Molecular Characterization of Legionellosis Drug Target Candidate Enzyme Phosphoglucosamine Mutase from Legionella pneumophila (strain Paris): An In Silico Approach

Md. Anayet Hasan,Md. Habibul Hasan Mazumder,Md. Arif Khan,Mohammad Uzzal Hossain,A. S. M. Homaun Kabir Chowdhury 한국유전체학회 2014 Genomics & informatics Vol.12 No.4

The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire’s disease. The increasingdevelopment of drug resistance against legionellosis has led to explore new novel drug targets. It has been found thatphosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the mostprobable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugarand nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this,the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means ofhomology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structurevalidation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondarystructural features were determined through self-optimized prediction method with alignment (SOPMA) and interactingnetworks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showedthat 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in thegenerously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 forERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorablebinding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensiveinvestigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.

Molecular Characterization of Legionellosis Drug Target Candidate Enzyme Phosphoglucosamine Mutase from Legionella pneumophila (strain Paris): An In Silico Approach

Hasan, Md. Anayet,Mazumder, Md. Habibul Hasan,Khan, Md. Arif,Hossain, Mohammad Uzzal,Chowdhury, A.S.M. Homaun Kabir Korea Genome Organization 2014 Genomics & informatics Vol.12 No.4

The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire's disease. The increasing development of drug resistance against legionellosis has led to explore new novel drug targets. It has been found that phosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the most probable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugar and nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this, the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means of homology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structure validation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondary structural features were determined through self-optimized prediction method with alignment (SOPMA) and interacting networks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showed that 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in the generously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 for ERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorable binding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensive investigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.

Anther Culture in Crop Plants: Progress and Perspectives

M. Thoihidul Islam(M. Thoihidul Islam ),Mohammad Rashid Arif(Mohammad Rashid Arif ),Md. Toufiq Hasan(Md. Toufiq Hasan ),Arif Hasan Khan Robin(Arif Hasan Khan Robin ) 한국육종학회 2023 Plant Breeding and Biotechnology Vol.11 No.2

A resurrection has started in haploid and double haploid research in the twenty-first century. The haploid and double haploid could be achieved through in vivo and in vitro anther and microspore culture techniques. Fixing the homozygosity is the most striking benefit of androgenesis. Various factors like genotypic dependency, growth condition, developmental stage of the microspore, pre-treatment, culture media, regeneration media, growth hormones, and various chemicals have a direct effect. Wheat, rice, Brassica, and tobacco are the notable crops where anther and microspore culture has been utilized. These haploidy and double haploidy through anther culture served many purposes of basic and applied research. Especially, double haploid cultivars have been cultivating around the globe. In addition, for chromosome mapping, QTL mapping, marker-assisted selection, marker-assisted backcrossing, mutation breeding, genome-wide association study, genomic engineering, and genome editing, androgenesis based haploid and double haploid plants have been exploited due to the effectiveness. Recently, researchers are trying to explain albinism that happens during anther culture from an epigenetic perspective. Further prospects of haploid and doubled haploid research through anther culture have been described in this review.

Trait Association, Genetic Analyses and Fatty Acid Profiles in Oilseed Producing Rapeseed-Mustard (Brassica spp.) Genotypes

Md. Abir Ul Islam,Juthy Abedin Nupur,Arif Hasan Khan Robin 한국육종학회 2020 Plant Breeding and Biotechnology Vol.8 No.4

Short duration oilseed Brassica varieties are important to increase cropping intensity as well as total oilseed production. In this research, genetic and multivariate analyses were conducted for 19 morphological characters of 48 rapeseed and mustardgenotypes. Evaluation of oil content and fatty acid profiles were done for ten selected rapeseed and mustard genotypes. Significantgenotypic variations were observed for all morphological characters except 1000 seeds weight. Days to 50% flowering, plant height,total number of siliqua per plant, number of seeds per siliqua, length of siliqua and days to maturity exhibited high broad senseheritability along with high genetic advance. Length of primary branches, number of primary branches, number of secondary branches,total number of siliqua per plant, number of siliqua per main axis and number of siliqua per primary branches had a significant andpositive correlation with yield per plant. According to principal component analysis and cluster analysis—BARI Sharisha-9, BD-110455, BD-7113, BD-6954 and BD-6953 were the earliest genotypes and BD-10112, M-395 and M-119-5 were comparatively highyielding genotypes. The genotypes BD-6953, BD-6954, BD-10455, BD-10112 and BD-7113 had comparatively lower erucic acid andsaturated fatty acid profiles that are regarded as better edible oil characteristics. The selected genotypes and associated traits could beutilized for developing short duration, high yielding and edible quality rapeseed-mustard varieties.

Altered Glucosinolate Profiles and Expression of Glucosinolate Biosynthesis Genes in Ringspot Resistant and Susceptible Cabbage Lines

MD Abuyusuf,Arif Hasan Khan Robin,Hoy-Taek Kim,Md. Rafiqul Islam,Jong-In Park,Ill-Sup Nou 한국원예학회 2018 한국원예학회 학술발표요지 Vol.2018 No.10

Gummy Stem Blight Resistance in Melon: Inheritance Pattern and Development of Molecular Markers

Md Zahid Hassan,Arif Hasan Khan Robin,Md Abdur Rahim,Sathishkumar Natarajan,Hoy-Taek Kim,Jong-In Park,Ill-Sup Nou 한국원예학회 2018 한국원예학회 학술발표요지 Vol.2018 No.10

In silico analysis and expression profifi ling revealed Rlm1¡ blackleg disease-resistant genes in Chromosome 6 of Brassica oleracea

Arif Hasan Khan Robin,Gopal Saha,Jong-In Park,Rawnak Laila,Md Abdur Rahim,Mita Bagchi,Hoy-Taek Kim,Hee-Jeong Jung,Ill-Sup Nou 한국원예학회 2021 Horticulture, Environment, and Biotechnology Vol.62 No.6

Blackleg disease caused by Leptosphaeria maculans aff ects oilseeds and vegetables species of the Brassicaceae family. Several resistant genes have been reported in Brassica species in the A and B genomes, but the resistant locus has yet tobe mapped in the vegetable species B. oleracea . Since both A and C genome Brassica species have high ancestral synteny,it is generally believed that functional resistance against blackleg could be present in B. oleracea . Rlm1 is a major resistantgene present in chromosome A07 of Brassica napus that interacts with the AvrLm1 avirulence gene of L. maculans forhypersensitive interaction. This study identifi ed 15 orthologous Rlm1 ′ genes in the genome of B. oleracea through genomebrowsing. Then, the relative expression of Rlm1 ′ genes was investigated in two resistant lines and two susceptible cabbagelines after the inoculation of two L. maculans isolates, 03–02 s and 00–100 s, bearing avirulence gene AvrLm1 . The selectedRlm1 ′ genes have nucleotide-binding site-toll/interleukin receptor (NBS-TIR), leucine-rich repeat (LRR), coiled-coil (CC),and pathogenesis-related domains in a 7.0-mega-base pair (Mbp) genomic segment of chromosome C06 of B. oleracea . ANBS family gene bearing a TIR domain, Bol040038 , was upregulated in the resistant cabbage line ‘BN4303’ at 6, 24, and48 h after inoculation in both isolates, indicating that this genes might off er resistance against both isolates. Three genes,namely, Bol023847 , Bol040045 , and Bol040066 , showed diff erential expression in both ‘BN4303’ and ‘BN4098’ resistantcabbage lines in response to both isolates. Ten genes were upregulated in both resistant cabbage lines, and two other genes,namely, Bol039924 and Bol040069 , were upregulated only in the resistant line ‘BN4098’ after the infection of the 00–100 sisolate. These results indicated that the putative Rlm1 ′ genes off er isolate-specifi c resistance. However, the mapping andfunctional analysis are required to determine the defi nitive role of the putative Rlm1 ′ genes.

Screening of melon genotypes identifies gummy stem blight resistance associated with Gsb1 resistant loci

Md Zahid Hassan,Arif Hasan Khan Robin,Md Abdur Rahim,Sathishkumar Natarajan,김효택,박종인,노일섭 한국식물생명공학회 2018 JOURNAL OF PLANT BIOTECHNOLOGY Vol.45 No.3

Gummy stem blight (GSB) is one of the most destructive and economically important, soil borne diseases of melon caused by the ascomycete fungus, Didymella bryoniae throughout the world. In Korea, however, no GSB resistant genotype has been reported yet. The study aimed to identify GSB resistant melon germplasm. We screened a total of 60 genotypes including 16 lines and 44 melon cultivars collected from USA and Korea. Among the 16 melon lines, four lines including ‘PI482399’, ‘PI140471’, ‘PI136170’ and ‘PI420145’, and two Korean cultivars viz. ‘Asia Papaya’ and ‘Supra’ showed complete resistance. We were aware that both genotypic and environmental variations could influence the phenotypic screening of resistance and susceptibility. We therefore, further assessed all genotypes using 20 SSR markers. The SSR marker ‘CMCT505’ linked to Gsb1 in chromosome 1 perfectly grouped resistant and susceptible lines indicating that resistance is probably due to the presence of Gsb1 gene. Cloning and sequencing of resistant and susceptible Gsb1 amplicons showed that there were 32-bp deletions in resistant line and 39-bp deletions in resistant cultivar compared to susceptible one. Thus, the resistant melon lines and cultivars identified in this study could be recommended for the melon breeding program. Furthermore, the SSR marker ‘CMCT505’ which is tightly linked with Gsb1 could be used for molecular screening of melon germplasm.

Screening of melon genotypes identifies gummy stem blight resistance associated with Gsb1 resistant loci

Hassan, Md Zahid,Robin, Arif Hasan Khan,Rahim, Md Abdur,Natarajan, Sathishkumar,Kim, Hoy-Taek,Park, Jong-In,Nou, Ill-Sup The Korean Society of Plant Biotechnology 2018 식물생명공학회지 Vol.45 No.3

Gummy stem blight (GSB) is one of the most destructive and economically important, soil borne diseases of melon caused by the ascomycete fungus, Didymella bryoniae throughout the world. In Korea, however, no GSB resistant genotype has been reported yet. The study aimed to identify GSB resistant melon germplasm. We screened a total of 60 genotypes including 16 lines and 44 melon cultivars collected from USA and Korea. Among the 16 melon lines, four lines including 'PI482399', 'PI140471', 'PI136170' and 'PI420145', and two Korean cultivars viz. 'Asia Papaya' and 'Supra' showed complete resistance. We were aware that both genotypic and environmental variations could influence the phenotypic screening of resistance and susceptibility. We therefore, further assessed all genotypes using 20 SSR markers. The SSR marker 'CMCT505' linked to Gsb1 in chromosome 1 perfectly grouped resistant and susceptible lines indicating that resistance is probably due to the presence of Gsb1 gene. Cloning and sequencing of resistant and susceptible Gsb1 amplicons showed that there were 32-bp deletions in resistant line and 39-bp deletions in resistant cultivar compared to susceptible one. Thus, the resistant melon lines and cultivars identified in this study could be recommended for the melon breeding program. Furthermore, the SSR marker 'CMCT505' which is tightly linked with Gsb1 could be used for molecular screening of melon germplasm.

Genome-wide analysis of Solanum lycopersicum L. cyclophilins

Khadiza Khatun,Arif Hasan Khan Robin,Md Rafiqul Islam,Subroto Das Jyoti,Do-Jin Lee,김창길,정미영 한국식물생명공학회 2022 JOURNAL OF PLANT BIOTECHNOLOGY Vol.49 No.1

Cyclophilins (CYPs) are highly conserved ubiquitous proteins belong to the peptidyl prolyl cis/trans isomerase (PPIase) superfamily. These proteins are present in a wide range of organisms; they contain a highly conserved peptidylprolyl cis/trans isomerase domain. A comprehensive database survey identified a total of 35 genes localized in all cellular compartments of Solanum lycopersicum L., but largely in the cytosol. Sequence alignment and conserved motif analyses of the SlCYP proteins revealed a highly conserved CLD motif. Evolutionary analysis predicted the clustering of a large number of gene pairs with high sequence similarity. Expression analysis using the RNA-Seq data showed that the majority of the SlCYP genes were highly expressed in mature leaves and blooming flowers, compared with their expression in other organs. This study provides a basis for the functional characterization of individual CYP genes in the future to elucidate their role(s) in protein refolding and long-distance signaling in tomatoes and in plant biology, in general