1
|
García-Martín J, García-Abad L, Santamaría RI, Díaz M. Functional connexion of bacterioferritin in antibiotic production and morphological differentiation in Streptomyces coelicolor. Microb Cell Fact 2024; 23:234. [PMID: 39182107 PMCID: PMC11344345 DOI: 10.1186/s12934-024-02510-1] [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: 04/26/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Several two-component systems of Streptomyces coelicolor, a model organism used for studying antibiotic production in Streptomyces, affect the expression of the bfr (SCO2113) gene that encodes a bacterioferritin, a protein involved in iron storage. In this work, we have studied the effect of the deletion mutant ∆bfr in S. coelicolor. RESULTS The ∆bfr mutant exhibits a delay in morphological differentiation and produces a lesser amount of the two pigmented antibiotics (actinorhodin and undecylprodigiosin) compared to the wild type on complex media. The effect of iron in minimal medium was tested in the wild type and ∆bfr mutant. Consequently, we also observed different levels of production of the two pigmented antibiotics between the two strains, depending on the iron concentration and the medium (solid or liquid) used. Contrary to expectations, no differences in intracellular iron concentration were detected between the wild type and ∆bfr mutant. However, a higher level of reactive oxygen species in the ∆bfr mutant and a higher tolerance to oxidative stress were observed. Proteomic analysis showed no variation in iron response proteins, but there was a lower abundance of proteins related to actinorhodin and ribosomal proteins, as well as others related to secondary metabolite production and differentiation. Additionally, a higher abundance of proteins related to various types of stress, such as respiration and hypoxia among others, was also revealed. Data are available via ProteomeXchange with identifier PXD050869. CONCLUSION This bacterioferritin in S. coelicolor (Bfr) is a new element in the complex regulation of secondary metabolism in S. coelicolor and, additionally, iron acts as a signal to modulate the biosynthesis of active molecules. Our model proposes an interaction between Bfr and iron-containing regulatory proteins. Thus, identifying these interactions would provide new information for improving antibiotic production in Streptomyces.
Collapse
Affiliation(s)
- Javier García-Martín
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), C/ Zacarías González, nº 2, Salamanca, 37007, Spain
| | - Laura García-Abad
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), C/ Zacarías González, nº 2, Salamanca, 37007, Spain
| | - Ramón I Santamaría
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), C/ Zacarías González, nº 2, Salamanca, 37007, Spain.
| | - Margarita Díaz
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), C/ Zacarías González, nº 2, Salamanca, 37007, Spain.
| |
Collapse
|
2
|
Cruz-Bautista R, Zelarayan-Agüero A, Ruiz-Villafán B, Escalante-Lozada A, Rodríguez-Sanoja R, Sánchez S. An overview of the two-component system GarR/GarS role on antibiotic production in Streptomyces coelicolor. Appl Microbiol Biotechnol 2024; 108:306. [PMID: 38656376 PMCID: PMC11043171 DOI: 10.1007/s00253-024-13136-z] [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: 01/09/2024] [Revised: 03/23/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
The Streptomyces genus comprises Gram-positive bacteria known to produce over two-thirds of the antibiotics used in medical practice. The biosynthesis of these secondary metabolites is highly regulated and influenced by a range of nutrients present in the growth medium. In Streptomyces coelicolor, glucose inhibits the production of actinorhodin (ACT) and undecylprodigiosin (RED) by a process known as carbon catabolite repression (CCR). However, the mechanism mediated by this carbon source still needs to be understood. It has been observed that glucose alters the transcriptomic profile of this actinobacteria, modifying different transcriptional regulators, including some of the one- and two-component systems (TCSs). Under glucose repression, the expression of one of these TCSs SCO6162/SCO6163 was negatively affected. We aimed to study the role of this TCS on secondary metabolite formation to define its influence in this general regulatory process and likely establish its relationship with other transcriptional regulators affecting antibiotic biosynthesis in the Streptomyces genus. In this work, in silico predictions suggested that this TCS can regulate the production of the secondary metabolites ACT and RED by transcriptional regulation and protein-protein interactions of the transcriptional factors (TFs) with other TCSs. These predictions were supported by experimental procedures such as deletion and complementation of the TFs and qPCR experiments. Our results suggest that in the presence of glucose, the TCS SCO6162/SCO6163, named GarR/GarS, is an important negative regulator of the ACT and RED production in S. coelicolor. KEY POINTS: • GarR/GarS is a TCS with domains for signal transduction and response regulation • GarR/GarS is an essential negative regulator of the ACT and RED production • GarR/GarS putatively interacts with and regulates activators of ACT and RED.
Collapse
Affiliation(s)
- Rodrigo Cruz-Bautista
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Augusto Zelarayan-Agüero
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Beatriz Ruiz-Villafán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Adelfo Escalante-Lozada
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ave. Universidad 2001, 62210, Cuernavaca, Mexico
| | - Romina Rodríguez-Sanoja
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico.
| |
Collapse
|
3
|
Yan YS, Zou LS, Wei HG, Yang MY, Yang YQ, Li XF, Xia HY. An atypical two-component system, AtcR/AtcK, simultaneously regulates the biosynthesis of multiple secondary metabolites in Streptomyces bingchenggensis. Appl Environ Microbiol 2024; 90:e0130023. [PMID: 38112424 PMCID: PMC10807435 DOI: 10.1128/aem.01300-23] [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: 08/09/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
Streptomyces bingchenggensis is an industrial producer of milbemycins, which are important anthelmintic and insecticidal agents. Two-component systems (TCSs), which are typically situated in the same operon and are composed of a histidine kinase and a response regulator, are the predominant signal transduction pathways involved in the regulation of secondary metabolism in Streptomyces. Here, an atypical TCS, AtcR/AtcK, in which the encoding genes (sbi_06838/sbi_06839) are organized in a head-to-head pair, was demonstrated to be indispensable for the biosynthesis of multiple secondary metabolites in S. bingchenggensis. With the null TCS mutants, the production of milbemycin and yellow compound was abolished but nanchangmycin was overproduced. Transcriptional analysis and electrophoretic mobility shift assays showed that AtcR regulated the biosynthesis of these three secondary metabolites by a MilR3-mediated cascade. First, AtcR was activated by phosphorylation from signal-triggered AtcK. Second, the activated AtcR promoted the transcription of milR3. Third, MilR3 specifically activated the transcription of downstream genes from milbemycin and yellow compound biosynthetic gene clusters (BGCs) and nanR4 from the nanchangmycin BGC. Finally, because NanR4 is a specific repressor in the nanchangmycin BGC, activation of MilR3 downstream genes led to the production of yellow compound and milbemycin but inhibited nanchangmycin production. By rewiring the regulatory cascade, two strains were obtained, the yield of nanchangmycin was improved by 45-fold to 6.08 g/L and the production of milbemycin was increased twofold to 1.34 g/L. This work has broadened our knowledge on atypical TCSs and provided practical strategies to engineer strains for the production of secondary metabolites in Streptomyces.IMPORTANCEStreptomyces bingchenggensis is an important industrial strain that produces milbemycins. Two-component systems (TCSs), which consist of a histidine kinase and a response regulator, are the predominant signal transduction pathways involved in the regulation of secondary metabolism in Streptomyces. Coupled encoding genes of TCSs are typically situated in the same operon. Here, TCSs with encoding genes situated in separate head-to-head neighbor operons were labeled atypical TCSs. It was found that the atypical TCS AtcR/AtcK played an indispensable role in the biosynthesis of milbemycin, yellow compound, and nanchangmycin in S. bingchenggensis. This atypical TCS regulated the biosynthesis of specialized metabolites in a cascade mediated via a cluster-situated regulator, MilR3. Through rewiring the regulatory pathways, strains were successfully engineered to overproduce milbemycin and nanchangmycin. To the best of our knowledge, this is the first report on atypical TCS, in which the encoding genes of RR and HK were situated in separate head-to-head neighbor operons, involved in secondary metabolism. In addition, data mining showed that atypical TCSs were widely distributed in actinobacteria.
Collapse
Affiliation(s)
- Yu-Si Yan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - Li-Sha Zou
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - He-Geng Wei
- Zhejiang Yongtai Technology Co., LTD., Taizhou, Zhejiang, China
| | - Meng-Yao Yang
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - Yun-Qi Yang
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - Xiao-Fang Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - Hai-Yang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| |
Collapse
|
4
|
Martins NDRC, Rodrigues da Silva A, Ratcliffe N, Evangelho VGO, Castro HC, Quinn GA. Streptomyces: a natural source of anti- Candida agents. J Med Microbiol 2023; 72. [PMID: 37991419 DOI: 10.1099/jmm.0.001777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Introduction. There is an urgent need to source new compounds that can combat the current threat of serious infection caused by Candida spp. and contend with the problem of antimicrobial resistance.
Gap. A synthesis of the evidence available from the current literature is needed to identify promising antifungal chemotherapeutics.
Aim. To highlight anti-Candida compounds derived from
Streptomyces
spp. (a well-known source of antimicrobial compounds) that could translate to potential candidates for future clinical practice.
Methodology. A comprehensive review was conducted across three scientific literature databases spanning a 13-year period.
Results. We identified 151 compounds with anti-Candida activity. Amongst these, 40 were reported with very strong inhibitory activity, having minimum inhibitory concentrations (MICs) against Candida spp. of <3.5 µg ml−1, 66 compounds were considered strong inhibitors and 45 compounds exhibited moderate inhibitory potential. From an analysis of the MICs, we deduced that the actinomycin-like compounds RSP01 and RSP02 were probably the most promising anti-Candida compounds. Other antifungals of note included filipin-like compounds, which demonstrated superior inhibition to amphotericin B and activity against Candida glabrata and Candida krusei, and bafilomycin derivatives, which had substantial inhibition against Candida parapsilosis.
Conclusion. It is essential to recognize the limitations inherent in the quest for new antifungals, which encompass toxicity, in vivo effectiveness and constraints associated with limited data access. However, further investigation through in-depth study and emerging technologies is of paramount importance, given that there are still many more compounds to discover. This review highlights the importance of antifungal compounds derived from
Streptomyces
, which demonstrate robust inhibition, and, in many cases, low toxicity, making them promising candidates for the development of novel antifungal agents.
Collapse
Affiliation(s)
| | - Aldo Rodrigues da Silva
- Programa de Pós-Graduação em Patologia, Hospital Universitário Antônio Pedro, Niterói, Brazil
| | - Norman Ratcliffe
- Programa de Pós-graduação em Ciências e Biotecnologia, LABiEMol, Universidade Federal Fluminense, Niterói, Brazil
- Swansea University, Wales, UK
| | | | - Helena Carla Castro
- Programa de Pós-Graduação em Patologia, Hospital Universitário Antônio Pedro, Niterói, Brazil
- Programa de Pós-graduação em Ciências e Biotecnologia, LABiEMol, Universidade Federal Fluminense, Niterói, Brazil
| | - Gerry A Quinn
- Institute of Biomedical Sciences, Ulster University, Coleraine, Ireland
| |
Collapse
|
5
|
Riascos C, Martínez-Carrasco A, Díaz M, Santamaría RI. Role of fourteen XRE-DUF397 pairs from Streptomyces coelicolor as regulators of antibiotic production and differentiation. New players in a complex regulatory network. Front Microbiol 2023; 14:1217350. [PMID: 37492264 PMCID: PMC10364602 DOI: 10.3389/fmicb.2023.1217350] [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: 05/05/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023] Open
Abstract
Bacteria of the genus Streptomyces have a plethora of transcriptional regulators, among which the xenobiotic response element (XRE) plays an important role. In this organism, XRE regulators are often followed downstream by small proteins of unknown function containing a DUF397 domain. It has been proposed that XRE/DUF397 pairs constitute type II toxin-antitoxin (TA) systems. However, previous work carried out by our group has shown that one of these systems is a strong activator of antibiotic production in S. coelicolor and other Streptomyces species. In this work, we have studied the overexpression of fourteen XRE/DUF397 pairs present in the S. coelicolor genome and found that none behave as a type II TA system. Instead, they act as pleiotropic regulators affecting, in a dependent manner, antibiotic production and morphological differentiation on different culture media. After deleting, individually, six XRE/DUF397 pairs (those systems producing more notable phenotypic changes when overexpressed: SCO2246/45, SCO2253/52, SCO4176/77, SCO4678/79, SCO6236/35, and SCO7615/16), the pair SCO7615/16 was identified as producing the most dramatic differences as compared to the wild-type strain. The SCO7615/16 mutant had a different phenotype on each of the media tested (R2YE, LB, NMMP, YEPD, and MSA). In particular, on R2YE and YEPD media, a bald phenotype was observed even after 7 days, with little or no actinorhodin (ACT) production. Lower ACT production was also observed on LB medium, but the bacteria were able to produce aerial mycelium. On NMMP medium, the mutant produced a larger amount of ACT as compared with the wild-type strain.
Collapse
|
6
|
Abanoz-Seçgin B, Otur Ç, Okay S, Kurt-Kızıldoğan A. The regulatory role of Fur-encoding SCLAV_3199 in iron homeostasis in Streptomyces clavuligerus. Gene 2023:147594. [PMID: 37364696 DOI: 10.1016/j.gene.2023.147594] [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: 03/14/2023] [Revised: 06/09/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Iron homeostasis is strictly regulated by complex cascades connected with secondary metabolism in bacteria. Ferric uptake regulators ('Fur's), siderophores, efflux systems, and two-component signal transduction systems are the leading players in response stimuli. However, these regulatory mechanisms remain to be elucidated in Streptomyces clavuligerus. Our study focused on unraveling a possible role of SCLAV_3199 which encodes a Fur family transcriptional regulator, particularly in iron regulation and at the global level in this species. We deleted the SCLAV_3199 gene in S. clavuligerus and compared gene expression differences with the wild-type strain based on iron availability by RNA-seq. We found a potential regulatory effect of SCLAV_3199 on many transcriptional regulators and transporters. Besides, the genes encoding iron sulfur binding proteins were overexpressed in the mutant in the presence of iron. Notably, catechol (SCLAV_5397), and hydroxamate-type (SCLAV_1952, SCLAV_4680) siderophore-related genes were upregulated in the mutant strain in iron scarcity. Concomitantly, S. clavuligerus Δ3199 produced 1.65 and 1.9 times more catechol and hydroxamate-type siderophores, respectively, than that of the wild type strain under iron depletion. Iron containing chemically defined medium did not favor antibiotic production in S. clavuligerus Δ3199 while fermentation in starch-asparagine medium led to improved cephamycin C (2.23-fold) and clavulanic acid (2.56-fold) production in the mutant compared to the control. However, better tunicamycin yield (2.64-fold) was obtained in trypticase soy broth-grown cultures of S. clavuligerus Δ3199. Our findings demonstrate that the SCLAV_3199 gene plays a significant role in regulating both iron homeostasis and secondary metabolite biosynthesis in S. clavuligerus.
Collapse
Affiliation(s)
- Büşra Abanoz-Seçgin
- Department of Agricultural Biotechnology, Ondokuz Mayıs University, Samsun 55139, Türkiye
| | - Çiğdem Otur
- Department of Agricultural Biotechnology, Ondokuz Mayıs University, Samsun 55139, Türkiye
| | - Sezer Okay
- Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara, 06230, Türkiye
| | | |
Collapse
|
7
|
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
|
8
|
Xu Z, Tian P. Rethinking Biosynthesis of Aclacinomycin A. Molecules 2023; 28:molecules28062761. [PMID: 36985733 PMCID: PMC10054333 DOI: 10.3390/molecules28062761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/22/2023] Open
Abstract
Aclacinomycin A (ACM-A) is an anthracycline antitumor agent widely used in clinical practice. The current industrial production of ACM-A relies primarily on chemical synthesis and microbial fermentation. However, chemical synthesis involves multiple reactions which give rise to high production costs and environmental pollution. Microbial fermentation is a sustainable strategy, yet the current fermentation yield is too low to satisfy market demand. Hence, strain improvement is highly desirable, and tremendous endeavors have been made to decipher biosynthesis pathways and modify key enzymes. In this review, we comprehensively describe the reported biosynthesis pathways, key enzymes, and, especially, catalytic mechanisms. In addition, we come up with strategies to uncover unknown enzymes and improve the activities of rate-limiting enzymes. Overall, this review aims to provide valuable insights for complete biosynthesis of ACM-A.
Collapse
|