The relationship between codon usage bias and salt resistant genes in Arabidopsis thaliana and Oryza sativa

Barozai, Muhammad Younas Khan

doi:10.19045/bspab.2012.12005

Cited by 15 publications

(8 citation statements)

References 22 publications

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“…In the light of the empirical formula for biogenesis and expression of the miRNAs suggested by Ambros et al [29], these miRNAs are considered as a valid candidate after justifying the criteria B, C and D. According to Ambros et al [29] only the criterion D is enough for homologous sequences to validate as potential miRNAs in other species. The present study is in agreement with the other research groups [21,[33][34][35][36] where similarity based search by applying comparative genomics has produced novel and interesting findings in plants genomics.…”

Section: The New Cowpea Mirnassupporting

confidence: 93%

In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.)

2017

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Cowpea ( Vigna unguiculata L.) is an important leguminous plant and a good diet due to presence of carbohydrate and high protein contents. Currently, only few cowpea microRNAs (miRNAs) are reported. This study is intended to identify and functionally analyze new miRNAs and their targets in cowpea. An in-silico based homology search approach was applied and a total of 46 new miRNAs belonging to 45 families were identified and functionally annotated from the cowpea expressed sequence tags (ESTs). All these potential miRNAs are reported here for the first time in cowpea. The 46 new miRNAs were also observed with stable hairpin structures with minimum free energy, ranging from −10 to −132 kcal mol −1 with an average of −40 kcal mol −1 . The length of new cowpea miRNAs are ranged from 18 to 26 nt with an average of 21 nt. The cowpea miRNA-vun-mir4414, is found as pre-miRNA cluster for the first time in cowpea. Furthermore, a set of 138 protein targets were also identified for these newly identified 46 cowpea miRNAs. These targets have significant role in various biological processes, like metabolism, transcription regulation as transcription factor, cell transport, signal transduction, growth & development and structural proteins. These findings are the significant basis to utilize and manage this important leguminous plant-cowpea for better nutritional properties and tolerance for biotic and abiotic stresses.

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Section: The New Cowpea Mirnassupporting

confidence: 93%

In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.)

2017

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“…Highly expressed genes have a much stronger codon usage bias and are encoded by optimal codons corresponding to abundant tRNAs, for more rapid and efficient translation. [12,52]. Codon bias is significantly correlated to gene expression, but independent of base composition.…”

Section: Degree Of Gene Expressionmentioning

confidence: 99%

“…In Arabidopsis, genes encoding abundant protein in vegetal cells such as photosynthetic and housekeeping genes had a highly G/C biased codon usage and genes with strong tissue-specific expression had a weaker A/Tbiased codon usage when compared to stress-regulated genes [59]. A unimodal correlation existed between the codon usage bias (CUB) and salt stress-resistant genes among plant species [52]. Tissue-specific genes exhibit significantly different synonymous codon usage in rice, due to GC content variation among tissues, although this effect is weak [8].…”

Section: Pattern Of Gene Expressionmentioning

confidence: 99%

Codon usage bias

2021

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Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism. Codon usage bias has evolved through mutation, natural selection, and genetic drift in various organisms. Genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions are some factors influencing codon bias. The factors shaping codon bias may also be involved in evolution of the universal genetic code. Codon-usage bias is critical factor determining gene expression and cellular function by influencing diverse processes such as RNA processing, protein translation and protein folding. Codon usage bias reflects the origin, mutation patterns and evolution of the species or genes. Investigations of codon bias patterns in genomes can reveal phylogenetic relationships between organisms, horizontal gene transfers, molecular evolution of genes and identify selective forces that drive their evolution. Most important application of codon bias analysis is in the design of transgenes, to increase gene expression levels through codon optimization, for development of transgenic crops. The review gives an overview of deviations of genetic code, factors influencing codon usage or bias, codon usage bias of nuclear and organellar genes, computational methods to determine codon usage and the significance as well as applications of codon usage analysis in biological research, with emphasis on plants.

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“…In addition, 98 of the novel miRNAs were involved in targeting transcription factors, such as MYB transcription factor, BZIP transcription factor bZIP21, homeoboxleucine zipper protein, translation initiation factor 6-2, transcription factor BIM2, heat stress transcription factor HSFA9, and homeobox protein Nkx-6.1, which are targeted by stu-miR5254, stu-miR1450, stu-miR1879, stu-miR2673, and stu-miR5819, respectively. This class of protein has been considered as a miRNA target in various studies in different plant species (Zeng et al, 2009;Frazier et al, 2010;Xie et al, 2010;Barozai et al, 2012).…”

Section: Targeted Genes Of New Potato Mirnasmentioning

confidence: 99%

Identification and functional analysis of new conserved microRNAs and their targets in potato (Solanum tuberosum L.)

Din¹,

Barozai²,

Baloch³

2014

Turk J Bot

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Introduction Potato (Solanum tuberosum) belongs to the family Solanaceae and is an important agricultural crop. It is the world's fourth largest food crop, following rice, wheat, and maize. Distributed worldwide with about 5000 varieties, the potato has its center of origin in the high Andes of South America. It is best known for its carbohydrate content in the form of starch, though it also contains important vitamins and minerals (Abbas et al., 2012). It plays a viable role in the worldwide sustainable food system, producing more food energy on less land with low cost of cultivation. It is the most important tuber crop in terms of production, accounting for about 45% of total world tuber crop production (Shewry, 2003) and parental marker studies in anther-derived progeny (Aziz, 2014a, 2014b). MicroRNAs (miRNAs) are single-stranded RNAs that are noncoding, endogenous, and 18 to 26 nt in length (Bartel, 2004). The intergenic genes of miRNAs are generated from endogenous stem-loop primary transcripts known as precursor miRNAs (pre-miRNAs) through actions of Dicer-like 1 (DCL1), an RNAse III enzyme. DCL1, along with other proteins, generates a mature miRNA from the cleavage of stem-looped pre-miRNA (Ambros, 2003). Mature miRNA further associates with argonaute proteins to develop an RNA-induced silencing complex (RISC). The RISC then functions as a guide molecule in the negative posttranscriptional gene, silencing through 2-way base pairing with target mRNAs. The base pairings are perfect or near perfect and lead to mRNA cleavage or translational repression, respectively. miRNAs are one of the largest gene families, accounting for approximately 1% of the genome (Bartel, 2004). Many recent studies have shown that miRNAs have vital roles in diverse regulatory pathways in plants and animals (Baloch and Din, 2014; Din and Barozai, 2014a). In plants, miRNAs regulate tissue differentiation and development, including leaf, root, stem, and flower tissues. They also regulate developmental timing from the vegetative to reproductive stages, as well as signal transduction and response to biotic and abiotic stresses, such as salinity, drought, cold, heat, and pathogens (Zhang et al., 2006; Baloch et al., 2013; Song et al., 2013). The miRNAs and their targets interact through complex regulatory networks. A single miRNA can bind to regulate several distinct mRNA targets and, conversely, Abstract: MicroRNAs (miRNAs) are tiny, endogenous, nonprotein-coding, and functionally negative regulators of posttranscriptional gene regulation. Potato (Solanum tuberosum L.) is a starchy and tuberous crop that is also important for its potassium and vitamin contents. Though potato is the world's fourth largest food crop, its miRNAs and their targets have not been well studied. Here we report a comparative genomics approach that was applied to explore miRNAs and their targeted proteins in potato. A total of 120 new miRNAs from 110 families were identified and characterized from the expressed sequence tags. All 120 miRNAs were observed, along wit...

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The relationship between codon usage bias and salt resistant genes in Arabidopsis thaliana and Oryza sativa

Cited by 15 publications

References 22 publications

In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.)

In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.)

Codon usage bias

Identification and functional analysis of new conserved microRNAs and their targets in potato (Solanum tuberosum L.)

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