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Applied Microbiology
Special Issues
Advances in Fundamentals and Application of Microbial Industrial Biotechnology
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Advances in Fundamentals and Application of Microbial Industrial Biotechnology

A special issue of Applied Microbiology (ISSN 2673-8007).

Deadline for manuscript submissions: 30 June 2026 | Viewed by 1057

Special Issue Editors

Prof. Dr. J.H. de Winde

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Guest Editor
Department of Molecular Biotechnology, Institute for Biology, Leiden University, 2333 BE Leiden, The Netherlands
Interests: microbial molecular genetics and metabolic engineering; applied genomics and systems biology; control of nutrient signalling and transport in baker’s yeast Saccharomyces cerevisiae; identification of novel enzymes in the filamentous fungus Aspergillus niger; molecular mechanisms of stress and solvent tolerance in Pseudomonas putida
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Arthur Ram

E-Mail Website
Guest Editor
Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
Interests: Aspergillus niger; plant cell wall degradation; transcription factors; plant cell wall aromatics; genome editing; enzyme production; cell factory
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial industrial biotechnology, also known as industrial microbiology, highlights the application of microorganisms to produce valuable products and facilitate processes—predominantly industrial. To date, the metabolic versatility and diversity of various bacteria, yeasts and fungi has been harnessed to synthesize, degrade and recycle a wide range of bio-based chemicals, fuels, pharmaceuticals, and other natural and non-natural materials. Microbial industrial biotechnology offers important alternatives to chemical processes for the synthesis and degradation of many materials and compounds, and thus provides invaluable contributions to the development of sustainable alternatives for an array of industrial products and processes.

Microbial industrial biotechnology combines scientific and engineering principles with microorganisms, creating valuable products and processes. Important aspects are in the discovery, engineering and application of new organisms and pathways, for the synthesis or repurposing of both natural and produced compounds. In the last decade, the arrival of innovative synthetic biology and metabolic engineering techniques—alongside the implementation of advanced bioinformatics and analytical technology—has boosted the development of a multitude of microbial biobased applications. Harnessing biodiversity, the engineering of enzymes and the reconstruction of new metabolic routes has allowed for the generation of innovative microbial cell factory concepts that feature synthesis and metabolization of a range of high-value molecules that have only recently been made accessible via biological processes.

This Special Issue, supported by both Microorganisms and Applied Microbiology, is open to state-of-the-art and revolutionizing commentaries, research papers, and reviews. These are expected to highlight important and novel developments in the broad field of microbial industrial biotechnology. Importantly, contributions will not be restricted to synthetic biology and metabolic engineering of novel enzymes, pathways and microorganisms. The engineering of microbial cell factories and biotechnological processes—for a variety of applications—are also welcome. All contributions are expected to clearly contribute to the advancement of microbial industrial biotechnology for a sustainable biobased economy.

You may choose our Joint Special Issue in Microorganisms.

Prof. Dr. J.H. de Winde
Prof. Dr. Arthur Ram
Guest Editors

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 250 words) can be sent to the Editorial Office for assessment.

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. Applied Microbiology 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 1200 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 industrial biotechnology
  • industrial microbiology
  • applied microbiology

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Published Papers (1 paper)

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Research

35 pages, 3865 KB  
Article
In Silico Interaction Profiling of Pseudomonas aeruginosa Elastase (LasB) with Structural Fragments of Synthetic Polymers
by Afrah I. Waheeb, Saleem Obaid Gatia Almawla, Mayada Abdullah Shehan, Sameer Ahmed Awad, Mohammed Mukhles Ahmed and Saja Saddallah Abduljaleel
Appl. Microbiol. 2026, 6(4), 51; https://doi.org/10.3390/applmicrobiol6040051 - 7 Apr 2026
Viewed by 398
Abstract
Background: The ability of synthetic plastics to persist in the environment and the accumulation of microplastics has intensified the need to explore biological mechanisms capable of interacting with, and possibly degrading, polymeric materials. Microbial enzymes that have extensive catalytic flexibility represent promising candidates [...] Read more.
Background: The ability of synthetic plastics to persist in the environment and the accumulation of microplastics has intensified the need to explore biological mechanisms capable of interacting with, and possibly degrading, polymeric materials. Microbial enzymes that have extensive catalytic flexibility represent promising candidates in this context. Aim: This study set out to examine the molecular interaction patterns and dynamical stability of Pseudomonas aeruginosa elastase (LasB) with representative structural fragments of typical synthetic plastics to assess the suitability of the enzyme to polymer-derived substrates. Methods: The crystallographic structure of LasB (PDB ID: 1EZM) was retrieved from the Protein Data Bank and pre-prepared with the help of AutoDock4.2.6 Tools. Those polymer-derived ligands that were associated with the major industrial plastics such as polyamide (PA), polyvinyl chloride (PVC), polycarbonate (PC), poly-ethylene terephthalate (PET), polymethyl methacrylate (PMMA), and polyurethane (PUR) were retrieved in the PubChem database and geometrically optimized with the help of the MMFF94 force field. AutoDock Vina, with a specific grid box around the catalytic pocket, including Zn2+ ion, was used to perform molecular docking simulations. PyMOL and BIOVIA Discovery Studio software were used to analyze binding conformations, interaction residues and types of intermolecular contacts. Phosphoramidon, a known metalloprotease inhibitor, served as a positive control to confirm the docking protocol. Additional assessment of the structural stability and conformational behavior of the enzyme–ligand complexes was conducted by molecular dynamics (MD) simulations with the Desmond engine and explicit solvent model in a 50 ns trajectory using the OPLS4 force field. RMSD, RMSF, radius of gyration, hydrogen bonding analysis and solvent accessibility parameters were used to measure structural stability. Results: The docking experiment showed varying binding affinities with the test polymers. Polycarbonate (−5.774 kcal/mol) and polyurethane (−5.707 kcal/mol) had the highest in-teractions with the LasB catalytic pocket, polyamide (−5.277 kcal/mol) and PET (−4.483 kcal/mol) followed PMMA and PVC, which had weaker affinities. The following were the important residues involved in interaction networks: Glu141, His140, Val137, Arg198, Tyr114, and Trp115 that were implicated in interaction networks with hydrophobic interactions, π-cation interactions and van der Waals forces that were the major stabilization forces. MD simulations had stabilized complexes, and RMSD values were found to be within acceptable ranges of stability, and ligand-specific changes (around 1.0-3.2 A), which is also in line with stable protein-ligand systems. Phosphoramidon used as a positive control had an RMSD of 1.205 A which is within this stability range. PCA determined various ligand-bound conformational states of LasB with PA in com-pact state, PC and PVC in intermediate states and PUR, PMMA and PET in ex-panded conformations, indicating structur-al stability and adaptability of the binding pocket. Conclusion: These findings show that LasB has a structurally flexible catalytic pocket that can accommodate a wide range of polymer-derived ligands. These results offer an insight into the recognition of enzymes with polymers at the molecular level and also indicate that LasB might help in the interaction of microorganisms with synthetic plastics in environmental systems. Full article
(This article belongs to the Special Issue Advances in Fundamentals and Application of Microbial Industrial Biotechnology)
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