Dataset Information

Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize.

ABSTRACT: Amino acid transporters (AATs) are essential membrane proteins that transfer amino acids across cells. They are necessary for plant growth and development. The lysine histidine transporter (LHT) gene family in maize (Zea mays) has not yet been characterized. According to sequence composition and phylogenetic placement, this study found 15 LHT genes in the maize genome. The ZmLHT genes are scattered across the plasma membrane. The study also analyzed the evolutionary relationships, gene structures, conserved motifs, 3D protein structure, a transmembrane domain, and gene expression of the 15 LHT genes in maize. Comprehensive analyses of ZmLHT gene expression profiles revealed distinct expression patterns in maize LHT genes in various tissues. This study's extensive data will serve as a foundation for future ZmLHT gene family research. This study might make easier to understand how LHT genes work in maize and other crops.

SUBMITTER: Rabby MG

PROVIDER: S-EPMC9064515 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize.

Rabby Md Golam MG Hossen Md Munnaf MM Kamal Md Mostafa MM Islam Md Numan MN

Genetics research 20220426

Amino acid transporters (AATs) are essential membrane proteins that transfer amino acids across cells. They are necessary for plant growth and development. The lysine histidine transporter (LHT) gene family in maize (Zea mays) has not yet been characterized. According to sequence composition and phylogenetic placement, this study found 15 LHT genes in the maize genome. The ZmLHT genes are scattered across the plasma membrane. The study also analyzed the evolutionary r ...[more]

PMID: 35528221

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Project description:BackgroundAnthocyanin is an important class of water-soluble pigments that are widely distributed in various tissues of plants, and it not only facilitates diverse color changes but also plays important roles in various biological processes. Maize silk, serving as an important reproductive organ and displaying a diverse range of colors, plays an indispensable role in biotic resistance through its possession of anthocyanin. However, the copy numbers, characteristics, and expression patterns of genes involved in maize anthocyanin biosynthesis are not fully understood. In this study, gene numbers, distribution, structure, cis-elements of the anthocyanin synthetic gene family were identified, and then the potential transcriptional factors were predicted by two analyzed methods. Finally, genes involved in maize silk pigment were screened by un-targeted metabolism analysis.ResultsTen gene families involved in the maize anthocyanin biosynthesis pathway were identified, and 142 synthetic genes were obtained. These anthocyanin biosynthetic genes have high copy numbers and are normally clustered on chromosomes. The promoters of these synthetic genes contain various cis-elements and the gene expression patterns and transcriptional regulatory networks were analyzed. These genes are distributed on different chromosomes and gene expression patterns vary across different tissues in maize. Specifically, these genes often exhibit higher expression in the stem, leaves, and seeds. Ten highly expressed genes in silks were identified. Based on un-targeted metabolites detection in the silks of four maize representative inbred lines with different colors, two main differential anthocyanin components were identified. Furthermore, the gene expression patterns of the ten highly expressed genes and their potential interacting transcriptional factors were analyzed across the four inbred lines.ConclusionsThe results in this study show a through picture of maize anthocyanin synthetic genes, and the structure and function of genes related to anthocyanin biosynthesis in maize could be further investigated.

Project description:BackgroundLong intergenic noncoding RNAs (lincRNAs) are endogenous non-coding RNAs (ncRNAs) that are transcribed from 'intergenic' regions of the genome and may play critical roles in regulating gene expression through multiple RNA-mediated mechanisms. MicroRNAs (miRNAs) are single-stranded small ncRNAs of approximately 21-24 nucleotide (nt) that are involved in transcriptional and post-transcriptional gene regulation. While miRNAs functioning as mRNA repressors have been studied in detail, the influence of miRNAs on lincRNAs has seldom been investigated in plants.MethodsLincRNAs as miRNA targets or decoys were predicted via GSTAr.pl script with a set of rules, and lincRNAs as miRNA targets were validated by degradome data. Conservation analysis of lincRNAs as miRNA targets or decoys were conducted using BLASTN and MAFFT. The function of lincRNAs as miRNA targets were predicted via a lincRNA-mRNA co-expression network, and the function of lincRNAs as miRNA decoys were predicted according to the competing endogenous RNA (ceRNA) hypothesis.ResultsIn this work, we developed a computational method and systematically predicted 466 lincRNAs as 165 miRNA targets and 86 lincRNAs as 58 miRNA decoys in maize (Zea mays L.). Furthermore, 34 lincRNAs predicted as 33 miRNA targets were validated based on degradome data. We found that lincRNAs acting as miRNA targets or decoys are a common phenomenon, which indicates that the regulated networks of miRNAs also involve lincRNAs. To elucidate the function of lincRNAs, we reconstructed a miRNA-regulated network involving 78 miRNAs, 117 lincRNAs and 8834 mRNAs. Based on the lincRNA-mRNA co-expression network and the competing endogenous RNA hypothesis, we predicted that 34 lincRNAs that function as miRNA targets and 86 lincRNAs that function as miRNA decoys participate in cellular and metabolic processes, and play role in catalytic activity and molecular binding functions.ConclusionsThis work provides a comprehensive view of miRNA-regulated networks and indicates that lincRNAs can participate in a layer of regulatory interactions as miRNA targets or decoys in plants, which will enable in-depth functional analysis of lincRNAs.

Dataset Information

Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize.

Publications

Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize.

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