Potential relations between post-spliced introns and mature mRNAs in the Caenorhabditis elegans genome

Bo, Suling; Li, Hong; Zhang, Qiang; Lu, Zhanyuan; Bao, Tonglaga; Zhao, Xiaoqing

doi:10.1016/j.jtbi.2019.01.031

Cited by 6 publications

(4 citation statements)

References 43 publications

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“…Previous studies have shown that exons directly encode proteins and that introns influence RNA synthesis during transcription ( Mattick and Gagen, 2001 ). Moreover, the postspliced introns interact with the corresponding coding sequences and play an important role in regulating mRNA transport and gene expression ( Le Hir et al., 2003 ; Zhao et al., 2013 ; Bo et al., 2019 ). Therefore, the evolution and functional role of FLS introns remain to be studied in the future.…”

Section: Discussionmentioning

confidence: 99%

GbFLSa overexpression negatively regulates proanthocyanin biosynthesis

Guo

Wu²,

Wang³

et al. 2023

Front. Plant Sci.

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Flavonoids are important secondary metabolites with extensive pharmacological functions. Ginkgo biloba L. (ginkgo) has attracted extensive attention because of its high flavonoid medicinal value. However, little is understood about ginkgo flavonol biosynthesis. Herein, we cloned the full-length gingko GbFLSa gene (1314 bp), which encodes a 363 amino acid protein that has a typical 2-oxoglutarate (2OG)-Fe(II) oxygenase region. Recombinant GbFLSa protein with a molecular mass of 41 kDa was expressed in Escherichia coli BL21(DE3). The protein was localized to the cytoplasm. Moreover, proanthocyanins, including catechin, epicatechin, epigallocatechin and gallocatechin, were significantly less abundant in transgenic poplar than in nontransgenic (CK) plants. In addition, dihydroflavonol 4-reductase, anthocyanidin synthase and leucoanthocyanidin reductase expression levels were significantly lower than those of their CK counterparts. GbFLSa thus encodes a functional protein that might negatively regulate proanthocyanin biosynthesis. This study helps elucidate the role of GbFLSa in plant metabolism and the potential molecular mechanism of flavonoid biosynthesis.

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Section: Discussionmentioning

confidence: 99%

GbFLSa overexpression negatively regulates proanthocyanin biosynthesis

Guo

Wu²,

Wang³

et al. 2023

Front. Plant Sci.

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“…Previous studies have shown that exons directly encode proteins and that introns affect RNA synthesis during transcription [ 39 , 40 ]. In addition, an interaction occurs between introns and the corresponding coding sequences after shearing, which plays an important role in the regulation of mRNA transport and gene expression [ 41 , 42 , 43 ]. Hence, the evolutionary and functional roles of the GbF3′5′H1 intron remain to be studied.…”

Section: Discussionmentioning

confidence: 99%

Overexpression of GbF3′5′H1 Provides a Potential to Improve the Content of Epicatechin and Gallocatechin

Wang

Yue

et al. 2020

Molecules

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The flavonoids in Ginkgo biloba L. (ginkgo) have important medicinal uses due to their antioxidant, antitumor, and blood circulation-promoting effects. However, the genetic mechanisms underlying flavonoid biosynthesis in ginkgo remain elusive. Flavonoid 3′, 5′-hydroxylase (F3′5′H) is an important enzyme in flavonoid synthesis. We detected a novel differentially expressed GbF3′5′H1 gene homologous to the F3′5′H enzyme involved in the flavonoid synthesis pathway through transcriptome sequencing. In this study, we characterized this gene, performed an expression analysis, and heterologously overexpressed GbF3′5′H1 in Populus. Our results showed that GbF3′5′H1 is abundant in the leaf and highly expressed during April. We also found four metabolites closely related to flavonoid biosynthesis. Importantly, the contents of 4′,5-dihydroxy-7-glucosyloxyflavanone, epicatechin, and gallocatechin were significantly higher in transgenic plants than in nontransgenic plants. Our findings revealed that the GbF3′5′H1 gene functions in the biosynthesis of flavonoid-related metabolites, suggesting that GbF3′5′H1 represents a prime candidate for future studies (e.g., gene-editing) aiming to optimize ginkgo flavonoid production, especially that of flavan-3-ols.

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“…The loss/gain of an intron does affect gene expression after splicing and plays a very important role in the evolution of the eukaryotic genome and the presence of new eukaryotic species ( Duret, 2001 ; Halligan and Keightley, 2006 ). The interaction between post-spliced introns and their CDS was studied in our early works ( Zhao et al, 2013 ; Zhang et al, 2016 ; Bo et al, 2019 ), but the 5′-UTR and 3′-UTR of mRNA are very important to gene expression. It is therefore very meaningful to study the interaction between introns and their corresponding mRNAs and to uncover how introns influence stages of gene expression after splicing by their interactions.…”

Section: Introductionmentioning

confidence: 99%

Ubiquitous conservative interaction patterns between post-spliced introns and their mRNAs revealed by genome-wide interspecies comparison

Sun²,

Li³

et al. 2023

Front. Genet.

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Introns, as important vectors of biological functions, can influence many stages of mRNA metabolism. However, in recent research, post-spliced introns are rarely considered. In this study, the optimal matched regions between introns and their mRNAs in nine model organism genomes were investigated with improved Smith–Waterman local alignment software. Our results showed that the distributions of mRNA optimal matched frequencies were highly consistent or universal. There are optimal matched frequency peaks in the UTR regions, which are obvious, especially in the 3′-UTR. The matched frequencies are relatively low in the CDS regions of the mRNA. The distributions of the optimal matched frequencies around the functional sites are also remarkably changed. The centers of the GC content distributions for different sequences are different. The matched rate distributions are highly consistent and are located mainly between 60% and 80%. The most probable value of the optimal matched segments is about 20 bp for lower eukaryotes and 30 bp for higher eukaryotes. These results show that there are abundant functional units in the introns, and these functional units are correlated structurally with all kinds of sequences of mRNA. The interaction between the post-spliced introns and their corresponding mRNAs may play a key role in gene expression.

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Potential relations between post-spliced introns and mature mRNAs in the Caenorhabditis elegans genome

Cited by 6 publications

References 43 publications

GbFLSa overexpression negatively regulates proanthocyanin biosynthesis

GbFLSa overexpression negatively regulates proanthocyanin biosynthesis

Overexpression of GbF3′5′H1 Provides a Potential to Improve the Content of Epicatechin and Gallocatechin

Ubiquitous conservative interaction patterns between post-spliced introns and their mRNAs revealed by genome-wide interspecies comparison

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