1
|
Balleux G, Höfte M, Arguelles-Arias A, Deleu M, Ongena M. Bacillus lipopeptides as key players in rhizosphere chemical ecology. Trends Microbiol 2024:S0966-842X(24)00197-5. [PMID: 39214821 DOI: 10.1016/j.tim.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Microbial natural products are widely explored for their therapeutic potential. Understanding the underlying evolutionary and adaptive forces driving their production remains a fundamental question in biology. Amphiphilic cyclic lipopeptides (CLPs), a prominent category of bacterial specialized metabolites, show strong antimicrobial activity, particularly against phytopathogens. It is thus assumed that these compounds are deployed by soil- or rhizosphere-dwelling bacteria as microbial weapons in competitive natural environments. Here, we challenge this reductionist perspective and present evidence that Bacillus CLPs are prominent chemical mediators of ecological interactions. They help Bacillus to communicate, compete, defend against predators, or cooperate and establish mutualistic relationships with other (micro)organisms. Additional parallel examples are highlighted in other genera, such as Pseudomonas. This broader perspective underscores the need for further investigation into the role of CLPs in shaping the adaptive strategies of key rhizobacterial species.
Collapse
Affiliation(s)
- Guillaume Balleux
- Microbial Processes and Interactions laboratory, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium.
| | - Monica Höfte
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
| | - Anthony Arguelles-Arias
- Microbial Processes and Interactions laboratory, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Magali Deleu
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions laboratory, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium.
| |
Collapse
|
2
|
Cheng J, Yin X, Wang L, Liu X, Yang F, Zhang L, Liu T. Decoding molecular mechanism of species-selective targeting of fungal versus human HSP90 using multiple replica molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2023:1-11. [PMID: 37850420 DOI: 10.1080/07391102.2023.2270687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
As a highly evolutionarily conserved molecular chaperone, heat shock protein (HSP90), plays an important role in virulence traits, representing a therapeutic target for the treatment of fungal infections. The close evolutionary relationship between fungi and their human hosts poses a key challenge for the development of selective antifungal agents. In this work, molecular docking, multiple replica microsecond-based molecular dynamics (MD) simulations, and binding free energy calculations were performed to decode molecular mechanism of species-selective targeting of fungal versus human HSP90 triggered by the compound A11. MD simulations reveal that binding of compound A11 to human HSP90 nucleotide-binding domain (NBD) leads to obvious conformational changes relative to fungal HSP90 NBD. Binding free energy calculations show that the binding of compound A11 to fungal HSP90 NBD is stronger than that to human HSP90 NBD. Per residue-based free energy decomposition analysis was used to evaluate the inhibitor - residue interaction profile. The results efficiently identify the hot spot residues that play vital roles in favorable binding of compound A11 to fungal HSP90 NBD. This study is expected to provide a useful guidance for the development of selective inhibitors toward fungal HSP90.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jinying Cheng
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Xue Yin
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Lulu Wang
- Department of Critical Care Medicine, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Xianxian Liu
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Fang Yang
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Liguo Zhang
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Tonggang Liu
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| |
Collapse
|
3
|
Kumari R, Singha LP, Shukla P. Biotechnological potential of microbial bio-surfactants, their significance, and diverse applications. FEMS MICROBES 2023; 4:xtad015. [PMID: 37614639 PMCID: PMC10442721 DOI: 10.1093/femsmc/xtad015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/16/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Globally, there is a huge demand for chemically available surfactants in many industries, irrespective of their detrimental impact on the environment. Naturally occurring green sustainable substances have been proven to be the best alternative for reducing reliance on chemical surfactants and promoting long-lasting sustainable development. The most frequently utilized green active biosurfactants, which are made by bacteria, yeast, and fungi, are discussed in this review. These biosurfactants are commonly originated from contaminated sites, the marine ecosystem, and the natural environment, and it holds great potential for environmental sustainability. In this review, we described the importance of biosurfactants for the environment, including their biodegradability, low toxicity, environmental compatibility, and stability at a wide pH range. In this review, we have also described the various techniques that have been utilized to characterize and screen the generation of microbial biosurfactants. Also, we reviewed the potential of biosurfactants and its emerging applications in the foods, cosmetics, pharmaceuticals, and agricultural industries. In addition, we also discussed the ways to overcome problems with expensive costs such as low-cost substrate media formulation, gravitational techniques, and solvent-free foam fractionation for extraction that could be employed during biosurfactant production on a larger scale.
Collapse
Affiliation(s)
- Renuka Kumari
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Lairenjam Paikhomba Singha
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer-305817, Rajasthan, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| |
Collapse
|
4
|
Heterophyllin B inhibits the malignant phenotypes of gastric cancer cells via CXCR4. Hum Cell 2023; 36:676-688. [PMID: 36539682 DOI: 10.1007/s13577-022-00824-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
Heterophyllin B (HB) is a cyclic lipopeptide that has been shown to have anticancer effects. This study intended to further explore the effects and modulatory mechanism of HB in gastric cancer (GC) cells. The binding relationship between HB and CXCR4 was investigated by network pharmacological analysis, molecular docking, and cellular thermal shift assay (CETSA)-WB assay. Cellular assays revealed that HB could restrain GC cell viability, proliferation, invasion and migration by binding to CXCR4. Further studies presented that HB could suppress PI3K/AKT signaling pathway via binding to CXCR4, thus repressing PD-L1 expression. In vivo experiments in nude mice demonstrated that HB constrained PI3K/AKT signaling pathway to suppress GC cell metastasis and PD-L1 expression. In summary, the key target of HB in GC treatment was CXCR4. Cell experiments were employed for the investigation of the mechanism by which HB repressed GC cells. The results confirmed that HB could constrain the malignant progression of GC by the binding of HB into CXCR4 and suppressed PD-L1 expression via hampering PI3K/AKT signaling pathway.
Collapse
|
5
|
LC-MS and Transcriptome Analysis of Lipopeptide Biosynthesis by Bacillus velezensis CMT-6 Responding to Dissolved Oxygen. Molecules 2022; 27:molecules27206822. [PMID: 36296415 PMCID: PMC9607200 DOI: 10.3390/molecules27206822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
Dissolved oxygen (DO) is an key factor for lipopeptide fermentation. To better understand the link between oxygen supply and lipopeptide productivity in Bacillus velezensis CMT-6, the mechanism of DO on the synthesis of antimicrobial lipopeptides by Bacillus velezensis CMT-6 was examined. The production of surfactin and iturin of CMT-6 was detected by liquid chromatography–mass spectrometer (LC-MS) under different DO conditions and transcriptome analysis was performed. At 100 and 200 rpm, the lipopeptides productions were 2753.62 mg/L and 3452.90 mg/L, respectively. There was no significant change in the yield of iturin but that of surfactin increased by 64.14%. Transcriptome analysis revealed that the enriched differential genes were concentrated in the GO term of oxidation–reduction process. The marked enrichment of the lipopeptides synthesis pathway, including microbial metabolism in diverse environments and carbon metabolism in the two-component system, were observed. More importantly, the expression levels of the four surfactin synthetase genes increased at higher DO, however, the iturin synthetase gene expression did not. Furthermore, modular surfactin synthetase was overexpressed (between 9- and 49-fold) at 200 rpm but not at 100 rpm, which is suggestive of efficient surfactin assembly resulting in surfactin overproduction. This study provides a theoretical basis for constructing engineering strains with high lipopeptide production to adapt to different DO.
Collapse
|
6
|
Heat Shock Protein 90 (HSP90) Inhibitors as Anticancer Medicines: A Review on the Computer-Aided Drug Discovery Approaches over the Past Five Years. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2147763. [PMID: 35685897 PMCID: PMC9173959 DOI: 10.1155/2022/2147763] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/08/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022]
Abstract
Cancer is a disease caused by the uncontrolled, abnormal growth of cells in different anatomic sites. In 2018, it was predicted that the worldwide cancer burden would rise to 18.1 million new cases and 9.6 million deaths. Anticancer compounds, often known as chemotherapeutic medicines, have gained much interest in recent cancer research. These medicines work through various biological processes in targeting cells at various stages of the cell's life cycle. One of the most significant roadblocks to developing anticancer drugs is that traditional chemotherapy affects normal cells and cancer cells, resulting in substantial side effects. Recently, advancements in new drug development methodologies and the prediction of the targeted interatomic and intermolecular ligand interaction sites have been beneficial. This has prompted further research into developing and discovering novel chemical species as preferred therapeutic compounds against specific cancer types. Identifying new drug molecules with high selectivity and specificity for cancer is a prerequisite in the treatment and management of the disease. The overexpression of HSP90 occurs in patients with cancer, and the HSP90 triggers unstable harmful kinase functions, which enhance carcinogenesis. Therefore, the development of potent HSP90 inhibitors with high selectivity and specificity becomes very imperative. The activities of HSP90 as chaperones and cochaperones are complex due to the conformational dynamism, and this could be one of the reasons why no HSP90 drugs have made it beyond the clinical trials. Nevertheless, HSP90 modulations appear to be preferred due to the competitive inhibition of the targeted N-terminal adenosine triphosphate pocket. This study, therefore, presents an overview of the various computational models implored in the development of HSP90 inhibitors as anticancer medicines. We hereby suggest an extensive investigation of advanced computational modelling of the three different domains of HSP90 for potent, effective inhibitor design with minimal off-target effects.
Collapse
|