Y12F mutation in Pseudomonas plecoglossicida S7 lipase enhances its thermal and pH stability for industrial applications: a combination of in silico and in vitro study

Choudhary, Prassan; Waseem, Mohammad; Kumar, Sunil; Subbarao, Naidu; Srivastava, Shilpi; Chakdar, Hillol

doi:10.1007/s11274-023-03518-2

Cited by 5 publications

(3 citation statements)

References 81 publications

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“…have been studied in recent years for their potential as biocontrol agents and for enhancing industrial enzyme production in extreme environments. [31][32][33][34][35] Metagenomic analysis indicated that the colonization of the microbial community in neem gum is a complex consequence and requires thorough investigation to understand the mechanism and guiding forces of colonization. In summary, it can be concluded that neem gum is a good source of diverse microorganisms which can have multiple agricultural and biotechnological applications.…”

Section: Discussionmentioning

confidence: 99%

Deciphering Azadirachta indica (Neem) Gum Microbiome using Metagenomic Approaches

Saxena¹,

Singh²,

Chakdar³

et al. 2023

J. Pure Appl. Microbiol.

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Indian lilac or neem (Azadirachta indica) is found in tropical and subtropical regions of the Indian subcontinent. Each part of the tree is a source of various phytochemicals. Neem gum is an exudate from mature parts of the plant stem. Biochemically, it has an acidic pH range (5–6) and is composed of monosaccharides, saponins, phenols, and tannins. This study aimed to elucidate the diversity of neem gum-associated microflora through high throughput metagenomics approach using 16S rRNA variable region sequencing. The bacterial community of neem gum was dominated by Firmicutes (~82%), Proteobacteria (~18%), and Actinobacteria (~0.02%). Among the genera, Lactococcus was found to be the most dominant bacterium. The predominance of Lactococcus in neem gum is probably due to its acidic nature, which provides a suitable microenvironment for its proliferation. In addition, Lactococcus and beneficial microorganisms such as Pseudomonas, Burkholderia, Pantoea, Klebsiella, and Methylobacterium were also present in the gum. This study highlights the fact that neem gum can be exploited as a unique source of microorganisms for biotechnological and agricultural applications.

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Section: Discussionmentioning

confidence: 99%

Deciphering Azadirachta indica (Neem) Gum Microbiome using Metagenomic Approaches

Saxena¹,

Singh²,

Chakdar³

et al. 2023

J. Pure Appl. Microbiol.

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“…However, the current research article has focused on identifying therapeutic lead molecules against E. cloacae and evaluating their interaction profile with potent drug targets. Computational studies have already been established to predict potential techniques and therapeutics in the field of medical research and diagnostic purposes (Sinha et al 2019 ; Godara and Kao 2020 ; Sharma et al 2021 ; Priyamvada et al 2022 ; Kaviraj et al 2022 ; Alam et al 2023 ; Choudhary et al 2023 ). Gene Interaction Network (GIN) approach integrated with structural bioinformatics can be useful in understanding the complex molecular interactions among the biomolecules present in the physiological systems (Naha et al 2022 ; Priyamvada et al 2022 ; Ashok and Ramaiah 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Translational protein RpsE as an alternative target for novel nucleoside analogues to treat MDR Enterobacter cloacae ATCC 13047: network analysis and molecular dynamics study

Debroy

Ramaiah

2023

World J Microbiol Biotechnol

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The pathogenic Enterobacter cloacae subsp. cloacae str. ATCC 13047 has contemporarily emerged as a multi-drug resistant strain. To formulate an effective treatment option, alternative therapeutic methods need to be explored. The present study focused on Gene Interaction Network study of 46 antimicrobial resistance genes to reveal the densely interconnecting and functional hub genes in E. cloacae ATCC 13047. The AMR genes were subjected to clustering, topological and functional enrichment analysis, revealing rpsE (RpsE), acrA (AcrA) and arnT (ArnT) as novel therapeutic drug targets for hindering drug resistance in the pathogenic strain. Network topology further indicated translational protein RpsE to be exploited as a promising drug-target candidate for which the structure was predicted, optimized and validated through molecular dynamics simulations (MDS). Absorption, distribution, metabolism and excretion screening recognized ZINC5441082 ( N -Isopentyladenosine) (Lead_1) and ZINC1319816 (cyclopentyl-aminopurinyl-hydroxymethyl-oxolanediol) (Lead_2) as orally bioavailable compounds against RpsE. Molecular docking and MDS confirmed the binding efficacy and protein−ligand complex stability. Furthermore, binding free energy (G bind ) calculations, principal component and free energy landscape analyses affirmed the predicted nucleoside analogues against RpsE protein to be comprehensively examined as a potential treatment strategy against E. cloacae ATCC 13047. Supplementary information The online version contains supplementary material available at 10.1007/s11274-023-03634-z.

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“…5 As industrial catalysts, enzymes should be heterogeneous biocatalysts (to facilitate enzyme recovery and reaction control), stable, active, selective, and specific for the applied targeted substrate and reaction under industrially relevant conditions. [1][2][3][4] Fortunately, there are many tools that enable to bridge this gap, such as metagenomics, that enables to utilize most biodiversity, [6][7][8][9] directed evolution, that permits to mimic natural selection but focusing on the enzyme and the feature that the researcher has selected in an accelerated way, [10][11][12] directed mutagenesis, [13][14][15][16] that enables to build new enzymes, even enzymes bearing several different enzymes 17 (e.g., plurizymes), [18][19][20][21] and some physicochemical tools. Among the last ones, chemical modification of the enzyme surface can reach diverse objectives, such as altering the enzyme surface features, the mobility of a specific section of the protein or introducing intra or intermolecular crosslinkings.…”

Section: Introductionmentioning

confidence: 99%

The effects of the chemical modification on immobilized lipase features are affected by the enzyme crowding in the support

Abellanas‐Perez,

Carballares,

Rocha‐Martin

et al. 2023

Biotechnology Progress

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In this article, we have analyzed the interactions between enzyme crowding on a given support and its chemical modification (ethylenediamine modification via the carbodiimide route and picryl sulfonic (TNBS) modification of the primary amino groups) on the enzyme activity and stability. Lipase from Thermomyces lanuginosus (TLL) and lipase B from Candida antarctica (CALB) were immobilized on octyl‐agarose beads at two very different enzyme loadings, one of them exceeding the capacity of the support, one well under this capacity. Chemical modifications of the highly loaded and lowly loaded biocatalysts gave very different results in terms of activity and stability, which could increase or decrease enzyme activity depending on the enzyme support loading. For example, both lowly loaded biocatalysts increased their activity after modification while the effect was the opposite for the highly loaded biocatalysts. Additionally, the modification with TNBS of highly loaded CALB biocatalyst increased its stability while decrease the activity.

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Y12F mutation in Pseudomonas plecoglossicida S7 lipase enhances its thermal and pH stability for industrial applications: a combination of in silico and in vitro study

Cited by 5 publications

References 81 publications

Deciphering Azadirachta indica (Neem) Gum Microbiome using Metagenomic Approaches

Deciphering Azadirachta indica (Neem) Gum Microbiome using Metagenomic Approaches

Translational protein RpsE as an alternative target for novel nucleoside analogues to treat MDR Enterobacter cloacae ATCC 13047: network analysis and molecular dynamics study

The effects of the chemical modification on immobilized lipase features are affected by the enzyme crowding in the support

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