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1.
Front Plant Sci ; 12: 721631, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34603351

RESUMO

The exploitation of heterosis through hybrid breeding is one of the major breeding objectives for productivity increase in crop plants. This research analyzes the genetic basis of heterosis in Brassica juncea by using a doubled haploid (DH) mapping population derived from F1 between two heterotic inbred parents, one belonging to the Indian and the other belonging to the east European gene pool, and their two corresponding sets of backcross hybrids. An Illumina Infinium Brassica 90K SNP array-based genetic map was used to identify yield influencing quantitative trait loci (QTL) related to plant architecture, flowering, and silique- and seed-related traits using five different data sets from multiple trials, allowing the estimation of additive and dominance effects, as well as digenic epistatic interactions. In total, 695 additive QTL were detected for the 14 traits in the three trials using five data sets, with overdominance observed to be the predominant type of effect in determining the expression of heterotic QTL. The results indicated that the design in the present study was efficient for identifying common QTL across multiple trials and populations, which constitute a valuable resource for marker-assisted selection and further research. In addition, a total of 637 epistatic loci were identified, and it was concluded that epistasis among loci without detectable main effects plays an important role in controlling heterosis in yield of B. juncea.

2.
Curr Pharm Des ; 27(45): 4610-4629, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34533439

RESUMO

BACKGROUND: Breast cancer is the most prevalent cancer amongst females across the globe, and with over 2 million new cases reported in 2018, it poses a huge economic burden to the already dwindling public health. A dearth of therapies in the pipeline to treat triple-negative breast cancers and acquisition of resistance against the existing line of treatments urge the need to strategize novel therapeutics in order to add new drugs to the pipeline. HDAC inhibitors (HDACi) is one such class of small molecule inhibitors that target histone deacetylases to bring about chromosomal remodelling and normalize dysregulated gene expression that marks breast cancer progression. OBJECTIVE: While four HDACi have been approved by the FDA for the treatment of different cancer types, no HDACi is specifically earmarked for clinical management of breast cancer. Owing to the differential HDAC expression pertaining to different types of breast cancers, isoform-selective HDAC inhibitors need to be discovered. CONCLUSION: This review attempts to set the stage for the rational structure-based discovery of isoform-selective HDACi by providing structural insights into different HDACs and their catalytic folds based on their classes and individual landscape. The development of inhibitors in accordance with the differential expression of HDAC isoforms exhibited in breast cancer cells is a promising strategy to rationally design selective and effective inhibitors, adopting a 'personalized-medicine' approach.

3.
3 Biotech ; 11(8): 373, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34367865

RESUMO

The antimicrobial resistant strains of several pathogens are major culprits of hospital-acquired nosocomial infections. An active and urgent action is necessary against these pathogens for the development of unique therapeutics. The cysteine biosynthetic pathway or genes (that are absent in humans) involved in the production of L-cysteine appear to be an attractive target for developing novel antibiotics. CysE, a Serine Acetyltransferase (SAT), catalyzes the first step of cysteine synthesis and is reported to be essential for the survival of persistence in several microbes including Mycobacterium tuberculosis. Structure determination provides fundamental insight into structure and function of protein and aid in drug design/discovery efforts. This review focuses on the overview of current knowledge of structure function, regulatory mechanism, and potential inhibitors (active site as well as allosteric site) of CysE. Despite having conserved structure, slight modification in CysE structure lead to altered the regulatory mechanism and hence affects the cysteine production. Due to its possible role in virulence and vital metabolism of pathogens makes it a potential target in the quest to develop novel therapeutics to treat multi-drug-resistant bacteria.

4.
Med Biol Eng Comput ; 59(5): 1035-1054, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33860445

RESUMO

In this work, we propose a heterogeneous committee (ensemble) of diverse members (classification approaches) to solve the problem of human epithelial (HEp-2) cell image classification using indirect Immunofluorescence (IIF) imaging. We hypothesize that an ensemble involving different feature representations can enable higher performance if individual members in the ensemble are sufficiently varied. These members are of two types: (1) CNN-based members, (2) traditional members. For the CNN members, we have employed the well-established ResNet, DenseNet, and Inception models, which have distinctive salient aspects. For the traditional members, we incorporate class-specific features which are characterized depending on visual morphological attributes, and some standard texture features. To select the members which are discriminating and not redundant, we use an information theoretic measure which considers the trade-off between individual accuracies and diversity among the members. For all selected members, a compelling fusion required to combine their outputs to reach a final decision. Thus, we also investigate various fusion methods that combine the opinion of the committee at different levels: maximum voting, product, decision template, Bayes, Dempster-Shafer, etc. The proposed method is evaluated using ICPR-2014 data which consists of more images than some previous datasets ICPR-2012 and demonstrate state-of-the-art performance. To check the effectiveness of the proposed methodology for other related datasets, we test our methodology with newly compiled large-scale HEp-2 dataset with 63K cell images and demonstrate comparable performance even with less number of training samples. The proposed method produces 99.80% and 86.03% accuracy respectively when tested on ICPR-2014 and a new large-scale data containing 63K samples. Graphical Abstract Overview of the proposed methodology.


Assuntos
Células Epiteliais , Teorema de Bayes , Humanos
5.
Plant Biotechnol J ; 19(3): 602-614, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33073461

RESUMO

Brassica juncea (AABB), commonly referred to as mustard, is a natural allopolyploid of two diploid species-B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ~100× PacBio single-molecule real-time (SMRT) long reads providing contigs with an N50 value of >5 Mb. Contigs were corrected for the misassemblies and scaffolded with BioNano optical mapping. We also assembled a draft genome of B. nigra (BB) variety Sangam using Illumina short-read sequencing and Oxford Nanopore long reads and used it to validate the assembly of the B genome of B. juncea. Two different linkage maps of B. juncea, containing a large number of genotyping-by-sequencing markers, were developed and used to anchor scaffolds/contigs to the 18 linkage groups of the species. The resulting chromosome-scale assembly of B. juncea Varuna is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content and gene block associations. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The B. juncea Varuna assembly will be of major value to the breeding work on oleiferous types of mustard that are grown extensively in south Asia and elsewhere.


Assuntos
Genoma de Planta , Mostardeira , Ásia , Mapeamento Cromossômico , Cromossomos , Genoma de Planta/genética , Mostardeira/genética , Melhoramento Vegetal
6.
J Biomol Struct Dyn ; 39(5): 1547-1560, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32093568

RESUMO

Tuberculosis posses a major threat for health practitioners due to lengthy treatment regimen, increase in the drug-resistant strains of Mycobacterium tuberculosis (M. tb) and unavailability of drugs for its persistent form. Therefore, there is an urgent need for discovery of new and improved anti-tubercular drugs. In M. tb, the two step de novo biosynthesis of L-cysteine, an essential metabolic pathway is reported to be up-regulated in the persistent phase of the organism, involves two enzymes CysE and CysK. Although, structural insights for rational drug discovery are available for the later, not much information is known for the former. This study proposes a 3-dimensional model of M. tb CysE followed by in-silico screening of 67,030 anti-tuberculosis bioactive compounds. Subsequently, post-processing of 1000 best hits was carried out and top 200 compounds thus obtained were docked into the active site cleft of E. coli homologue as a control, but revealed unexpected results. Differences in the active site architectures and comparative analysis of molecular electrostatic potentials between the two CysEs provide molecular basis for the compounds C1, C3, C4 and C7 exhibiting preferential binding for M. tb CysE. In addition, shorter N-terminus along with positive and irregular trimeric base of M. tb CysE indicates its biological assembly as trimer. Based on mapping of residues involved in cysteine sensitivity on to the model structure of M. tb CysE, it is hypothesized that feedback inhibition of this homologue by cysteine may be affected.Communicated by Ramaswamy H. Sarma.


Assuntos
Mycobacterium tuberculosis , Serina O-Acetiltransferase , Antituberculosos/farmacologia , Domínio Catalítico , Escherichia coli/metabolismo , Simulação de Dinâmica Molecular , Mycobacterium tuberculosis/metabolismo , Serina O-Acetiltransferase/metabolismo
7.
Artigo em Inglês | MEDLINE | ID: mdl-32548107

RESUMO

Availability of purified drug target is a prerequisite for its structural and functional characterization. However, aggregation of recombinant protein as inclusion bodies (IBs) is a common problem during the large scale production of overexpressed protein in heterologous host. Such proteins can be recovered from IB pool using some mild solubilizing agents such as low concentration of denaturants or detergents, alcohols and osmolytes. This study reports optimization of solubilization buffer for recovery of soluble and biologically active recombinant mycobacterial Rv1915/ICL2a from IBs. Even though the target protein could be solubilized successfully with mild agents (sarcosine and ßME) without using denaturants, it failed to bind on Ni-NTA resin. The usual factors such as loss of His6-tag due to proteolysis, masking of the tag due to its location or protein aggregation were investigated, but the actual explanation, provided through bioinformatics analysis, turned out to be presence of intrinsically disordered protein regions (IDPRs) at the C-terminus. These regions due to their inability to fold into ordered structure may lead to non-specific protein aggregation and hence reduced binding to Ni-NTA affinity matrix. With this rationale, 90 residues from the C-terminal of Rv1915/ICL2 were truncated, the variant successfully purified and characterized for ICL and MICL activities, supporting the disordered nature of Rv1915/ICL2a C-terminal. When a region that has definite structure associated in some mycobaterial strains such as CDC 1551 and disorder in others for instance Mycobacterium tuberculosis H37Rv, it stands to reason that larger interface in the later may have implication in binding to other cellular partner.

8.
Plant J ; 103(5): 1885-1893, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32530074

RESUMO

The development of more productive crops will be key to addressing the challenges that climate change, population growth and diminishing resources pose to global food security. Advanced 'omics techniques can help to accelerate breeding by facilitating the identification of genetic markers for use in marker-assisted selection. Here, we present the validation of a new Associative Transcriptomics platform in the important oilseed crop Brassica juncea. To develop this platform, we established a pan-transcriptome reference for B. juncea, to which we mapped transcriptome data from a diverse panel of B. juncea accessions. From this panel, we identified 355 050 single nucleotide polymorphism variants and quantified the abundance of 93 963 transcripts. Subsequent association analysis of functional genotypes against a number of important agronomic and quality traits revealed a promising candidate gene for seed weight, BjA.TTL, as well as additional markers linked to seed colour and vitamin E content. The establishment of the first full-scale Associative Transcriptomics platform for B. juncea enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops.


Assuntos
Produção Agrícola/métodos , Mostardeira/genética , Poliploidia , Característica Quantitativa Herdável , Transcriptoma/genética , Perfilação da Expressão Gênica , Genes de Plantas/genética , Estudos de Associação Genética , Marcadores Genéticos/genética , Mostardeira/crescimento & desenvolvimento , Polimorfismo de Nucleotídeo Único/genética , Sementes/crescimento & desenvolvimento
9.
Int J Biol Macromol ; 151: 1240-1249, 2020 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-31751684

RESUMO

The emergence and spread of multidrug-resistant strains of Klebsiella pneumoniae is a major concern that necessitates the development of unique therapeutics. The essential requirement of serine acetyltransferase (SAT/CysE) for survival of several human pathogens makes it a very promising target for inhibitor designing and drug discovery. In this study, as an initial step to structure-based drug discovery, CysE from K. pneumonia was structurally and biochemically characterized. Subsequently, blind docking of selected natural products into the X-ray crystallography determined 3D structure of the target was carried out. Experimental validation of the inhibitory potential of the top-scorers established quercetin as an uncompetitive inhibitor of Kpn CysE. Molecular dynamics simulations carried out to elucidate the binding mode of quercetin reveal that this small molecule binds at the trimer-trimer interface of hexameric CysE, a site physically distinct from the active site of the enzyme. Detailed analysis of conformational differences incurred in Kpn CysE structure on binding to quercetin provides mechanistic understanding of allosteric modulation. Binding of quercetin to CysE leads to conformation changes in the active site loops and proximal loops that affect its internal dynamics and consequently its affinity for substrate/co-factor binding, justifying the reduced enzyme activity.


Assuntos
Antibacterianos/química , Klebsiella pneumoniae/enzimologia , Serina O-Acetiltransferase/química , Regulação Alostérica/efeitos dos fármacos , Antibacterianos/farmacologia , Clonagem Molecular , Estabilidade Enzimática , Expressão Gênica , Humanos , Cinética , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Conformação Molecular , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Desnaturação Proteica , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Serina O-Acetiltransferase/antagonistas & inibidores , Serina O-Acetiltransferase/genética , Serina O-Acetiltransferase/isolamento & purificação , Relação Estrutura-Atividade
10.
Asian J Psychiatr ; 45: 125-128, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31586818

RESUMO

To evaluate the validity and reliability of Hindi version of Montreal cognitive assessment (H-MoCA) as a screening tool to detect mild cognitive impairment among older adults of India. The study was conducted in three phases, namely content validation of H-MoCA reliability estimation, internal consistency and test- retest reliability. Qualitative and quantitative validation through expert review resulted in modification of H-MoCA which was tested on purposive sample of 30 subjects, and analysis was done for internal consistency reliability, then the scale was re-administered to the same group to establish test-retest reliability. Internal consistency was reported in terms of Cronbach's alpha (α) and test-retest reliability in terms of intra class correlation coefficient (ICC). Qualitative review and Content validation ratio (Lawshe) validate the content of H-MoCA with CVR of 0.99. The scale has good internal consistency, Cronbach's alpha (α) = 0.64 and high test-retest reliability, intra class correlation coefficient (ICC) = 0.87. Thus the Hindi translated version of MoCA is a valid and reliable tool for detecting mild cognitive impairment.


Assuntos
Disfunção Cognitiva/diagnóstico , Testes de Estado Mental e Demência , Feminino , Humanos , Índia , Masculino , Pessoa de Meia-Idade , Reprodutibilidade dos Testes
11.
Int J Biol Macromol ; 141: 927-936, 2019 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-31505209

RESUMO

Tuberculosis (TB) is one of the leading causes of death worldwide. Long duration of TB therapy, results in the persistence and development of drug resistant strains of causative organism Mycobacterium tuberculosis (Mtb). Novel drug targets against persistent Mtb is an immediate need for overcoming this global menace. Isocitrate lyase (ICL), the first enzyme of glyoxylate pathway, is essential for persistent Mtb and absent in humans, hence a propitious target for drug development. Pathogenic Mtb H37Rv, have two types of ICLs - ICL1 encoded by icl (Rv0467) is well characterized and homologous to eubacterial enzyme whereas ICL2 encoded by aceA is more related to eukaryotic isocitrate lyase. To compound it, the aceA gene is split into two ORFs namely rv1915/aceAa and rv1916/aceAb. No translational product has been reported for the later and therefore, in vivo existence of Rv1916/ICL2b is debatable. This study reports recombinant production of Rv1916 in heterologous host E. coli BL21 (DE3) for structure function studies. The studies categorically demonstrate that akin to Mtb ICL1, recombinant Rv1916 also possess dual ICL and methylisocitrate lyase (MICL) activities in vitro. Based on in silico analysis, a putative function linked to secondary metabolite synthesis is assigned to unique mycobacterial domain IV.


Assuntos
Proteínas de Bactérias/química , Isocitrato Liase/química , Modelos Moleculares , Mycobacterium tuberculosis/enzimologia , Conformação Proteica , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/isolamento & purificação , Proteínas de Bactérias/metabolismo , Isocitrato Liase/genética , Isocitrato Liase/isolamento & purificação , Isocitrato Liase/metabolismo , Cinética , Mycobacterium tuberculosis/classificação , Mycobacterium tuberculosis/genética , Filogenia , Relação Quantitativa Estrutura-Atividade , Proteínas Recombinantes
12.
J Genet ; 98(2)2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31204703

RESUMO

Being an economical and nutritional crop, Capsicum appeases people's peppery taste and is found to bewidely distributed all over the world having vast diversity. In the present study, genetic polymorphism, cross transferability (CT) and genetic diversity were examined among the 54 different accessions of Capsicum species including 49 of Capsicum annuum, three of C. baccatum and two of C. frutescens, using a set of 36 start codon targeted (SCoT) primers. Of the total, 35 SCoT markers showed successful amplification profile among chilli germplasms and an average primer polymorphism was reported as 81.52% which ranged from 50% (SCoT-6) to 100% (SCoT-11). A total of 365 amplicons were obtained with an average of 10.43 bands per primer and the length of the bands ranged from 150 bp to 1.2 kb. Further, polymorphic information content value of SCoT markers ranged from 0.42 (for SCoT-25) to 0.86 (SCoT-27) with an average of 0.78. The average value of CT of SCoT markers was 44.08% ranged from 14.25% to 57.26% among different chilli accessions. A dendrogram was constructed and established genetic relationship among 54 capsicum species, with the help of translation initiation codon polymorphisms or SCoT primer amplification. This study suggests the effectiveness of SCoT marker system for characterizing and assessing genetic diversity of Capsicum germplasm, which can be used for evolutionary studies and to identify agronomically important traits.


Assuntos
Capsicum/genética , Códon de Iniciação , Cruzamentos Genéticos , Polimorfismo Genético , Amplificação de Genes , Marcadores Genéticos , Variação Genética , Genoma de Planta , Genômica/métodos , Filogenia
13.
Theor Appl Genet ; 132(8): 2223-2236, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31049632

RESUMO

KEY MESSAGE: BjuWRR1, a CNL-type R gene, was identified from an east European gene pool line of Brassica juncea and validated for conferring resistance to white rust by genetic transformation. White rust caused by the oomycete pathogen Albugo candida is a significant disease of crucifer crops including Brassica juncea (mustard), a major oilseed crop of the Indian subcontinent. Earlier, a resistance-conferring locus named AcB1-A5.1 was mapped in an east European gene pool line of B. juncea-Donskaja-IV. This line was tested along with some other lines of B. juncea (AABB), B. rapa (AA) and B. nigra (BB) for resistance to six isolates of A. candida collected from different mustard growing regions of India. Donskaja-IV was found to be completely resistant to all the tested isolates. Sequencing of a BAC spanning the locus AcB1-A5.1 showed the presence of a single CC-NB-LRR protein encoding R gene. The genomic sequence of the putative R gene with its native promoter and terminator was used for the genetic transformation of a susceptible Indian gene pool line Varuna and was found to confer complete resistance to all the isolates. This is the first white rust resistance-conferring gene described from Brassica species and has been named BjuWRR1. Allelic variants of the gene in B. juncea germplasm and orthologues in the Brassicaceae genomes were studied to understand the evolutionary dynamics of the BjuWRR1 gene.


Assuntos
Resistência à Doença/genética , Genes de Plantas , Mostardeira/genética , Mostardeira/microbiologia , Oomicetos/fisiologia , Doenças das Plantas/microbiologia , Proteínas/genética , Alelos , Sequência de Aminoácidos , Sequência de Bases , Evolução Molecular , Regulação da Expressão Gênica de Plantas , Estudos de Associação Genética , Marcadores Genéticos , Variação Genética , Oomicetos/isolamento & purificação , Plantas Geneticamente Modificadas , Proteínas/química , Proteínas/metabolismo , Transformação Genética
14.
J Neurosci Rural Pract ; 10(1): 94-100, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30765978

RESUMO

Background: Serum interleukin (IL)-6 has been found to be associated with sleep quality, mood, and survival in patients with solid tumors. Results in these studies were confounded by knowledge of diagnosis to study subjects. Moreover, such data among subjects with hematological malignancies and data regarding restless legs syndrome is limited. The present study was, therefore, conducted to assess the sleep quality, depression, and restless leg syndrome in hematological malignancies and to study if there is any role of IL6 associated with it. Methods: Sixty-six subjects having hematological malignancy were included in this study after excluding the potential confounders. Sleep quality was examined using Pittsburg Sleep Quality Index, depression by the Patient Health Questionnaire-9. Diagnosis of RLS was made through clinical examination. Serum for measurement of IL-6 was collected at baseline and after 1 month of initiation of chemotherapy. Patients were followed up for 6 months. Results: Average age of study subjects was 50.16 years with male predominance. Nearly 22.7% had clinical depression, 28.8% had poor quality sleep, and restless legs syndrome (RLS) was reported in 6.1% cases. Nearly 22.7% patients died at 6 months. Disturbed sleep at baseline was associated with depression (odds ratio [OR] =7.89) and poor 6 months survival. Serum IL-6 did not show any association with sleep quality, restless-legs-syndrome, and depression. However, baseline high level of serum IL-6 (OR = 26.06) and low level after chemotherapy (OR = 0.03) were associated with poor survival at 6 months. Conclusion: Poor quality sleep, depression, and RLS are prevalent among adult subjects with hematological malignancies. Sleep disturbance, high pretreatment inflammatory and lowering of inflammatory load after chemotherapy increase likelihood for poor prognosis. Serum IL-6 did not show any association with sleep quality, restless legs syndrome and depression.

15.
Prep Biochem Biotechnol ; 49(4): 368-374, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30734630

RESUMO

The emergence of drug resistance in Streptococcus pneumoniae (Spn) is a global health threat and necessitates discovery of novel therapeutics. The serine acetyltransferase (also known as CysE) is an enzyme of cysteine biosynthesis pathway and is reported to be essential for the survival of several pathogenic bacteria. Therefore, it appears to be a very attractive target for structure-function understanding and inhibitor design. This study describes the molecular cloning of cysE from Spn in the pET21c vector and efforts carried out for expression and purification of active recombinant CysE. Significant expression of recombinant Spn cysE could be achieved in codon optimized BL21(DE3)-RIL strain as opposed to conventional BL21(DE3) strain. Analysis of codon adaptation index (CAI) with levels of eukaryotic genes and prokaryotic cysEs expressed in heterologous E. coli host suggests that codon optimized E. coli BL21(DE3)-RIL may be a better host for expressing genes with low CAI. Here, an efficient protocol has been developed for recovery of recombinant Spn CysE in soluble and biologically active form by the usage of nonionic detergent Triton X-100 at a concentration as low as 1%. Altogether, this study reports a simple strategy for producing functionally active Spn CysE in E. coli.


Assuntos
Clonagem Molecular/métodos , Serina O-Acetiltransferase/biossíntese , Streptococcus pneumoniae/enzimologia , Sequência de Bases , Códon , Detergentes/química , Escherichia coli/genética , Octoxinol/química , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Serina O-Acetiltransferase/química , Serina O-Acetiltransferase/genética , Serina O-Acetiltransferase/isolamento & purificação
16.
3 Biotech ; 9(2): 44, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30675454

RESUMO

CysK (O-acetylserine sulfhydrylase) is a pyridoxal-5' phosphate-dependent enzyme which catalyzes the second step of the de novo cysteine biosynthesis pathway by converting O-acetyl serine (OAS) into l-cysteine in the presence of sulfide. The first step of the cysteine biosynthesis involves formation of OAS from serine and acetyl CoA by CysE (serine acetyltransferase). Apart from role of CysK in cysteine biosynthesis, recent studies have revealed various additional roles of this enzyme in bacterial physiology. Other than the suggested regulatory role in cysteine production, other activities of CysK include involvement of CysK-in contact-dependent toxin activation in Gram-negative pathogens, as a transcriptional regulator of CymR by stabilizing the CymR-DNA interactions, in biofilm formation by providing cysteine and via another mechanism not yet understood, in ofloxacin and tellurite resistance as well as in cysteine desulfurization. Some of these activities involve binding of CysK to another cellular partner, where the complex is regulated by the availability of OAS and/or sulfide (H2S). The aim of this study is to present an overview of current knowledge of multiple functions performed by CysK and identifying structural features involved in alternate functions. Due to possible role in disease, promoting or inhibiting a "moonlighting" function of CysK could be a target for developing novel therapeutic interventions.

17.
Front Plant Sci ; 10: 1690, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31998351

RESUMO

White rust, causal agent oomycete Albugo candida, is a significant disease of the cultivated Brassica species. The Indian gene pool lines of oilseed mustard, Brassica juncea, are highly susceptible to the pathogen. Resistance to A. candida has been reported in the east European gene pool lines of mustard and mapped to LG A4 in line Heera and LG A5 in line Donskaja-IV. A new resistance-conferring locus to A. candida isolate AcB1 has been mapped to LG A6 of B. juncea line Tumida-a Chinese vegetable type mustard using an F1DH mapping population that has been developed from a Tumida × Varuna (susceptible Indian gene pool line) cross. A molecular map containing 8,303 genic and GBS markers was used to map the resistance trait to an interval of 63.0 cM-70.8 cM on LG A6. Genome assemblies of Tumida and Varuna were used to find the genes present within the flanking markers discerned by genetic mapping. The most likely candidate gene in the mapped interval is BjuA046215, a CC-NBS-LRR (CNL) type R gene that encodes a protein with all the specific subdomains of the proteins encoded by such genes. Alleles of BjuA046215 in Varuna and other lines of the Indian and the east European gene pools encode proteins that have truncated LRR domains. Analysis of the syntenic regions in some of the Brassicaceae genomes and phylogenetic analysis of CNL type R genes showed BjuA046215 to be closely related to a recently described white rust resistance-conferring R gene BjuWRR1 in B. juncea Donskaja-IV, both belonging to the CNL-D group of R genes. Related R genes in Arabidopsis thaliana confer resistance to another oomycete, Peronospora parasitica.

18.
3 Biotech ; 8(12): 504, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30555765

RESUMO

Structure-based drug discovery has emerged as a powerful tool in computational drug discovery and has gained rapid acceleration due to the development of better algorithms for high-end computation in an affordable time. Molecular docking and virtual screening methods are routinely used for the purpose but computing the ligand binding energies with inbuilt scoring functions accurately is still a limitation. Although, MMPBSA and MMGBSA are routinely employed tools for achieving accurate binding free energies, they are applied on well-equilibrated explicitly solvated systems and are computationally expensive and time-consuming. This study compares different post-processing protocols performed on an in-silico screened benchmarked P. falciparum Dihydrofolate reductase (PfDHFR) dataset with AutoDockVina. The docked and implicitly solvated complexes were subjected to (1) rescoring, (2) energy minimization and (3) Binding Estimation After Refinement (BEAR) algorithm. Subsequently, binding free energies were computed using three different tools-MMPBSA, MMGBSA and "g_mmpbsa". Surprisingly, rescoring alone displays lower accuracy than the inherent scoring function of the AutoDockVina. However, encouraging results were seen after post-processing with the other two protocols. The results suggest that MMPBSA applied on energy minimized conformations is able to achieve 42-fold reductions in computational time as opposed to the BEAR algorithm with comparable accuracy.

19.
Front Plant Sci ; 9: 1448, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30386353

RESUMO

Increasing oil content in oilseed mustard (Brassica juncea) is a major breeding objective-more so, in the lines that have "0" erucic acid content (< 2% of the seed oil) as earlier studies have shown negative pleiotropic effect of erucic acid loci on the oil content, both in oilseed mustard and rapeseed. We report here QTL analysis of oil content in eight different mapping populations involving seven different parents-including a high oil content line J8 (~49%). The parental lines of the mapping populations contained wide variation in oil content and erucic acid content. The eight mapping populations were categorized into two sets-five populations with individuals segregating for erucic acid (SE populations) and the remaining three with zero erucic acid segregants (ZE populations). Meta-analysis of QTL mapped in individual SE populations identified nine significant C-QTL, with two of these merging most of the major oil QTL that colocalized with the erucic acid loci on the linkage groups A08 and B07. QTL analysis of oil content in ZE populations revealed a change in the landscape of the oil QTL compared to the SE populations, in terms of altered allelic effects and phenotypic variance explained by ZE QTL at the "common" QTL and observation of "novel" QTL in the ZE background. The important loci contributing to oil content variation, identified in the present study could be used in the breeding programmes for increasing the oil content in high erucic and "0" erucic backgrounds.

20.
Int J Biol Macromol ; 111: 1010-1018, 2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-29366889

RESUMO

Drug resistance to almost all antibiotics of Shigella flexneri, a major cause of shigellosis in developing countries, necessitates continuous discovery of novel therapeutics. This study reports a structure-function analysis of a potential drug target serine acetyltransferase (CysE), an enzyme of de novo cysteine biosynthesis pathway that is absent in humans. Analysis of CysE sequences of S. flexneri species and serotypes displayed only two variants that differed by a single amino acid substitution at position 241. Structural inspection of the available crystal structure disclosed this site to be distinct from the substrate/cofactor binding pockets or dimer/trimer interfaces. This study discovers that V241 variant of S. flexneri CysE has nearly null enzymatic activity. The observation is explained by molecular dynamic studies which reveal that the disorder generated by A241V substitution is the basis of dissociation of the quaternary assembly of S. flexneri CysE leading to loss of enzymatic activity and stability. The study provides the first evidence that position 241 of CysE, affects the catalytic efficiency of enzyme and suggests this locus as a 'hot spot' for the propagation of conformational changes. It may be postulated that transient quaternary structure of CysE maybe another mechanism for regulating the intracellular level of cysteine.


Assuntos
Cisteína/biossíntese , Disenteria Bacilar/enzimologia , Serina O-Acetiltransferase/química , Shigella flexneri/enzimologia , Sequência de Aminoácidos , Clonagem Molecular , Cisteína/genética , Farmacorresistência Bacteriana/genética , Estabilidade Enzimática , Escherichia coli/genética , Humanos , Simulação de Dinâmica Molecular , Mutação , Estrutura Quaternária de Proteína , Serina O-Acetiltransferase/genética , Shigella flexneri/genética , Shigella flexneri/patogenicidade
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