1
|
Saito S, Arai MA. Methodology for awakening the potential secondary metabolic capacity in actinomycetes. Beilstein J Org Chem 2024; 20:753-766. [PMID: 38633912 PMCID: PMC11022428 DOI: 10.3762/bjoc.20.69] [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: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
Secondary metabolites produced by actinomycete strains undoubtedly have great potential for use in applied research areas such as drug discovery. However, it is becoming difficult to obtain novel compounds because of repeated isolation around the world. Therefore, a new strategy for discovering novel secondary metabolites is needed. Many researchers believe that actinomycetes have as yet unanalyzed secondary metabolic activities, and the associated undiscovered secondary metabolite biosynthesis genes are called "silent" genes. This review outlines several approaches to further activate the metabolic potential of actinomycetes.
Collapse
Affiliation(s)
- Shun Saito
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Midori A Arai
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| |
Collapse
|
2
|
Patil RS, Sharma S, Bhaskarwar AV, Nambiar S, Bhat NA, Koppolu MK, Bhukya H. TetR and OmpR family regulators in natural product biosynthesis and resistance. Proteins 2023. [PMID: 37874037 DOI: 10.1002/prot.26621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.
Collapse
Affiliation(s)
- Rachit S Patil
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Siddhant Sharma
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Aditya V Bhaskarwar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Souparnika Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Niharika A Bhat
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Mani Kanta Koppolu
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Hussain Bhukya
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| |
Collapse
|
3
|
Wang M, Li CJ, Zhang Z, Li PP, Yang LL, Zhi XY. The evolution of morphological development is congruent with the species phylogeny in the genus Streptomyces. Front Microbiol 2023; 14:1102250. [PMID: 37065118 PMCID: PMC10090380 DOI: 10.3389/fmicb.2023.1102250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
As the canonical model organism to dissect bacterial morphological development, Streptomyces species has attracted much attention from the microbiological society. However, the evolution of development-related genes in Streptomyces remains elusive. Here, we evaluated the distribution of development-related genes, thus indicating that the majority of these genes were ubiquitous in Streptomyces genomes. Furthermore, the phylogenetic topologies of related strict orthologous genes were compared to the species tree of Streptomyces from both concatenation and single-gene tree analyses. Meanwhile, the reconciled gene tree and normalization based on the number of parsimony-informative sites were also employed to reduce the impact of phylogenetic conflicts, which was induced by uncertainty in single-gene tree inference based merely on the sequence and the bias in the amount of phylogenetic information caused by variable numbers of parsimony-informative sites. We found that the development-related genes had higher congruence to the species tree than other strict orthologous genes. Considering that the development-related genes could also be tracked back to the common ancestor of Streptomyces, these results suggest that morphological development follows the same pattern as species divergence.
Collapse
Affiliation(s)
- Min Wang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- Zhaotong Health Vocational College, Zhaotong, China
| | - Cong-Jian Li
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Zhen Zhang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Pan-Pan Li
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- *Correspondence: Xiao-Yang Zhi,
| |
Collapse
|
4
|
Mendauletova A, Latham JA. Biosynthesis of the redox cofactor mycofactocin is controlled by the transcriptional regulator MftR and induced by long-chain acyl-CoA species. J Biol Chem 2021; 298:101474. [PMID: 34896395 PMCID: PMC8728441 DOI: 10.1016/j.jbc.2021.101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/11/2022] Open
Abstract
Mycofactocin (MFT) is a ribosomally synthesized and post-translationally-modified redox cofactor found in pathogenic mycobacteria. While MFT biosynthetic proteins have been extensively characterized, the physiological conditions under which MFT biosynthesis is required are not well understood. To gain insights into the mechanisms of regulation of MFT expression in Mycobacterium smegmatis mc2155, we investigated the DNA-binding and ligand-binding activities of the putative TetR-like transcription regulator, MftR. In this study, we demonstrated that MftR binds to the mft promoter region. We used DNase I footprinting to identify the 27 bp palindromic operator located 5′ to mftA and found it to be highly conserved in Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium ulcerans, and Mycobacterium marinum. To determine under which conditions the mft biosynthetic gene cluster (BGC) is induced, we screened for effectors of MftR. As a result, we found that MftR binds to long-chain acyl-CoAs with low micromolar affinities. To demonstrate that oleoyl-CoA induces the mft BGC in vivo, we re-engineered a fluorescent protein reporter system to express an MftA–mCherry fusion protein. Using this mCherry fluorescent readout, we show that the mft BGC is upregulated in M. smegmatis mc2155 when oleic acid is supplemented to the media. These results suggest that MftR controls expression of the mft BGC and that MFT production is induced by long-chain acyl-CoAs. Since MFT-dependent dehydrogenases are known to colocalize with acyl carrier protein/CoA-modifying enzymes, these results suggest that MFT might be critical for fatty acid metabolism or cell wall reorganization.
Collapse
Affiliation(s)
- Aigera Mendauletova
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - John A Latham
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA.
| |
Collapse
|
5
|
Vicente CM, Girardet JM, Hôtel L, Aigle B. Molecular Dynamics to Elucidate the DNA-Binding Activity of AlpZ, a Member of the Gamma-Butyrolactone Receptor Family in Streptomyces ambofaciens. Front Microbiol 2020; 11:1255. [PMID: 32714286 PMCID: PMC7343708 DOI: 10.3389/fmicb.2020.01255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/18/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cláudia M. Vicente
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- *Correspondence: Cláudia M. Vicente,
| | | | | | - Bertrand Aigle
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Bertrand Aigle,
| |
Collapse
|
6
|
Misaki Y, Yamamoto S, Suzuki T, Iwakuni M, Sasaki H, Takahashi Y, Inada K, Kinashi H, Arakawa K. SrrB, a Pseudo-Receptor Protein, Acts as a Negative Regulator for Lankacidin and Lankamycin Production in Streptomyces rochei. Front Microbiol 2020; 11:1089. [PMID: 32582072 PMCID: PMC7296167 DOI: 10.3389/fmicb.2020.01089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/30/2020] [Indexed: 11/15/2022] Open
Abstract
Streptomyces rochei 7434AN4, a producer of lankacidin (LC) and lankamycin (LM), carries many regulatory genes including a biosynthesis gene for signaling molecules SRBs (srrX), an SRB receptor gene (srrA), and a SARP (Streptomyces antibiotic regulatory protein) family activator gene (srrY). Our previous study revealed that the main regulatory cascade goes from srrX through srrA to srrY, leading to LC production, whereas srrY further regulates a second SARP gene srrZ to synthesize LM. In this study we extensively investigated the function of srrB, a pseudo-receptor gene, by analyzing antibiotic production and transcription. Metabolite analysis showed that the srrB mutation increased both LC and LM production over four-folds. Transcription, gel shift, and DNase I footprinting experiments revealed that srrB and srrY are expressed under the SRB/SrrA regulatory system, and at the later stage, SrrB represses srrY expression by binding to the promoter region of srrY. These findings confirmed that SrrB acts as a negative regulator of the activator gene srrY to control LC and LM production at the later stage of fermentation in S. rochei.
Collapse
Affiliation(s)
- Yuya Misaki
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shouji Yamamoto
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Toshihiro Suzuki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Miyuki Iwakuni
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiroaki Sasaki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yuzuru Takahashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kuninobu Inada
- Natural Science Center for Basic Research and Development, Hiroshima University, Higashi-Hiroshima, Japan
| | - Haruyasu Kinashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kenji Arakawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| |
Collapse
|
7
|
Kapoor I, Olivares P, Nair SK. Biochemical basis for the regulation of biosynthesis of antiparasitics by bacterial hormones. eLife 2020; 9:e57824. [PMID: 32510324 PMCID: PMC7347384 DOI: 10.7554/elife.57824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/06/2020] [Indexed: 11/23/2022] Open
Abstract
Diffusible small molecule microbial hormones drastically alter the expression profiles of antibiotics and other drugs in actinobacteria. For example, avenolide (a butenolide) regulates the production of avermectin, derivatives of which are used in the treatment of river blindness and other parasitic diseases. Butenolides and γ-butyrolactones control the production of pharmaceutically important secondary metabolites by binding to TetR family transcriptional repressors. Here, we describe a concise, 22-step synthetic strategy for the production of avenolide. We present crystal structures of the butenolide receptor AvaR1 in isolation and in complex with avenolide, as well as those of AvaR1 bound to an oligonucleotide derived from its operator. Biochemical studies guided by the co-crystal structures enable the identification of 90 new actinobacteria that may be regulated by butenolides, two of which are experimentally verified. These studies provide a foundation for understanding the regulation of microbial secondary metabolite production, which may be exploited for the discovery and production of novel medicines.
Collapse
Affiliation(s)
- Iti Kapoor
- Department of Biochemistry, University of Illinois at Urbana ChampaignUrbanaUnited States
| | - Philip Olivares
- Department of Biochemistry, University of Illinois at Urbana ChampaignUrbanaUnited States
- Institute for Genomic Biology, University of Illinois at Urbana ChampaignUrbanaUnited States
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana ChampaignUrbanaUnited States
- Institute for Genomic Biology, University of Illinois at Urbana ChampaignUrbanaUnited States
- Center for Biophysics and Computational Biology, University of Illinois at Urbana ChampaignUrbanaUnited States
| |
Collapse
|
8
|
van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
Collapse
|
9
|
Daniel-Ivad M, Pimentel-Elardo S, Nodwell JR. Control of Specialized Metabolism by Signaling and Transcriptional Regulation: Opportunities for New Platforms for Drug Discovery? Annu Rev Microbiol 2018; 72:25-48. [PMID: 29799791 DOI: 10.1146/annurev-micro-022618-042458] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Specialized metabolites are bacterially produced small molecules that have an extraordinary diversity of important biological activities. They are useful as biochemical probes of living systems, and they have been adapted for use as drugs for human afflictions ranging from infectious diseases to cancer. The biosynthetic genes for these molecules are controlled by a dense network of regulatory mechanisms: Cell-cell signaling and nutrient sensing are conspicuous features of this network. While many components of these mechanisms have been identified, important questions about their biological roles remain shrouded in mystery. In addition to identifying new molecules and solving their mechanisms of action (a central preoccupation in this field), we suggest that addressing questions of quorum sensing versus diffusion sensing and identifying the dominant nutritional and environmental cues for specialized metabolism are important directions for research.
Collapse
Affiliation(s)
- M Daniel-Ivad
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
| | - S Pimentel-Elardo
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
| | - J R Nodwell
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
| |
Collapse
|
10
|
Arakawa K. Manipulation of metabolic pathways controlled by signaling molecules, inducers of antibiotic production, for genome mining in Streptomyces spp. Antonie van Leeuwenhoek 2018; 111:743-751. [PMID: 29476430 DOI: 10.1007/s10482-018-1052-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/19/2018] [Indexed: 10/18/2022]
Abstract
Streptomyces is well characterized by an ability to produce a wide variety of secondary metabolites including antibiotics, whose expression is strictly controlled by small diffusible signaling molecules at nano-molar concentrations. The signaling molecules identified to date are classified into three skeletons; γ-butyrolactones, furans, and γ-butenolides. Accumulated data suggest the structural diversity of the signaling molecules in Streptomyces species and their potential in activating cryptic secondary metabolite biosynthetic pathways. Several genome mining approaches to activate silent biosynthetic gene clusters have been reported for natural product discovery. This review updates recent examples on genetic manipulation including blockage of metabolic pathways together with inactivation of transcriptional repressor genes.
Collapse
Affiliation(s)
- Kenji Arakawa
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan.
| |
Collapse
|
11
|
Lu F, Hou Y, Zhang H, Chu Y, Xia H, Tian Y. Regulatory genes and their roles for improvement of antibiotic biosynthesis in Streptomyces. 3 Biotech 2017; 7:250. [PMID: 28718097 DOI: 10.1007/s13205-017-0875-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/07/2017] [Indexed: 01/23/2023] Open
Abstract
The numerous secondary metabolites in Streptomyces spp. are crucial for various applications. For example, cephamycin C is used as an antibiotic, and avermectin is used as an insecticide. Specifically, antibiotic yield is closely related to many factors, such as the external environment, nutrition (including nitrogen and carbon sources), biosynthetic efficiency and the regulatory mechanisms in producing strains. There are various types of regulatory genes that work in different ways, such as pleiotropic (or global) regulatory genes, cluster-situated regulators, which are also called pathway-specific regulatory genes, and many other regulators. The study of regulatory genes that influence antibiotic biosynthesis in Streptomyces spp. not only provides a theoretical basis for antibiotic biosynthesis in Streptomyces but also helps to increase the yield of antibiotics via molecular manipulation of these regulatory genes. Currently, more and more emphasis is being placed on the regulatory genes of antibiotic biosynthetic gene clusters in Streptomyces spp., and many studies on these genes have been performed to improve the yield of antibiotics in Streptomyces. This paper lists many antibiotic biosynthesis regulatory genes in Streptomyces spp. and focuses on frequently investigated regulatory genes that are involved in pathway-specific regulation and pleiotropic regulation and their applications in genetic engineering.
Collapse
|
12
|
|
13
|
van der Meij A, Worsley SF, Hutchings MI, van Wezel GP. Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev 2017; 41:392-416. [DOI: 10.1093/femsre/fux005] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/02/2017] [Indexed: 12/13/2022] Open
|
14
|
Bhukya H, Jana AK, Sengupta N, Anand R. Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence. J Struct Biol 2017; 198:134-146. [PMID: 28343010 DOI: 10.1016/j.jsb.2017.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/13/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs from S. coelicolor. CprB is implicated as a receptor of γ-butyrolactones, a class of quorum sensing molecules, responsible for initiating secondary metabolic pathways. In order to understand the molecular mechanism of DNA recognition, the X-ray structure of CprB in complex with its biological relevant operator sequence was solved to a resolution of 3.95Å. Furthermore, to refine and compliment the results, atomistic molecular dynamics simulations were carried out using the X-ray structure as the template. The studies reveal that CprB binds to DNA as dimer of dimers with this mode of interaction results in minimal distortion in the DNA, enabling these proteins to recognize multiple sequences with varying affinity. Another crucial finding from our simulation results was that the positively charged N-terminal arm of CprB brings extra stability to the protein-DNA complex by interacting with the minor-groove of the DNA and anchoring itself to the phosphate backbone. Corroborating electrophoretic mobility shift assay and fluorescence anisotropy experiments showed that the mutant ΔN6-CprB exhibited about 7-8 fold reduced DNA binding. Comparison with other TetR-FTRs reveals that this strategy is also employed by over 25% of TetR-FTRs, where N-terminal anchoring mechanism is used to enhance selectivity for a particular DNA sequence.
Collapse
Affiliation(s)
- Hussain Bhukya
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Asis K Jana
- India Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Neelanjana Sengupta
- Dept. of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, W. Bengal, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| |
Collapse
|
15
|
Rolland JL, Stien D, Sanchez-Ferandin S, Lami R. Quorum Sensing and Quorum Quenching in the Phycosphere of Phytoplankton: a Case of Chemical Interactions in Ecology. J Chem Ecol 2016; 42:1201-1211. [PMID: 27822708 DOI: 10.1007/s10886-016-0791-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 09/20/2016] [Accepted: 10/05/2016] [Indexed: 12/28/2022]
Abstract
The interactions between bacteria and phytoplankton regulate many important biogeochemical reactions in the marine environment, including those in the global carbon, nitrogen, and sulfur cycles. At the microscopic level, it is now well established that important consortia of bacteria colonize the phycosphere, the immediate environment of phytoplankton cells. In this microscale environment, abundant bacterial cells are organized in a structured biofilm, and exchange information through the diffusion of small molecules called semiochemicals. Among these processes, quorum sensing plays a particular role as, when a sufficient abundance of cells is reached, it allows bacteria to coordinate their gene expression and physiology at the population level. In contrast, quorum quenching mechanisms are employed by many different types of microorganisms that limit the coordination of antagonistic bacteria. This review synthesizes quorum sensing and quorum quenching mechanisms evidenced to date in the phycosphere, emphasizing the implications that these signaling systems have for the regulation of bacterial communities and their activities. The diversity of chemical compounds involved in these processes is examined. We further review the bacterial functions regulated in the phycosphere by quorum sensing, which include biofilm formation, nutrient acquisition, and emission of algaecides. We also discuss quorum quenching compounds as antagonists of quorum sensing, their function in the phycosphere, and their potential biotechnological applications. Overall, the current state of the art demonstrates that quorum sensing and quorum quenching regulate a balance between a symbiotic and a parasitic way of life between bacteria and their phytoplankton host.
Collapse
Affiliation(s)
- Jean Luc Rolland
- Interactions-Hôtes-Pathogènes-Environnements (IHPE), Ifremer, CNRS, UPVD, Université de Montpellier, UMR 5244, 34090, Montpellier, France
| | - Didier Stien
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Sophie Sanchez-Ferandin
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Raphaël Lami
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France.
| |
Collapse
|
16
|
Sultan SP, Kitani S, Miyamoto KT, Iguchi H, Atago T, Ikeda H, Nihira T. Characterization of AvaR1, a butenolide-autoregulator receptor for biosynthesis of a Streptomyces hormone in Streptomyces avermitilis. Appl Microbiol Biotechnol 2016; 100:9581-9591. [DOI: 10.1007/s00253-016-7781-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/25/2016] [Accepted: 08/02/2016] [Indexed: 10/21/2022]
|
17
|
Romero-Rodríguez A, Robledo-Casados I, Sánchez S. An overview on transcriptional regulators in Streptomyces. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1017-39. [PMID: 26093238 DOI: 10.1016/j.bbagrm.2015.06.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 12/19/2022]
Abstract
Streptomyces are Gram-positive microorganisms able to adapt and respond to different environmental conditions. It is the largest genus of Actinobacteria comprising over 900 species. During their lifetime, these microorganisms are able to differentiate, produce aerial mycelia and secondary metabolites. All of these processes are controlled by subtle and precise regulatory systems. Regulation at the transcriptional initiation level is probably the most common for metabolic adaptation in bacteria. In this mechanism, the major players are proteins named transcription factors (TFs), capable of binding DNA in order to repress or activate the transcription of specific genes. Some of the TFs exert their action just like activators or repressors, whereas others can function in both manners, depending on the target promoter. Generally, TFs achieve their effects by using one- or two-component systems, linking a specific type of environmental stimulus to a transcriptional response. After DNA sequencing, many streptomycetes have been found to have chromosomes ranging between 6 and 12Mb in size, with high GC content (around 70%). They encode for approximately 7000 to 10,000 genes, 50 to 100 pseudogenes and a large set (around 12% of the total chromosome) of regulatory genes, organized in networks, controlling gene expression in these bacteria. Among the sequenced streptomycetes reported up to now, the number of transcription factors ranges from 471 to 1101. Among these, 315 to 691 correspond to transcriptional regulators and 31 to 76 are sigma factors. The aim of this work is to give a state of the art overview on transcription factors in the genus Streptomyces.
Collapse
Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Ivonne Robledo-Casados
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico.
| |
Collapse
|
18
|
Mao XM, Luo S, Zhou RC, Wang F, Yu P, Sun N, Chen XX, Tang Y, Li YQ. Transcriptional regulation of the daptomycin gene cluster in Streptomyces roseosporus by an autoregulator, AtrA. J Biol Chem 2015; 290:7992-8001. [PMID: 25648897 DOI: 10.1074/jbc.m114.608273] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Daptomycin is a cyclic lipopeptide antibiotic produced by Streptomyces roseosporus. To reveal the transcriptional regulatory mechanism of daptomycin biosynthesis, we used the biotinylated dptE promoter (dptEp) as a probe to affinity isolate the dptEp-interactive protein AtrA, a TetR family transcriptional regulator, from the proteome of mycelia. AtrA bound directly to dptEp to positively regulate gene cluster expression and daptomycin production. Meanwhile, both ΔatrA and ΔadpA mutants showed bald phenotype and null production of daptomycin. AdpA positively regulated atrA expression by direct interaction with atrA promoter (atrAp), and removal of ArpA in S. roseosporus, a homolog of the A-factor receptor, resulted in accelerated morphological development and increased daptomycin production, suggesting that atrA was the target of AdpA to mediate the A-factor signaling pathway. Furthermore, AtrA was positively autoregulated by binding to its own promoter atrAp. Thus, for the first time at the transcriptional level, we have identified an autoregulator, AtrA, that directly mediates the A-factor signaling pathway to regulate the proper production of daptomycin.
Collapse
Affiliation(s)
- Xu-Ming Mao
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, Department of Chemical and Biomolecular Engineering, UCLA, Los, Angeles, California 90095, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Shuai Luo
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Ri-Cheng Zhou
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Feng Wang
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Pin Yu
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Ning Sun
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| | - Xiao-Xia Chen
- the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and the Hangzhou Huadong Medicine Group Biotechnology Institute Company, Ltd., Hangzhou 310011, China
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, UCLA, Los, Angeles, California 90095
| | - Yong-Quan Li
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058, China, the Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou 310058, China, and
| |
Collapse
|
19
|
Zou Z, Du D, Zhang Y, Zhang J, Niu G, Tan H. A γ-butyrolactone-sensing activator/repressor, JadR3, controls a regulatory mini-network for jadomycin biosynthesis. Mol Microbiol 2014; 94:490-505. [PMID: 25116816 DOI: 10.1111/mmi.12752] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2014] [Indexed: 01/12/2023]
Abstract
Two regulatory genes, jadR2 and jadR3, in the jadomycin (jad) biosynthetic gene cluster of Streptomyces venezuelae encode homologues of γ-butyrolactone receptor. JadR2 was previously shown to be a pseudo γ-butyrolactone receptor. jadR3 is situated at the upstream of jadW123 encoding putative enzymes for γ-butyrolactone biosynthesis. Disruption of jadR3 resulted in markedly decreased production of jadomycin. Transcriptional analysis revealed that JadR3 represses jadW1, jadR2 and jadR3 but activates jadR1, the key activator gene for jadomycin biosynthesis. DNase I footprinting showed that JadR3 has four binding sites in the intergenic regions of jadR2-jadR1 and jadR3-jadW1. A JadR3 interactive molecule, SVB1, was purified from a large-scale fermentation and its structure found to be the same as SCB3, a γ-butyrolactone from Streptomyces coelicolor, and was absent from a jadW123 mutant lacking jadomycin production. Addition of SVB1 or extract from S. coelicolor to the mutant restored jadomycin production. Overall, our results revealed that the association of JadR3 and SVB1 plays an important role in controlling a regulatory mini-network governing jadomycin biosynthesis, providing new insights into the ways in which γ-butyrolactone/receptor systems modulate antibiotic biosynthesis in Streptomyces.
Collapse
Affiliation(s)
- Zhengzhong Zou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | | | | | | | | |
Collapse
|
20
|
Biswas A, Swarnkar RK, Hussain B, Sahoo SK, Pradeepkumar PI, Patwari GN, Anand R. Fluorescence Quenching Studies of γ-Butyrolactone Binding Protein (CprB) from Streptomyces coelicolor A3(2). J Phys Chem B 2014; 118:10035-42. [DOI: 10.1021/jp503589h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anwesha Biswas
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Ravi K. Swarnkar
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Bhukya Hussain
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Suraj K. Sahoo
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - P. I. Pradeepkumar
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - G. Naresh Patwari
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Ruchi Anand
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| |
Collapse
|
21
|
Bhukya H, Bhujbalrao R, Bitra A, Anand R. Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2). Nucleic Acids Res 2014; 42:10122-33. [PMID: 25092919 PMCID: PMC4150764 DOI: 10.1093/nar/gku587] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Antibiotic production and resistance pathways in Streptomyces are dictated by the interplay of transcriptional regulatory proteins that trigger downstream responses via binding to small diffusible molecules. To decipher the mode of DNA binding and the associated allosteric mechanism in the sub-class of transcription factors that are induced by γ-butyrolactones, we present the crystal structure of CprB in complex with the consensus DNA element to a resolution of 3.25 Å. Binding of the DNA results in the restructuring of the dimeric interface of CprB, inducing a pendulum-like motion of the helix-turn-helix motif that inserts into the major groove. The crystal structure revealed that, CprB is bound to DNA as a dimer of dimers with the mode of binding being analogous to the broad spectrum multidrug transporter protein QacR from the antibiotic resistant strain Staphylococcus aureus. It was demonstrated that the CprB displays a cooperative mode of DNA binding, following a clamp and click model. Experiments performed on a subset of DNA sequences from Streptomyces coelicolor A3(2) suggest that CprB is most likely a pleiotropic regulator. Apart from serving as an autoregulator, it is potentially a part of a network of proteins that modulates the γ-butyrolactone synthesis and antibiotic regulation pathways in S. coelicolor A3(2).
Collapse
Affiliation(s)
- Hussain Bhukya
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India
| | - Ruchika Bhujbalrao
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Aruna Bitra
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| |
Collapse
|
22
|
Mak S, Xu Y, Nodwell JR. The expression of antibiotic resistance genes in antibiotic-producing bacteria. Mol Microbiol 2014; 93:391-402. [PMID: 24964724 DOI: 10.1111/mmi.12689] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2014] [Indexed: 12/01/2022]
Abstract
Antibiotic-producing bacteria encode antibiotic resistance genes that protect them from the biologically active molecules that they produce. The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. It appears that there have been at least two general solutions to this problem. In many cases, the expression of resistance genes is tightly linked to that of antibiotic biosynthetic genes. In others, the resistance genes can be induced by their cognate antibiotics or by intermediate molecules from their biosynthetic pathways. The regulatory mechanisms that couple resistance to antibiotic biosynthesis are mechanistically diverse and potentially relevant to the origins of clinical antibiotic resistance.
Collapse
Affiliation(s)
- Stefanie Mak
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | | | | |
Collapse
|
23
|
Abstract
The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.
Collapse
|
24
|
Rabyk MV, Ostash BO, Fedorenko VO. Gene networks regulating secondary metabolism in actinomycetes: Pleiotropic regulators. CYTOL GENET+ 2014. [DOI: 10.3103/s0095452714010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
25
|
Kimura N. Metagenomic approaches to understanding phylogenetic diversity in quorum sensing. Virulence 2014; 5:433-42. [PMID: 24429899 DOI: 10.4161/viru.27850] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Quorum sensing, a form of cell-cell communication among bacteria, allows bacteria to synchronize their behaviors at the population level in order to control behaviors such as luminescence, biofilm formation, signal turnover, pigment production, antibiotics production, swarming, and virulence. A better understanding of quorum-sensing systems will provide us with greater insight into the complex interaction mechanisms used widely in the Bacteria and even the Archaea domain in the environment. Metagenomics, the use of culture-independent sequencing to study the genomic material of microorganisms, has the potential to provide direct information about the quorum-sensing systems in uncultured bacteria. This article provides an overview of the current knowledge of quorum sensing focused on phylogenetic diversity, and presents examples of studies that have used metagenomic techniques. Future technologies potentially related to quorum-sensing systems are also discussed.
Collapse
Affiliation(s)
- Nobutada Kimura
- Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba, Ibaraki Japan
| |
Collapse
|
26
|
Cuthbertson L, Ahn SK, Nodwell JR. Deglycosylation as a mechanism of inducible antibiotic resistance revealed using a global relational tree for one-component regulators. ACTA ACUST UNITED AC 2013; 20:232-40. [PMID: 23438752 DOI: 10.1016/j.chembiol.2012.11.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/22/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
Abstract
The ligands that interact with the vast majority of small-molecule binding transcription factors are unknown, a significant gap in our understanding of sensory perception by cells. TetR-family regulators (TFRs) are found in most prokaryotes and are involved in regulating virtually every aspect of prokaryotic life however only a few TFRs have been characterized. We report the application of phylogenomics to the identification of cognate ligands for TFRs. Using phylogenomics we identify a TFR, KijR, that responds to the antibiotic kijanimicin. We go on to show that KijR represses a gene, kijX, which confers resistance to kijanimicin. Finally we show that KijX inactivates kijanimicin by the hydrolytic removal of sugar residues. This is a demonstration of antibiotic resistance by deglycosylation.
Collapse
Affiliation(s)
- Leslie Cuthbertson
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | | | | |
Collapse
|
27
|
|
28
|
Pleiotropic control of secondary metabolism and morphological development by KsbC, a butyrolactone autoregulator receptor homologue in Kitasatospora setae. Appl Environ Microbiol 2012; 78:8015-24. [PMID: 22961899 DOI: 10.1128/aem.02355-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The γ-butyrolactone autoregulator signaling cascades have been shown to control secondary metabolism and/or morphological development among many Streptomyces species. However, the conservation and variation of the regulatory systems among actinomycetes remain to be clarified. The genome sequence of Kitasatospora setae, which also belongs to the family Streptomycetaceae containing the genus Streptomyces, has revealed the presence of three homologues of the autoregulator receptor: KsbA, which has previously been confirmed to be involved only in secondary metabolism; KsbB; and KsbC. We describe here the characterization of ksbC, whose regulatory cluster closely resembles the Streptomyces virginiae barA locus responsible for the autoregulator signaling cascade. Deletion of the gene ksbC resulted in lowered production of bafilomycin and a defect of aerial mycelium formation, together with the early and enhanced production of a novel β-carboline alkaloid named kitasetaline. A putative kitasetaline biosynthetic gene cluster was identified, and its expression in a heterologous host led to the production of kitasetaline together with JBIR-133, the production of which is also detected in the ksbC disruptant, and JBIR-134 as novel β-carboline alkaloids, indicating that these genes were biosynthetic genes for β-carboline alkaloid and thus are the first such genes to be discovered in bacteria.
Collapse
|
29
|
Characterization of a new ScbR-like γ-butyrolactone binding regulator (SlbR) in Streptomyces coelicolor. Appl Microbiol Biotechnol 2012; 96:113-21. [PMID: 22246527 DOI: 10.1007/s00253-011-3803-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 11/27/2011] [Accepted: 11/28/2011] [Indexed: 10/14/2022]
Abstract
γ-Butyrolactones in Streptomyces are well recognized as bacterial hormones, and they affect secondary metabolism of Streptomyces. γ-Butyrolactone receptors are considered important regulatory proteins, and various γ-butyrolactone synthases and receptors have been reported in Streptomyces. Here, we characterized a new regulator, SCO0608, that interacted with SCB1 (γ-butyrolactone of Streptomyces coelicolor) and bound to the scbR/A and adpA promoters. The SCO0608 protein sequences are not similar to those of any known γ-butyrolactone binding proteins in Streptomyces such as ScbR from S. coelicolor or ArpA from Streptomyces griseus. Interestingly, SCO0608 functions as a repressor of antibiotic biosynthesis and spore formation in R5 complex media. We showed the existence of another type of γ-butyrolactone receptor in Streptomyces, and this SCO0608 was named ScbR-like γ-butyrolactone binding regulator (SlbR) in S. coelicolor.
Collapse
|
30
|
Characterisation of a γ-butyrolactone receptor of Streptomyces tacrolimicus: effect on sporulation and tacrolimus biosynthesis. Appl Microbiol Biotechnol 2011; 92:971-84. [PMID: 21792593 DOI: 10.1007/s00253-011-3466-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/22/2011] [Accepted: 06/22/2011] [Indexed: 10/18/2022]
Abstract
Streptomyces tacrolimicus (ATCC 55098) was reported to produce the immunosuppressant tacrolimus. The wild-type strain sporulates sparsely and produces very low levels of this immunosuppressant. The lack of genetic knowledge of this strain has hampered strain improvement. In this work, we have cloned the gene encoding a γ-butyrolactone receptor protein (Gbr). The gbr gene is linked to two genes encoding two subunits of the dihydroxyacetone kinase, putatively involved in the biosynthesis of the dihydroxyacetone phosphate precursor of γ-butyrolactone but is not flanked by γ-butyrolactone synthetase genes. The Gbr protein was overexpressed in Escherichia coli and purified. Electrophoretic mobility shift assays showed that Gbr binds to a specific autoregulatory element sequence located 338 bp upstream of the gbr gene, indicating that its expression is self-regulated. The deletion mutant Δgbr showed a very early and intense sporulation in two different media. A phenotype similar to that of the wild-type strain was restored by complementation of the Δgbr mutant with a wild-type gbr allele. Duplication of the gbr gene resulted in a slower sporulation. The Δgbr mutant produced much lower amount (32%) of tacrolimus quantified by high performance liquid chromatography. This analysis, using an optimised system, allowed the resolution of tacrolimus from ascomycin and other contaminant metabolites. Our results indicate that the Gbr protein regulates negatively the sporulation and positively the production of tacrolimus.
Collapse
|
31
|
van Wezel GP, McDowall KJ. The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Nat Prod Rep 2011; 28:1311-33. [PMID: 21611665 DOI: 10.1039/c1np00003a] [Citation(s) in RCA: 315] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Streptomycetes and other actinobacteria are renowned as a rich source of natural products of clinical, agricultural and biotechnological value. They are being mined with renewed vigour, supported by genome sequencing efforts, which have revealed a coding capacity for secondary metabolites in vast excess of expectations that were based on the detection of antibiotic activities under standard laboratory conditions. Here we review what is known about the control of production of so-called secondary metabolites in streptomycetes, with an emphasis on examples where details of the underlying regulatory mechanisms are known. Intriguing links between nutritional regulators, primary and secondary metabolism and morphological development are discussed, and new data are included on the carbon control of development and antibiotic production, and on aspects of the regulation of the biosynthesis of microbial hormones. Given the tide of antibiotic resistance emerging in pathogens, this review is peppered with approaches that may expand the screening of streptomycetes for new antibiotics by awakening expression of cryptic antibiotic biosynthetic genes. New technologies are also described that have potential to greatly further our understanding of gene regulation in what is an area fertile for discovery and exploitation
Collapse
|
32
|
Willey JM, Gaskell AA. Morphogenetic Signaling Molecules of the Streptomycetes. Chem Rev 2010; 111:174-87. [DOI: 10.1021/cr1000404] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joanne M. Willey
- Department of Biology, Hofstra University, Hempstead, New York 11549, United States, and Hofstra University-North Shore-Long Island Jewish School of Medicine, Hempstead, New York 11549, United States
| | - Alisa A. Gaskell
- Department of Biology, Hofstra University, Hempstead, New York 11549, United States, and Hofstra University-North Shore-Long Island Jewish School of Medicine, Hempstead, New York 11549, United States
| |
Collapse
|
33
|
Laskaris P, Tolba S, Calvo-Bado L, Wellington EM, Wellington L. Coevolution of antibiotic production and counter-resistance in soil bacteria. Environ Microbiol 2010; 12:783-96. [PMID: 20067498 DOI: 10.1111/j.1462-2920.2009.02125.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We present evidence for the coexistence and coevolution of antibiotic resistance and biosynthesis genes in soil bacteria. The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. strA and vph were found either within a biosynthetic gene cluster or independently. Streptomyces griseus strains possessing the streptomycin cluster formed part of a clonal complex. All S. griseus strains possessing solely strA belonged to two clades; both were closely related to the streptomycin producers. Other more distantly related S. griseus strains did not contain strA. S. griseus strains with only vph also formed two clades, but they were more distantly related to the producers and to one another. The expression of the strA gene was constitutive in a resistance-only strain whereas streptomycin producers showed peak strA expression in late log phase that correlates with the switch on of streptomycin biosynthesis. While there is evidence that antibiotics have diverse roles in nature, our data clearly support the coevolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources.
Collapse
Affiliation(s)
- Paris Laskaris
- Department of Biological Sciences, University of Warwick, Coventry, UK
| | | | | | | | | |
Collapse
|
34
|
Abstract
Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.
Collapse
Affiliation(s)
- Paul D Straight
- Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843, USA.
| | | |
Collapse
|
35
|
Cell-free Escherichia coli-based system to screen for quorum-sensing molecules interacting with quorum receptor proteins of Streptomyces coelicolor. Appl Environ Microbiol 2009; 75:6367-72. [PMID: 19684180 DOI: 10.1128/aem.00019-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quorum sensing (QS) is mediated by small molecules and involved in diverse cellular functions, such as virulence, biofilm formation, secondary metabolism, and cell differentiation. In this study, we developed a rapid and effective screening tool based on a cell-free Escherichia coli-based expression system to identify QS molecules of Streptomyces. The binding of QS molecules to gamma-butyrolactone receptor ScbR was monitored by changes in the expression levels of the green fluorescent protein reporter in E. coli cell extract. Using this assay system, we could successfully confirm SCB1, a gamma-butyrolactone molecule in Streptomyces coelicolor, binding to its known receptor, ScbR. In addition, we have shown that N-hexanoyl-DL-homoserine lactone, one of the QS molecules in many gram-negative bacteria, can regulate ScbR and trigger precocious antibiotic production in S. coelicolor. Our new method can be applied to other strains for which a screening tool for QS molecules has not yet been developed.
Collapse
|
36
|
Wang XJ, Guo SL, Guo WQ, Xi D, Xiang WS. Role of nsdA in negative regulation of antibiotic production and morphological differentiation in Streptomyces bingchengensis. J Antibiot (Tokyo) 2009; 62:309-13. [PMID: 19444300 DOI: 10.1038/ja.2009.33] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To investigate the function of nsdA in Streptomyces bingchengensis, it was cloned and sequenced, which presented an 89.89% identity with that of S. coelicolor. The lambdaRED-mediated PCR-targeting technique was used to create nsdA replacement in the S. bingchengensis_226541 chromosome. The nsdA disruption mutant, BC29, was obtained, which produced more pigment and spores than did the ancestral strain. HPLC analysis revealed that the disruption of nsdA efficiently increased milbemycin A(4) production and nanchangmycin production by 1.5-fold and 9-fold, respectively. Complementation of the nsdA mutation restored the phenotype and antibiotic production. These results showed that nsdA negatively affected sporulation and antibiotic production in S. bingchengensis.
Collapse
Affiliation(s)
- Xiang-Jing Wang
- School of Life Science, Northeast Agricultural University, Harbin, China
| | | | | | | | | |
Collapse
|
37
|
Abstract
Antibiotic production is regulated by numerous signals, including the so-called bacterial hormones found in antibiotic producing organisms such as Streptomyces. These signals, the gamma-butyrolactones, are produced in very small quantities, which has hindered their structural elucidation and made it difficult to assess whether they are being produced. In this chapter, we describe a rapid small-scale extraction method from either solid or liquid cultures in scales of one plate or 50 ml of medium. Also described is a bioassay to detect the gamma-butyrolactones by determining either the production of pigmented antibiotic of Streptomyces coelicolor or kanamycin resistant growth on addition of the gamma-butyrolactones. We also describe some insights into the identification of the gamma-butyrolactone receptor and its targets and also the gel retardation conditions with three differently labeled probes.
Collapse
|
38
|
Anzai K, Ohno M, Nakashima T, Kuwahara N, Suzuki R, Tamura T, Komaki H, Miyadoh S, Harayama S, Ando K. Taxonomic distribution of Streptomyces species capable of producing bioactive compounds among strains preserved at NITE/NBRC. Appl Microbiol Biotechnol 2008; 80:287-95. [DOI: 10.1007/s00253-008-1510-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 04/14/2008] [Accepted: 04/16/2008] [Indexed: 12/01/2022]
|
39
|
Isolation and characterization of bamA genes, homologues of the γ-butyrolactone autoregulator-receptor gene in Amycolatopsis mediterranei, a rifamycin producer. Biotechnol Lett 2008; 30:2019-24. [DOI: 10.1007/s10529-008-9794-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 06/20/2008] [Accepted: 06/24/2008] [Indexed: 10/21/2022]
|
40
|
Choi SU, Kim MK, Ha HS, Hwang YI. In vivo functions of the gamma-butyrolactone autoregulator receptor in Streptomyces ambofaciens producing spiramycin. Biotechnol Lett 2007; 30:891-7. [PMID: 18058070 DOI: 10.1007/s10529-007-9613-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 11/21/2007] [Indexed: 11/30/2022]
Abstract
A gene encoding a gamma-butyrolactone autoregulator receptor was cloned in to E. coli from Streptomyces ambofaciens producing spiramycin, a macrolide antibiotic used in both veterinary medicine and human medicine. A 714-bp intact receptor gene (saaR) was obtained by PCR and genomic Southern hybridization with the 100-bp PCR product as a probe. To clarify the in vivo function of saaR, a saaR-disrupted strain was constructed by means of homologous recombination, and phenotypes were compared with those of the wild-type strain. The number of saaR-disruptant spores was 4-fold less than that of the wild-type strain. In addition, saaR deletion from the S. ambofaciens chromosome resulted in complete loss of spiramycin production suggesting that saaR is a rare positive regulator, controlling both spiramycin biosynthesis and sporulation.
Collapse
Affiliation(s)
- Sun-Uk Choi
- Department of Food Science and Biotechnology, Kyungnam University, Masan, 631-701, Republic of Korea
| | | | | | | |
Collapse
|
41
|
Horinouchi S, Beppu T. Hormonal control by A-factor of morphological development and secondary metabolism in Streptomyces. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2007; 83:277-295. [PMID: 24367152 PMCID: PMC3859367 DOI: 10.2183/pjab/83.277] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Accepted: 10/25/2007] [Indexed: 06/03/2023]
Abstract
Streptomyces griseus, a well-known industrial producer of streptomycin, is a member of the genus Streptomyces, which shows a complex life cycle resembling that of fungi. A-factor, a C13 γ-butyrolactone compound, was discovered as a self-regulatory factor or a bacterial hormone to induce morphological differentiation and production of secondary metabolites, including streptomycin, in this organism. Accumulating evidence has revealed an A-factor-triggered signal cascade, which is composed of several key steps or components. These include: (i) AfsA catalyzing a crucial step of A-factor biosynthesis, (ii) the A-factor-specific receptor (ArpA), which acts as a transcriptional repressor for adpA, (iii) adpA, a sole target of ArpA, which encodes a global transcriptional activator AdpA, and (iv) a variety of members of the AdpA regulon, a set of the genes regulated by AdpA. A-factor is biosynthesized via five reaction steps, in which AfsA catalyzes acyl transfer between a β-ketoacyl-acyl carrier protein and the hydroxyl group of dihydroxyacetone phosphate. The receptor ArpA, belonging to the TetR family, is a homodimer, each subunit of which contains a helix-turn-helix DNA-binding motif and an A-factor-binding pocket. The three-dimensional structure and conformational change upon binding A-factor are elucidated, on the basis of X-ray crystallography of CprB, an ArpA homologue. AdpA, belonging to the AraC/XylS transcriptional activator family, binds operators upstream from the promoters of a variety of the target genes and activates their transcription, thus forming the AdpA regulon. Members of the AdpA regulon includes the pathway-specific transcriptional activator gene strR that activates the whole streptomycin biosynthesis gene cluster, in addition to a number of genes that direct the multiple cellular functions required for cellular differentiation in a concerted manner. A variety of A-factor homologues as well as homologues of afsA/arpA are distributed widely among Streptomyces, indicating the significant role of this type of molecular signaling in the ecosystem and evolutional processes.
Collapse
Affiliation(s)
- Sueharu Horinouchi
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo,
Japan
| | - Teruhiko Beppu
- Advanced Research Institute for the Science and Humanities, Nihon University, Tokyo,
Japan
| |
Collapse
|
42
|
Arakawa K, Mochizuki S, Yamada K, Noma T, Kinashi H. gamma-Butyrolactone autoregulator-receptor system involved in lankacidin and lankamycin production and morphological differentiation in Streptomyces rochei. MICROBIOLOGY-SGM 2007; 153:1817-1827. [PMID: 17526839 DOI: 10.1099/mic.0.2006/002170-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An afsA homologue (srrX) and three gamma-butyrolactone receptor gene homologues (srrA, srrB and srrC) are coded on the giant linear plasmid pSLA2-L in Streptomyces rochei 7434AN4, a producer of two polyketide antibiotics, lankacidin and lankamycin. Construction of gene disruptants and their phenotypic study revealed that srrX and srrA make a gamma-butyrolactone receptor system in this strain. Addition of a gamma-butyrolactone fraction to an srrX-deficient mutant restored the production of lankacidin and lankamycin, indicating that the SrrX protein is not necessary for this event. In addition to a positive effect on antibiotic production, srrX showed a negative effect on morphological differentiation. The receptor gene srrA reversed both effects of srrX, while the second receptor gene homologue srrC had only a positive function in spore formation. Furthermore, disruption of the third homologue srrB greatly increased the production of lankacidin and lankamycin. Electron microscopic analysis showed that aerial mycelium formation stopped at a different stage in the srrA and srrC mutants. Overall, these results indicated that srrX, srrA, srrB and srrC constitute a complex regulatory system for antibiotic production and morphological differentiation in S. rochei.
Collapse
Affiliation(s)
- Kenji Arakawa
- Department of Molecular Biotechnology, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Susumu Mochizuki
- Department of Molecular Biotechnology, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Kohei Yamada
- Department of Molecular Biotechnology, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Takenori Noma
- Department of Molecular Biotechnology, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Haruyasu Kinashi
- Department of Molecular Biotechnology, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| |
Collapse
|
43
|
Abstract
Gamma-butyrolactones regulate secondary metabolism and, sometimes, sporulation in actinomycetes by binding to specific receptor proteins, causing their dissociation from DNA targets and releasing the latter from transcriptional repression. Previously, in engineered strains of Streptomyces lividans, we showed that TylP, a deduced gamma-butyrolactone receptor, downregulated reporter gene expression driven by tylP, tylQ or tylS promoter DNA. These genes all control tylosin production in Streptomyces fradiae. Thus, at early stages of fermentation, TylQ represses tylR whereas TylS is needed for transcriptional activation of tylR. Importantly, TylR is the key activator of tylosin-biosynthetic genes. Here, we show that HIS-tagged TylP binds to specific DNA sequences, similar to the targets for authentic gamma-butyrolactone receptors, in the promoters of tylP, tylQ and tylS. Moreover, such binding is disrupted by material produced in S. fradiae and extractable by organic solvent. That putative gamma-butyrolactone material was not produced when orf18 * was disrupted within the S. fradiae genome and only about 1% of that activity survived inactivation of orf16 *, suggesting roles for the respective gene products in gamma-butyrolactone synthesis. Continued synthesis of tylosin by the disrupted strains contrasts with other reports that loss of gamma-butyrolactones abolishes antibiotic production.
Collapse
Affiliation(s)
- Dawn R D Bignell
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, UK
| | | | | |
Collapse
|
44
|
Li W, Ying X, Guo Y, Yu Z, Zhou X, Deng Z, Kieser H, Chater KF, Tao M. Identification of a gene negatively affecting antibiotic production and morphological differentiation in Streptomyces coelicolor A3(2). J Bacteriol 2006; 188:8368-75. [PMID: 17041057 PMCID: PMC1698255 DOI: 10.1128/jb.00933-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SC7A1 is a cosmid with an insert of chromosomal DNA from Streptomyces coelicolor A3(2). Its insertion into the chromosome of S. coelicolor strains caused a duplication of a segment of ca. 40 kb and delayed actinorhodin antibiotic production and sporulation, implying that SC7A1 carried a gene negatively affecting these processes. The subcloning of SC7A1 insert DNA resulted in the identification of the open reading frame SCO5582 as nsdA, a gene negatively affecting Streptomyces differentiation. The disruption of chromosomal nsdA caused the overproduction of spores and of three of four known S. coelicolor antibiotics of quite different chemical types. In at least one case (that of actinorhodin), this was correlated with premature expression of a pathway-specific regulatory gene (actII-orf4), implying that nsdA in the wild-type strain indirectly repressed the expression of the actinorhodin biosynthesis cluster. nsdA expression was up-regulated upon aerial mycelium initiation and was strongest in the aerial mycelium. NsdA has DUF921, a Streptomyces protein domain of unknown function and a conserved SXR site. A site-directed mutation (S458A) in this site in NsdA abolished its function. Blast searching showed that NsdA homologues are present in some Streptomyces genomes. Outside of streptomycetes, NsdA-like proteins have been found in several actinomycetes. The disruption of the nsdA-like gene SCO4114 had no obvious phenotypic effects on S. coelicolor. The nsdA orthologue SAV2652 in S. avermitilis could complement the S. coelicolor nsdA-null mutant phenotype.
Collapse
Affiliation(s)
- Wencheng Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
Bacteria use a variety of means to communicate with one another and with their eukaryotic hosts. In some cases, social interactions allow bacteria to synchronize the behavior of all of the members of the group and thereby act like multicellular organisms. By contrast, some bacterial social engagements promote individuality among members within the group and thereby foster diversity. Here we explore the molecular mechanisms underpinning some recently discovered bacterial communication systems. These include long- and short-range chemical signaling channels; one-way, two-way, and multi-way communication; contact-mediated and contact-inhibited signaling; and the use and spread of misinformation or, more dramatically, even deadly information.
Collapse
Affiliation(s)
- Bonnie L Bassler
- Howard Hughes Medical Institute and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | | |
Collapse
|
46
|
Takano E. Gamma-butyrolactones: Streptomyces signalling molecules regulating antibiotic production and differentiation. Curr Opin Microbiol 2006; 9:287-94. [PMID: 16675291 DOI: 10.1016/j.mib.2006.04.003] [Citation(s) in RCA: 245] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 04/20/2006] [Indexed: 12/31/2022]
Abstract
Small signalling molecules called gamma-butyrolactones are mainly produced by Streptomyces species in which they regulate antibiotic production and morphological differentiation. Their molecular mechanism of action has recently been unravelled in several streptomycetes, revealing a diverse and complex system. Gamma-butyrolactones and their receptors also occur in some other Actinobacteria, suggesting that this is a general regulatory system for antibiotic production. The gamma-butyrolactones bind to receptors, many of which are involved in regulation of specific antibiotic biosynthesis clusters. The importance of understanding how secondary metabolites are regulated and how environmental and physiological signals are sensed highlights the relevance of studying this system.
Collapse
Affiliation(s)
- Eriko Takano
- Mikrobiologie/Biotechnologie, Eberhard-Karls-Universität Tübingen, Elfriede-Aulhorn Str 6, 72076 Tübingen, Germany.
| |
Collapse
|
47
|
Kawabuchi M, Hara Y, Nihira T, Yamada Y. Production of butyrolactone autoregulators by Streptomyces coelicolor A3(2). FEMS Microbiol Lett 2006. [DOI: 10.1111/j.1574-6968.1997.tb12756.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
48
|
Lee KM, Lee CK, Choi SU, Park HR, Kitani S, Nihira T, Hwang YI. Cloning and in vivo functional analysis by disruption of a gene encoding the gamma-butyrolactone autoregulator receptor from Streptomyces natalensis. Arch Microbiol 2005; 184:249-57. [PMID: 16228193 DOI: 10.1007/s00203-005-0047-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 09/15/2005] [Accepted: 09/19/2005] [Indexed: 11/24/2022]
Abstract
A gene encoding a gamma-butyrolactone autoregulator receptor, which has a common activity as DNA-binding transcriptional repressors controlling secondary metabolism and/or morphological differentiation in Streptomyces, was cloned from a natamycin producer, Streptomyces natalensis. PCR using the primers designed for the two highly conserved regions of Streptomyces autoregulator receptors (BarA, FarA, ScbR, and ArpA) gave a 102-bp band. The sequence of this band had a high similarity to the expected region of a receptor gene. By genomic Southern hybridization with the 102-bp insert as a probe, a 687-bp intact receptor gene (sngR) was obtained from S. natalensis. To clarify the in vivo function of sngR, a sngR-disrupted strain was constructed, and the phenotypes were compared with those of the wild-type strain. The sngR-disruptants started natamycin production 6 h earlier and showed a 4.6-fold higher production of natamycin than the wild-type strain. In addition, the sporulation began earlier and the number of spores was tenfold more abundant than that of the wild-type strain. All the phenotypes were restored back to the original phenotypes of the wild-type strain by complementation with the intact sngR, indicating that the autoregulator receptor protein of S. natalensis acts as a primary negative regulator both on the biosynthesis of natamycin and sporulation.
Collapse
Affiliation(s)
- Kang-Mu Lee
- Department of Food Science and Biotechnology, Division of Life Science, Kyungnam University, 449 Wolyong-Dong, Masan 631-701, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
49
|
Yang YH, Joo HS, Lee K, Liou KK, Lee HC, Sohng JK, Kim BG. Novel method for detection of butanolides in Streptomyces coelicolor culture broth, using a His-tagged receptor (ScbR) and mass spectrometry. Appl Environ Microbiol 2005; 71:5050-5. [PMID: 16151086 PMCID: PMC1214611 DOI: 10.1128/aem.71.9.5050-5055.2005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gamma-butyrolactone derivative molecules in Streptomyces play a crucial role in cell density control, secondary metabolism, and cell differentiation. As their synthesis level in the cell is very low compared to those of similar N-acyl homoserine lactone molecules from gram-negative bacteria, it is very hard to analyze them even with several hundredfold concentration of the culture broth. We have developed a very quick and easy detection method using an affinity capture technique with His-tagged receptor proteins and electrospray tandem mass spectrometry. Using Streptomyces coelicolor as a model system, SCB1 was detected from only 100 ml of the culture broth after solvent extraction. This method can be further applied to detection and quantitative analysis of butanolides and inhibitor screening of the receptor molecules.
Collapse
Affiliation(s)
- Yung-Hun Yang
- School of Chemical and Biological Engineering, Seoul National University, Shillim Dong, San 56-1, Kwan-ak Gu, Seoul, Korea
| | | | | | | | | | | | | |
Collapse
|
50
|
Ohnishi Y, Yamazaki H, Kato JY, Tomono A, Horinouchi S. AdpA, a central transcriptional regulator in the A-factor regulatory cascade that leads to morphological development and secondary metabolism in Streptomyces griseus. Biosci Biotechnol Biochem 2005; 69:431-9. [PMID: 15784968 DOI: 10.1271/bbb.69.431] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) is a microbial hormone that triggers aerial mycelium formation and secondary metabolism in Streptomyces griseus. A-factor produced in a growth-dependent manner switches on the transcription of adpA encoding a transcriptional activator by binding to the A-factor receptor protein (ArpA), which has bound the adpA promoter, and dissociating the DNA-bound ArpA from the DNA. AdpA then activates a number of genes with various functions required for morphological development and secondary metabolism, forming an AdpA regulon. AdpA, which contains a ThiJ/PfpI/DJ-1-like dimerization domain at its N-terminal portion and an AraC/XylS-type DNA-binding domain at its C-terminal portion, is a representative of a large subfamily of the AraC/XylS family. AdpA binds various positions with respect to the transcriptional start points of the target genes and recruits RNA polymerase to the specific promoter region, and facilitates the isomerization of the RNA polymerase-DNA complex into an open complex competent for transcriptional initiation. The AdpA-binding consensus sequence is 5'-TGGCSNGWWY-3' (S: G or C; W: A or T; Y: T or C; N: any nucleotide). The DNA-binding specificity of AdpA in conjunction with that of other AraC/XylS family members is also discussed.
Collapse
Affiliation(s)
- Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Japan.
| | | | | | | | | |
Collapse
|