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Wu ZF, Wang BJ, Ni JW, Sun ZN, Zhang XR, Xiong HM. Green Fluorescent Carbon Dots with Critically Controlled Surface States: Make Silk Shine via Feeding Silkworms. NANO LETTERS 2024; 24:9675-9682. [PMID: 39058271 DOI: 10.1021/acs.nanolett.4c02426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Feeding silkworms with functional materials as additives to produce naturally modified silk is a facile, diverse, controllable, and environmentally friendly method with a low cost of time and investment. Among various additives, carbon dots (CDs) show unique advantages due to their excellent biocompatibility and fluorescence stability. Here, a new type of green fluorescent carbon dots (G-CDs) is synthesized with a high oil-water partition ratio of 147, a low isoelectric point of 5.16, an absolute quantum yield of 71%, and critically controlled surface states. After feeding with G-CDs, the silkworms weave light yellow cocoons whose green fluorescence is visible to the naked eye under UV light. The luminous silk is sewn onto the cloth to create striking patterns with beautiful fluorescence. Such G-CDs have no adverse effect on the survival rate and the life cycle of silkworms and enable their whole bodies to glow under UV light. Based on the strong fluorescence, chemical stability, and biological safety, G-CDs are found in the digestive tracts, silk glands, feces, cocoons, and even moth bodies. G-CDs accumulate in the posterior silk glands where fibroin protein is secreted, indicating its stronger combination with fibroin than sericin, which meets the requirements for practical applications.
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Affiliation(s)
- Zhao-Fan Wu
- Department of Chemistry and Shanghai Key Laboratory of Molecular and Catalysis and Innovative Materials, Fudan University, Shanghai 200438, P. R. China
| | - Bao-Juan Wang
- Department of Chemistry and Shanghai Key Laboratory of Molecular and Catalysis and Innovative Materials, Fudan University, Shanghai 200438, P. R. China
| | - Jia-Wen Ni
- Department of Chemistry and Shanghai Key Laboratory of Molecular and Catalysis and Innovative Materials, Fudan University, Shanghai 200438, P. R. China
| | - Zhao-Nan Sun
- Department of Chemistry and Shanghai Key Laboratory of Molecular and Catalysis and Innovative Materials, Fudan University, Shanghai 200438, P. R. China
| | - Xi-Rong Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular and Catalysis and Innovative Materials, Fudan University, Shanghai 200438, P. R. China
| | - Huan-Ming Xiong
- Department of Chemistry and Shanghai Key Laboratory of Molecular and Catalysis and Innovative Materials, Fudan University, Shanghai 200438, P. R. China
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McQueen C, Hughes GL, Pownall ME. Skeletal muscle differentiation drives a dramatic downregulation of RNA polymerase III activity and differential expression of Polr3g isoforms. Dev Biol 2019; 454:74-84. [PMID: 31173763 DOI: 10.1016/j.ydbio.2019.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/09/2019] [Accepted: 06/03/2019] [Indexed: 12/27/2022]
Abstract
Gene regulatory networks underpinning skeletal muscle determination and differentiation have been extensively investigated, providing molecular insights into how cell lineages are established during development. These studies have exclusively focused on the transcriptome downstream of RNA polymerase II (Pol II). RNA polymerase III (Pol III) drives the production of tRNAs and other small RNAs essential for the flow of genetic information from gene to protein and we have found that a specific isoform of a subunit unique to Pol III is expressed early in the myogenic lineage. This points to the possibility that additional regulatory networks exist to control the production of Pol III transcripts during skeletal muscle differentiation. We describe the differential expression of Polr3g and its alternate isoform Polr3gL during embryonic development and using a custom tRNA microarray, we demonstrate their distinct activity on the synthesis of tRNA isoacceptors. We show that Pol III dependent transcripts are dramatically down-regulated during the differentiation of skeletal muscle, as are mRNAs coding for Pol III associated proteins Brf1 and Brf2, while Polr3gL is up-regulated alongside contractile protein genes. Forcing Polr3g expression in this context results in a partial reversal of myogenic differentiation.
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Affiliation(s)
- Caitlin McQueen
- Biology Department, University of York, York, YO10 5DD, United Kingdom
| | - Gideon L Hughes
- Biology Department, University of York, York, YO10 5DD, United Kingdom
| | - Mary E Pownall
- Biology Department, University of York, York, YO10 5DD, United Kingdom.
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3
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Marín M, Fernández-Calero T, Ehrlich R. Protein folding and tRNA biology. Biophys Rev 2017; 9:573-588. [PMID: 28944442 PMCID: PMC5662057 DOI: 10.1007/s12551-017-0322-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022] Open
Abstract
Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.
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Affiliation(s)
- Mónica Marín
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Tamara Fernández-Calero
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Bioinformatics Unit, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Ricardo Ehrlich
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
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Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties? Life (Basel) 2016; 6:life6010009. [PMID: 26901226 PMCID: PMC4810240 DOI: 10.3390/life6010009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 01/18/2023] Open
Abstract
Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process.
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Baumgartner R, Umlauf E, Veitinger M, Guterres S, Rappold E, Babeluk R, Mitulović G, Oehler R, Zellner M. Identification and validation of platelet low biological variation proteins, superior to GAPDH, actin and tubulin, as tools in clinical proteomics. J Proteomics 2013; 94:540-51. [DOI: 10.1016/j.jprot.2013.10.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/27/2013] [Accepted: 10/10/2013] [Indexed: 12/21/2022]
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Behura SK, Severson DW. Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes. Biol Rev Camb Philos Soc 2012; 88:49-61. [PMID: 22889422 DOI: 10.1111/j.1469-185x.2012.00242.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.
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Affiliation(s)
- Susanta K Behura
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
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Zhang G, Lukoszek R, Mueller-Roeber B, Ignatova Z. Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation. Nucleic Acids Res 2010; 39:3331-9. [PMID: 21138970 PMCID: PMC3082873 DOI: 10.1093/nar/gkq1257] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues.
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Affiliation(s)
- Gong Zhang
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476 Potsdam, Potsdam, Germany
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Czech A, Fedyunin I, Zhang G, Ignatova Z. Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations. MOLECULAR BIOSYSTEMS 2010; 6:1767-72. [PMID: 20617253 DOI: 10.1039/c004796c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations that alter the amino acid sequence are known to potentially exert deleterious effects on protein function, whereas substitutions of nucleotides without amino acid change are assumed to be neutral for the protein's functionality. However, cumulative evidence suggests that synonymous substitutions might also induce phenotypic variability by affecting splicing accuracy, translation fidelity, and conformation and function of proteins. tRNA isoacceptors mediate the translation of codons to amino acids, and asymmetric tRNA abundance causes variations in the rate of translation of each single triplet. Consequently, the effect of a silent point mutation in the coding region could be significant due to differential abundances of the cognate tRNA(s), emphasizing the importance of precise assessment of tRNA composition. Here, we provide an overview of the methods used to quantitatively determine the concentrations of tRNA species and discuss synonymous mutations in the context of tRNA composition of the cell, thus providing a new twist on the detrimental impact of the silent mutations.
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Affiliation(s)
- Andreas Czech
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14467 Potsdam-Golm, Germany
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The International Silkworm Genome Consortium. The genome of a lepidopteran model insect, the silkworm Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2008; 38:1036-45. [PMID: 19121390 DOI: 10.1016/j.ibmb.2008.11.004] [Citation(s) in RCA: 493] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 11/28/2008] [Accepted: 11/28/2008] [Indexed: 05/21/2023]
Abstract
Bombyx mori, the domesticated silkworm, is a major insect model for research, and the first lepidopteran for which draft genome sequences became available in 2004. Two independent data sets from whole-genome shotgun sequencing were merged and assembled together with newly obtained fosmid- and BAC-end sequences. The remarkably improved new assembly is presented here. The 8.5-fold sequence coverage of an estimated 432 Mb genome was assembled into scaffolds with an N50 size of approximately 3.7 Mb; the largest scaffold was 14.5 million base pairs. With help of a high-density SNP linkage map, we anchored 87% of the scaffold sequences to all 28 chromosomes. A particular feature was the high repetitive sequence content estimated to be 43.6% and that consisted mainly of transposable elements. We predicted 14,623 gene models based on a GLEAN-based algorithm, a more accurate prediction than the previous gene models for this species. Over three thousand silkworm genes have no homologs in other insect or vertebrate genomes. Some insights into gene evolution and into characteristic biological processes are presented here and in other papers in this issue. The massive silk production correlates with the existence of specific tRNA clusters, and of several sericin genes assembled in a cluster. The silkworm's adaptation to feeding on mulberry leaves, which contain toxic alkaloids, is likely linked to the presence of new-type sucrase genes, apparently acquired from bacteria. The silkworm genome also revealed the cascade of genes involved in the juvenile hormone biosynthesis pathway, and a large number of cuticular protein genes.
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10
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Abstract
The persistent difficulties in the production of protein at high levels in heterologous systems, as well as the inability to understand pathologies associated with protein aggregation, highlight our limited knowledge on the mechanisms of protein folding in vivo. Attempts to improve yield and quality of recombinant proteins are diverse, frequently involving optimization of the cell growth temperature, the use of synonymous codons and/or the co-expression of tRNAs, chaperones and folding catalysts among others. Although protein secondary structure can be determined largely by the amino acid sequence, protein folding within the cell is affected by a range of factors beyond amino acid sequence. The folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins and ligands, the ribosome, translocation through a pore membrane, redox conditions, among others. The translation rate as well as the translation machinery itself can dramatically affect protein folding, and thus the structure and function of the protein product. This review addresses current efforts to better understand how the use of synonymous codons in the mRNA and the availability of tRNAs can modulate translation kinetics, affecting the folding, the structure and the biological activity of proteins.
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Affiliation(s)
- Monica Marin
- Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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11
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Thompson DM, Lu C, Green PJ, Parker R. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA (NEW YORK, N.Y.) 2008; 14:2095-103. [PMID: 18719243 PMCID: PMC2553748 DOI: 10.1261/rna.1232808] [Citation(s) in RCA: 435] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2008] [Accepted: 06/30/2008] [Indexed: 05/19/2023]
Abstract
Recent results have identified a diversity of small RNAs in a wide range of organisms. In this work, we demonstrate that Saccharomyces cerevisiae contains a small RNA population consisting primarily of tRNA halves and rRNA fragments. Both 5' and 3' fragments of tRNAs are detectable by Northern blot analysis, suggesting a process of endonucleolytic cleavage. tRNA and rRNA fragment production in yeast is most pronounced during oxidative stress conditions, especially during entry into stationary phase. Similar tRNA fragments are also observed in human cell lines and in plants during oxidative stress. These results demonstrate that tRNA cleavage is a conserved aspect of the response to oxidative stress.
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Affiliation(s)
- Debrah M Thompson
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
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12
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Andrioli LP, Gorab E, Amabis JM. The DNA puff 4C expresses a salivary secretion protein in Trichosia pubescens (Diptera; Sciaridae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2008; 67:76-86. [PMID: 18076109 DOI: 10.1002/arch.20222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
DNA puffs are genomic regions of polytene chromosomes that undergo developmentally controlled DNA amplification and transcription in salivary glands of sciarid flies. Here, we tested the hypothesis that DNA puff genes code for salivary proteins in Trichosia pubescens. To do that, we generated antibodies against saliva and immunoscreened a cDNA library made from salivary glands. We isolated clones corresponding to DNA puff regions, including clone D-50 that contained the entire coding sequence of the previously isolated C4B1 gene from puff 4C. Indeed, we showed that puff 4C is a DNA puff region detecting its local transcription and its extra rounds of DNA incorporation compared to neighboring regions. We further confirmed D-50 clone identity in Western blots reacted with the anti-saliva anitiserum. We detected a recombinant protein expressed by this clone that had the expected size for a full-length product of the gene. We end with a discussion of the relationship between DNA puff genes and their products.
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Affiliation(s)
- Luiz Paulo Andrioli
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
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13
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Abstract
Comparison of the amino acid composition of cell-proteins using 17 amino acids has been used to investigate the biological evolution of organisms such as bacteria, blue-green alga, green alga, fungi, slime mold, protozoa and vertebrates. The degree of difference in the amino acid ratios between any two groups reflects the degree of divergency in biological evolution. The amino acid composition of the Gram-negative bacteria (Escherichia coli, Klebsiella, Proteus, and Vibrio alginolyticus) was identical. However, the amino acid composition of Staphylococcus aureus and Bacillus subtilis, which are Gram-positive bacteria, differed from each other and from the Gram-negative bacteria. The amino acid composition of the blue-green alga (Cyanobacterium, Chroococidiopsis) was quite similar to that of E. coli. A marked difference in the amino acid composition was observed between E. coli and green alga (Chlorella), and significant differences were observed between E. coli and other organisms, such as fungi, protozoa (Tetrahymena), slime mold (Dictyostelium discoideum) and vertebrates. In conclusion, the change in cellular amino acid composition reflects the divergence which has occurred during biological evolution, whereas a basic pattern of amino acid composition is maintained in spite of a long period of evolutional divergence among the various organisms. Thus, it is proposed that the primitive life forms established at the end of prebiotic evolution had a similar amino acid composition.
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Affiliation(s)
- K Sorimachi
- Department of Microbiology, Dokkyo University School of Medicine, Tochigi, Japan
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14
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Ting S, Dignam J. Post-transcriptional regulation of glutamyl-prolyl-tRNA synthetase in rat salivary gland. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37066-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Leung J, Sinclair DA, Hayashi S, Tener GM, Grigliatti TA. Informational redundancy of tRNA(4Ser) and tRNA(7Ser) genes in Drosophila melanogaster and evidence for intergenic recombination. J Mol Biol 1991; 219:175-88. [PMID: 1903816 DOI: 10.1016/0022-2836(91)90560-s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Variant tRNA genes have been widely observed in multicellular eukaryotes. Recent biochemical studies have shown that some of them are expressed in a tissue- or a stage-specific manner. These findings would thus imply that certain modified tRNAs may be crucial for the development of the organism. Using Drosophila melanogaster as a model, we have taken a combined genetic and molecular approach to examine critically the possible biological functions of tRNA(4, 7Ser) genes. We showed that at least 50% of the total templates can be deleted from the genome without inducing abnormal phenotypes such as Minute, or a decrease in viability. In addition, two of the tRNASer variant genes that are unique in sequence are also completely dispensable. This strongly implies that even though they may be expressed in vivo, they play no essential role in the development of the fruitfly. By comparison with some of the corresponding tRNA genes in another sibling species, Drosophila erecta, our results suggest strongly that the variants are products non-reciprocal exchanges among the tRNA(4, 7Ser), genes. Such intergenic recombination events may have a major influence in the concerted evolution of the two gene families.
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Affiliation(s)
- J Leung
- Department of Zoology, University of British Columbia, Vancouver, Canada
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Wood L, Hatzenbuhler N, Peterson R, Vogeli G. Isolation of a mouse genomic clone containing four tRNACys-encoding genes. Gene 1991; 98:249-52. [PMID: 2016065 DOI: 10.1016/0378-1119(91)90181-a] [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: 12/29/2022]
Abstract
A cluster of four tRNACys-encoding genes with the anticodon GCA was found on a murine genomic clone containing an 18-kb DNA insert. Three of the four genes encode the identical tRNA, whereas the fourth gene has an altered nucleotide (nt) sequence. Two of the genes within a 2-kb PvuII fragment have the same polarity and are separated by only 921 bp. These two tRNAs have a different primary sequence. The changes in the nt sequences occur within three stems of the tRNA cloverleaf structure and weaken the strength of the H-bonds within the stems. All four genes (designated i-iv) have the 3' structural element that has been proposed as the transcription termination signal [Bogenhagen and Brown, Cell 24 (1981) 261-270]. The remainder of the flanking regions of the three identical tRNAs are very similar to each other, whereas the flanking regions of the fourth tRNA are distinctly different.
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Affiliation(s)
- L Wood
- Molecular Biology Research, Upjohn Company, Kalamazoo, MI 49007
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17
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Chang PK, Dignam JD. Primary structure of alanyl-tRNA synthetase and the regulation of its mRNA levels in Bombyx mori. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)45301-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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18
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O'Neill GP, Söll D. Expression of the Synechocystis sp. strain PCC 6803 tRNA(Glu) gene provides tRNA for protein and chlorophyll biosynthesis. J Bacteriol 1990; 172:6363-71. [PMID: 2121711 PMCID: PMC526821 DOI: 10.1128/jb.172.11.6363-6371.1990] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the cyanobacterium Synechocystis sp. strain PCC 6803 (Synechocystis 6803) delta-aminolevulinic acid (ALA), the sole precursor for the synthesis of the porphyrin rings of heme and chlorophyll, is formed from glutamate activated by acylation to tRNA(Glu) (G. P. O'Neill, D. M. Peterson, A. Schön, M. W. Chen, and D. Söll, J. Bacteriol. 170:3810-3816, 1988; S. Rieble and S. I. Beale, J. Biol. Chem. 263:8864-8871, 1988). We report here that Synechocystis 6803 possesses a single tRNA(Glu) gene which was transcribed as monomeric precursor tRNA and matured into the two tRNA(Glu) species. They differed in the extent of modification of the first anticodon base, 5-methylaminomethyl-2-thiouridine (O'Neill et al., 1988). The two tRNA species had equivalent capacities to stimulate the tRNA-dependent formation of ALA in Synechocystis 6803 and to provide glutamate for protein biosynthesis in an Escherichia coli-derived translation system. These results are in support of a dual role of tRNA(Glu). The levels of tRNA(Glu) were examined by Northern (RNA) blot analysis of cellular RNA and by aminoacylation assays in cultures of Synechocystis 6803 in which the amount of chlorophyll synthesized was modulated over a 10-fold range by various illumination regimens or by the addition of inhibitors of chlorophyll and ALA biosynthesis. In these cultures, the level of tRNA(Glu) was always a constant fraction of the total tRNA population, suggesting that tRNA(Glu) and chlorophyll levels are regulated independently. In addition, the tRNA(Glu) was always fully aminoacylated in vivo.
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Affiliation(s)
- G P O'Neill
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
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19
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Schmutzler C, Gross HJ. Genes, variant genes, and pseudogenes of the human tRNA(Val) gene family are differentially expressed in HeLa cells and in human placenta. Nucleic Acids Res 1990; 18:5001-8. [PMID: 2402432 PMCID: PMC332105 DOI: 10.1093/nar/18.17.5001] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pre-tRNAs(Val) were identified in unfractionated tRNA preparations from HeLa cells and human placenta and their 5' leader structures were deduced from the nucleotide sequences of the corresponding cDNAs. Several of these precursors can be assigned to nine out of the eleven members of the human tRNA(Val) gene family characterized so far, which demonstrates that these gene loci are actively transcribed in vivo. Among the expressed genes there are (a) genes for the two known tRNA(Val) isoacceptor species from human placenta, (b) gene variants that exhibit sequence alterations as compared to conventional genes, and (c) pseudogenes that produce processing-deficient precursors which are not matured to tRNAs. The transcription products of several yet unknown tRNA(Val) genes have also been detected. Furthermore, different expression patterns are observed in the two cell types studied. These data allow for the first time an insight into the in vivo expression of a human tRNA gene family.
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Affiliation(s)
- C Schmutzler
- Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Würzburg, FRG
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20
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Byrne BM, Gruber M, Ab G. The evolution of egg yolk proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1989; 53:33-69. [PMID: 2682782 DOI: 10.1016/0079-6107(89)90005-9] [Citation(s) in RCA: 225] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Viswanathan S, Dignam SS, Dignam JD. Control of the levels of alanyl-, glycyl-, and seryl-tRNA synthetases in the silkgland of Bombyx mori. Dev Biol 1988; 129:350-7. [PMID: 3417042 DOI: 10.1016/0012-1606(88)90382-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have examined the levels of glycyl-, alanyl-, and seryl-tRNA synthetases and the levels of their corresponding translatable mRNAs in the posterior and middle silkglands of the silkworm, Bombyx mori. Analysis of Western blots reveals that the change in the abundance of these enzymes during the fifth instar in crude extracts derived from posterior and middle silkgland correlates with changes in enzymatic activity; most of the change in activity for seryl- and alanyl-tRNA synthetases can be accounted for by the corresponding change in enzyme concentration, while the apparent specific activity of glycyl-tRNA synthetase appears to be elevated in the posterior silkgland. Accompanying the changes in enzyme activity and enzyme concentration are changes in the levels of the corresponding mRNAs as determined by immunoprecipitation of in vitro translation products. The levels of all three enzymes are 10 to 20 times higher in the posterior and middle silkglands than in ovarian tissue. A form of alanyl-tRNA synthetase with a slightly higher apparent molecular weight is detected in the posterior silkgland early in the fifth instar and in ovarian tissue.
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Affiliation(s)
- S Viswanathan
- Department of Biochemistry, University of Mississippi Medical Center, Jackson 39216-4505
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Viswanathan S, Dignam JD. Seryl-tRNA synthetase from Bombyx mori. Purification and properties. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)57425-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Palmer JM, Folk WR. Isolation and sequence analysis of a nuclear tRNA(met-i) gene from soybean. PLANT MOLECULAR BIOLOGY 1987; 8:47-51. [PMID: 24302523 DOI: 10.1007/bf00016433] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/1986] [Revised: 08/07/1986] [Accepted: 08/19/1986] [Indexed: 06/02/2023]
Abstract
A gene encoding the initiator methionine transfer RNA (tRNA(met-i)) has been isolated from a soybean genomic library. The nucleotide sequence of the gene is colinear with the previously determined sequence of bean and wheat germ tRNA(met-i) (3, 8) except for a transversion at site 51/63 in stem IV. Microinjection of the soybean gene into Xenopus oocytes caused the transcription of an RNA product equal in size to mature Xenopus tRNA(met-i). Hybridization of a restriction fragment containing the tRNA(met-i) gene to digests of soybean DNA reveals that the gene occurs in only one to a few copies per haploid genome.
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Affiliation(s)
- J M Palmer
- Department of Microbiology, University of Texas, 78712, Austin, TX, U.S.A
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Leung J, Addison WR, Delaney AD, MacKay RM, Miller RC, Spiegelman GB, Grigliatti TA, Tener GM. Drosophila melanogaster tRNAVal3b genes and their allogenes. Gene 1985; 34:207-17. [PMID: 3924738 DOI: 10.1016/0378-1119(85)90129-5] [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: 01/08/2023]
Abstract
Drosophila tRNAVal3b genes have been analyzed with respect to their nucleotide sequence and in vitro transcription efficiency. Plasmid pDt78R contains a single tRNA gene derived from the major tRNAVal3b gene cluster at chromosome band 84D. Its sequence corresponds to that of the tRNAVal3b. Two other plasmids, pDt41R and pDt48, each contain a tRNAVal3b-like gene from the minor tRNAVal3b gene cluster at chromosome bands 90BC. They contain the expected CAC anticodon, but their sequence differs from the tRNA at four positions. In homologous cell-free extracts, the tRNAVal3b variant genes in pDt41R and pDt48 are transcribed an order of magnitude more efficiently than the tRNAVal3b gene in pDt78R. However, the variant genes do not appear to contribute significantly to the in vivo tRNA pool [Larsen et al.: Mol. Gen. Genet. 185 (1982) 390-396]. We propose the term allogenes to describe families of related DNA sequences that may code for variant forms of a standard tRNA isoaccepting species.
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KAULENAS MINDAUGASS. Molecular Biology: Protein Synthesis. Biochemistry 1985. [DOI: 10.1016/b978-0-08-030811-1.50014-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Silk Synthesis. Biochemistry 1985. [DOI: 10.1016/b978-0-08-030811-1.50023-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Mizutani T, Narihara T, Hashimoto A. Purification and properties of bovine liver seryl-tRNA synthetase. ACTA ACUST UNITED AC 1984; 143:9-13. [PMID: 6565588 DOI: 10.1111/j.1432-1033.1984.tb08331.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Seryl-tRNA synthetase was purified 1800-fold from bovine liver extract by ultracentrifugation at 150 000 X g, chromatography on DEAE-cellulose, fractional precipitation with ammonium sulfate, gel chromatography on Sephacryl S-300, adsorption chromatography on hydroxyapatite, affinity chromatography on blue-Sepharose and finally on Matrex gel red A. The relative molecular mass, Mr, in the denatured state was estimated as 87 000 by sodium dodecyl sulfate disc gel electrophoresis; in the active state the Mr, was estimated as 170 000 for the dimeric native enzyme (alpha 2 type) by chromatography on Sephacryl S-300. The amino acid composition of the enzyme was determined. The Km values for ATP and serine were 0.49 mM and 30 microM, respectively. The Km values for tRNASerIGA and tRNASerCmCA were 1.40 microM and 1.25 microM, respectively. Sequences common to the two isoaccepting tRNASer molecules are discussed in relation to the recognition mechanism of the purified seryl-tRNA synthetase.
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Dignam SS, Dignam JD. Glycyl- and alanyl-tRNA synthetases from Bombyx mori. Purification and properties. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43007-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Evidence that translational control mechanisms operate to optimize antifreeze protein production in the winter flounder. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)43724-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Okamoto H, Ishikawa E, Suzuki Y. Structural analysis of sericin genes. Homologies with fibroin gene in the 5' flanking nucleotide sequences. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33412-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Chevallier A, Garel JP. Differential synthesis rates of tRNA species in the silk gland of Bombyx mori are required to promote tRNA adaptation to silk messages. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 124:477-82. [PMID: 7106102 DOI: 10.1111/j.1432-1033.1982.tb06618.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In studying the mechanism of tRNA adaptation to silk fibroin and sericin mRNA translation, we investigated the accumulation rates of tRNA species rapidly labeled in vivo in the posterior and middle silk glands of the silkworm Bombyx mori during the last larval instar. We found that the rates of synthesis of total and individual tRNA species labeled with [3H]uridine during the growth and the secretion phases and separated by electrophoresis on polyacrylamide gels, are specific for each tRNA species and each tissue. We noted continuous variations of the tRNA levels designed to reflect changes in the population of mRNAs. The tRNA adaptation to silk mRNAs is completed roughly at the end of the growth phase and at the beginning of the secretion phase (day four of the Vth instar). Its stabilization during the secretion phase occurs by a reversal of the relative rates of predominant tRNA species, mainly tRNAGly. The sum total of the synthetic rates for each tRNA species corroborates their known adaptive distribution during the secretion phase of silk proteins. In addition, when coupled to the similarity of their turnover rates, observed previously, the data support a transcriptional control of tRNA genes.
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