scholarly journals The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870

2019 ◽  
Author(s):  
Joni Frederick ◽  
Fritha Hennessy ◽  
Uli Horn ◽  
Pilar de la Torre Cortés ◽  
Marcel van den Broek ◽  
...  
Keyword(s):  
Nitrile Hydratase ◽  
Model Organism ◽  
Protein Sequences ◽  
Gene Clusters ◽  
Gram Positive Bacteria ◽  
Wide Range ◽  
Peptide Synthetase ◽  
Potential Applications ◽  
Rhodococcus Jostii Rha1 ◽  
Nitrile Hydrolysis

Abstract Background Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst. Results The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci. Conclusions The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.

scholarly journals The complete genome sequence of the nitrile biocatalyst Rhodococcus rhodochrous ATCC BAA-870

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Joni Frederick ◽  
Fritha Hennessy ◽  
Uli Horn ◽  
Pilar de la Torre Cortés ◽  
Marcel van den Broek ◽  
...  
Keyword(s):  
Nitrile Hydratase ◽  
Model Organism ◽  
Protein Sequences ◽  
Gene Clusters ◽  
Rhodococcus Rhodochrous ◽  
Gram Positive Bacteria ◽  
Wide Range ◽  
Peptide Synthetase ◽  
Potential Applications ◽  
Nitrile Hydrolysis

Abstract Background Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst. Results The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci. Conclusions The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.

scholarly journals The biotechnological relevance of Rhodococcus rhodochrous. The complete genomic sequence of nitrile biocatalyst strain ATCC BAA-870.

2019 ◽  
Author(s):  
Joni Frederick ◽  
Fritha Hennessy ◽  
Uli Horn ◽  
Pilar de la Torre Cortés ◽  
Marcel van den Broek ◽  
...  
Keyword(s):  
Nitrile Hydratase ◽  
Genomic Sequence ◽  
Model Organism ◽  
Protein Sequences ◽  
Gene Clusters ◽  
Rhodococcus Rhodochrous ◽  
Functional Roles ◽  
Wide Range ◽  
Potential Applications ◽  
Nitrile Hydrolysis

Abstract Background Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The expressed nitrilase, nitrile hydratase and amidase activities have shown stereoselective preferences for beta-substituted nitrile compounds. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst. Results The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, and several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster. Based on COG functional categories of proteins using RAST annotation, the main distributions of predicted annotated genes belong to known subsystems encoding amino acids and derivatives (19.7%), carbohydrates (13.4%), fatty acids, lipids and isoprenoids (12.2%), and cofactors, vitamins, prosthetic groups and pigments (9.4%). However, 74% of RAST annotated genes are not assigned clear functional roles within known metabolic pathways, and 38% of genes are annotated as hypothetical. BASys annotation predicts that 55% of annotated genes have an unknown function. The R. rhodochrous ATCC BAA-870 genome contains one possible CRISPR, identified by CRISPRCasFinder. Conclusions The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases. The capacity of this strain to hydrolyse nitriles resides upon a plasmid, containing a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase.

scholarly journals Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4504
Author(s):  
Muhanna Al-shaibani ◽  
Radin Maya Saphira Radin Mohamed ◽  
Nik Sidik ◽  
Hesham Enshasy ◽  
Adel Al-Gheethi ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Bioactive Compounds ◽  
Extreme Environments ◽  
Software Tool ◽  
Gene Clusters ◽  
Well Being ◽  
Bioactive Substances ◽  
Diverse Range ◽  
Wide Range ◽  
Potential Applications

The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities’ well-being.

Insights into bio-synthesis of nanoparticles by Shewanella genus

2021 ◽  
Author(s):  
Vishnu D. Rajput ◽  
Tatiana Minkina ◽  
Richard Kimber ◽  
Vipin Kumar Singh ◽  
Sudhir Shende ◽  
...  
Keyword(s):  
Focal Point ◽  
Low Cost ◽  
Model Organism ◽  
Metal Species ◽  
Synthesis Methods ◽  
Influence Of Process Parameters ◽  
Synthesis Of Nanoparticles ◽  
Current State ◽  
Wide Range ◽  
Potential Applications

The exploitation of microorganisms for the fabrication of nanoparticles (NPs) has garnered considerable research interest globally. The microbiological transformation of metals and metal salts into respective NPs can be achieved under environmentally benign conditions, offering a more sustainable alternative to chemical synthesis methods. Species of the metal-reducing bacterial genus Shewanella are able to couple the oxidation of various electron donors including lactate, pyruvate and hydrogen, to the reduction of a wide range of metal species, resulting in biomineralization of a multitude of metal NPs. Single metal-based NPs as well as composite materials with properties equivalent or even superior to physically and chemically produced NPs have been synthesized by a number of Shewanella species. A mechanistic understanding of electron transfer mediated bioreduction of metals into respective NPs by Shewanella is crucial in maximizing NP yields and directing the synthesis to produce fine-tuned NPs with tailored properties. In addition, thorough investigations into the influence of process parameters controlling the biosynthesis is another focal point for optimizing the process of NP generation. Synthesis of metal-based NPs using Shewanella species offers a low-cost, eco-friendly alternative to current physiochemical methods. This article aims to shed light on the contribution of Shewanella as a model organism in the biosynthesis of a variety of NPs, and critically reviews the current state of knowledge on factors controlling their synthesis, characterization, potential applications in different sectors and future prospects.

scholarly journals Controlled Autolysis and Enzyme Release in a Recombinant Lactococcal Strain Expressing the Metalloendopeptidase Enterolysin A

2004 ◽  
Vol 70 (3) ◽  
pp. 1744-1748 ◽  
Author(s):  
Rita M. Hickey ◽  
R. Paul Ross ◽  
Colin Hill
Keyword(s):  
Large Scale ◽  
Production Systems ◽  
Expression System ◽  
Fold Increase ◽  
Lytic Enzyme ◽  
Enzyme Release ◽  
Gram Positive Bacteria ◽  
Wide Range ◽  
Potential Applications ◽  
A Cell

ABSTRACT This study concerns the exploitation of the lytic enzyme enterolysin A (EntL), produced by Enterococcus faecalis strain DPC5280, to elicit the controlled autolysis of starter lactococci. EntL, a cell wall metalloendopeptidase secreted by some E. faecalis strains, can kill a wide range of gram-positive bacteria, including lactococci. The controlled expression of entL, which encodes EntL, was achieved using a nisin-inducible expression system in a lactococcal host. Zymographic analysis of EntL activity demonstrated that active enzyme is produced by the recombinant lactococcal host. Indeed, expression of EntL resulted in almost complete autolysis of the host strain 2 h after induction with nisin. Model cheese experiments using a starter strain in addition to the inducible enterolysin-producing strain showed a 27-fold increase in activity with respect to the release of lactate dehydrogenase in the strain overexpressing EntL, demonstrating the potential of EntL production in large-scale cheese production systems. Indeed, the observation that a wide range of lactic bacteria are sensitive to EntL suggests that EntL-induced autolysis has potential applications with a variety of lactic acid bacteria and could be a basis for probiotic delivery systems.

scholarly journals A Slot-Die Technique for the Preparation of Continuous, High-Area, Chitosan-Based Thin Films

Polymers ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1566
Author(s):  
Oliver J. Pemble ◽  
Maria Bardosova ◽  
Ian M. Povey ◽  
Martyn E. Pemble
Keyword(s):  
Thin Films ◽  
Mechanical Properties ◽  
High Volume ◽  
Mechanical Anisotropy ◽  
Diverse Range ◽  
Direction Parallel ◽  
High Area ◽  
Wide Range ◽  
Slot Die ◽  
Potential Applications

Chitosan-based films have a diverse range of potential applications but are currently limited in terms of commercial use due to a lack of methods specifically designed to produce thin films in high volumes. To address this limitation directly, hydrogels prepared from chitosan, chitosan-tetraethoxy silane, also known as tetraethyl orthosilicate (TEOS) and chitosan-glutaraldehyde have been used to prepare continuous thin films using a slot-die technique which is described in detail. By way of preliminary analysis of the resulting films for comparison purposes with films made by other methods, the mechanical strength of the films produced was assessed. It was found that as expected, the hybrid films made with TEOS and glutaraldehyde both show a higher yield strength than the films made with chitosan alone. In all cases, the mechanical properties of the films were found to compare very favorably with similar measurements reported in the literature. In order to assess the possible influence of the direction in which the hydrogel passes through the slot-die on the mechanical properties of the films, testing was performed on plain chitosan samples cut in a direction parallel to the direction of travel and perpendicular to this direction. It was found that there was no evidence of any mechanical anisotropy induced by the slot die process. The examples presented here serve to illustrate how the slot-die approach may be used to create high-volume, high-area chitosan-based films cheaply and rapidly. It is suggested that an approach of the type described here may facilitate the use of chitosan-based films for a wide range of important applications.

scholarly journals Health Benefits of Uses and Applications of Moringa oleifera in Bakery Products

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 318
Author(s):  
Paula García Milla ◽  
Rocío Peñalver ◽  
Gema Nieto
Keyword(s):  
Moringa Oleifera ◽  
Essential Amino Acids ◽  
Bakery Products ◽  
Unani Medicine ◽  
Functional Value ◽  
Organoleptic Characteristics ◽  
Wide Range ◽  
Potential Applications ◽  
Medicinal Properties ◽  
Excellent Source

Moringa oleifera belongs to the Moringaceae family and is the best known of the native Moringa oleifera genus. For centuries, it has been used as a system of Ayurvedic and Unani medicine and has a wide range of nutritional and bioactive compounds, including proteins, essential amino acids, carbohydrates, lipids, fibre, vitamins, minerals, phenolic compounds, phytosterols and others. These characteristics allow it to have pharmacological properties, including anti-diabetic, anti-inflammatory, anticarcinogenic, antioxidant, cardioprotective, antimicrobial and hepatoprotective properties. The entire Moringa oleifera plant is edible, including its flowers, however, it is not entirely safe, because of compounds that have been found mainly in the root and bark, so the leaf was identified as the safest. Moringa oleifera is recognised as an excellent source of phytochemicals, with potential applications in functional and medicinal food preparations due to its nutritional and medicinal properties; many authors have experimented with incorporating it mainly in biscuits, cakes, brownies, meats, juices and sandwiches. The results are fascinating, as the products increase their nutritional value; however, the concentrations cannot be high, as this affects the organoleptic characteristics of the supplemented products. The aim of this study is to review the application of Moringa oleifera in bakery products, which will allow the creation of new products that improve their nutritional and functional value.

scholarly journals Plant antimicrobial peptides: structures, functions, and applications

2021 ◽  
Vol 62 (1) ◽  
Author(s):  
Junpeng Li ◽  
Shuping Hu ◽  
Wei Jian ◽  
Chengjian Xie ◽  
Xingyong Yang
Keyword(s):  
Antimicrobial Activity ◽  
Antimicrobial Peptides ◽  
Agricultural Production ◽  
Food Additives ◽  
Antimicrobial Activities ◽  
Gram Positive Bacteria ◽  
Potential Applications ◽  
Potential Applicability ◽  
Bacteria And Fungi ◽  
Positively Charged

AbstractAntimicrobial peptides (AMPs) are a class of short, usually positively charged polypeptides that exist in humans, animals, and plants. Considering the increasing number of drug-resistant pathogens, the antimicrobial activity of AMPs has attracted much attention. AMPs with broad-spectrum antimicrobial activity against many gram-positive bacteria, gram-negative bacteria, and fungi are an important defensive barrier against pathogens for many organisms. With continuing research, many other physiological functions of plant AMPs have been found in addition to their antimicrobial roles, such as regulating plant growth and development and treating many diseases with high efficacy. The potential applicability of plant AMPs in agricultural production, as food additives and disease treatments, has garnered much interest. This review focuses on the types of plant AMPs, their mechanisms of action, the parameters affecting the antimicrobial activities of AMPs, and their potential applications in agricultural production, the food industry, breeding industry, and medical field.

scholarly journals Applicability of Honey on Silkworms (Bombyx mori) and Quality Improvement of Its Biomaterials

2021 ◽  
Vol 11 (10) ◽  
pp. 4613
Author(s):  
Gabriela-Maria Baci ◽  
Alexandra-Antonia Cucu ◽  
Adela Ramona Moise ◽  
Daniel Severus Dezmirean
Keyword(s):  
Quality Improvement ◽  
Bombyx Mori ◽  
Human Health ◽  
Recombinant Proteins ◽  
Therapeutic Agent ◽  
Life Sciences ◽  
Model Organism ◽  
Medical Field ◽  
Wide Range ◽  
Ancient Times

Since ancient times, honey has been considered one of the most illustrious and esteemed natural products. Honey plays two key roles; specifically, it is an appreciated nutritional product, and also exhibits a wide range of beneficial properties for human health as a therapeutic agent. Furthermore, it has been shown that honey has valuable effects on the biological and physiological features of mulberry silkworms (Bombyx mori). Bombyx mori exhibits importance not only for the economy, but it also serves as an important biotechnological bioreactor for the production of recombinant proteins that have a great impact in the medical field and beyond. It also represents an important model organism for life sciences. In view of the fact that silk fibroin serves as a natural biopolymer that displays high biocompatibility with human organisms and due to honey’s various and remarkable properties for human health, the two elements are currently used together in order to develop ideal biomaterials for a wide range of purposes. In this review, by discussing the applicability of honey on Bombyx mori and beyond, the importance of honey for life sciences and related fields is spotlighted.

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