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Tatematsu KI, Uchino K, Sezutsu H, Tamura T. Effect of ATG initiation codon context motifs on the efficiency of translation of mRNA derived from exogenous genes in the transgenic silkworm, Bombyx mori. SPRINGERPLUS 2014; 3:136. [PMID: 25674439 PMCID: PMC4320137 DOI: 10.1186/2193-1801-3-136] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/03/2014] [Indexed: 01/17/2023]
Abstract
The context sequence motif surrounding the ATG initiation codon influences mRNA translation efficiency and affects protein production; however, the optimal sequence differs among species. To determine the optimal sequence for production of recombinant proteins in a transgenic silkworm, we compared 14-nucleotide context motifs around the ATG (ATG-context) in 50 silkworm genes and found the following consensus: (A/T)AN(A/T)ATCAAAatgN. We were also able to define the least-common motif: CCN(C/G)CGN(C/T/G)(G/C/T)(T/G)atgC, which served as a negative control. To examine the regulatory role of these motifs in protein expression, we constructed reporter plasmids containing different ATG-context motifs together with either the luciferase gene or an enhanced green fluorescent protein (EGFP) gene. These constructs were then used for comparison of luciferase reporter activity and EGFP production in BmN4 cells in vitro as well as in transgenic silkworms in vivo. We detected 10-fold higher luciferase activity in BmN4 cells transfected with the consensus ATG-context motif construct, compared to the negative control plasmid. ELISA measurements of EGFP translation products with the corresponding constructs in BmN4 cells showed consistently similar results. Interestingly, the translation efficiency of the novel consensus ATG-context motif did not show the highest activity in the transgenic silkworms in vivo, except for the fat body. The highest efficiency in the middle and posterior silk glands was produced by the sericin 1 context. Our results show that the ATG-context motifs differ among silkworm tissues. This result is important for the further improvement of the transgenic silkworm system for the production of recombinant proteins.
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Affiliation(s)
- Ken-Ichiro Tatematsu
- Transgenic Silkworm Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634 Japan
| | - Keiro Uchino
- Transgenic Silkworm Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634 Japan
| | - Hideki Sezutsu
- Transgenic Silkworm Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634 Japan
| | - Toshiki Tamura
- Transgenic Silkworm Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634 Japan
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Patakottu BR, Singh PK, Malhotra P, Chauhan VS, Patankar S. In vivo analysis of translation initiation sites in Plasmodium falciparum. Mol Biol Rep 2011; 39:2225-32. [PMID: 21643747 DOI: 10.1007/s11033-011-0971-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 05/26/2011] [Indexed: 11/30/2022]
Abstract
Regulation of gene expression in the malaria parasite Plasmodium falciparum is tightly controlled and little is known about the many steps involved. One step i.e. translation initiation is also poorly understood and in P. falciparum, choice of the translation initiation site (TIS) is a critical decision largely due to the high frequency of AUGs in the relatively long 5' untranslated regions of parasite mRNAs. The sequences surrounding the TIS have a major role to play in translation initiation and this report evaluates these sequences by mutational analysis of the heat shock protein 86 gene, transient transfection and reporter assays in the parasite. We find that purines at the -3 and +4 positions are essential for efficient translation in P. falciparum, similar to other eukaryotes. Interestingly, a U at the -1 position results in 2.5-fold higher reporter activity compared to wild type. Certain classes of protein biosynthetic genes show higher frequencies of U at the -1 position, suggesting that these genes may exhibit higher levels of translation. This work defines the optimal sequences for TIS choice and has implications for the design of efficient expression vectors in an important human pathogen.
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Affiliation(s)
- Balakota Reddy Patakottu
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Syomin BV, Ivanova LA, Popenko VI, Ilyin YV. Structural protein GAG of the gypsy retrovirus forms virus-like particles in the bacterial cell. Mol Biol 2011. [DOI: 10.1134/s0026893311030150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lukaszewicz M, Feuermann1 M, Jérouville B, Stas A, Boutry M. In vivo evaluation of the context sequence of the translation initiation codon in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2000; 154:89-98. [PMID: 10725562 DOI: 10.1016/s0168-9452(00)00195-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Statistical analysis of the AUG initiation codon context in several plant organisms identified a nucleotide preference in some positions around the AUG. Sixteen AUG contexts were studied using transient expression in tobacco, maize and Norway spruce. Besides the importance of A or G at position -3, we revealed the role of positions -2, -1 for which AA or CC were found to be the best for tobacco and maize, respectively. GC (positions +4, +5) were also found to be important in both tobacco and maize. Finally, we identified a variation in context efficiency according to cell type, since A was better than G at position -3 in tobacco leaf protoplasts, while both nucleotides were equally efficient in tobacco suspension cells.
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Affiliation(s)
- M Lukaszewicz
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Place Croix du Sud 2-20, B-1348, Louvain-La-Neuve, Belgium
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Foster JM, Yudkin B, Lockyer AE, Roberts DB. Cloning and sequence analysis of GmII, a Drosophila melanogaster homologue of the cDNA encoding murine Golgi alpha-mannosidase II. Gene 1995; 154:183-6. [PMID: 7890162 DOI: 10.1016/0378-1119(94)00867-r] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Using the murine cDNA that encodes Golgi alpha-mannosidase II (GlcNAc transferase I-dependent alpha 1,3[alpha 1,6] mannosidase; EC 3.2.1.114) as a probe to screen a cDNA library made from Drosophila melanogaster (Dm) embryos, we have isolated GmII, the Dm sequence homologue. The 3926-bp cDNA has an open reading frame of 3327 bp and predicts a polypeptide of approx. 127 kDa, a mass similar to that of the murine protein. The deduced mouse and Dm amino acid (aa) sequences share extensive similarity across their entire lengths and are both type-II transmembrane (TM) proteins with short cytoplasmic tails, single TM domains and large hydrophilic C-terminal domains. A region of approx. 200 aa, within the C-terminal domain, has considerable similarity to a corresponding region from several other alpha-mannosidases. GmII has been localized to a single site (85D14-18) on the right arm of chromosome 3.
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Affiliation(s)
- J M Foster
- Department of Biochemistry, Oxford University, UK
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Feng Y, Lakkis L, Devys D, Warren ST. Quantitative comparison of FMR1 gene expression in normal and premutation alleles. Am J Hum Genet 1995; 56:106-13. [PMID: 7825564 PMCID: PMC1801331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We report studies on FMR1 gene expression in cells derived from male premutation carriers. Transcription of FMR1 genes with CGG-repeat lengths within the premutation range was demonstrated to be normal. Repeat lengths are faithfully transcribed into FMR1 mRNAs, which have steady-state levels, as measured by RNase protection, similar to those of normal cells. Premutation transcripts also are shown to have normal turnover, with the FMR1 mRNA half-life estimated to be 12 h. Measurement of FMR1 protein was also found to be in similar abundance in normal and premutation cell lines. These data support the nonpenetrant status of premutation carriers of fragile X syndrome and suggest that the occasional case reports to the contrary may reflect either other causes, including low-level mosaicism for larger, methylated FMR1 alleles, or simply coincidence.
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Affiliation(s)
- Y Feng
- Howard Hughes Medical Institute, Emory University School of Medicine, Atlanta, GA 30322
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Ye X, Cavener DR. Isolation and characterization of the Drosophila melanogaster gene encoding translation-initiation factor eIF-2 beta. Gene 1994; 142:271-4. [PMID: 8194763 DOI: 10.1016/0378-1119(94)90273-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Drosophila melanogaster cDNA clones encoding the beta subunit of translation initiation factor 2 (eIF-2) were isolated and sequenced. The longest cDNA predicts a protein of 312 amino acids (aa), which possesses a putative RNA-binding motif and a highly charged N-terminal region composed of three basic polylysine blocks. The aa sequence comparison of D. melanogaster eIF-2 beta with its human and yeast counterparts demonstrates a high degree of similarity, especially within the C-terminal region. Northern analysis indicates quasi-constitutive expression of eIF-2 beta throughout D. melanogaster development.
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Affiliation(s)
- X Ye
- Department of Molecular Biology, Vanderbilt University, Nashville, TN 37235
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Qu S, Cavener DR. Isolation and characterization of the Drosophila melanogaster eIF-2 alpha gene encoding the alpha subunit of translation initiation factor eIF-2. Gene 1994; 140:239-42. [PMID: 8144032 DOI: 10.1016/0378-1119(94)90550-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Genomic and cDNA clones encoding the Drosophila melanogaster alpha-subunit of translational initiation factor 2 (eIF-2 alpha) were isolated. The D. melanogaster eIF-2 alpha gene encodes a 341 amino-acid (aa) protein that shares 57 and 44% identity to its human and yeast homologues, respectively. The regulatory phosphorylation site at Ser50 is embedded in a segment of 19 conserved aa residues. Analysis of the genomic DNA and cDNA clones indicated that eIF-2 alpha is a single-copy gene and its coding region is interrupted by a 260-bp intron. The D. melanogaster eIF-2 alpha mRNA is 1350 nt in length and is expressed throughout development.
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Affiliation(s)
- S Qu
- Department of Molecular Biology, Vanderbilt University, Nashville, TN 37235
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Pantopoulos K, Johansson HE, Hentze MW. The role of the 5' untranslated region of eukaryotic messenger RNAs in translation and its investigation using antisense technologies. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1994; 48:181-238. [PMID: 7938549 PMCID: PMC7133200 DOI: 10.1016/s0079-6603(08)60856-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This chapter discusses the recent advances in the field of translational control and the possibility of applying the powerful antisense technology to investigate some of the unanswered questions, especially those pertaining to the role of the 5’untranslated region ( UTR) on translation initiation. Translational regulation is predominantly exerted during the initiation phase that is considered to be the rate-limiting step. Two types of translational regulation can be distinguished: global, in which the initiation rate of (nearly) all cellular messenger RNA (mRNA) is controlled and selective, in which the translation rate of specific mRNAs varies in response to the biological stimuli. In most cases of global regulation, control is exerted via the phosphorylation state of certain initiation factors, whereas only a few examples of selective regulation have been characterized well enough to define the underlying molecular events. Interestingly, cis-acting regulatory sequences, affecting translation initiation, have been found not only in the 5’UTRs of selectively regulated mRNAs, but also in the 3’UTRs. Thus, in addition to the protein encoding open reading frames, both the 5’ and 3’UTRs of mRNAs must be considered for their effect on translation.
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Key Words
- alas, 5-aminolevulinate synthase
- bfgf, basic fibroblast growth factor
- bip, immunoglobulin-binding protein
- cat, chloramphenicol acetyltransferase
- dai, double-stranded rna-activated inhibitor
- ealas, erythroid-specific form of alas
- frp, ferritin repressor protein
- gcd, general control derepressible
- gcn, general control nonderepressible
- gef, guanine-nucleotide exchange factor
- grp, glucose-regulated protein
- hgh, human growth hormone
- icam, intracellular adhesion molecule
- ire, iron-responsive element
- ire-bp, iron-responsive element-binding protein
- ires, internal ribosomal entry site
- irf, iron regulatory factor
- irp, iron regulatory protein
- la, lupus erythematosus antigen
- lap, liver-enriched activating protein
- lip, liver-enriched inhibitory protein
- mep, methyl phosphonate
- pa, phosphoramidate
- pdgf, platelet-derived growth factor
- pest, phosphotriester
- pll, poly(1-lysine)
- po, phosphodiester
- ps, phosphorothioate
- ps2, phosphorodithioate
- ssl, suppressor of stem-loop
- tce, translational control element
- tgf, transforming growth factor
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Affiliation(s)
- K Pantopoulos
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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Abstract
This article reviews current knowledge on the mechanisms affecting the fidelity of initiation codon selection, and discusses the effects of structural features in the 5′-non-coding region on the efficiency of translation of messenger RNA molecules.
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Affiliation(s)
- M Kozak
- Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Piscataway 08854
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Rosenthal E. Sequence analysis of translationally controlled maternal mRNAs from Urechis caupo. DEVELOPMENTAL GENETICS 1993; 14:485-91. [PMID: 8111976 DOI: 10.1002/dvg.1020140609] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Fertilization of Urechis caupo oocytes stimulates dramatic changes in the pattern of protein synthesis. This shift is brought about entirely through selective translation of the large pool of maternal mRNAs synthesized and stored during oogenesis. My laboratory has identified cDNA clones to more than 20 different Urechis maternal mRNAs. These have been used to determine whether the complementary mRNAs are translated in oocytes or embryos, and to analyze the polyadenylation status of the mRNAs at different stages. For 14 of the mRNAs, multiple, overlapping cDNA clones were isolated, and the complete sequence of the mRNA molecule was determined. Of these 14 mRNAs, half are from the subset that is translated in growing and full-grown oocytes, but not in embryos. These 7 mRNAs have poly(A) tails before fertilization. The other 7 are from the subset that is not translated at any time before fertilization, and has very short poly(A) tails in oocytes. After fertilization these mRNAs are recruited onto polysomes and extensively polyadenylated. The sequence data from the two classes of maternal mRNAs was compared in an attempt to identify consensus sequences that could regulate translation directly, or indirectly, by controlling polyadenylation or secondary structure formation. Two features of the sequences correlate very well with the translation and polyadenylation of the different mRNAs--the identity of the base immediately preceding the AUG start codon, and the presence of the sequences UUUUA and UUUUUA in the 3' untranslated region.
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Affiliation(s)
- E Rosenthal
- Pacific Biomedical Research Center, Kewalo Marine Laboratory, University of Hawaii, Honolulu 96813
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