1
|
Firrincieli A, Tornatore E, Piacenza E, Cappelletti M, Saiano F, Pavia FC, Alduina R, Zannoni D, Presentato A. The actinomycete Kitasatospora sp. SeTe27, subjected to adaptive laboratory evolution (ALE) in the presence of selenite, varies its cellular morphology, redox stability, and tolerance to the toxic oxyanion. CHEMOSPHERE 2024; 354:141712. [PMID: 38484991 DOI: 10.1016/j.chemosphere.2024.141712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
The effects of oxyanions selenite (SeO32-) in soils are of high concern in ecotoxicology and microbiology as they can react with mineral particles and microorganisms. This study investigated the evolution of the actinomycete Kitasatospora sp. SeTe27 in response to selenite. To this aim, we used the Adaptive Laboratory Evolution (ALE) technique, an experimental approach that mimics natural evolution and enhances microbial fitness for specific growth conditions. The original strain (wild type; WT) isolated from uncontaminated soil gave us a unique model system as it has never encountered the oxidative damage generated by the prooxidant nature of selenite. The WT strain exhibited a good basal level of selenite tolerance, although its growth and oxyanion removal capacity were limited compared to other environmental isolates. Based on these premises, the WT and the ALE strains, the latter isolated at the end of the laboratory evolution procedure, were compared. While both bacterial strains had similar fatty acid profiles, only WT cells exhibited hyphae aggregation and extensively produced membrane-like vesicles when grown in the presence of selenite (challenged conditions). Conversely, ALE selenite-grown cells showed morphological adaptation responses similar to the WT strain under unchallenged conditions, demonstrating the ALE strain improved resilience against selenite toxicity. Whole-genome sequencing revealed specific missense mutations in genes associated with anion transport and primary and secondary metabolisms in the ALE variant. These results were interpreted to show that some energy-demanding processes are attenuated in the ALE strain, prioritizing selenite bioprocessing to guarantee cell survival in the presence of selenite. The present study indicates some crucial points for adapting Kitasatospora sp. SeTe27 to selenite oxidative stress to best deal with selenium pollution. Moreover, the importance of exploring non-conventional bacterial genera, like Kitasatospora, for biotechnological applications is emphasized.
Collapse
Affiliation(s)
- Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via San Camillo de Lellis snc, 01100, Viterbo, Italy.
| | - Enrico Tornatore
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| | - Elena Piacenza
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
| | - Filippo Saiano
- Department of Agricultural, Food and Forestry Sciences (SAAF), University of Palermo, Viale delle Scienze Ed. 4, 90128, Palermo, Italy.
| | - Francesco Carfì Pavia
- Department of Engineering, University of Palermo, Viale delle Scienze Ed. 8, 90128, Palermo, Italy.
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
| | - Alessandro Presentato
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| |
Collapse
|
2
|
Cruz-Bautista R, Ruíz-Villafán B, Romero-Rodríguez A, Rodríguez-Sanoja R, Sánchez S. Trends in the two-component system's role in the synthesis of antibiotics by Streptomyces. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12623-z. [PMID: 37341754 DOI: 10.1007/s00253-023-12623-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
Despite the advances in understanding the regulatory networks for secondary metabolite production in Streptomyces, the participation of the two-component systems (TCS) in this process still requires better characterization. These sensing systems and their responses to environmental stimuli have been described by evaluating mutant strains with techniques that allow in-depth regulatory responses. However, defining the stimulus that triggers their activation is still a task. The transmembrane nature of the sensor kinases and the high content of GC in the streptomycetes represent significant challenges in their study. In some examples, adding elements to the assay medium has determined the respective ligand. However, a complete TCS description and characterization requires specific amounts of the involved proteins that are most difficult to obtain. The availability of enough sensor histidine kinase concentrations could facilitate the identification of the ligand-protein interaction, and besides would allow the establishment of its phosphorylation mechanisms and determine their tridimensional structure. Similarly, the advances in the development of bioinformatics tools and novel experimental techniques also promise to accelerate the TCSs description and provide knowledge on their participation in the regulation processes of secondary metabolite formation. This review aims to summarize the recent advances in the study of TCSs involved in antibiotic biosynthesis and to discuss alternatives to continue their characterization. KEY POINTS: • TCSs are the environmental signal transducers more abundant in nature. • The Streptomyces have some of the highest number of TCSs found in bacteria. • The study of signal transduction between SHKs and RRs domains is a big challenge.
Collapse
Affiliation(s)
- Rodrigo Cruz-Bautista
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
| | - Beatriz Ruíz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
| |
Collapse
|
3
|
Jin S, Hui M, Lu Y, Zhao Y. An overview on the two-component systems of Streptomyces coelicolor. World J Microbiol Biotechnol 2023; 39:78. [PMID: 36645528 DOI: 10.1007/s11274-023-03522-6] [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: 12/01/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023]
Abstract
The two-component system (TCS) found in various organisms is a regulatory system, which is involved in the response by the organism to stimuli, thereby regulating the internal behavior of the cell. It is commonly found in prokaryotes and is an important signaling system in bacteria. TCSs are involved in the regulation of physiological and morphological differentiation of the industrially important microbes from the genus Streptomyces, which produce a vast array of bioactive secondary metabolites (SMs). Genetic engineering of TCSs can substantially increase the yield of target SMs, which is valuable for industrial-scale production. Research on TCS has mainly been completed in the model strain Streptomyces coelicolor. In this review, we summarize the recent advances in the functional identification and elucidation of the regulatory mechanisms of various TCSs in S. coelicolor, with a focus on their roles in the biosynthesis of important SMs.
Collapse
Affiliation(s)
- Shangping Jin
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China
| | - Ming Hui
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 100 Guilin Road, 200234, Shanghai, China.
| | - Yawei Zhao
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China.
| |
Collapse
|
4
|
Sánchez de la Nieta R, Santamaría RI, Díaz M. Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled. Int J Mol Sci 2022; 23:ijms232315085. [PMID: 36499414 PMCID: PMC9739842 DOI: 10.3390/ijms232315085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Bacteria of the Streptomyces genus constitute an authentic biotech gold mine thanks to their ability to produce a myriad of compounds and enzymes of great interest at various clinical, agricultural, and industrial levels. Understanding the physiology of these organisms and revealing their regulatory mechanisms is essential for their manipulation and application. Two-component systems (TCSs) constitute the predominant signal transduction mechanism in prokaryotes, and can detect a multitude of external and internal stimuli and trigger the appropriate cellular responses for adapting to diverse environmental conditions. These global regulatory systems usually coordinate various biological processes for the maintenance of homeostasis and proper cell function. Here, we review the multiple TCSs described and characterized in Streptomyces coelicolor, one of the most studied and important model species within this bacterial group. TCSs are involved in all cellular processes; hence, unravelling the complex regulatory network they form is essential for their potential biotechnological application.
Collapse
|
5
|
Global Chromosome Topology and the Two-Component Systems in Concerted Manner Regulate Transcription in Streptomyces. mSystems 2021; 6:e0114221. [PMID: 34783581 PMCID: PMC8594442 DOI: 10.1128/msystems.01142-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Bacterial gene expression is controlled at multiple levels, with chromosome supercoiling being one of the most global regulators. Global DNA supercoiling is maintained by the orchestrated action of topoisomerases. In Streptomyces, mycelial soil bacteria with a complex life cycle, topoisomerase I depletion led to elevated chromosome supercoiling, changed expression of a significant fraction of genes, delayed growth, and blocked sporulation. To identify supercoiling-induced sporulation regulators, we searched for Streptomyces coelicolor transposon mutants that were able to restore sporulation despite high chromosome supercoiling. We established that transposon insertion in genes encoding a novel two-component system named SatKR reversed the sporulation blockage resulting from topoisomerase I depletion. Transposition in satKR abolished the transcriptional induction of the genes within the so-called supercoiling-hypersensitive cluster (SHC). Moreover, we found that activated SatR also induced the same set of SHC genes under normal supercoiling conditions. We determined that the expression of genes in this region impacted S. coelicolor growth and sporulation. Interestingly, among the associated products is another two-component system (SitKR), indicating the potential for cascading regulatory effects driven by the SatKR and SitKR two-component systems. Thus, we demonstrated the concerted activity of chromosome supercoiling and a hierarchical two-component signaling system that impacts gene activity governing Streptomyces growth and sporulation. IMPORTANCEStreptomyces microbes, soil bacteria with complex life cycle, are the producers of a broad range of biologically active compounds (e.g., antibiotics). Streptomyces bacteria respond to various environmental signals using a complex transcriptional regulation mechanism. Understanding regulation of their gene expression is crucial for Streptomyces application as industrial organisms. Here, on the basis of the results of extensive transcriptomics analyses, we describe the concerted gene regulation by global DNA supercoiling and novel two-component system. Our data indicate that regulated genes encode growth and sporulation regulators. Thus, we demonstrate that Streptomyces bacteria link the global regulatory strategies to adjust life cycle to unfavorable conditions.
Collapse
|
6
|
Liu M, Xu W, Zhu Y, Cui X, Pang X. The Response Regulator MacR and its Potential in Improvement of Antibiotic Production in Streptomyces coelicolor. Curr Microbiol 2021; 78:3696-3707. [PMID: 34426858 DOI: 10.1007/s00284-021-02633-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/11/2021] [Indexed: 11/29/2022]
Abstract
We previously reported that the two-component system MacRS regulates morphogenesis and production of the blue-pigmented antibiotic actinorhodin (ACT) in Streptomyces coelicolor. In this study, the role of MacRS was further extended to include control of the production of the red-pigmented antibiotic undecylprodigiosin (RED) and the calcium-dependent antibiotic (CDA), and control of other important cellular activities. Our data indicated that disruption of the MacRS TCS reduced production not only of ACT but also of RED and CDA. RNA-Seq analysis revealed that genes involved in both secondary metabolism and primary metabolism are differentially expressed in the MacRS deletion mutant ΔmacRS. Moreover, we found that genes of the Zur regulon are also markedly downregulated in ΔmacRS, suggesting a role for macRS in zinc homeostasis. In addition to previously identified MacR sites with strong matches to the MacR consensus recognition sequence, a genome-wide search revealed over one hundred less-stringent matches, including potential sites upstream of absR1, crgA, and smeA. Electrophoretic mobility shift assays demonstrated that MacR binds some of these sites in vitro. Although there is no strong MacR site upstream of the ACT regulatory gene actII-orf4 (sco5085), we showed that an engineered MacR site enhanced ACT production, providing an approach for modulating production of useful compounds. Altogether, our work suggests an important role for MacRS in a range of cellular activities in Streptomyces and its potential application in strain engineering.
Collapse
Affiliation(s)
- Meng Liu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Wenhao Xu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yanping Zhu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiqing Cui
- Deqiang Biology Co. Ltd, Harbin, 150060, China.
| | - Xiuhua Pang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
7
|
Shi M, Chen L, Zhang W. Regulatory Diversity and Functional Analysis of Two-Component Systems in Cyanobacterium Synechocystis sp. PCC 6803 by GC-MS Based Metabolomics. Front Microbiol 2020; 11:403. [PMID: 32256471 PMCID: PMC7090099 DOI: 10.3389/fmicb.2020.00403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/26/2020] [Indexed: 12/02/2022] Open
Abstract
Two-component signal transduction systems are still poorly functionally characterized in the model cyanobacterium Synechocystis sp. PCC 6803. To address the issue, a GC-MS based comparative metabolomic analysis was conducted on a library of 44 knockout mutants for the response regulators (RRs) in Synechocystis. The metabolomic profiling analysis showed that 7 RRs mutants, namely Δslr1909, Δsll1291, Δslr6040, Δsll1330, Δslr2024, Δslr1584, and Δslr1693, were significantly different at metabolomic level, although their growth patterns are similar to the wild type under the normal autotrophic growth condition, suggesting regulatory diversity of RRs at metabolite level in Synechocystis. Additionally, a detailed metabolomic analysis coupled with RT-PCR verification led to useful clues for possible function of these 7 RRs, which were found involved in regulation of multiple aspects of cellular metabolisms in Synechocystis. Moreover, an integrative metabolomic and evolutionary analysis of all RR showed that four groups of RR genes clustered together in both metabolomic and evolutionary trees, suggesting of possible functional conservation of these RRs during the evolutionary process. Meanwhile, six groups of RRs with close evolutionary origin were found with different metabolomic profiles, suggesting possible functional changes during evolution. In contrast, more than 10 groups of RR genes with different clustering patterns in the evolutionary tree were found clustered together in metabolomics-based tree, suggesting possible functional convergences during the evolution. This study provided a metabolomic view of RR function, and the most needed functional clues for further characterization of these regulatory proteins in Synechocystis.
Collapse
Affiliation(s)
- Mengliang Shi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| |
Collapse
|
8
|
Multi-level regulation of coelimycin synthesis in Streptomyces coelicolor A3(2). Appl Microbiol Biotechnol 2019; 103:6423-6434. [PMID: 31250060 PMCID: PMC6667686 DOI: 10.1007/s00253-019-09975-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 11/03/2022]
Abstract
Despite being a yellow pigment visible to the human eye, coelimycin (CPK) remained to be an undiscovered secondary metabolite for over 50 years of Streptomyces research. Although the function of this polyketide is still unclear, we now know that its "cryptic" nature is attributed to a very complex and precise mechanism of cpk gene cluster regulation in the model actinomycete S. coelicolor A3(2). It responds to the stringent culture density and timing of the transition phase by the quorum-sensing butanolide system and to the specific nutrient availability/uptake signals mediated by the global (pleiotropic) regulators; many of which are two-component signal transduction systems. The final effectors of this regulation cascade are predicted to be two cluster-situated Streptomyces antibiotic regulatory proteins (SARPs) putatively activating the expression of type I polyketide synthase (PKS I) genes. After its synthesis, unstable, colorless antibiotic coelimycin A reacts with specific compounds in the medium losing its antibacterial properties and giving rise to yellow coelimycins P1 and P2. Here we review the current knowledge on coelimycin synthesis regulation in Streptomyces coelicolor A3(2). We focus on the regulatory feedback loop which interconnects the butanolide system with other cpk cluster-situated regulators. We also present the effects exerted on cpk genes expression by the global, pleiotropic regulators, and the regulatory connections between cpk and other biosynthetic gene clusters.
Collapse
|
9
|
Lu T, Zhu Y, Zhang P, Sheng D, Cao G, Pang X. SCO5351 is a pleiotropic factor that impacts secondary metabolism and morphological development in Streptomyces coelicolor. FEMS Microbiol Lett 2018; 365:5040222. [DOI: 10.1093/femsle/fny150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/16/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Ting Lu
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Yanping Zhu
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Peipei Zhang
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Duohong Sheng
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Guangxiang Cao
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, China
| | - Xiuhua Pang
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| |
Collapse
|