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Rehman, Hafiz Mamoon,Nawaz, Muhammad Amjad,Shah, Zahid Hussain,Yang, Seung Hwan,Chung, Gyuhwa Elsevier 2018 Plant science Vol.267 No.-
<P><B>Abstract</B></P> <P>Triterpenoid saponins are one of the most highly accumulated groups of functional components in soybean (<I>Glycine max</I>) and the oxidative reactions during their biosynthesis are required for their aglycone diversity. Natural mutants of soyasaponins in wild soybean (<I>Glycine soja</I>) are valuable resources for establishing the soyasaponin biosynthesis pathway and breeding new soybean varieties. In this study, we investigated the genetic mechanism behind the absence of group A saponins in a Korean wild soybean mutant, CWS5095. Whole genome sequencing (WGS) of CWS5095 identified four point mutations [Val6 → Asp, Ile231 → Thr, His294 → Gln, and Arg376 → Lys] in <I>CYP72A69</I> (<I>Glyma15g39090</I>), which oxygenate the C-21 position of soyasapogenol B or other intermediates to produce soyasapogenol A, leading to group A saponin production. An <I>in vitro</I> enzyme activity assay of single-sited mutated clones indicated that the Arg376 > Lys mutation (a highly conserved mutation based on a nucleotide change from G → A at the 1,127th position) may lead to loss of gene function in the <I>sg-5</I> mutant. A very high normalized expression value of 377 reads per kilo base per million (RPKM) of <I>Glyma15g39090</I> in the hypocotyl axis at the early maturation seed-development stage confirmed their abundant presence in seed hypocotyls. A molecular dynamics analysis of the Arg376 > Lys mutation based on the <I>CYP3A4</I> (a human CYP450) protein structure found that it was responsible for the increase in axis length toward the heme (active site), which is critically important for biological activity and ligand binding. Our results provide important information on how to eradicate bitter and astringent saponins in soybean by utilizing the reported mutation in <I>Glyma15g39090</I>, and its importance for seed hypocotyl development based on transcript abundance.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The reported <I>sg</I>-5 mutant provides a unique genetic resource to eradicate group A saponins, which are bitter and astringent in taste. </LI> <LI> <I>CYP72A69</I> gene, oxygenate the C-21 position of soyasapogenol B to produce soyasapogenol A. </LI> <LI> Arg376 > Lys mutation in a <I>CYP72A69</I> gene in soybean may lead to loss of gene function in the <I>sg</I>-5 mutant. </LI> <LI> Arg376 > Lys mutation based on the <I>CYP3A4</I> (a human CYP450) protein structure change the axis length toward the heme (active site). </LI> </UL> </P>
Mamoon Rehman, H.,Amjad Nawaz, M.,Bao, L.,Hussain Shah, Z.,Lee, J.M.,Ahmad, M.Q.,Chung, G.,Yang, S.H. G. Fischer 2016 Journal of plant physiology Vol.206 No.-
<P>Family-1 UDP-glycosyltransferases (EC 2.4.1.x; UGTs) are enzymes that glycosylate aglycones into glycoside-associated compounds with improved transport and water solubility. This glycosylation mechanism is vital to plant functions, such as regulation of hormonal homeostasis, growth and development, xenobiotic detoxification, stress response, and biosynthesis of secondary metabolites. Here, we report a genome-wide analysis of soybean that identified 149 putative UGTs based on 44 conserved plant secondary product glycosyl-transferase (PSPG) motif amino acid sequences. Phylogenetic analysis against 22 referenced UGTs from Arabidopsis and maize clustered the putative UGTs into 15 major groups (A-O); J, K, and N were not represented, but the UGTs were distributed across all chromosomes except chromosome 04. Leucine was the most abundant amino acid across all 149 UGT peptide sequences. Two conserved introns (C-1 and C-2) were detected in the most intron-containing UGTs. Publicly available microarray data on their maximum expression in the seed developmental stage were further confirmed using Affymetrix soybean IVT array and RNA sequencing data. The UGT expression models were designed, based on reads per kilobase of gene model per million mapped read (RPKM) values confirmed their maximally varied expression at globular and early maturation stages of seed development. (C) 2016 Elsevier GmbH. All rights reserved.</P>
Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean
Nawaz, Muhammad Amjad,Rehman, Hafiz Mamoon,Baloch, Faheem Shehzad,Ijaz, Babar,Ali, Muhammad Amjad,Khan, Iqrar Ahmad,Lee, Jeong Dong,Chung, Gyuhwa,Yang, Seung Hwan G. Fischer 2017 Journal of plant physiology Vol. No.
<P><B>Abstract</B></P> <P>The plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference <I>Arabidopsis</I> CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18). Soybean CS expansion occurred in 66 duplication events. Additionally, we identified 95 simple sequence repeat makers related to 44 CSs. We next performed digital expression analysis using publically available datasets to understand potential CS functions in soybean. We found that CSs were highly expressed during soybean seed development, a pattern confirmed with an Affymatrix soybean IVT array and validated with RNA-seq profiles. Within CS groups, CESAs had higher relative expression than CSLs. Soybean CS models were designed based on maximum average RPKM values. Gene co-expression networks were developed to explore which CSs could work together in soybean. Finally, RT-PCR analysis confirmed the expression of 15 selected CSs during all four seed developmental stages.</P>
Nawaz, Muhammad Amjad,Yang, Seung Hwan,Rehman, Hafiz Mamoon,Baloch, Faheem Shehzad,Lee, Jeong Dong,Park, Jong Hyun,Chung, Gyuhwa Elsevier 2017 Biochemical systematics and ecology Vol.71 No.-
<P><B>Abstract</B></P> <P>Korea is considered one of the centers of genetic diversity for cultivated as well as wild soybeans. Natural habitats of wild soybeans are distributed across the Korean mainland and the islands surrounding the Korean peninsula. In this study, the genetic diversity of 100 mainland Korean wild soybean accessions was evaluated by using 42 simple sequence repeat markers covering 17 soybean chromosomes. All analyzed loci were polymorphic and a total of 114 alleles were found. The observed average genetic diversity was low (0.4). The results showed that the 100 selected accessions did not exactly follow the geographical distribution. These results were further confirmed by the phylogeny inferred from five morphological characteristics (i.e., leaf shape, leaf area, plant shape, seed area, and 100-seed weight). Together, the genetic and morphological evaluations suggested conclusively that the selected population did not follow the geographical distribution pattern. The present study could provide useful information for the <I>ex situ</I> conservation and exploitation of wild soybean accessions in soybean improvement stratagems, and will aid in further understanding about the phylogeography of the species in the Korean center of diversity.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Microsatellite analysis and morphological characterization of Korean wild soybean was done. </LI> <LI> Korean mainland wild soybeans have low genetic diversity. </LI> <LI> Selected populations do not follow geographical distribution pattern. </LI> </UL> </P>
정규화,Bao Le,Muhammad Amjad Nawaz,Hafiz Mamoon Rehman,Thu Le,양승환,Kirill S. Golokhvast,손은호 한국유전학회 2016 Genes & Genomics Vol.38 No.12
Auxin response factors (ARFs) encode one of the most abundant groups of auxin-mediated response transcription factors in higher plants and play a major role in various biological processes. The success of whole genome sequencing allows for comprehensive phylogenetic analysis of ARF genes in plants. Here, we identified 80 ARF genes belonging to five different groups in legume species, soybean (Glycine max, 55) and common bean (Phaseolus vulgaris, 25), based on phylogenetic analysis and supported by motif analysis. There is no member ARF of common bean in group V which contained two members from soybean, GmARF12 and GmARF55. The duplication events among two species were also observed by using Ks values. A majority of the ARF genes (96.1 %; 38 GmARFs and 56.0 %, 14 PvARFs) were segmentally duplicated while only two and one of ARF G. max and P. vulgaris genes were tandemly duplicated, respectively. In addition, expression profiling indicated that ARF genes in soybean and common bean perform various functions in plant growth and development, excluding flowering development. Furthermore, diversity of cis-elements in promoter regions also revealed differential expression of ARF proteins.
Molecular Elucidation of Two Novel Seed Specific Flavonoid Glycosyltransferases in Soybean
Gyuhwa Chung;Seung Hwan Yang,Hafiz Mamoon Rehman,Muhammad Amjad Nawaz,Zahid Hussain Shah 한국식물학회 2018 Journal of Plant Biology Vol.61 No.5
Flavonoids are specialized plant secondarymetabolites that are mainly present as glycoconjugates andfunction as attractants to pollinators and symbionts, UVprotectants, allelochemicals, and have antimicrobial andantiherbivore activity for plant health. Because of theheterogeneity of UDP-glycosyltransferases (UGTs) forglycosylation in plants, their function in flavonoid glycosylationremains largely unknown in soybean and other legumes,particularly that of the UGT92 genes. Here, we identified 152putative UGT92 genes across 48 plant species and elucidatedtheir mode of duplication, expansion/deletion pattern,alignment, phylogenetic analysis, and genome-wide distribution. Two novel UGT-encoding genes Glyma14g04790 (UGT92G1)and Glyma15g03670 (UGT92G2) were isolated fromsoybean and their heterologous expression was optimized inEscherichia. coli. Both genes exhibited catalytic activitytoward quercetin, kaempferol, and myricetin, with UDPglucoseas the sugar donor and were characterized asflavanol-specific UGTs. High expression of both UGTswas observed in adaxial and abaxial parenchyma, suspensorcells, and adaxial and abaxial epidermis cells during seeddevelopment, suggesting that they are seed-specific flavanolglycosyltransferases in soybean. Co-expression analysis ofUGT92 genes with their first and second neighborhood genesprovided a basis for their network elucidation in soybean. Weprovide valuable information on the role of UGT92 in seeddevelopment via the glycosylation of multiple flavanols andthe potential metabolic engineering of flavonoid compoundsin both plants and E. coli.