Quantitative adaptation of isoacceptor tRNAs to mRNA codons of alanine, glycine and serine

Silkworm (Bombyx mori) is a lepidopteran-holometabolic model organism. To understand its developmental biochemistry, we characterized the larval hemolymph metabonome from the third instar to prepupa stage using 1H NMR spectroscopy whilst hemolymph fatty acid composition using GC-FID/MS. We unambiguously assigned more than 60 metabolites, among which tyrosine-o-β-glucuronide, mesaconate, homocarnosine, and picolinate were reported for the first time from the silkworm hemolymph. Phosphorylcholine was the most abundant metabolite in all developmental stages with exception for the periods before the third and fourth molting. We also found obvious developmental dependence for the hemolymph metabonome involving multiple pathways including protein biosyntheses, glycolysis, TCA cycle, the metabolisms of choline amino acids, fatty acids, purines, and pyrimidines. Most hemolymph amino acids had two elevations during the feeding period of the fourth instar and prepupa stage. Trehalose was the major blood sugar before day 8 of the fifth instar, whereas glucose became the major blood sugar after spinning. C16:0, C18:0 and its unsaturated forms were dominant fatty acids in hemolymph. The developmental changes of hemolymph metabonome were associated with dietary nutrient intakes, biosyntheses of cell membrane, pigments, proteins, and energy metabolism. These findings offered essential biochemistry information in terms of the dynamic metabolic changes during silkworm development.

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“…Gly level had different behavior here probably due to silkworms’ capability to convert Ala, Thr, and Ser into Gly. 61,62 …”

Section: Discussionmentioning

confidence: 99%

Developmental Changes for the Hemolymph Metabolome of Silkworm (Bombyx mori L.)

Zhou

Hao

et al. 2015

J. Proteome Res.

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“…Other restrictions on codon choice might be due to factors such as chromatin assembly, protection of DNA against mutagenic damage, or regulation of repHcation and transcription. Most notable is the predominance of tRNA^'', tRNA^'', and tRNA^'' species during the decoding of fibroin mRNA in the posterior part of the gland Garel 1976;Garel et al 1977) and the predominance of tRNA^"', tRNA^'^, and tRNA^'^ species during sericin synthesis in the middle part of the gland ) (see Table 8-6). The studies of Garel et al (1974) and Garel (1976) have shown that there is a positive correlation between the frequency of the codons used in these mRNAs and the relative concentration of the tRNA species.…”

Section: Trna Profiles In Multicellular Eukaryotesmentioning

confidence: 99%

Biased Codon Usage: An Exploration of Its Role in Optimization of Translation

Boer¹,

Kastelein²

1986

Maximizing Gene Expression

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“…To meet such high protein synthetic demands, posterior silk gland cells undergo a functional adaptation to meet the cellular needs of specialized tRNAs [23,24]. Consequently, together with high levels of RNA polymerase II activity, there is concomitant increase in pol III activity.…”

Section: Discussionmentioning

confidence: 99%

Characterization of RNA polymerase III transcription factor TFIIIC from the mulberry silkworm, Bombyx mori

Srinivasan

Gopinathan

2002

European Journal of Biochemistry

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Fractionation of nuclear extracts from posterior silk glands of mulberry silkworm Bombyx mori, resolved the transcription factor TFIIIC into two components (designated here as TFIIIC and TFIIIC1) as in HeLa cell nuclear extracts. The reconstituted transcription of tRNA genes required the presence of both components. The affinity purified TFIIIC is a heteromeric complex comprising of five subunits ranging from 44 to 240 kDa. Of these, the 51-kDa subunit could be specifically crosslinked to the B box of tRNA Gly 1 . Purified swTFIIIC binds to the B box sequences with an affinity in the same range as of yTFIIIC or hTFII-IC2. Although an histone acetyl transferase (HAT) activity was associated with the TFIIIC fractions during the initial stages of purification, the HAT activity, unlike the human TFIIIC preparations, was separated at the final DNA affinity step. The tRNA transcription from DNA template was independent of HAT activity but the repressed transcription from chromatin template could be partially restored by external supplementation of the dissociated HAT activity. This is the first report on the purification and characterization of TFIIIC from insect systems.Keywords: Bombyx mori; chromatin transcription; histone acetyl transferase activity pol III transcription; transcription factor.RNA polymerase III (pol III) synthesizes small, untranslated, stable RNAs such as tRNAs, 5S rRNA, and a variety of other cellular and viral RNAs. At least two transcription factors, TFIIIB and TFIIIC are necessary for the transcription of tRNA genes. The basal promoter elements, for pol III transcription are two internal conserved regions comprising of the A and B box sequences, located within the tRNA coding region, which are recognized and bound by TFIIIC to initiate the transcription process [1].The most detailed and mechanistically elaborate information about transcription factor IIIC is available for yeast followed by the human cell lines [2,3]. In Saccharomyces cerevisiae, TFIIIC (scTFIIIC) is a multisubunit protein comprising of six subunits with an aggregate mass of 520 kDa. The largest subunit (138 kDa) binds to the B box and the third largest one (95 kDa) binds to the A box [4,5]. The genes encoding these subunits are essential for yeast cell viability [3].Human TFIIIC is more complex than the yeast factor and executes additional functions. hTFIIIC can be resolved into two components, TFIIIC1 and TFIIIC2, on ion exchange or oligonucleotide affinity columns [6,7]. The initial recognition of tRNA promoters is achieved by TFIIIC2, which binds to the B box and then serves to recruit TFIIIC1 and TFIIIB [8]. TFIIIC2 from HeLa cells consists of five polypeptides of 220, 110, 103, 90, and 63 kDa of which the largest one binds to the tRNA gene [9]. Regions of homology between the largest TFIIIC subunits, tau 138 from yeast and TFIIIC220 from human, have been demonstrated recently and these conserved residues appear to be of functional significance [10]. TFIIIC102 and TFIIIC63 interact with each other as well as with hTFIIIB9...

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Quantitative adaptation of isoacceptor tRNAs to mRNA codons of alanine, glycine and serine

Cited by 65 publications

References 29 publications

Developmental Changes for the Hemolymph Metabolome of Silkworm (Bombyx mori L.)

Developmental Changes for the Hemolymph Metabolome of Silkworm (Bombyx mori L.)

Biased Codon Usage: An Exploration of Its Role in Optimization of Translation

Characterization of RNA polymerase III transcription factor TFIIIC from the mulberry silkworm, Bombyx mori

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