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Yin Z, Li M, Niu C, Yu M, Xie X, Haimiti G, Guo W, Shi J, He Y, Ding J, Zhang F. Design of multi-epitope vaccine candidate against Brucella type IV secretion system (T4SS). PLoS One 2023; 18:e0286358. [PMID: 37561685 PMCID: PMC10414599 DOI: 10.1371/journal.pone.0286358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/22/2023] [Indexed: 08/12/2023] Open
Abstract
Brucellosis is a common zoonosis, which is caused by Brucella infection, and Brucella often infects livestock, leading to abortion and infertility. At present, human brucellosis remains one of the major public health problems in China. According to previous research, most areas in northwest China, including Xinjiang, Tibet, and other regions, are severely affected by Brucella. Although there are vaccines against animal Brucellosis, the effect is often poor. In addition, there is no corresponding vaccine for human Brucellosis infection. Therefore, a new strategy for early prevention and treatment of Brucella is needed. A multi-epitope vaccine should be developed. In this study, we identified the antigenic epitopes of the Brucella type IV secretion system VirB8 and Virb10 using an immunoinformatics approach, and screened out 2 cytotoxic T lymphocyte (CTL) epitopes, 9 helper T lymphocyte (HTL) epitopes, 6 linear B cell epitopes, and 6 conformational B cell epitopes. These advantageous epitopes are spliced together through different linkers to construct a multi-epitope vaccine. The silico tests showed that the multi-epitope vaccine was non-allergenic and had a strong interaction with TLR4 molecular docking. In immune simulation results, the vaccine construct may be useful in helping brucellosis patients to initiate cellular and humoral immunity. Overall, our findings indicated that the multi-epitope vaccine construct has a high-quality structure and suitable characteristics, which may provide a theoretical basis for the development of a Brucella vaccine.
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Affiliation(s)
- Zhengwei Yin
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Min Li
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Ce Niu
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Xinjiang, China
| | - Xinru Xie
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Gulishati Haimiti
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Wenhong Guo
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Juan Shi
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Yueyue He
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Xinjiang, China
| | - Jianbing Ding
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Fengbo Zhang
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
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2
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Komarova ES, Dontsova OA, Pyshnyi DV, Kabilov MR, Sergiev PV. Flow-Seq Method: Features and Application in Bacterial Translation Studies. Acta Naturae 2022; 14:20-37. [PMID: 36694903 PMCID: PMC9844084 DOI: 10.32607/actanaturae.11820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/11/2022] [Indexed: 01/22/2023] Open
Abstract
The Flow-seq method is based on using reporter construct libraries, where a certain element regulating the gene expression of fluorescent reporter proteins is represented in many thousands of variants. Reporter construct libraries are introduced into cells, sorted according to their fluorescence level, and then subjected to next-generation sequencing. Therefore, it turns out to be possible to identify patterns that determine the expression efficiency, based on tens and hundreds of thousands of reporter constructs in one experiment. This method has become common in evaluating the efficiency of protein synthesis simultaneously by multiple mRNA variants. However, its potential is not confined to this area. In the presented review, a comparative analysis of the Flow-seq method and other alternative approaches used for translation efficiency evaluation of mRNA was carried out; the features of its application and the results obtained by Flow-seq were also considered.
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Affiliation(s)
- E. S. Komarova
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - O. A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437 Russia
| | - D. V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119234 Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
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3
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Kalinina AA, Kolesnikov AV, Kozyr AV, Kulikova NL, Zamkova MA, Kazansky DB, Khromykh LM. Preparative Production and Purification of Recombinant Human Cyclophilin A. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:259-268. [PMID: 35526853 DOI: 10.1134/s0006297922030063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
In this work, we developed the method of preparative production of recombinant human cyclophilin A (rhCypA) in Escherichia coli. The full-length cDNA encoding the gene of human CypA (CYPA) was amplified by RT-PCR from the total RNA of human T cell lymphoma Jurkat. The nucleotide sequence of CYPA was optimized to provide highly effective translation in E. coli. Recombinant CYPA DNA was cloned into the pET22b(+) vector, and the resulted expression plasmid was used to transform E. coli strain BL21(DE3)Gold. The recombinant producer strain of E. coli produced soluble rhCypA in the bacterial cytoplasm. The synthesis efficiency of rhCypA was up to 50% of the total cell protein allowing to produce rhCypA in the amount of 1 g per liter of the culture. We also developed the method for rhCypA purification, consisting of a single-step tandem anion exchange chromatography on DEAE- and Q-Sepharose columns. The protein purity was 95% according to electrophoresis (SDS-PAGE), and its contamination with endotoxin did not exceed 0.05 ng per 1 mg of the protein that met the requirements of European pharmacopoeia for injectable preparations. The produced recombinant protein exhibited functional features of native CypA, i.e., isomerase activity and chemokine activity as assessed by stimulation of migration of mouse bone marrow hematopoietic stem cells in vivo. The generated producer strain of E. coli is a super-producer and could be used for large-scale experimental studies of rhCypA and in its preclinical and clinical trials as a drug.
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Affiliation(s)
- Anastasiia A Kalinina
- N. N. Blokhin National Medical Research Center of Oncology, the Ministry of Health of the Russian Federation, Moscow, 115478, Russia
| | - Alexander V Kolesnikov
- State Research Center of Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia
| | - Arina V Kozyr
- State Research Center of Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia
| | - Natalia L Kulikova
- Institute of Immunological Engineering, Lyubuchany, Moscow Region, 142380, Russia
| | - Maria A Zamkova
- N. N. Blokhin National Medical Research Center of Oncology, the Ministry of Health of the Russian Federation, Moscow, 115478, Russia
| | - Dmitry B Kazansky
- N. N. Blokhin National Medical Research Center of Oncology, the Ministry of Health of the Russian Federation, Moscow, 115478, Russia
| | - Ludmila M Khromykh
- N. N. Blokhin National Medical Research Center of Oncology, the Ministry of Health of the Russian Federation, Moscow, 115478, Russia.
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Osterman IA, Chervontseva ZS, Evfratov SA, Sorokina AV, Rodin VA, Rubtsova MP, Komarova ES, Zatsepin TS, Kabilov MR, Bogdanov AA, Gelfand MS, Dontsova OA, Sergiev PV. Translation at first sight: the influence of leading codons. Nucleic Acids Res 2020; 48:6931-6942. [PMID: 32427319 PMCID: PMC7337518 DOI: 10.1093/nar/gkaa430] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/31/2023] Open
Abstract
First triplets of mRNA coding region affect the yield of translation. We have applied the flowseq method to analyze >30 000 variants of the codons 2-11 of the fluorescent protein reporter to identify factors affecting the protein synthesis. While the negative influence of mRNA secondary structure on translation has been confirmed, a positive role of rare codons at the beginning of a coding sequence for gene expression has not been observed. The identity of triplets proximal to the start codon contributes more to the protein yield then more distant ones. Additional in-frame start codons enhance translation, while Shine-Dalgarno-like motifs downstream the initiation codon are inhibitory. The metabolic cost of amino acids affects the yield of protein in the poor medium. The most efficient translation was observed for variants with features resembling those of native Escherichia coli genes.
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Affiliation(s)
- Ilya A Osterman
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Zoe S Chervontseva
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,A.A.Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | | | - Alena V Sorokina
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia
| | | | - Maria P Rubtsova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ekaterina S Komarova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,A.A.Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | - Olga A Dontsova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Petr V Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
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Volkenborn K, Kuschmierz L, Benz N, Lenz P, Knapp A, Jaeger KE. The length of ribosomal binding site spacer sequence controls the production yield for intracellular and secreted proteins by Bacillus subtilis. Microb Cell Fact 2020; 19:154. [PMID: 32727460 PMCID: PMC7392706 DOI: 10.1186/s12934-020-01404-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/13/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Bacillus subtilis is widely used for the industrial production of recombinant proteins, mainly due to its high secretion capacity, but higher production yields can be achieved only if bottlenecks are removed. To this end, a crucial process is translation initiation which takes place at the ribosome binding site enclosing the Shine Dalgarno sequence, the start codon of the target gene and a short spacer sequence in between. Here, we have studied the effects of varying spacer sequence lengths in vivo on the production yield of different intra- and extracellular proteins. RESULTS The shuttle vector pBSMul1 containing the strong constitutive promoter PHpaII and the optimal Shine Dalgarno sequence TAAGGAGG was used as a template to construct a series of vectors with spacer lengths varying from 4 to 12 adenosines. For the intracellular proteins GFPmut3 and β-glucuronidase, an increase of spacer lengths from 4 to 7-9 nucleotides resulted in a gradual increase of product yields up to 27-fold reaching a plateau for even longer spacers. The production of secreted proteins was tested with cutinase Cut and swollenin EXLX1 which were N-terminally fused to one of the Sec-dependent signal peptides SPPel, SPEpr or SPBsn. Again, longer spacer sequences resulted in up to tenfold increased yields of extracellular proteins. Fusions with signal peptides SPPel or SPBsn revealed the highest production yields with spacers of 7-10nt length. Remarkably, fusions with SPEpr resulted in a twofold lower production yield with 6 or 7nt spacers reaching a maximum with 10-12nt spacers. This pattern was observed for both secreted proteins fused to SPEpr indicating a dominant role also of the nucleotide sequence encoding the respective signal peptide for translation initiation. This conclusion was corroborated by RT qPCR revealing only slightly different amounts of transcript. Also, the effect of a putative alternative translation initiation site could be ruled out. CONCLUSION Our results confirm the importance of the 5' end sequence of a target gene for translation initiation. Optimizing production yields thus may require screenings for optimal spacer sequence lengths. In case of secreted proteins, the 5' sequence encoding the signal peptide for Sec-depended secretion should also be considered.
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Affiliation(s)
- Kristina Volkenborn
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), C/o Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Laura Kuschmierz
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Environmental Microbiology and Biotechnology-Molecular Enzyme Technology and Biochemistry, University Duisburg-Essen, 45141, Essen, Germany
| | - Nuka Benz
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), C/o Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Patrick Lenz
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Bioeconomy Science Center (BioSC), C/o Forschungszentrum Jülich, 52425, Jülich, Germany.
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), C/o Forschungszentrum Jülich, 52425, Jülich, Germany
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6
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Behloul N, Wei W, Baha S, Liu Z, Wen J, Meng J. Effects of mRNA secondary structure on the expression of HEV ORF2 proteins in Escherichia coli. Microb Cell Fact 2017; 16:200. [PMID: 29137642 PMCID: PMC5686824 DOI: 10.1186/s12934-017-0812-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022] Open
Abstract
Background Viral protein expression in Escherichia coli (E. coli) is a powerful tool for structural/functional studies as well as for vaccine and diagnostics development. However, numerous factors such as codon bias, mRNA secondary structure and nucleotides distribution, have been indentified to hamper this heterologous expression. Results In this study, we combined computational and biochemical methods to analyze the influence of these factors on the expression of different segments of hepatitis E virus (HEV) ORF 2 protein and hepatitis B virus surface antigen (HBsAg). Three out of five HEV antigens were expressed while all three HBsAg fragments were not. The computational analysis revealed a significant difference in nucleotide distribution between expressed and non-expressed genes; and all these non-expressing constructs shared similar stable 5′-end mRNA secondary structures that affected the accessibility of both Shine-Dalgarno (SD) sequence and start codon AUG. By modifying the 5′-end of HEV and HBV non-expressed genes, there was a significant increase in the total free energy of the mRNA secondary structures that permitted the exposure of the SD sequence and the start codon, which in turn, led to the successful expression of these genes in E. coli. Conclusions This study demonstrates that the mRNA secondary structure near the start codon is the key limiting factor for an efficient expression of HEV ORF2 proteins in E. coli. It describes also a simple and effective strategy for the production of viral proteins of different lengths for immunogenicity/antigenicity comparative studies during vaccine and diagnostics development. Electronic supplementary material The online version of this article (10.1186/s12934-017-0812-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nouredine Behloul
- Department of Microbiology and Immunology, School of Medicine, Southeast University, 87 DingJiaQiao Road, Nanjing, 210009, Jiangsu, China
| | - Wenjuan Wei
- Department of Microbiology and Immunology, School of Medicine, Southeast University, 87 DingJiaQiao Road, Nanjing, 210009, Jiangsu, China
| | - Sarra Baha
- Department of Microbiology and Immunology, School of Medicine, Southeast University, 87 DingJiaQiao Road, Nanjing, 210009, Jiangsu, China
| | - Zhenzhen Liu
- Department of Microbiology and Immunology, School of Medicine, Southeast University, 87 DingJiaQiao Road, Nanjing, 210009, Jiangsu, China
| | - Jiyue Wen
- Department of Pharmacology, Anhui Medical University, Hefei, 230032, China
| | - Jihong Meng
- Department of Microbiology and Immunology, School of Medicine, Southeast University, 87 DingJiaQiao Road, Nanjing, 210009, Jiangsu, China.
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Selimoglu SM, Kasap M, Akpinar G, Karadenizli A. Overcoming difficulties on synthesis of cardiac troponin-I. Prep Biochem Biotechnol 2017; 47:94-99. [PMID: 27070210 DOI: 10.1080/10826068.2016.1172894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Human cardiac troponin-I (cTnI) is one of the most sensitive and specific indicators, used in the diagnosis of myocardial infarction. To produce the protein efficiently, Escherichia coli and Pichia pastoris systems were used. Initial trials for the expression in E. coli were not successful, although different expression vectors with different promoters were tested. This led us to use P. pastoris for the expression. After several trials with two different expression strains of P. pastoris, it was concluded that P. pastoris was also not an optimal expression host for cTnI. Comprehensive analysis of the expression systems indicated that an efficient expression is only possible when the gene is optimized for expression in E. coli. For this purpose, the gene was optimized in-silico, but edited manually afterwards. It was synthesized and cloned into pQE-2 vector. Expression was performed using routine experimental conditions. Thus, cTnI could be efficiently expressed from the optimized gene in E. coli. The expression and purification were practical and may be used for commercial purposes since a total yield of 25µg highly pure protein per milliliter of culture could be obtained. The protein was in its ready-to-use form for many biological applications, including as a standard in diagnostic tests and an antigen for antibody production.
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Affiliation(s)
- S Mert Selimoglu
- a Department of Medical Biology , Kocaeli University Medical School , Umuttepe Kocaeli , Turkey
| | - Murat Kasap
- b DEKART Proteomics Laboratory, Department of Medical Biology , Kocaeli University Medical School , Umuttepe Kocaeli , Turkey
| | - Gurler Akpinar
- b DEKART Proteomics Laboratory, Department of Medical Biology , Kocaeli University Medical School , Umuttepe Kocaeli , Turkey
| | - Aynur Karadenizli
- c Department of Medical Microbiology , Kocaeli University Medical School , Umuttepe Kocaeli , Turkey
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8
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Alternative Translation Initiation of a Haloarchaeal Serine Protease Transcript Containing Two In-Frame Start Codons. J Bacteriol 2016; 198:1892-901. [PMID: 27137502 DOI: 10.1128/jb.00202-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/26/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Recent studies have shown that haloarchaea employ leaderless and Shine-Dalgarno (SD)-less mechanisms for translation initiation of leaderless transcripts with a 5' untranslated region (5' UTR) of <10 nucleotides (nt) and leadered transcripts with a 5' UTR of ≥10 nt, respectively. However, whether the two mechanisms can operate on the same naturally occurring haloarchaeal transcript carrying multiple potential start codons is unknown. In this study, the transcript of the sptA gene (encoding an extracellular serine protease of Natrinema sp. strain J7-2) was experimentally determined and found to contain two potential in-frame AUG codons (AUG(1) and AUG(2)) located 5 and 29 nt, respectively, downstream of the transcription start site. Mutational analysis revealed that both AUGs can function as the translation start codon for production of active SptA, although AUG(1) is more efficient than AUG(2) for translation initiation. Insertion of a stable stem-loop structure between the two AUGs completely abolished initiation at AUG(1) but did not affect initiation at AUG(2), indicating that AUG(2)-initiated translation does not involve ribosome scanning from the 5' end of the transcript. Furthermore, the efficiency of AUG(2)-initiated translation was not influenced by an upstream SD-like sequence. In addition, both AUG(1) and AUG(2) contribute to transcript stability, probably by recruiting ribosomes to protect the transcript against degradation. These data suggest that depending on which of two in-frame start codons is used, the sptA transcript can act as either a leaderless or a leadered transcript for SptA production in haloarchaea. IMPORTANCE In eukaryotes and bacteria, alternative translation start sites contribute to proteome complexity and can be used as a functional mechanism to increase translation efficiency. However, little is known about alternative translation initiation in archaea. Our results demonstrate that leaderless and SD-less mechanisms can be used for translation initiation of the sptA transcript from two in-frame start codons, raising the possibility that in haloarchaea, alternative translation initiation on one transcript functions to increase translation efficiency and/or contribute to proteome complexity.
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9
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Gualerzi CO, Pon CL. Initiation of mRNA translation in bacteria: structural and dynamic aspects. Cell Mol Life Sci 2015; 72:4341-67. [PMID: 26259514 PMCID: PMC4611024 DOI: 10.1007/s00018-015-2010-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 01/12/2023]
Abstract
Initiation of mRNA translation is a major checkpoint for regulating level and fidelity of protein synthesis. Being rate limiting in protein synthesis, translation initiation also represents the target of many post-transcriptional mechanisms regulating gene expression. The process begins with the formation of an unstable 30S pre-initiation complex (30S pre-IC) containing initiation factors (IFs) IF1, IF2 and IF3, the translation initiation region of an mRNA and initiator fMet-tRNA whose codon and anticodon pair in the P-site following a first-order rearrangement of the 30S pre-IC produces a locked 30S initiation complex (30SIC); this is docked by the 50S subunit to form a 70S complex that, following several conformational changes, positional readjustments of its ligands and ejection of the IFs, becomes a 70S initiation complex productive in initiation dipeptide formation. The first EF-G-dependent translocation marks the beginning of the elongation phase of translation. Here, we review structural, mechanistic and dynamical aspects of this process.
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MESH Headings
- Bacteria/genetics
- Bacteria/metabolism
- Binding Sites/genetics
- Codon, Initiator/genetics
- Codon, Initiator/metabolism
- Models, Genetic
- Nucleic Acid Conformation
- Peptide Initiation Factors/genetics
- Peptide Initiation Factors/metabolism
- Protein Biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- Ribosomes/metabolism
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Affiliation(s)
| | - Cynthia L Pon
- Laboratory of Genetics, University of Camerino, 62032, Camerino, Italy.
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10
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Kramer P, Gäbel K, Pfeiffer F, Soppa J. Haloferax volcanii, a prokaryotic species that does not use the Shine Dalgarno mechanism for translation initiation at 5'-UTRs. PLoS One 2014; 9:e94979. [PMID: 24733188 PMCID: PMC3986360 DOI: 10.1371/journal.pone.0094979] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/21/2014] [Indexed: 11/30/2022] Open
Abstract
It was long assumed that translation initiation in prokaryotes generally occurs via the so-called Shine Dalgarno (SD) mechanism. Recently, it became clear that translation initiation in prokaryotes is more heterogeneous. In the haloarchaeon Haloferax volcanii, the majority of transcripts is leaderless and most transcripts with a 5′-UTR lack a SD motif. Nevertheless, a bioinformatic analysis predicted that 20–30% of all genes are preceded by a SD motif in haloarchaea. To analyze the importance of the SD mechanism for translation initiation in haloarchaea experimentally the monocistronic sod gene was chosen, which contains a 5′-UTR with an extensive SD motif of seven nucleotides and a length of 19 nt, the average length of 5′UTRs in this organism. A translational fusion of part of the sod gene with the dhfr reporter gene was constructed. A mutant series was generated that matched the SD motif from zero to eight positions, respectively. Surprisingly, there was no correlation between the base pairing ability between transcripts and 16S rRNA and translational efficiency in vivo under several different growth conditions. Furthermore, complete replacement of the SD motif by three unrelated sequences did not reduce translational efficiency. The results indicate that H. volcanii does not make use of the SD mechanism for translation initiation in 5′-UTRs. A genome analysis revealed that while the number of SD motifs in 5′-UTRs is rare, their fraction within open reading frames is high. Possible biological functions for intragenic SD motifs are discussed, including re-initiation of translation at distal genes in operons.
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Affiliation(s)
- Piet Kramer
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Katrin Gäbel
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | | | - Jörg Soppa
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
- * E-mail:
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11
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Osterman IA, Evfratov SA, Sergiev PV, Dontsova OA. Comparison of mRNA features affecting translation initiation and reinitiation. Nucleic Acids Res 2013; 41:474-86. [PMID: 23093605 PMCID: PMC3592434 DOI: 10.1093/nar/gks989] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 09/22/2012] [Accepted: 09/27/2012] [Indexed: 11/17/2022] Open
Abstract
Regulation of gene expression at the level of translation accounts for up to three orders of magnitude in its efficiency. We systematically compared the impact of several mRNA features on translation initiation at the first gene in an operon with those for the second gene. Experiments were done in a system with internal control based on dual cerulean and red (CER/RFP) fluorescent proteins. We demonstrated significant differences in the efficiency of Shine Dalgarno sequences acting at the leading gene and at the following genes in an operon. The majority of frequent intercistronic arrangements possess medium SD dependence, medium dependence on the preceding cistron translation and efficient stimulation by A/U-rich sequences. The second cistron starting immediately after preceding cistron stop codon displays unusually high dependence on the SD sequence.
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Affiliation(s)
| | | | - Petr V. Sergiev
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia
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Gaspar P, Oliveira JL, Frommlet J, Santos MAS, Moura G. EuGene: maximizing synthetic gene design for heterologous expression. Bioinformatics 2012; 28:2683-4. [PMID: 22847936 DOI: 10.1093/bioinformatics/bts465] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
UNLABELLED Numerous software applications exist to deal with synthetic gene design, granting the field of heterologous expression a significant support. However, their dispersion requires the access to different tools and online services in order to complete one single project. Analyzing codon usage, calculating codon adaptation index (CAI), aligning orthologs and optimizing genes are just a few examples. A software application, EuGene, was developed for the optimization of multiple gene synthetic design algorithms. In a seamless automatic form, EuGene calculates or retrieves genome data on codon usage (relative synonymous codon usage and CAI), codon context (CPS and codon pair bias), GC content, hidden stop codons, repetitions, deleterious sites, protein primary, secondary and tertiary structures, gene orthologs, species housekeeping genes, performs alignments and identifies genes and genomes. The main function of EuGene is analyzing and redesigning gene sequences using multi-objective optimization techniques that maximize the coding features of the resulting sequence. AVAILABILITY EuGene is freely available for non-commercial use, at http://bioinformatics.ua.pt/eugene.
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Affiliation(s)
- Paulo Gaspar
- DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
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Radzi Noor M, Soulimane T. Bioenergetics at extreme temperature: Thermus thermophilus ba(3)- and caa(3)-type cytochrome c oxidases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:638-49. [PMID: 22385645 DOI: 10.1016/j.bbabio.2011.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/11/2011] [Accepted: 08/12/2011] [Indexed: 10/28/2022]
Abstract
Seven years into the completion of the genome sequencing projects of the thermophilic bacterium Thermus thermophilus strains HB8 and HB27, many questions remain on its bioenergetic mechanisms. A key fact that is occasionally overlooked is that oxygen has a very limited solubility in water at high temperatures. The HB8 strain is a facultative anaerobe whereas its relative HB27 is strictly aerobic. This has been attributed to the absence of nitrate respiration genes from the HB27 genome that are carried on a mobilizable but highly-unstable plasmid. In T. thermophilus, the nitrate respiration complements the primary aerobic respiration. It is widely known that many organisms encode multiple biochemically-redundant components of the respiratory complexes. In this minireview, the presence of the two cytochrome c oxidases (CcO) in T. thermophilus, the ba(3)- and caa(3)-types, is outlined along with functional considerations. We argue for the distinct evolutionary histories of these two CcO including their respective genetic and molecular organizations, with the caa(3)-oxidase subunits having been initially 'fused'. Coupled with sequence analysis, the ba(3)-oxidase crystal structure has provided evolutionary and functional information; for example, its subunit I is more closely related to archaeal sequences than bacterial and the substrate-enzyme interaction is hydrophobic as the elevated growth temperature weakens the electrostatic interactions common in mesophiles. Discussion on the role of cofactors in intra- and intermolecular electron transfer and proton pumping mechanism is also included.
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Affiliation(s)
- Mohamed Radzi Noor
- Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland
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14
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Abstract
Translation initiation is a crucial step of protein synthesis which largely defines how the composition of the cellular transcriptome is converted to the proteome and controls the response and adaptation to environmental stimuli. The efficiency of translation of individual mRNAs, and hence the basal shape of the proteome, is defined by the structures of the mRNA translation initiation regions. Initiation efficiency can be regulated by small molecules, proteins, or antisense RNAs, underscoring its importance in translational control. Although initiation has been studied in bacteria for decades, many aspects remain poorly understood. Recent evidence has suggested an unexpected diversity of pathways by which mRNAs can be recruited to the bacterial ribosome, the importance of structural dynamics of initiation intermediates, and the complexity of checkpoints for mRNA selection. In this review, we discuss how the ribosome shapes the landscape of translation initiation by non-linear kinetic processing of the transcriptome information. We summarize the major pathways by which mRNAs enter the ribosome depending on the structure of their 5' untranslated regions, the assembly and the structure of initiation intermediates, the individual and synergistic roles of initiation factors, and the mechanisms of mRNA and initiator tRNA selection.
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Affiliation(s)
- Pohl Milón
- Department of Physical Biochemistry, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
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Quality control of mRNA decoding on the bacterial ribosome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 86:95-128. [PMID: 22243582 DOI: 10.1016/b978-0-12-386497-0.00003-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ribosome is a major player in providing accurate gene expression in the cell. The fidelity of substrate selection is tightly controlled throughout the translation process, including the initiation, elongation, and termination phases. Although each phase of translation involves different players, that is, translation factors and tRNAs, the general principles of selection appear surprisingly similar for very different substrates. At essentially every step of translation, differences in complex stabilities as well as induced fit are sources of selectivity. A view starts to emerge of how the ribosome uses local and global conformational switches to govern induced-fit mechanisms that ensure fidelity. This review describes the mechanisms of tRNA and mRNA selection at all phases of protein synthesis in bacteria.
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Matsuda D, Mauro VP. Determinants of initiation codon selection during translation in mammalian cells. PLoS One 2010; 5:e15057. [PMID: 21124832 PMCID: PMC2991327 DOI: 10.1371/journal.pone.0015057] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 10/15/2010] [Indexed: 11/24/2022] Open
Abstract
Factors affecting translation of mRNA contribute to the complexity of eukaryotic proteomes. In some cases, translation of a particular mRNA can generate multiple proteins. However, the factors that determine whether ribosomes initiate translation from the first AUG codon in the transcript, from a downstream codon, or from multiple sites are not completely understood. Various mRNA properties, including AUG codon-accessibility and 5′ leader length have been proposed as potential determinants that affect where ribosomes initiate translation. To explore this issue, we performed studies using synthetic mRNAs with two in-frame AUG codons−both in excellent context. Open reading frames initiating at AUG1 and AUG2 encode large and small isoforms of a reporter protein, respectively. Translation of such an mRNA in COS-7 cells was shown to be 5′ cap-dependent and to occur efficiently from both AUG codons. AUG codon-accessibility was modified by using two different elements: an antisense locked nucleic acid oligonucleotide and an exon-junction complex. When either element was used to mask AUG1, the ratio of the proteins synthesized changed, favoring the smaller (AUG2-initiated) protein. In addition, we observed that increased leader length by itself changed the ratio of the proteins and favored initiation at AUG1. These observations demonstrate that initiation codon selection is affected by various factors, including AUG codon-accessibility and 5′ leader length, and is not necessarily determined by the order of AUG codons (5′→3′). The modulation of AUG codon accessibility may provide a powerful means of translation regulation in eukaryotic cells.
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Affiliation(s)
- Daiki Matsuda
- Department of Neurobiology, The Scripps Research Institute and The Skaggs Institute for Chemical Biology, La Jolla, California, United States of America
| | - Vincent P. Mauro
- Department of Neurobiology, The Scripps Research Institute and The Skaggs Institute for Chemical Biology, La Jolla, California, United States of America
- * E-mail:
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Kaw MK, Blumenthal RM. Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator. BMC Mol Biol 2010; 11:87. [PMID: 21092102 PMCID: PMC2997769 DOI: 10.1186/1471-2199-11-87] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 11/19/2010] [Indexed: 01/09/2023] Open
Abstract
Background Most type II restriction-modification (RM) systems have two independent enzymes that act on the same DNA sequence: a modification methyltransferase that protects target sites, and a restriction endonuclease that cleaves unmethylated target sites. When RM genes enter a new cell, methylation must occur before restriction activity appears, or the host's chromosome is digested. Transcriptional mechanisms that delay endonuclease expression have been identified in some RM systems. A substantial subset of those systems is controlled by a family of small transcription activators called C proteins. In the PvuII system, C.PvuII activates transcription of its own gene, along with that of the downstream endonuclease gene. This regulation results in very low R.PvuII mRNA levels early after gene entry, followed by rapid increase due to positive feedback. However, given the lethal consequences of premature REase accumulation, transcriptional control alone might be insufficient. In C-controlled RM systems, there is a ± 20 nt overlap between the C termination codon and the R (endonuclease) initiation codon, suggesting possible translational coupling, and in many cases predicted RNA hairpins could occlude the ribosome binding site for the endonuclease gene. Results Expression levels of lacZ translational fusions to pvuIIR or pvuIIC were determined, with the native pvuII promoter having been replaced by one not controlled by C.PvuII. In-frame pvuIIC insertions did not substantially decrease either pvuIIC-lacZ or pvuIIR-lacZ expression (with or without C.PvuII provided in trans). In contrast, a frameshift mutation in pvuIIC decreased expression markedly in both fusions, but mRNA measurements indicated that this decrease could be explained by transcriptional polarity. Expression of pvuIIR-lacZ was unaffected when the pvuIIC stop codon was moved 21 nt downstream from its WT location, or 25 or 40 bp upstream of the pvuIIR initiation codon. Disrupting the putative hairpins had no significant effects. Conclusions The initiation of translation of pvuIIR appears to be independent of that for pvuIIC. Direct tests failed to detect regulatory rules for either gene overlap or the putative hairpins. Thus, at least during balanced growth, transcriptional control appears to be sufficiently robust for proper regulation of this RM system.
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Affiliation(s)
- Meenakshi K Kaw
- Department of Medical Microbiology and Immunology, University of Toledo Health Science Campus, 3100 Transverse Drive, Toledo, OH 43614-2598, USA
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18
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Sarilla S, Habib SY, Tollefsen DM, Friedman DB, Arnett DR, Verhamme IM. Glycosaminoglycan-binding properties and kinetic characterization of human heparin cofactor II expressed in Escherichia coli. Anal Biochem 2010; 406:166-75. [PMID: 20670608 DOI: 10.1016/j.ab.2010.07.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
Abstract
Irreversible inactivation of alpha-thrombin (T) by the serpin, heparin cofactor II (HCII), is accelerated by ternary complex formation with the glycosaminoglycans (GAGs) heparin and dermatan sulfate (DS). Low expression of human HCII in Escherichia coli was optimized by silent mutation of 27 rare codons and five secondary Shine-Dalgarno sequences in the cDNA. The inhibitory activities of recombinant HCII, and native and deglycosylated plasma HCII, and their affinities for heparin and DS were compared. Recombinant and deglycosylated HCII bound heparin with dissociation constants (K(D)) of 6+/-1 and 7+/-1 microM, respectively, approximately 6-fold tighter than plasma HCII, with K(D) 40+/-4 microM. Binding of recombinant and deglycosylated HCII to DS, both with K(D) 4+/-1 microM, was approximately 4-fold tighter than for plasma HCII, with K(D) 15+/-4 microM. Recombinant HCII, lacking N-glycosylation and tyrosine sulfation, inactivated alpha-thrombin with a 1:1 stoichiometry, similar to plasma HCII. Second-order rate constants for thrombin inactivation by recombinant and deglycosylated HCII were comparable, at optimal GAG concentrations that were lower than those for plasma HCII, consistent with its weaker GAG binding. This weaker binding may be attributed to interference of the Asn(169)N-glycan with the HCII heparin-binding site.
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Affiliation(s)
- Suryakala Sarilla
- Department of Pathology, Vanderbilt University School of Medicine, C3321A Medical Center North, Nashville, TN 37232, USA
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Abstract
The presence of nucleotide hybridization between the 3′ end of 16S rRNA and mRNA sequence upstream of the start codon is well known in bacteria. In this paper, we detect the presence of such hybridization sites inside the coding regions of E. coli genes, and analyze their proximity to clusters of slow-translating codons. We study this phenomenon in genes of high and low expression separately. Based on our findings, we propose an explanation for the presence of RNA hybridization within the translated regions of bacterial genes.
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Affiliation(s)
- Lalit Ponnala
- Computational Biology Service Unit, Cornell University, Ithaca NY USA
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Surkov S, Nilsson H, Rasmussen LCV, Sperling-Petersen HU, Isaksson LA. Translation initiation region dependency of translation initiation in Escherichia coli by IF1 and kasugamycin. FEBS J 2010; 277:2428-39. [DOI: 10.1111/j.1742-4658.2010.07657.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Translational Bypassing – Peptidyl-tRNA Re-pairing at Non-overlapping Sites. RECODING: EXPANSION OF DECODING RULES ENRICHES GENE EXPRESSION 2010. [DOI: 10.1007/978-0-387-89382-2_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Nishizawa A, Nakayama M, Uemura T, Fukuda Y, Kimura S. Ribosome-binding site interference caused by Shine-Dalgarno-like nucleotide sequences in Escherichia coli cells. J Biochem 2009; 147:433-43. [PMID: 19910312 DOI: 10.1093/jb/mvp187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Two-cistronic expression plasmids are useful for high-level expression of heterologous genes in Escherichia coli cells by preventing the inhibition of translational initiation. In the process of constructing a two-cistronic expression plasmid pCbSTCR-4 containing the fragments of the porcine cytochrome b(5) (Psb5) and NADPH-cytochrome P450 reductase (PsCPR) genes as the first and second cistrons, respectively, the presence of a specific region in the first cistron that lowered the accumulation level of the PsCPR was suggested [Kimura, S., et al. (2005) J. Biochem. 137, 523-533]. In this study, a disturbing nucleotide sequence similar to a Shine-Dalgarno (SD) sequence (SD-like sequence), AGGAG, was identified at the 5'-upstream region near the SD sequence for the second cistron. Silent mutations in the SD-like sequence that lowered the similarity to a typical SD sequence increased the accumulation level of PsCPR. SD-like sequences introduced into mono-cistronic expression plasmids for the Psb5 and PsCPR genes also decreased the accumulation level of these proteins. The SD-like sequence also decreased the accumulation level of the insoluble PsCPR protein. This type of ribosome-binding site interference is useful not only for precise control of protein accumulation but also for increasing the soluble form of recombinant proteins in E. coli cells.
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Raymond A, Lovell S, Lorimer D, Walchli J, Mixon M, Wallace E, Thompkins K, Archer K, Burgin A, Stewart L. Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer. BMC Biotechnol 2009; 9:37. [PMID: 19383143 PMCID: PMC2680836 DOI: 10.1186/1472-6750-9-37] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 04/21/2009] [Indexed: 01/29/2023] Open
Abstract
Background With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript. Results In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38α), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in both E. coli and a cell-free wheat germ translation system. We also compare the protein expression levels in E. coli for a set of 11 different proteins with greatly varied G:C content and codon bias. Conclusion The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from Bacillus subtilis. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.
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Affiliation(s)
- Amy Raymond
- deCODE biostructures Inc, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.
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Banerjee S, Salunkhe SS, Apte-Deshpande AD, Mandi NS, Mandal G, Padmanabhan S. Over-expression of proteins using a modified pBAD24 vector in E. coli expression system. Biotechnol Lett 2009; 31:1031-6. [PMID: 19330488 DOI: 10.1007/s10529-009-9976-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 02/27/2009] [Accepted: 03/09/2009] [Indexed: 10/21/2022]
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Wills NM, O'Connor M, Nelson CC, Rettberg CC, Huang WM, Gesteland RF, Atkins JF. Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA. EMBO J 2008; 27:2533-44. [PMID: 18772887 DOI: 10.1038/emboj.2008.170] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 08/06/2008] [Indexed: 11/09/2022] Open
Abstract
Half the ribosomes translating the mRNA for phage T4 gene 60 topoisomerase subunit bypass a 50 nucleotide coding gap between codons 46 and 47. The pairing of codon 46 with its cognate peptidyl-tRNA anticodon dissociates, and following mRNA slippage, peptidyl-tRNA re-pairs to mRNA at a matched triplet 5' adjacent to codon 47, where translation resumes. Here, in studies with gene 60 cassettes, it is shown that the peptidyl-tRNA anticodon does not scan the intervening sequence for potential complementarity. However, certain coding gap mutants allow peptidyl-tRNA to scan sequences in the bypassed segment. A model is proposed in which the coding gap mRNA enters the ribosomal A-site and forms a structure that precludes peptidyl-tRNA scanning of its sequence. Dissipation of this RNA structure, together with the contribution of 16S rRNA anti-Shine-Dalgarno sequence pairing with GAG, facilitates peptidyl-tRNA re-pairing to mRNA.
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Affiliation(s)
- Norma M Wills
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
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Zamora-Romo E, Cruz-Vera LR, Vivanco-Domínguez S, Magos-Castro MA, Guarneros G. Efficient expression of gene variants that harbour AGA codons next to the initiation codon. Nucleic Acids Res 2007; 35:5966-74. [PMID: 17726048 PMCID: PMC2034473 DOI: 10.1093/nar/gkm643] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In an effort to improve the knowledge about the rules which direct the effect of the early ORF sequences on translation efficiency, we have analyzed the effect of pairs of the six arginine codons at the second and third positions on the expression of lacZ variants. Whereas the pairs of identical AGA or AGG codons were favorable for the gene expression, identical pairs of each of the four CGN codons were very inefficient. This result was unexpected because tandems of AGA or AGG codons located in more internal gene positions provoke deficient expression whilst internally located CGU and CGC are the most abundant and efficiently translated arginine codons. The mixed combinations of AGA and each of the CGN codons usually resulted in efficient rates of lacZ expression independently of the peptidyl-tRNA propensity to dissociate from the ribosome. Thus, the variant harboring the pair of AGA codons was expressed as efficiently as the variant carrying a pair of AAA codons in the same positions, a configuration reported as one of the most common and efficient for gene expression. We explain these results assuming that the presence of adenines in these early positions enhance gene expression. As expected, specific mRNA levels correlated with the intensity of lacZ expression for each variant. However, the induction of lacZ AGA AGA gene in pth cells accumulated peptidyl-tRNAArg4 as well as a short 5′-proximal lacZ mRNA fragment suggesting ribosome stalling due to depletion of aminoacylated-tRNAArg4.
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Affiliation(s)
- Efraín Zamora-Romo
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D. F. and Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA
| | - Luis Rogelio Cruz-Vera
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D. F. and Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA
| | - Serafín Vivanco-Domínguez
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D. F. and Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA
| | - Marco Antonio Magos-Castro
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D. F. and Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA
| | - Gabriel Guarneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D. F. and Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA
- *To whom correspondence should be addressed. +52 55 5061 3338+52 55 5061 3392
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Villalobos A, Ness JE, Gustafsson C, Minshull J, Govindarajan S. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 2006; 7:285. [PMID: 16756672 PMCID: PMC1523223 DOI: 10.1186/1471-2105-7-285] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Accepted: 06/06/2006] [Indexed: 12/02/2022] Open
Abstract
Background Direct synthesis of genes is rapidly becoming the most efficient way to make functional genetic constructs and enables applications such as codon optimization, RNAi resistant genes and protein engineering. Here we introduce a software tool that drastically facilitates the design of synthetic genes. Results Gene Designer is a stand-alone software for fast and easy design of synthetic DNA segments. Users can easily add, edit and combine genetic elements such as promoters, open reading frames and tags through an intuitive drag-and-drop graphic interface and a hierarchical DNA/Protein object map. Using advanced optimization algorithms, open reading frames within the DNA construct can readily be codon optimized for protein expression in any host organism. Gene Designer also includes features such as a real-time sliding calculator of oligonucleotide annealing temperatures, sequencing primer generator, tools for avoidance or inclusion of restriction sites, and options to maximize or minimize sequence identity to a reference. Conclusion Gene Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de novo creation of genetic constructs.
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Affiliation(s)
- Alan Villalobos
- DNA 2.0, Inc. 1430 O'Brien Drive Suite E, Menlo Park, CA 94025, USA
| | - Jon E Ness
- DNA 2.0, Inc. 1430 O'Brien Drive Suite E, Menlo Park, CA 94025, USA
| | - Claes Gustafsson
- DNA 2.0, Inc. 1430 O'Brien Drive Suite E, Menlo Park, CA 94025, USA
| | - Jeremy Minshull
- DNA 2.0, Inc. 1430 O'Brien Drive Suite E, Menlo Park, CA 94025, USA
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