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Molecular Research on Bacteria: 2nd Edition
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Molecular Research on Bacteria: 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 20 December 2026 | Viewed by 2290

Special Issue Editor

Dr. Giovanni Stelitano

E-Mail Website
Guest Editor
Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata 9, 27100 Pavia, Italy
Interests: bacterial biochemistry; enzymes; target identification; drug development; mycobacteria; infectious diseases; antimicrobial resistance; metabolites; computational approaches
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, "Molecular Research on Bacteria."

Research on bacteria remains an open field today due to the identification of emerging new species and clinical isolates resistant to most antibiotics in use. Fortunately, therapeutic approaches are evolving with the integration of new strategies, such as antivirulence therapies, drug repurposing, and phage therapy. On the other hand, new research is focusing on the use of non-pathogenic bacteria for beneficial purposes, such as bioremediation and biorestoration. This Special Issue aims to collate original papers and reviews on bacteria research, with particular relevance on the molecular level.

Dr. Giovanni Stelitano
Guest Editor

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • bacteria
  • molecular biology
  • infections
  • antimicrobials
  • bacterial enzymes
  • bioremediation
  • enzyme evolution and adaptation

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Published Papers (3 papers)

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20 pages, 2056 KB  
Article
Direct Production of 2-Butanol from Glucose by Recombinant Klebsiella pneumoniae Strains
by Emanoel Gergov, Alexander Arsov, Kaloyan Petrov, Lidia Tsigoriyna and Penka Petrova
Int. J. Mol. Sci. 2026, 27(6), 2892; https://doi.org/10.3390/ijms27062892 - 23 Mar 2026
Viewed by 404
Abstract
2-Butanol is a promising biofuel due to its favorable properties and lower microbial toxicity compared to other butanol isomers. However, microbial production remains challenging due to the absence of a native biochemical pathway for directly converting sugars into 2-butanol. To achieve this goal, [...] Read more.
2-Butanol is a promising biofuel due to its favorable properties and lower microbial toxicity compared to other butanol isomers. However, microbial production remains challenging due to the absence of a native biochemical pathway for directly converting sugars into 2-butanol. To achieve this goal, glucose should be directed through the 2,3-butanediol (2,3-BD) pathway, involving α-acetolactate synthase, α-acetolactate decarboxylase, and butanediol dehydrogenase for the formation of meso-2,3-BD, followed by diol dehydratase-catalyzed conversion of meso-2,3-BD to butanone and alcohol dehydrogenase-mediated reduction in butanone to 2-butanol. In this study, we report the development of six new recombinant strains based on Klebsiella pneumoniae G31, in which the metabolic pathway for converting glucose to meso-2,3-BD was extended to 2-butanol. All engineered strains harbored the vitamin B12-dependent diol dehydratase complex (pduCDEGH) from Lentilactobacillus diolivorans DSM 14421 under its native promoter control. In addition, pduQ from the same strain, and adh from Clostridium beijerinckii DSM 51 encoding alcohol dehydrogenases were expressed under native, T7, or Ptac promoters. The highest yield of 2-butanol from glucose was achieved by K. pneumoniae K6 carrying the adh gene under the control of the T7 promoter—437 mg/L. Using 2-butanone as a substrate, K6 again produced the highest titer of 2-butanol (3.9 g/L), followed by the recombinant K8 (with adh under the Ptac promoter), and notably, by the native K. pneumoniae strains. Therefore, although pduQ encodes a key alcohol dehydrogenase in L. diolivorans, it has weaker properties than adh for the K. pneumoniae host in all promoter configurations. As the high expression levels of adh under T7 promoter control were driven by the native bacterial RNA polymerase, this promoter–host combination appears particularly suitable for developing other strains of industrial relevance. Full article
(This article belongs to the Special Issue Molecular Research on Bacteria: 2nd Edition)
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19 pages, 11607 KB  
Article
The Effect of clpP Gene Disruption on Cell Morphology, Growth, and the Ability to Synthesize Cellulose of Komagataeibacter xylinus E25
by Marzena Jędrzejczak-Krzepkowska, Karolina Ludwicka and Stanislaw Bielecki
Int. J. Mol. Sci. 2025, 26(24), 12047; https://doi.org/10.3390/ijms262412047 - 15 Dec 2025
Viewed by 745
Abstract
Komagataeibacter species are the best producers of bacterial nanocellulose membranes (BNC)—amazing biomaterial with unique properties and applications in the medical and food industries. The molecular mechanisms of BNC synthesis control remain poorly understood and the need for BNC production and structure improvement is [...] Read more.
Komagataeibacter species are the best producers of bacterial nanocellulose membranes (BNC)—amazing biomaterial with unique properties and applications in the medical and food industries. The molecular mechanisms of BNC synthesis control remain poorly understood and the need for BNC production and structure improvement is growing. Looking for the genes significant for biosynthesis, we studied the unexplored effect of ClpP proteolytic subunit inactivation on Komagataeibacter xylinus E25 cell morphology and production of BNC. A mutant with a disrupted clpP gene and a complemented strain were obtained. The colonies of the mutant cells, in contrast to the wild-type and complemented ones, were smaller, irregular, and were surrounded by a polymeric noncellulosic envelope. Additionally, the mutant cells were longer and organized in chains, showing different growth and production dynamics of BNC when grown under standard conditions. We also observed worse growth and production of BNC at 5 °C above optimal temperature and in the presence of increased levels of ethanol. E25 mutant cells were characterized by lower viability under stress conditions. The 3D microstructure of BNC displayed thicker fibers and denser packing and contained more hard-to-extract exopolysaccharides (HE-EPSs). Based on the outcomes, we conclude that the effect of ClpP on K. xylinus decreased resistance to stress and lowered the BNC production level. Full article
(This article belongs to the Special Issue Molecular Research on Bacteria: 2nd Edition)
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16 pages, 1680 KB  
Article
Effect of the Bacterial Chaperones SecB and Trigger Factor (TF) on the Folding Dynamics and In Vitro Translocation of Cytoplasmic and Secretory Model Proteins
by Ying Xu, Haitham Sedky, Dries Smets, Jochem Smit, Spyridoula Karamanou, Anastassios Economou and Kurt Vermeire
Int. J. Mol. Sci. 2025, 26(23), 11485; https://doi.org/10.3390/ijms262311485 - 27 Nov 2025
Viewed by 820
Abstract
Nascent polypeptides selected for export are synthesized in the cytoplasm by ribosomes and inserted into or translocated across membranes to reach their correct location. Exported proteins delay their folding and remain soluble during their cytoplasmic transit to the membrane. In bacteria, most secretory [...] Read more.
Nascent polypeptides selected for export are synthesized in the cytoplasm by ribosomes and inserted into or translocated across membranes to reach their correct location. Exported proteins delay their folding and remain soluble during their cytoplasmic transit to the membrane. In bacteria, most secretory proteins require additional support from cytosolic chaperones such as trigger factor (TF) and SecB to promote their translocation competence. Here, we investigate the effect of TF and SecB on the folding dynamics and in vitro translocation of secretory and cytoplasmic model proteins PpiA and PpiB, respectively. Global hydrogen—deuterium exchange mass spectrometry (HDX-MS) experiments reveal that SecB delays the folding of slow-folding PpiA proteins but has no effect on fast folders like PpiB. In vitro protein translocation results show that TF inhibits the Sec-dependent translocation of mature PpiA/B and derivative proteins, as well as some secretory preproteins carrying a signal peptide (SP), whereas SecB has no clear effect under the same conditions. However, SecB proves to be dominant over TF in protein translocation in vitro. Finally, for the secretory preprotein proPpiA, SecB prevents SP-induced aggregation. Our findings indicate that the combined properties of signal peptides and mature domains dictate chaperone specificity and translocation efficiency, with both TF and SecB acting in a substrate-specific manner. Full article
(This article belongs to the Special Issue Molecular Research on Bacteria: 2nd Edition)
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