Characterization of Lysinibacillus fusiformis strain S4C11: In vitro, in planta, and in silico analyses reveal a plant-beneficial microbe

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

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Design, Synthesis, Characterization of New Carbamates of 4-Nitrophenylchloroformate and Their Antimicrobial and Antioxidant Activities: an In Vitro and In Silico Approach

Chemistry Africa ◽

10.1007/s42250-020-00211-x ◽

2021 ◽

Author(s):

P. Hari Babu ◽

Ch. Venkataramaiah ◽

C. Naga Raju ◽

P. V. Chalapathi

Keyword(s):

In Silico ◽

Antioxidant Activities ◽

Design Synthesis

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In Silico Analyses of Rice Thionin Genes and the Antimicrobial Activity of OsTHION15 Against Phytopathogens

Phytopathology ◽

10.1094/phyto-06-17-0217-r ◽

2019 ◽

Vol 109 (1) ◽

pp. 27-35

Author(s):

Krissana Boonpa ◽

Suparuk Tantong ◽

Kamonwan Weerawanich ◽

Pawinee Panpetch ◽

Onanong Pringsulaka ◽

...

Keyword(s):

Antimicrobial Activity ◽

Stress Responses ◽

In Silico ◽

Pathogenic Bacteria ◽

Hyphal Growth ◽

In Planta ◽

Recombinant Peptide ◽

Plant Disease Control ◽

Helminthosporium Oryzae ◽

In Silico Analyses

Thionins are a family of antimicrobial peptides. We performed in silico expression analyses of the 44 rice (Oryza sativa) thionins (OsTHIONs). Modulated expression levels of OsTHIONs under different treatments suggest their involvement in many processes, including biotic, abiotic, and nutritional stress responses, and in hormone signaling. OsTHION15 (LOC_Os06g32600) was selected for further characterization based on several in silico analyses. OsTHION15 in O. sativa subsp. indica ‘KDML 105’ was expressed in all of the tissues and organs examined, including germinating seed, leaves, and roots of seedlings and mature plants, and inflorescences. To investigate the antimicrobial activity of OsTHION15, we produced a recombinant peptide in Escherichia coli Rosetta-gami (DE3). The recombinant OsTHION15 exhibited inhibitory activities toward rice-pathogenic bacteria such as Xanthomonas oryzae pv. oryzae and Pectobacterium carotovorum pv. atroseptica, with minimum inhibitory concentrations of 112.6 and 14.1 µg ml−1, respectively. A significant hyphal growth inhibition was also observed toward Fusarium oxysporum f. sp. cubense and Helminthosporium oryzae. In addition, we demonstrated the in planta antibacterial activity of this peptide in Nicotiana benthamiana against X. campestris pv. glycines. These activities suggest the possible application of OsTHION15 in plant disease control.

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Isolation and Characterization of a Pseudomonas syringae Strain with Antagonistic Activities Against Pseudomonas syringae pv. glycinea in Vitro and in Planta

Developments in Plant Pathology - Pseudomonas Syringae Pathovars and Related Pathogens ◽

10.1007/978-94-011-5472-7_114 ◽

1997 ◽

pp. 629-634

Author(s):

Rudolf May ◽

Beate Völksch ◽

Grit Kampmann ◽

Jörg Nüske

Keyword(s):

Pseudomonas Syringae ◽

In Planta ◽

Isolation And Characterization

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Characterization of medicinal plant-associated biocontrol Bacillus subtilis (SSL2) by liquid chromatography-mass spectrometry and evaluation of compounds by in silico and in vitro methods

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1581091 ◽

2019 ◽

Vol 38 (2) ◽

pp. 500-510 ◽

Cited By ~ 3

Author(s):

Hardik Naik Jinal ◽

Natarajan Amaresan

Keyword(s):

Mass Spectrometry ◽

Bacillus Subtilis ◽

Liquid Chromatography ◽

Medicinal Plant ◽

In Silico ◽

Liquid Chromatography Mass Spectrometry ◽

In Vitro Methods ◽

Chromatography Mass Spectrometry

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In silico design and in vitro characterization of a recombinant antigen for specific recognition of NMP22

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2019.08.065 ◽

2019 ◽

Vol 140 ◽

pp. 69-77 ◽

Cited By ~ 1

Author(s):

Alireza Bonakdar ◽

Fatemeh Sahebazzamani ◽

Mohammad Javad Rasaee ◽

Saman Hosseinkhani ◽

Fatemeh Rahbarizadeh ◽

...

Keyword(s):

In Silico ◽

Recombinant Antigen ◽

In Silico Design ◽

Specific Recognition ◽

In Vitro Characterization

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Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode

Biochemical Journal ◽

10.1042/bcj20190288 ◽

2019 ◽

Vol 476 (12) ◽

pp. 1843-1856 ◽

Cited By ~ 1

Author(s):

Cyril Hamiaux ◽

Lesley Larsen ◽

Hui Wen Lee ◽

Zhiwei Luo ◽

Prachi Sharma ◽

...

Keyword(s):

In Silico ◽

Binding Mode ◽

Crystal Structure Analysis ◽

Tolfenamic Acid ◽

In Vitro Assays ◽

Inhibition Mechanism ◽

In Planta ◽

Competitive Antagonist ◽

In Silico Docking

Abstract Strigolactones (SLs) are multifunctional plant hormones regulating essential physiological processes affecting growth and development. In vascular plants, SLs are recognized by α/β hydrolase-fold proteins from the D14/DAD2 (Dwarf14/Decreased Apical Dominance 2) family in the initial step of the signaling pathway. We have previously discovered that N-phenylanthranilic acid derivatives (e.g. tolfenamic acid) are potent antagonists of SL receptors, prompting us to design quinazolinone and quinazolinedione derivatives (QADs and QADDs, respectively) as second-generation antagonists. Initial in silico docking studies suggested that these compounds would bind to DAD2, the petunia SL receptor, with higher affinity than the first-generation compounds. However, only one of the QADs/QADDs tested in in vitro assays acted as a competitive antagonist of SL receptors, with reduced affinity and potency compared with its N-phenylanthranilic acid ‘parent’. X-ray crystal structure analysis revealed that the binding mode of the active QADD inside DAD2's cavity was not that predicted in silico, highlighting a novel inhibition mechanism for SL receptors. Despite a ∼10-fold difference in potency in vitro, the QADD and tolfenamic acid had comparable activity in planta, suggesting that the QADD compensates for lower potency with increased bioavailability. Altogether, our results establish this QADD as a novel lead compound towards the development of potent and bioavailable antagonists of SL receptors.

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