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Mattiello SP, Barth VC, Scaria J, Ferreira CAS, Oliveira SD. Fluoroquinolone and beta-lactam antimicrobials induce different transcriptome profiles in Salmonella enterica persister cells. Sci Rep 2023; 13:18696. [PMID: 37907566 PMCID: PMC10618250 DOI: 10.1038/s41598-023-46142-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023] Open
Abstract
Here, we investigate the transcriptome profiles of two S. Enteritidis and one S. Schwarzengrund isolates that present different persister levels when exposed to ciprofloxacin or ceftazidime. It was possible to note a distinct transcript profile among isolates, time of exposure, and treatment. We could not find a commonly expressed transcript profile that plays a role in persister formation after S. enterica exposure to beta-lactam or fluoroquinolone, as only three DEGs presented the same behavior under the conditions and isolates tested. It appears that the formation of persisters in S. enterica after exposure to ciprofloxacin is linked to the overexpression of genes involved in the SOS response (recA), cell division inhibitor (sulA), iron-sulfur metabolism (hscA and iscS), and type I TA system (tisB). On the other hand, most genes differentially expressed in S. enterica after exposure to ceftazidime appeared to be downregulated and were part of the flagellar assembly apparatus, citrate cycle (TCA cycle), glycolysis/gluconeogenesis, carbon metabolism, bacterial secretion system, quorum sensing, pyruvate metabolism pathway, and biosynthesis of secondary metabolites. The different transcriptome profiles found in S. enterica persisters induced by ciprofloxacin and ceftazidime suggest that these cells modulate their response differently according to each stress.
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Affiliation(s)
- S P Mattiello
- Laboratório de Imunologia e Microbiologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga, 6681, Porto Alegre, 90619-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
- College of Mathematics and Science, The University of Tennessee Southern, UTS, Pulaski, TN, USA
- Department of Veterinary and Biomedical Sciences, South Dakota State University, SDSU, Brookings, SD, USA
| | - V C Barth
- Laboratório de Imunoterapia, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - J Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, SDSU, Brookings, SD, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, USA
| | - C A S Ferreira
- Laboratório de Imunologia e Microbiologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga, 6681, Porto Alegre, 90619-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - S D Oliveira
- Laboratório de Imunologia e Microbiologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga, 6681, Porto Alegre, 90619-900, Brazil.
- Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.
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Lubbers M, van Wezel GP, Claessen D. Reproducible switching between a walled and cell wall-deficient lifestyle of actinomycetes using gradient agar plates. J Microbiol Methods 2023; 204:106660. [PMID: 36563750 DOI: 10.1016/j.mimet.2022.106660] [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: 11/16/2022] [Revised: 12/17/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
The cell wall is a shape-defining structure that envelopes almost all bacteria, protecting them from biotic and abiotic stresses. Paradoxically, some filamentous actinomycetes have a natural ability to shed their cell wall under influence of hyperosmotic stress. These wall-deficient cells can revert to their walled state when transferred to a medium without osmoprotection but often lyse due to their fragile nature. Here, we designed plates with an osmolyte gradient to reduce cell lysis and thereby facilitating the transition between a walled and wall-deficient state. These gradient plates allow determining of the osmolyte concentration where switching takes place, thereby enabling careful and reproducible comparison between mutants affected by switching. Exploring these transitions could give valuable insights into the ecology of actinomycetes and their biotechnological applications.
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Affiliation(s)
- Maarten Lubbers
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Gilles P van Wezel
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Dennis Claessen
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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Xu X, Dong B, Peng L, Gao C, He Z, Wang C, Zeng J. Anti-tuberculosis drug development via targeting the cell envelope of Mycobacterium tuberculosis. Front Microbiol 2022; 13:1056608. [PMID: 36620019 PMCID: PMC9810820 DOI: 10.3389/fmicb.2022.1056608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis possesses a dynamic cell envelope, which consists of a peptidoglycan layer, a mycolic acid layer, and an arabinogalactan polysaccharide. This envelope possesses a highly complex and unique structure representing a barrier that protects and assists the growth of M. tuberculosis and allows its adaptation to the host. It regulates the immune response of the host cells, causing their damage. Therefore, the cell envelope of M. tuberculosis is an attractive target for vaccine and drug development. The emergence of multidrug-resistant as well as extensively drug resistant tuberculosis and co-infection with HIV prevented an effective control of this disease. Thus, the discovery and development of new drugs is a major keystone for TB treatment and control. This review mainly summarizes the development of drug enzymes involved in the biosynthesis of the cell wall in M. tuberculosis, and other potential drug targets in this pathway, to provide more effective strategies for the development of new drugs.
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Affiliation(s)
- Xinyue Xu
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Baoyu Dong
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lijun Peng
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chao Gao
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.,Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiqun He
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chuan Wang
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Call SN, Andrews LB. CRISPR-Based Approaches for Gene Regulation in Non-Model Bacteria. Front Genome Ed 2022; 4:892304. [PMID: 35813973 PMCID: PMC9260158 DOI: 10.3389/fgeed.2022.892304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 01/08/2023] Open
Abstract
CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) have become ubiquitous approaches to control gene expression in bacteria due to their simple design and effectiveness. By regulating transcription of a target gene(s), CRISPRi/a can dynamically engineer cellular metabolism, implement transcriptional regulation circuitry, or elucidate genotype-phenotype relationships from smaller targeted libraries up to whole genome-wide libraries. While CRISPRi/a has been primarily established in the model bacteria Escherichia coli and Bacillus subtilis, a growing numbering of studies have demonstrated the extension of these tools to other species of bacteria (here broadly referred to as non-model bacteria). In this mini-review, we discuss the challenges that contribute to the slower creation of CRISPRi/a tools in diverse, non-model bacteria and summarize the current state of these approaches across bacterial phyla. We find that despite the potential difficulties in establishing novel CRISPRi/a in non-model microbes, over 190 recent examples across eight bacterial phyla have been reported in the literature. Most studies have focused on tool development or used these CRISPRi/a approaches to interrogate gene function, with fewer examples applying CRISPRi/a gene regulation for metabolic engineering or high-throughput screens and selections. To date, most CRISPRi/a reports have been developed for common strains of non-model bacterial species, suggesting barriers remain to establish these genetic tools in undomesticated bacteria. More efficient and generalizable methods will help realize the immense potential of programmable CRISPR-based transcriptional control in diverse bacteria.
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Affiliation(s)
- Stephanie N. Call
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lauren B. Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, United States
- *Correspondence: Lauren B. Andrews,
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