Biotechnology

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Browsing Biotechnology by Author "Abiy Zegeye"

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    Comparative in Silico Study of Lodging-Resistant Genes of Tef (Eragrostis Tef (Zucc.) Trotter) Against Wheat, Barley and Rice
    (Addis Ababa University, 2024-07) Tigist Shewafera; Abiy Zegeye
    Tef (Eragrostis tef), a cereal crop indigenous to Ethiopia, is essential in ensuring food and nutrition security. It is well-known for its gluten-free properties, rendering it suitable for individuals with celiac disease. However, tef is highly susceptible to lodging that negatively impacts its productivity. Efforts to develop varieties that are lodging-resistant have had limited success; particularly, because there have been a dearth of targeted genetic interventions. The aim of this study is to computationally predict and characterize six lodging-resistant genes (Rht1, BRI1, COMT1, CAD8C, CESA1 and CESA4) and the corresponding polypeptides of tef vis-à-vis three economically important cereal crops. The study began by selecting three economically important crops, namely: wheat, barley and rice and their six lodging-resistant genes. Using in silico probes, six homologous candidate lodging-resistant genes were retrieved from tef subgenomes. The candidate tef lodging-resistant nucleotide sequences were analyzed to computationally predict their gene structures and then comparatively analyzed against their homologues in the selected three crops. Putative polypeptide sequences of the six lodging-resistant genes, derived from their obtained predicted tef genes, were subjected to further amino acid level analysis to identify variations unique to tef, map the variations to specific functional or structural domains, predict the potential effects of the said variations and examine the possible impact of significant variations on the 3 dimensional structure of the proteins. Multiple sequence alignment of polypeptide sequences revealed distinct amino acid differences unique to tef in key functional and structural domains encoded by these lodging-resistant genes, with potential implications for tef's lodging susceptibility attributes. Variant effect predictions of counterfactual amino acid variations point to a subset of the unique tef variations having significant likelihood of causing damage in four of the six proteins: Rht1, BRI1, COMT1 and CESA1. Further examination of significant variation effects on the 3D structures of the four proteins revealed possible effects on the secondary structure of the polypeptides. Overall, the findings provide insights into several of tef's genetic variations related to lodging resistance features. Further experimental validation studies are needed to confirm these findings and elucidate the precise roles of these genes in tef's lodging susceptibility.
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    Deciphering the Conserved Cis-Regulatory Elements of Major Milk Protein Genes by Computational Analysis
    (Addis Ababa University, 2024-04) Addis Tekaw; Abiy Zegeye
    Milk genes are exclusively expressed in MECs during lactation, regulated by lactogenic hormones like prolactin that act through specific TFs. The recruitment of TF is determined by cis-regulatory motifs in their gene promoters; but there is limited evidence of shared motifs among the major milk gene across species. In this study, Jalview, Meme-Suite, TomTom, and GOMo software were utilized to construct phylogenetic trees, discover motifs, identify TFs, and determine GO terms, respectively, in the 2kb upstream putative promoter region of CSN1S1, CSN1S2, CSN2, CSN3, LALBA and BLG milk genes among twenty-three mammalian species. The analysis revealed three common TFBSs for STAT1, STAT5a, and STAT5b TFs in all milk genes across the species studied, except for BLG, within the region -390 to -80bp from the canonical TSS, with a few shared TFBSs located in the distal promoter region upstream of -600bp. STAT3 was also detected in CSN1S1, CSN2, CSN3, and LALBA genes, sharing binding sites with STAT1, STAT5a, and STAT5b. Furthermore, TFBSs for Sox9 and Sox6 TFs were found to be shared between the LALBA and BLG putative promoters within -400 to -100bp. Moreover, GO analysis linked GPCR with regulatory motifs in all six milk genes across 23 species, essential for enhancing STAT5 phosphorylation through Gαq activation in the JAK-STAT pathway. The totality of the result suggests that the relative abundance of STAT5 and STAT3 proteins may play a role in regulating the expression level of caseins and LALBA commensurate with the stage of lactation. Together, these results offer valuable insights into the potential of the milk genes’ promoter for constructing eukaryotic expression vectors and provide essential information for transgenic studies.