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Microorganisms
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Microbial Biocatalysis and Biodegradation
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Microbial Biocatalysis and Biodegradation

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 18034

Special Issue Editor

Prof. Dr. Andrew Willetts

E-Mail Website
Guest Editor
College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, UK
Interests: microbial biochemistry; microbial biocatalysis; microbial biodegradation: chemoenzymatic synthesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial biocatalysis and biodegradation reflect facets of the global biogeochemical carbon cycle; each can have useful/valuable practical applications in microbial biotechnology, for instance, in chemoenzymatic synthesis and bioremediation, respectively. The goal of this Special Issues is to provide some current insights in these areas of microbiology, from the molecular level of individual enzymes to the level of whole ecosystems. Particular emphasis will be placed on beneficial advances resulting from the introduction of new technologies, including both those that have evolved specifically in the post-genomic era (e.g., protein engineering by directed evolution) and those that have grown out of greater knowledge and understanding of enzyme structure–function relationships (e.g., combinatorial active-site mutation and iterative saturation mutagenesis). In addition, we hope to include examples of appropriate strategies that enhance the robustness of individual microbial enzymes used in biocatalysis, as well as of microbial cultures or ecosystems used for bioremediation.

Case studies to be covered could include the role of microbial biocatalysis in the production of bulk chemicals (e.g., acrylamide), fine chemicals (e.g., flavours and fragrances), pharmaceuticals (e.g., esomeprazole and simvastatin), and drug metabolites for pharmacokinetic studies, in addition to the relative merits of biostimulation and bioaugmentation as different strategies to promote bioremediation and/or waste recycling.

Prof. Dr. Andrew Willetts
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbial biocatalysis
  • chemoenzymatic synthesis
  • directed evolution
  • active site mutation
  • bioremediation
  • waste recycling

Published Papers (7 papers)

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Research

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12 pages, 831 KiB  
Article
Inter-Species Redox Coupling by Flavin Reductases and FMN-Dependent Two-Component Monooxygenases Undertaking Nucleophilic Baeyer–Villiger Biooxygenations
by Andrew Willetts
Microorganisms 2023, 11(1), 71; https://doi.org/10.3390/microorganisms11010071 - 27 Dec 2022
Cited by 3 | Viewed by 1722
Abstract
Using highly purified enzyme preparations throughout, initial kinetic studies demonstrated that the isoenzymic 2,5- and 3,6-diketocamphane mono-oxygenases from Pseudomonas putida ATCC 17453 and the LuxAB luciferase from Vibrio fischeri ATCC 7744 exhibit commonality in being FMN-dependent two-component monooxygenases that promote redox coupling by [...] Read more.
Using highly purified enzyme preparations throughout, initial kinetic studies demonstrated that the isoenzymic 2,5- and 3,6-diketocamphane mono-oxygenases from Pseudomonas putida ATCC 17453 and the LuxAB luciferase from Vibrio fischeri ATCC 7744 exhibit commonality in being FMN-dependent two-component monooxygenases that promote redox coupling by the transfer of flavin reductase-generated FMNH2 by rapid free diffusion. Subsequent studies confirmed the comprehensive inter-species compatibility of both native and non-native flavin reductases with each of the tested monooxygenases. For all three monooxygenases, non-native flavin reductases from Escherichia coli ATCC 11105 and Aminobacter aminovorans ATCC 29600 were confirmed to be more efficient donators of FMNH2 than the corresponding tested native flavin reductases. Some potential practical implications of these outcomes are considered for optimising FMNH2-dependent biooxygenations of recognised practical and commercial value. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation)
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20 pages, 12811 KiB  
Article
From Rest to Growth: Life Collisions of Gordonia polyisoprenivorans 135
by Nataliya E. Suzina, Vladimir V. Sorokin, Valentina N. Polivtseva, Violetta V. Klyueva, Elena V. Emelyanova and Inna P. Solyanikova
Microorganisms 2022, 10(2), 465; https://doi.org/10.3390/microorganisms10020465 - 18 Feb 2022
Cited by 4 | Viewed by 2065
Abstract
In the process of evolution, living organisms develop mechanisms for population preservation to survive in unfavorable conditions. Spores and cysts are the most obvious examples of dormant forms in microorganisms. Non-spore-forming bacteria are also capable of surviving in unfavorable conditions, but the patterns [...] Read more.
In the process of evolution, living organisms develop mechanisms for population preservation to survive in unfavorable conditions. Spores and cysts are the most obvious examples of dormant forms in microorganisms. Non-spore-forming bacteria are also capable of surviving in unfavorable conditions, but the patterns of their behavior and adaptive reactions have been studied in less detail compared to spore-forming organisms. The purpose of this work was to study the features of transition from dormancy to active vegetative growth in one of the non-spore-forming bacteria, Gordonia polisoprenivorans 135, which is known as a destructor of such aromatic compounds as benzoate, 3-chlorobenzoate, and phenol. It was shown that G. polyisoprenivorans 135 under unfavorable conditions forms cyst-like cells with increased thermal resistance. Storage for two years does not lead to complete cell death. When the cells were transferred to fresh nutrient medium, visible growth was observed after 3 h. Immobilized cells stored at 4 °C for at least 10 months regenerated their metabolic activity after only 30 min of aeration. A study of the ultrathin organization of resting cells by transmission electron microscopy combined with X-ray microanalysis revealed intracytoplasmic electron-dense spherical membrane ultrastructures with significant similarity to previously described acidocalcisomas. The ability of some resting G. polyisoprenivorans 135 cells in the population to secrete acidocalcisome-like ultrastructures into the extracellular space was also detected. These structures contain predominantly calcium (Ca) and, to a lesser extent, phosphorus (P), and are likely to serve as depots of vital macronutrients to maintain cell viability during resting and provide a quick transition to a metabolically active state under favorable conditions. The study revealed the features of transitions from active growth to dormant state and vice versa of non-spore-forming bacteria G. polyisoprenivorans 135 and the possibility to use them as the basis of biopreparations with a long shelf life. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation)
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11 pages, 3085 KiB  
Article
Polyhydroxyalkanoate (PHA) Production in Pseudomonas sp. phDV1 Strain Grown on Phenol as Carbon Sources
by Iliana Kanavaki, Athina Drakonaki, Ermis Dionisios Geladas, Apostolos Spyros, Hao Xie and Georgios Tsiotis
Microorganisms 2021, 9(8), 1636; https://doi.org/10.3390/microorganisms9081636 - 30 Jul 2021
Cited by 24 | Viewed by 3869
Abstract
Pseudomonas strains have a variety of potential uses in bioremediation and biosynthesis of biodegradable plastics. Pseudomonas sp. strain phDV1, a Gram-negative phenol degrading bacterium, has been found to utilize monocyclic aromatic compounds as sole carbon source via the meta-cleavage pathway. The degradation [...] Read more.
Pseudomonas strains have a variety of potential uses in bioremediation and biosynthesis of biodegradable plastics. Pseudomonas sp. strain phDV1, a Gram-negative phenol degrading bacterium, has been found to utilize monocyclic aromatic compounds as sole carbon source via the meta-cleavage pathway. The degradation of aromatic compounds comprises an important step in the removal of pollutants. The present study aimed to investigate the ability of the Pseudomonas sp. strain phDV1 to produce polyhydroxyalkanoates (PHAs) and examining the effect of phenol concentration on PHA production. The bacterium was cultivated in minimal medium supplemented with different concentrations of phenol ranging from 200–600 mg/L. The activity of the PHA synthase, the key enzyme which produces PHA, was monitored spectroscopically in cells extracts. Furthermore, the PHA synthase was identified by mass spectrometry in cell extracts analyzed by SDS-PAGE. Transmission electron micrographs revealed abundant electron-transparent intracellular granules. The isolated biopolymer was confirmed to be polyhydroxybutyrate (PHB) by FTIR, NMR and MALDI-TOF/TOF analyses. The ability of strain Pseudomonas sp. phDV1 to remove phenol and to produce PHB makes the strain a promising biocatalyst in bioremediation and biosynthesis of biodegradable plastics. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation)
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11 pages, 1986 KiB  
Article
A Host-Vector System for the Expression of a Thermostable Bacterial Lipase in a Locally Isolated Meyerozyma guilliermondii SMB
by Abu Bakar Salleh, Siti Marha Baharuddin, Raja Noor Zaliha Raja Abd Rahman, Thean Chor Leow, Mahiran Basri and Siti Nurbaya Oslan
Microorganisms 2020, 8(11), 1738; https://doi.org/10.3390/microorganisms8111738 - 06 Nov 2020
Cited by 1 | Viewed by 2543
Abstract
Screening for a new yeast as an alternative host is expected to solve the limitations in the present yeast expression system. A yeast sample which was isolated from the traditional food starter ‘ragi’ from Malaysia was identified to contain Meyerozyma guilliermondii strain SMB. [...] Read more.
Screening for a new yeast as an alternative host is expected to solve the limitations in the present yeast expression system. A yeast sample which was isolated from the traditional food starter ‘ragi’ from Malaysia was identified to contain Meyerozyma guilliermondii strain SMB. This yeast-like fungus strain SMB was characterized to assess its suitability as an expression host. Lipase activity was absent in this host (when assayed at 30 °C and 70 °C) and Hygromycin B (50 μg/mL) was found to be its best selection marker. Then, the hyg gene (Hygromycin B) was used to replace the sh ble gene (Zeocin) expression cassette in a Komagataella phaffii expression vector (designated as pFLDhα). A gene encoding the mature thermostable lipase from Bacillus sp. L2 was cloned into pFLDhα, followed by transformation into strain SMB. The optimal expression of L2 lipase was achieved using YPTM (Yeast Extract-Peptone-Tryptic-Methanol) medium after 48 h with 0.5% (v/v) methanol induction, which was 3 times faster than another K. phaffii expression system. In conclusion, a new host-vector system was established as a platform to express L2 lipase under the regulation of PFLD1. It could also be promising to express other recombinant proteins without inducers. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation)
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16 pages, 6306 KiB  
Article
Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope
by Tom Halliwell, Karl Fisher, Karl A. P. Payne, Stephen E. J. Rigby and David Leys
Microorganisms 2020, 8(9), 1344; https://doi.org/10.3390/microorganisms8091344 - 02 Sep 2020
Cited by 5 | Viewed by 2705
Abstract
Reductive dehalogenases are responsible for the reductive cleavage of carbon-halogen bonds during organohalide respiration. A variety of mechanisms have been proposed for these cobalamin and [4Fe-4S] containing enzymes, including organocobalt, radical, or cobalt-halide adduct based catalysis. The latter was proposed for the oxygen-tolerant [...] Read more.
Reductive dehalogenases are responsible for the reductive cleavage of carbon-halogen bonds during organohalide respiration. A variety of mechanisms have been proposed for these cobalamin and [4Fe-4S] containing enzymes, including organocobalt, radical, or cobalt-halide adduct based catalysis. The latter was proposed for the oxygen-tolerant Nitratireductor pacificus pht-3B catabolic reductive dehalogenase (NpRdhA). Here, we present the first substrate bound NpRdhA crystal structures, confirming a direct cobalt–halogen interaction is established and providing a rationale for substrate preference. Product formation is observed in crystallo due to X-ray photoreduction. Protein engineering enables rational alteration of substrate preference, providing a future blue print for the application of this and related enzymes in bioremediation. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation)
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14 pages, 15104 KiB  
Article
Light Regulation of Two New Manganese Peroxidase-Encoding Genes in Trametes polyzona KU-RNW027
by Piyangkun Lueangjaroenkit, Emi Kunitake, Makiko Sakka, Tetsuya Kimura, Churapa Teerapatsakul, Kazuo Sakka and Lerluck Chitradon
Microorganisms 2020, 8(6), 852; https://doi.org/10.3390/microorganisms8060852 - 05 Jun 2020
Cited by 6 | Viewed by 2346
Abstract
To better understand the light regulation of ligninolytic systems in Trametes polyzona KU-RNW027, ligninolytic enzymes-encoding genes were identified and analyzed to determine their transcriptional regulatory elements. Elements of light regulation were investigated in submerged culture. Three ligninolytic enzyme-encoding genes, mnp1, mnp2, [...] Read more.
To better understand the light regulation of ligninolytic systems in Trametes polyzona KU-RNW027, ligninolytic enzymes-encoding genes were identified and analyzed to determine their transcriptional regulatory elements. Elements of light regulation were investigated in submerged culture. Three ligninolytic enzyme-encoding genes, mnp1, mnp2, and lac1, were found. Cloning of the genes encoding MnP1 and MnP2 revealed distinct deduced amino acid sequences with 90% and 86% similarity to MnPs in Lenzites gibbosa, respectively. These were classified as new members of short-type hybrid MnPs in subfamily A.2 class II fungal secretion heme peroxidase. A light responsive element (LRE), composed of a 5′-CCRCCC-3′ motif in both mnp promoters, is reported. Light enhanced MnP activity 1.5 times but not laccase activity. The mnp gene expressions under light condition increased 6.5- and 3.8-fold, respectively. Regulation of laccase gene expression by light was inconsistent with the absence of LREs in their promoter. Blue light did not affect gene expressions but impacted their stability. Reductions of MnP and laccase production under blue light were observed. The details of the molecular mechanisms underlying enzyme production in this white-rot fungus provide useful knowledge for wood degradation relative to illumination condition. These novel observations demonstrate the potential of enhancing ligninolytic enzyme production by this fungus for applications with an eco-friendly approach to bioremediation. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation)
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Review

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34 pages, 8556 KiB  
Review
The Isoenzymic Diketocamphane Monooxygenases of Pseudomonas putida ATCC 17453—An Episodic History and Still Mysterious after 60 Years
by Andrew Willetts
Microorganisms 2021, 9(12), 2593; https://doi.org/10.3390/microorganisms9122593 - 15 Dec 2021
Cited by 2 | Viewed by 1823
Abstract
Researching the involvement of molecular oxygen in the degradation of the naturally occurring bicyclic terpene camphor has generated a six-decade history of fascinating monooxygenase biochemistry. While an extensive bibliography exists reporting the many varied studies on camphor 5-monooxygenase, the initiating enzyme of the [...] Read more.
Researching the involvement of molecular oxygen in the degradation of the naturally occurring bicyclic terpene camphor has generated a six-decade history of fascinating monooxygenase biochemistry. While an extensive bibliography exists reporting the many varied studies on camphor 5-monooxygenase, the initiating enzyme of the relevant catabolic pathway in Pseudomonas putida ATCC 17453, the equivalent recorded history of the isoenzymic diketocamphane monooxygenases, the enzymes that facilitate the initial ring cleavage of the bicyclic terpene, is both less extensive and more enigmatic. First referred to as ‘ketolactonase—an enzyme for cyclic lactonization’—the enzyme now classified as 2,5-diketocamphane 1,2-monooxygenase (EC 1.14.14.108) holds a special place in the history of oxygen-dependent biochemistry, being the first biocatalyst confirmed to undertake a biooxygenation reaction equivalent to the peracid-catalysed Baeyer–Villiger chemical oxidation first reported in the late 19th century. However, following that auspicious beginning, the biochemistry of EC 1.14.14.108, and its isoenzymic partner 3,6-diketocamphane 1,6-monooxygenase (EC 1.14.14.155) was dogged for many years by the mistaken belief that the enzymes were true flavoproteins that function with a tightly-bound flavin cofactor in the active site. This misconception led to a number of erroneous interpretations of relevant experimental data. It is only in the last decade, initially as the result of pure serendipity, that these enzymes have been confirmed to be members of a relatively recently discovered class of oxygen-dependent enzymes, the flavin-dependent two-component monooxygenases. This has promoted a renaissance of interest in the enzymes, resulting in programmes of research that have significantly expanded current knowledge of both their mode of action and regulation in camphor-grown P. putida ATCC 17453. However, some features of the biochemistry of the isoenzymic diketocamphane monooxygenases remain currently unexplained. It is the episodic history of these enzymes and some of what remains unresolved that are the principal subjects of this review. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation)
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