has an important role in membrane protein topogenesis.
Collapse
Affiliation(s)
- Evan Mercier
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
10
|
Abstract
Ribosome display has proven to be a powerful in vitro selection and evolution method for generating high-affinity binders from libraries of folded proteins. It works entirely in vitro, and this has two important consequences. First, since no transformation of any cells is required, libraries with much greater diversity can be handled than with most other techniques. Second, since a library does not have to be cloned and transformed, it is very convenient to introduce random errors in the library by PCR-based methods and select improved binders. Thus, a true directed evolution, an iteration between randomization and selection over several generations, can be conveniently carried out, e.g., for affinity maturation, either on a given clone or on the whole library. Ribosome display has been successfully applied to antibody single-chain Fv fragments (scFv), which can be selected not only for specificity but also for stability and catalytic activity. High-affinity binders with new target specificity can be obtained from highly diverse libraries in only a few selection rounds. In this protocol, the selection from the library and the process of affinity maturation and off-rate selection are explained in detail.
Collapse
|
11
|
Geng G, Yu C, Li X, Yuan X. Variable 3'polyadenylation of Wheat yellow mosaic virus and its novel effects on translation and replication. Virol J 2019; 16:23. [PMID: 30786887 PMCID: PMC6383263 DOI: 10.1186/s12985-019-1130-z] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/13/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Polyadenylation influences many aspects of mRNA as well as viral RNA. variable polyadenylation at the 3' end have been reported in RNA viruses. It is interesting to identify the characteristic and potential role of 3' polyadenylation of Wheat yellow mosaic virus (WYMV), which has been reported to contain two genomic RNAs with 3' poly(A) tails and caused severe disease on wheat in East Asia region. METHODS 3' RACE was used to identify sequences of the 3' end in WYMV RNAs from naturally infected wheat by WYMV. In vitro translation assay was performed to analyze effect of UTRs of WYMV with or without 3'polyadenylation on translation. In vitro replication mediated by WYMV NIb protein were performed to evaluate effect of variable polyadenylation on replication. RESULTS Variable polyadenylation in WYMV RNAs was identified via 3' RACE. WYMV RNAs in naturally infected wheat in China simultaneously present with regions of long, short, or no adenylation at the 3' ends. The effects of variable polyadenylation on translation and replication of WYMV RNAs were evaluated. 5'UTR and 3'UTR of WYMV RNA1 or RNA2 synergistically enhanced the translation of the firefly luciferase (Fluc) gene in in vitro WGE system, whereas additional adenylates had an oppositive effect on this enhancement on translation mediated by UTRs of WYMV. Additional adenylates remarkably inhibited the synthesis of complementary strand from viral genome RNA during the in vitro replication mediated by WYMV NIb protein. CONCLUSIONS 3' end of WYMV RNAs present variable polyadenylation even no polyadenylation. 3' polyadenylation have opposite effect on translation mediated by UTRs of WYMV RNA1 or RNA2. 3' polyadenylation have negative effect on minus-strand synthesis of WYMV RNA in vitro. Variable polyadenylation of WYMV RNAs may provide sufficient selection on the template for translation and replication.
Collapse
Affiliation(s)
- Guowei Geng
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| | - Chengming Yu
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| | - Xiangdong Li
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| | - Xuefeng Yuan
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| |
Collapse
|
12
|
Widowati EW, Bamberg-Lemper S, Becker W. Mutational analysis of two residues in the DYRK homology box of the protein kinase DYRK1A. BMC Res Notes 2018; 11:297. [PMID: 29764512 PMCID: PMC5952693 DOI: 10.1186/s13104-018-3416-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/09/2018] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Dual specificity tyrosine phosphorylation-regulated kinases (DYRK) contain a characteristic sequence motif (DYRK homology box, DH box) that is located N-terminal of the catalytic domain and supports the autophosphorylation of a conserved tyrosine during maturation of the catalytic domain. Two missense mutations in the DH box of human DYRK1B were recently identified as causative of a rare familiar form of metabolic syndrome. We have recently shown that these amino acid exchanges impair maturation of the kinase domain. Here we report the characterization of DYRK1A point mutants (D138P, K150C) that correspond to the pathogenic DYRK1B variants (H90P, R102C). RESULTS When expressed in HeLa cells, DYRK1A-D138P and K150C showed no significant difference from wild type DYRK1A regarding the activating tyrosine autophosphorylation or catalytic activity towards exogenous substrates. However, both DYRK1A variants were underphosphorylated on tyrosine when expressed in a bacterial cell free in vitro translation system. These results suggest that D138 and K150 participate in the maturation of the catalytic domain of DYRK1A albeit the mutation of these residues is compensated under physiological conditions.
Collapse
Affiliation(s)
- Esti Wahyu Widowati
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Aachen, Germany
- Chemistry Study Program, Faculty of Science and Technology, State Islamic University (UIN) Sunan Kalijaga, Yogyakarta, Indonesia
| | | | - Walter Becker
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Aachen, Germany
| |
Collapse
|
13
|
Abstract
Methylated RNA nucleotides were recently discovered to be highly abundant in RNAs. The effects of these methylations were mainly attributed to altered mRNA stabilities, protein-binding affinities, or RNA structures. The direct impact of RNA modifications on the performance of the ribosome has not been investigated so far. In this chapter, we describe an approach that allows introducing RNA modifications site-specifically into coding sequences of mRNAs and determining their effect on the translation machinery in a well-defined bacterial in vitro system.
Collapse
Affiliation(s)
- Thomas P Hoernes
- Division of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, Innsbruck, 6020, Austria
| | - Matthias D Erlacher
- Division of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, Innsbruck, 6020, Austria.
| |
Collapse
|
14
|
Tsuji S, Ichihashi N. Translation activity of chimeric ribosomes composed of Escherichia coli and Bacillus subtilis or Geobacillus stearothermophilus subunits. Biochem Biophys Rep 2017; 10:325-328. [PMID: 28955760 PMCID: PMC5614676 DOI: 10.1016/j.bbrep.2017.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 01/23/2017] [Revised: 05/09/2017] [Accepted: 05/11/2017] [Indexed: 11/24/2022] Open
Abstract
Ribosome composition, consisting of rRNA and ribosomal proteins, is highly conserved among a broad range of organisms. However, biochemical studies focusing on ribosomal subunit exchangeability between organisms remain limited. In this study, we show that chimeric ribosomes, composed of Escherichia coli and Bacillus subtilis or E. coli and Geobacillus stearothermophilus subunits, are active for β-galactosidase translation in a highly purified E. coli translation system. Activities of the chimeric ribosomes showed only a modest decrease when using E. coli 30 S subunits, indicating functional conservation of the 50 S subunit between these bacterial species. A highly sensitive translation assay was established. B. subtilis 50S subunit is active for translation in an E. coli system. G. stearothermophilus 50S subunit is active for translation in an E. coli system.
Collapse
Affiliation(s)
- Sayaka Tsuji
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norikazu Ichihashi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Corresponding author at: Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
15
|
Abstract
Aberrant histone deacetylase (HDAC) activity often correlates with neoplastic transformation and inhibition of HDACs by small molecules has emerged as a promising strategy to treat hematological malignancies in particular. Treatment with HDAC inhibitors (HDACis) often prompts tumor cells to undergo apoptosis, thereby causing a caspase-dependent cleavage of target proteins. An unexpectedly large number of proteins are in vivo caspase substrates and defining caspase-mediated substrate specificity is a major challenge. In this chapter we demonstrate that the hematopoietic transcription factor PU.1 becomes cleaved after treatment of acute myeloid leukemia (AML) cells with the HDACis LBH589 (panobinostat) or MS-275 (entinostat). To define caspase specificity for PU.1, an in vitro caspase assay including caspases 1-10 with in vitro-translated PU.1 is described in detail.
Collapse
Affiliation(s)
- Fabian Treude
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Tobias Gladbach
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Jacqueline Plaster
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Jörg Hartkamp
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
| |
Collapse
|
16
|
Machida K, Shigeta T, Kobayashi A, Masumoto A, Hidaka Y, Imataka H. Cell-free analysis of polyQ-dependent protein aggregation and its inhibition by chaperone proteins. J Biotechnol 2016; 239:1-8. [PMID: 27702574 DOI: 10.1016/j.jbiotec.2016.09.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 09/23/2016] [Accepted: 09/30/2016] [Indexed: 11/21/2022]
Abstract
Protein misfolding and aggregation is one of the major causes of neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease and Huntington's disease. So far protein aggregation related to these diseases has been studied using animals, cultured cells or purified proteins. In this study, we show that a newly synthesized polyglutamine protein implicated in Huntington's disease forms large aggregates in HeLa cells, and successfully recapitulate the process of this aggregation using a translation-based system derived from HeLa cell extracts. When the cell-free translation system was pre-incubated with recombinant human cytosolic chaperonin CCT, or the Hsc70 chaperone system (Hsc70s: Hsc70, Hsp40, and Hsp110), aggregate formation was inhibited in a dose-dependent manner. In contrast, when these chaperone proteins were added in a post-translational manner, aggregation was not prevented. These data led us to suggest that chaperonin CCT and Hsc70s interact with nascent polyglutamine proteins co-translationally or immediately after their synthesis in a fashion that prevents intra- and intermolecular interactions of aggregation-prone polyglutamine proteins. We conclude that the in vitro approach described here can be usefully employed to analyze the mechanisms that provoke polyglutamine-driven protein aggregation and to screen for molecules to prevent it.
Collapse
|
17
|
Haque M, Stanfield B, Kousoulas KG. Bovine herpesvirus type-1 glycoprotein K (gK) interacts with UL20 and is required for infectious virus production. Virology 2016; 499:156-164. [PMID: 27661734 DOI: 10.1016/j.virol.2016.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 06/18/2016] [Revised: 08/27/2016] [Accepted: 09/06/2016] [Indexed: 02/05/2023]
Abstract
We have previously shown that the HSV-1 gK and UL20 proteins interact and function in virion envelopment, membrane fusion, and neuronal entry. Alignment of the predicted secondary structures of gKs encoded by BoHV-1, HSV-1, HSV-2, EHV-1 and VZV indicated a high degree of domain conservation. Two BoHV-1 gK-null mutant viruses were created by either gK gene deletion or stop codon insertion. In addition, a V5 epitope-tag was inserted at the carboxyl terminus of gK gene to detect gK. The engineered gK-null mutant viruses failed to replicate and produce viral plaques. Co-immunoprecipitation of gK and UL20 expressed via different methods revealed that gK and UL20 physically interacted in the presence or absence of other viral proteins. Confocal microscopy showed that gK and UL20 colocalized in infected cells. These results indicate that BoHV-1 gK and UL20 may function in a similar manner to other alphaherpesvirus orthologues specified by HSV-1, PRV and EHV-1.
Collapse
Affiliation(s)
- Muzammel Haque
- Department of Pathobiological Sciences and Division of Biotechnology and Molecular Medicine, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Brent Stanfield
- Department of Pathobiological Sciences and Division of Biotechnology and Molecular Medicine, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Konstantin G Kousoulas
- Department of Pathobiological Sciences and Division of Biotechnology and Molecular Medicine, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, United States
| |
Collapse
|
18
|
Schoborg JA, Clark LG, Choudhury A, Hodgman CE, Jewett MC. Yeast knockout library allows for efficient testing of genomic mutations for cell-free protein synthesis. Synth Syst Biotechnol 2016; 1:2-6. [PMID: 29062921 PMCID: PMC5640588 DOI: 10.1016/j.synbio.2016.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 09/10/2015] [Revised: 01/27/2016] [Accepted: 02/12/2016] [Indexed: 12/31/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems from crude lysates have benefitted from modifications to their enzyme composition. For example, functionally deleting enzymes in the source strain that are deleterious to CFPS can improve protein synthesis yields. However, making such modifications can take substantial time. As a proof-of-concept to accelerate prototyping capabilities, we assessed the feasibility of using the yeast knockout collection to identify negative effectors in a Saccharomyces cerevisiae CFPS platform. We analyzed extracts made from six deletion strains that targeted the single deletion of potentially negative effectors (e.g., nucleases). We found a statistically significant increase in luciferase yields upon loss of function of GCN3, PEP4, PPT1, NGL3, and XRN1 with a maximum increase of over 6-fold as compared to the wild type. Our work has implications for yeast CFPS and for rapidly prototyping strains to enable cell-free synthetic biology applications.
Collapse
Key Words
- ANOVA, analysis of variance
- ATP, adenosine triphosphate
- CFPS, cell-free protein synthesis
- CRISPR, clustered regularly interspaced short palindromic repeats
- Cell-free biology
- Cell-free protein synthesis
- In vitro translation
- NTP, nucleoside triphosphate
- OD, optical density
- Protein expression
- SC, synthetic complete media
- Saccharomyces cerevisiae
- Synthetic biology
- YKO, yeast knockout
- cAMP, cyclic adenosine monophosphate
- eIF, eukaryotic initiation factor
Collapse
Affiliation(s)
- Jennifer A. Schoborg
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Lauren G. Clark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Alaksh Choudhury
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
- Masters in Biotechnology Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
| | - C. Eric Hodgman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
- Masters in Biotechnology Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 N. St Clair St, Suite 1200, Chicago, IL 60611-3068, USA
- Simpson Querrey Institute, Northwestern University, 303 E. Superior St, Suite 11-131, Chicago, IL 60611-2875, USA
- Corresponding author. 2145 Sheridan Road, Tech E-136, Evanston, IL 60208-3120, USA.2145 Sheridan RoadTech E-136EvanstonIL60208-3120USA
| |
Collapse
|
19
|
Bollinger JG, Stergachis AB, Johnson RS, Egertson JD, MacCoss MJ. Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards. Methods Mol Biol 2016; 1410:207-21. [PMID: 26867746 DOI: 10.1007/978-1-4939-3524-6_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In targeted proteomics, the development of robust methodologies is dependent upon the selection of a set of optimal peptides for each protein-of-interest. Unfortunately, predicting which peptides and respective product ion transitions provide the greatest signal-to-noise ratio in a particular assay matrix is complicated. Using in vitro synthesized proteins as analytical standards, we report here an empirically driven method for the selection of said peptides in a human plasma assay matrix.
Collapse
Affiliation(s)
- James G Bollinger
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA
| | - Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA
| | - Jarrett D Egertson
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA.
| |
Collapse
|
20
|
Miller C, Bröcker MJ, Prat L, Ip K, Chirathivat N, Feiock A, Veszprémi M, Söll D. A synthetic tRNA for EF-Tu mediated selenocysteine incorporation in vivo and in vitro. FEBS Lett 2015; 589:2194-9. [PMID: 26160755 DOI: 10.1016/j.febslet.2015.06.039] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [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: 04/13/2015] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
Abstract
Incorporation of selenocysteine (Sec) in bacteria requires a UGA codon that is reassigned to Sec by the Sec-specific elongation factor SelB and a conserved mRNA motif (SECIS element). These requirements severely restrict the engineering of selenoproteins. Earlier, a synthetic tRNASec was reported that allowed canonical Sec incorporation by EF-Tu; however, serine misincorporation limited its scope. We report a superior tRNASec variant (tRNAUTuX) that facilitates EF-Tu dependent stoichiometric Sec insertion in response to UAG both in vivo in Escherichia coli and in vitro in a cellfree protein synthesis system. We also demonstrate recoding of several sense codons in a SelB supplemented cell-free system. These advances in Sec incorporation will aid rational design and directed evolution of selenoproteins.
Collapse
Affiliation(s)
- Corwin Miller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Markus J Bröcker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Laure Prat
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Kevan Ip
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Napon Chirathivat
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Alexander Feiock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Miklós Veszprémi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|
21
|
Ueda H, Dong J. From fluorescence polarization to Quenchbody: Recent progress in fluorescent reagentless biosensors based on antibody and other binding proteins. Biochim Biophys Acta 2014; 1844:1951-1959. [PMID: 24931832 DOI: 10.1016/j.bbapap.2014.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/07/2014] [Accepted: 06/06/2014] [Indexed: 12/31/2022]
Abstract
Recently, antibody-based fluorescent biosensors are receiving considerable attention as a suitable biomolecule for diagnostics, namely, homogeneous immunoassay and also as an imaging probe. To date, several strategies for "reagentless biosensors" based on antibodies and natural and engineered binding proteins have been described. In this review, several approaches are introduced including a recently described fluorescent antibody-based biosensor Quenchbody, which works on the principle of fluorescence quenching of attached dye and its antigen-dependent release. The merits and possible demerits of each approach are discussed. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
Collapse
Affiliation(s)
- Hiroshi Ueda
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 Japan.
| | - Jinhua Dong
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 Japan
| |
Collapse
|
22
|
Schoborg JA, Hodgman CE, Anderson MJ, Jewett MC. Substrate replenishment and byproduct removal improve yeast cell-free protein synthesis. Biotechnol J 2014; 9:630-40. [PMID: 24323955 DOI: 10.1002/biot.201300383] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/11/2013] [Accepted: 12/06/2013] [Indexed: 12/21/2022]
Abstract
Cell-free protein synthesis (CFPS) platforms are now considered a powerful tool for synthesizing a variety of proteins at scales from pL to 100 L with accelerated process development pipelines. We previously reported the advancement of a novel yeast-based CFPS platform. Here, we studied factors that cause termination of yeast CFPS batch reactions. Specifically, we characterized the substrate and byproduct concentrations in batch, fed-batch, and semi-continuous reaction formats through high-performance liquid chromatography (HPLC) and chemical assays. We discovered that creatine phosphate, the secondary energy substrate, and nucleoside triphosphates were rapidly degraded during batch CFPS, causing a significant drop in the reaction's energy charge (E.C.) and eventual termination of protein synthesis. As a consequence of consuming creatine phosphate, inorganic phosphate accumulated as a toxic byproduct. Additionally, we measured amino acid concentrations and found that aspartic acid was rapidly consumed. By adopting a semi-continuous reaction format, where passive diffusion enables substrate replenishment and byproduct removal, we achieved over a 70% increase in active superfolder green fluorescent protein (sfGFP) as compared with the batch system. This study identifies targets for the future improvement of the batch yeast CFPS reaction. Moreover, it outlines a detailed, generalized method to characterize and improve other CFPS platforms.
Collapse
Affiliation(s)
- Jennifer A Schoborg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | | | | | | |
Collapse
|
23
|
Becker JP, Weiss J, Theile D. Cisplatin, oxaliplatin, and carboplatin unequally inhibit in vitro mRNA translation. Toxicol Lett 2013; 225:43-7. [PMID: 24275384 DOI: 10.1016/j.toxlet.2013.11.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 09/27/2013] [Revised: 11/04/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
Abstract
DNA is considered the preferential target of platinum containing cytostatics such as cisplatin, oxaliplatin, and carboplatin. Despite profound knowledge on the interaction between platinum drugs and DNA, there is little data on the interaction with mRNA and even less on the potential differences among these antineoplastic agents to inhibit protein synthesis. We therefore established an in vitro translation system using in vitro transcribed mRNA encoding green fluorescent protein (GFP) to evaluate the effects of exposure of GFP mRNA to 0-100 μM of cisplatin, oxaliplatin, or carboplatin. We additionally investigated the interaction between these drugs and mRNA through evaluation of crossing-points during quantitative real-time polymerase chain reactions. In contrast to oxaliplatin or carboplatin, 100 μM cisplatin significantly increased crossing-points by about 3 cycles (P<0.01) and profoundly attenuated translation of GFP mRNA (P<0.05). Oxaliplatin showed a trend to reduce GFP mRNA translation, whereas carboplatin entirely failed to influence it. In conclusion, this study for the very first time documents different effects of platinum cytostatics on mRNA translation and demonstrates mRNA to be a functionally relevant target of at least cisplatin.
Collapse
Affiliation(s)
- Jonas Philipp Becker
- Department of Clinical Pharmacology and Pharmacoepidemiology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Johanna Weiss
- Department of Clinical Pharmacology and Pharmacoepidemiology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany.
| | - Dirk Theile
- Department of Clinical Pharmacology and Pharmacoepidemiology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| |
Collapse
|
24
|
Kiberstis PA, Pessi A, Atherton E, Jackson R, Hunter T, Zimmern D. Analysis of in vitro and in vivo products of the TMV 30kDa open reading frame using antisera raised against a synthetic peptide. FEBS Lett 1983; 164:355-360. [PMID: 33785967 PMCID: PMC8006913 DOI: 10.1016/0014-5793(83)80316-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The peptide Tyr-Ser-Glu-Ala-Thr-Val-Ala-Glu-Ser-Asp-Ser-Phe (the predicted C-terminal 11 amino acids of the TMV 30kDa open reading frame plus an additional N-terminal Tyr residue) was synthesized by solid phase methods and used to raise antisera in rabbits. These antisera precipitated 4 major proteins (p30, p28, p19 and 18.5kDa) from in vitro translation products of TMV short rod RNA, but only one, of apparent M r = 30500, from TMV-infected tobacco protoplasts. This protein was made between 8 and 16 h post infection, and had [35S]Met-labelled tryptic peptides identical to those of in vitro synthesized p30.
Collapse
Affiliation(s)
| | - Antonello Pessi
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH
| | - Eric Atherton
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH
| | - Richard Jackson
- Biochemistry Department, University of Cambridge, Tennis Court Road, Cambridge CB2 IQW, England
| | - Tony Hunter
- The Salk Institute, PO Box 85800, San Diego, CA 92138, USA
| | - David Zimmern
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH
| |
Collapse
|