scholarly journals Analisis Single Nucleotide Polymorphism Gen Faktor Transkripsi MYB dalam Biosintesis Antosianin Kulit Buah Mangga (Analysis of Single Nucleotide Polymorphism Gene Transcription Factor MYB in Mango Skin Anthocyanin Biosynthesis)

2021 ◽  
Vol 31 (1) ◽  
pp. 1
Author(s):  
Findy Ashgi ◽  
Adi Pancoro

<p>Perkembangan pasar bebas berdampak terhadap selera produk-produk pertanian, seperti warna buah mangga. Antosianin merupakan senyawa yang bertanggung jawab dalam menginduksi warna pada buah. Senyawa ini diregulasi oleh gen faktor transkripsi MYB. Mutasi Single Nucleotide Polymorphism (SNP) daerah ekson gen MYB dapat mengubah asam amino yang memengaruhi aktivitas enzim yang mengakibatkan munculnya variasi fenotipe warna buah di antara individu-individu dalam spesies yang sama. Penelitian ini bertujuan menemukan SNP pada gen MYB dari kulit buah mangga varietas Arum Manis, Gedong Gincu, Manalagi, Golek, dan Cengkir. Penelitian dilakukan dengan tiga tahap utama, yaitu isolasi DNA kulit buah mangga, Polymerase Chain Reaction (PCR), dan proses sekuensing oleh Macrogen Inc. (Singapore). Hasil multiple sequence alignment asam amino gen faktor transkripsi MYB menunjukkan adanya perbedaan basa yang mengakibatkan munculnya stop codon dari SNP 337 A→T dan SNP 338 A→G yang memengaruhi fenotipe warna kulit buah. SNP yang memunculkan stop codon dapat direkomendasikan untuk membedakan fenotipe pigmentasi antosianin pada kulit buah mangga Gedong Gincu yang bewarna merah dengan warna kulit buah mangga yang lainnya. Adanya SNP menyebabkan prematur stop codon yang terjadi pada gen faktor transkripsi MYB dan diduga berpengaruh terhadap pigmentasi antosianin.</p><p><strong>Keywords</strong></p><p>Mangga; SNP; Faktor transkripsi; Antosianin; MYB</p><p><strong>Abstract </strong></p><p>The development of free markets gives an impact on appetite for agricultural products, such as the color of mangoes fruit skin. Anthocyanins are compounds that are responsible for giving color to the fruit skin, these compounds are regulated by the MYB transcription factor genes. Single Nucleotide Polymorphism (SNP) mutations in the exon region of the MYB gene can change amino acids that affect enzyme activity, resulting in phenotypic variations in fruit color among individuals in the same species. This study aims to find SNP in MYB genes from mango peel varieties Arum Manis, Gedong Gincu, Manalagi, Golek, and Cengkir. The research was conducted in three main stages, namely isolation of mango peel DNA, Polymerase Chain Reaction (PCR), and sequencing process by Macrogen Inc (Singapore). The results of multiple sequence alignment of the amino acid MYB transcription factor genes showed a base difference which resulted in the appearance of a stop codon from SNP 337 A→T and SNP 338 A→G which affected the phenotype of fruit skin color. The SNP that raises the stop codon can be recommended to differentiate the anthocyanin pigmentation phenotype on the red skin of the mango Gedong Gincu from the skin color of other mangoes. The presence of SNP causes premature stop codon that occurs in the MYB transcription factor gene and is thought to have an effect on anthocyanin pigmentation.</p><p> </p>

2021 ◽  
Author(s):  
Junping Yu ◽  
Guolong Zhao ◽  
Wei Li ◽  
Ying Zhang ◽  
Peng Wang ◽  
...  

Abstract Soybean [Glycine max (L.) Merr.] is an important crop providing vegetable oils and proteins. Increasing demand on soy products heightens the urgency of soybean yield improvement. Hybrid breeding with male sterility system is an effective method to improve crop production. Cloning of genic male sterile (GMS) gene combined with biotechnology method can contribute to constructing GMS-based hybrid Seed Production Technology (SPT) to promote soybean performance and yield. In this research, we identified a soybean GMS locus, GmMS6, by combining bulked segregant analysis (BSA)-sequencing and map-based cloning technology. GmMS6 encodes an R2R3 MYB transcription factor, whose mutant allele in ms6 (Ames1) harbors a single nucleotide polymorphism (SNP) substitution, leading to the 76th Leucine to Histidine change in the DNA binding domain. Phylogenetic analysis demonstrates GmMS6 is a homolog of Tapetal Development and Function 1 (TDF1)/MYB35 that is an anther development key factor co-evolved with angiosperm. It has a recently duplicated homolog GmMS6LIKE (GmMS6L), both of which can rescue the male fertility of Arabidopsis homologous mutant attdf1 while GmMS6L76H cannot, denoting that both proteins are functional and L76 is a critical residue for TDF1’s function. However, compared to anther specific expressed GmMS6, GmMS6L is constitutively expressed at a very low level, explaining deficiency of GmMS6 alone causes pollen abortion. Moreover, the expression levels of major regulatory and structural genes for anther development are significantly decreased in ms6, unveiling that GmMS6 is a core transcription factor regulating soybean anther development.


PLoS Genetics ◽  
2015 ◽  
Vol 11 (4) ◽  
pp. e1005152 ◽  
Author(s):  
Diana M. Calderón-Noreña ◽  
Alberto González-Novo ◽  
Sara Orellana-Muñoz ◽  
Pilar Gutiérrez-Escribano ◽  
Yolanda Arnáiz-Pita ◽  
...  

2010 ◽  
Vol 76 (9) ◽  
pp. 2783-2790 ◽  
Author(s):  
A. Van Stelten ◽  
J. M. Simpson ◽  
T. J. Ward ◽  
K. K. Nightingale

ABSTRACT Listeria monocytogenes utilizes internalin A (InlA; encoded by inlA) to cross the intestinal barrier to establish a systemic infection. Multiple naturally occurring mutations leading to a premature stop codon (PMSC) in inlA have been reported worldwide, and these mutations are causally associated with attenuated virulence. Five inlA PMSC mutations recently discovered among isolates from France and the United States were included as additional markers in our previously described inlA single-nucleotide polymorphism (SNP) genotyping assay. This assay was used to screen >1,000 L. monocytogenes isolates from ready-to-eat (RTE) foods (n = 502) and human listeriosis cases (n = 507) for 18 inlA PMSC mutations. A significantly (P < 0.0001) greater proportion of RTE food isolates (45.0%) carried a PMSC mutation in inlA compared to human clinical isolates (5.1%). The proportion of L. monocytogenes with or without PMSC mutations in inlA was similar among isolates from different RTE food categories except for deli meats, which included a marginally higher proportion (P = 0.12) of isolates carrying a PMSC in inlA. We also analyzed the distribution of epidemic clone (EC) strains, which have been linked to the majority of listeriosis outbreaks worldwide and are overrepresented among sporadic cases in the United States. We observed a significant (P < 0.05) overrepresentation of EC strains in deli and seafood salads and a significant (P < 0.05) underrepresentation of EC strains in smoked seafood. These results provide important data to predict the human health risk of exposure to L. monocytogenes strains that differ in pathogenic potential through consumption of contaminated RTE foods.


2020 ◽  
Author(s):  
A M U B Mahfuz ◽  
Md. Arif Khan

ABSTRACTT-box transcription factor 5 (TBX5) gene encodes the transcription factor TBX5 which plays a crucial role in the development of the heart and upper limbs. Alternative splicing resulting in several isoforms regulate the functions of this gene during the developmental process. Damaging single nucleotide variants in this gene alter the structure and disturb the functions of TBX5 and ultimately cause Holt-Oram Syndrome (HOS), an autosomal dominant disease where various congenital malformations of the heart (with or without conduction defects), upper limbs and shoulder girdles are observed. Besides HOS, TBX5 single nucleotide variants can also be associated with Dilated Cardiomyopathy, Atrial Fibrillation, and Tetralogy of Fallot without skeletal deformity.By exploiting available Single Nucleotide Polymorphism information in dbSNP, this study was designed to identify in silico the deleterious TBX5 SNPs, and predict their structural and functional consequences, and alteration of biochemical properties on the candidate protein. For this purpose, various reliable in silico analysis tools such as PROVEAN, SIFT, PolyPhen-2, MutPred2, PredictSNP1, PredictSNP2, MetaLR, MetaSVM, REVEL, ConSurf, NetsurfP-2.0, iStable 2.0, Missense3D, UTRdb, MirSNP, and Human Splicing Finder (HSF) have been used. 58 missense substitutions were found damaging by both sequence homology-based tools SIFT (Sorting Intolerant from Tolerant) and PROVEAN (Protein Variation Effect Analyzer), and structure homology-based tool PolyPhen-2 (Polymorphism Phenotyping-2). Among these 58 substitutions, 13 are already annotated as Pathogenic/Likely Pathogenic in ClinVar database, and so they were excluded. Then, the rest 45 high confidence substitutions were further scrutinized by various disease association predicting meta servers. Next, conservation profile of the native amino acid residues, their surface & solvent accessibility, and stability and structural integrity of the protein upon mutation were assessed. Analysis of 1 stop loss SNP, and 2 nonsense SNPs were done by PredictSNP2. Analysis of SNPs in the UTR region were done using UTRdb and MirSNP, and splice site SNPs were evaluated by Human Splicing Finder (HSF). This study provides a comprehensive list of most deleterious SNPs onTBX5 gene. The results from this study can help in early diagnosis of HOS and in relevant genetic counseling.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2250-2250
Author(s):  
Anurag Saxena ◽  
Keith Bonham ◽  
Evan Neuls ◽  
Oksana Moshynska

Abstract Lower expression of Bax protein in various human malignancies is associated with poor response to treatment and shorter disease-free survival. We (Cancer Lett2002; 187:199–205) and others (J Clin Oncol; 23:1514–21) have shown the association of a single nucleotide polymorphism (SNP) in the BAX promoter (G125A) with reduced protein expression and treatment resistance in chronic lymphocytic leukemia (CLL). Using luciferase reporter gene assay we demonstrated that this SNP significantly reduced BAX promoter activity (Oncogene2005; 24:2042–9). Our aim was to determine the effect of this polymorphism on the binding of transcription factors. For electrophoretic mobility shift (EMSA), HeLa and K562 nuclear extracts, and for chromatin immunoprecipitation (ChIP), K562 cells were used to study their ability to bind to a radiolabeled DNA probe corresponding to the BAX promoter region with G nucleotide at the position 125 or bearing G125A SNP. Super-shift assay was performed to determine the transcription factor involved in binding. Competition assays were performed to determine differences in the binding ability of the two probes. A panel of antibodies was tested by super-shift and ChIP assays, non-specific antibodies served as negative controls. Two major band shifts were detected by EMSA. The mobility of the detected complexes was different from those observed with GC1 probe, specific for Sp1/Sp3, suggesting the involvement of transcription factors other than Sp1/ Sp3. This was confirmed in super-shift assay and ChIP assay by incubating DNA probes with Sp1 or/ and Sp3 antibodies. We also found in the competition assays that the cold probes competed differently for binding. The findings provide evidence of the ability of G125A SNP to influence transcription factor binding in vitro (as shown in EMSA experiments) and in vivo (in ChIP experiments).


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