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Stevenson CEM, Lawson DM. Analysis of Protein-DNA Interactions Using Surface Plasmon Resonance and a ReDCaT Chip. Methods Mol Biol 2021; 2263:369-379. [PMID: 33877608 DOI: 10.1007/978-1-0716-1197-5_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The recognition of specific DNA sequences by proteins is crucial to fundamental biological processes such as DNA replication, transcription, and gene regulation. The technique of surface plasmon resonance (SPR) is ideally suited for the measurement of these interactions because it is quantitative, simple to implement, reproducible, can be automated, and requires very little sample. This typically involves the direct capture of biotinylated DNA to a streptavidin (SA) chip before flowing over the protein of interest and monitoring the interaction. However, once the DNA has been immobilized on the chip, it cannot be removed without damaging the chip surface. Moreover, if the protein-DNA interaction is strong, then it may not be possible to remove the protein from the DNA without damaging the chip surface. Given that the chips are costly, this will limit the number of samples that can be tested. Therefore, we have developed a Reusable DNA Capture Technology, or ReDCaT chip, that enables a single streptavidin chip to be used multiple times making the technique simple, quick, and cost effective. The general steps to prepare the ReDCaT chip, run a simple binding experiment, and analysis of data will be described in detail. Some additional applications will also be introduced.
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Affiliation(s)
- Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK.
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
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Vior NM, Cea-Torrescassana E, Eyles TH, Chandra G, Truman AW. Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator. Front Microbiol 2020; 11:495. [PMID: 32273872 PMCID: PMC7113386 DOI: 10.3389/fmicb.2020.00495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/06/2020] [Indexed: 01/18/2023] Open
Abstract
Bottromycin is a ribosomally synthesized and post-translationally modified peptide (RiPP) produced by several streptomycetes, including the plant pathogen Streptomyces scabies. There is significant interest in this molecule as it possesses strong antibacterial activity against clinically relevant multidrug resistant pathogens and is structurally distinct from all other antibiotics. However, studies into its efficacy are hampered by poor yields. An understanding of how bottromycin biosynthesis is regulated could aid the development of strategies to increase titres. Here, we use 5′-tag-RNA-seq to identify the transcriptional organization of the gene cluster, which includes an internal transcriptional start site that precedes btmD, the gene that encodes the bottromycin precursor peptide. We show that the gene cluster does not encode a master regulator that controls pathway expression and instead encodes a regulatory gene, btmL, which functions as a modulator that specifically affects the expression of btmD but not genes up- or downstream of btmD. In order to identify non-cluster associated proteins involved in regulation, proteins were identified that bind to the main promoter of the pathway, which precedes btmC. This study provides insights into how this deceptively complex pathway is regulated in the absence of a pathway specific master regulator, and how it might coordinate with the central metabolism of the cell.
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Affiliation(s)
- Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Tom H Eyles
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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Lee JH, Jeong H, Kim Y, Lee HS. Corynebacterium glutamicum whiA plays roles in cell division, cell envelope formation, and general cell physiology. Antonie van Leeuwenhoek 2019; 113:629-641. [DOI: 10.1007/s10482-019-01370-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/30/2019] [Indexed: 10/25/2022]
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AdpAsd, a Positive Regulator for Morphological Development and Toyocamycin Biosynthesis in Streptomyces diastatochromogenes 1628. Curr Microbiol 2018; 75:1345-1351. [DOI: 10.1007/s00284-018-1529-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/14/2018] [Indexed: 10/28/2022]
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Bauer JS, Fillinger S, Förstner K, Herbig A, Jones AC, Flinspach K, Sharma C, Gross H, Nieselt K, Apel AK. dRNA-seq transcriptional profiling of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis NRRL18488 and general analysis of the transcriptome. RNA Biol 2017; 14:1617-1626. [PMID: 28665778 DOI: 10.1080/15476286.2017.1341020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
FK506 (tacrolimus) is a valuable immunosuppressant produced by several Streptomyces strains. In the genome of the wild type producer Streptomyces tsukubaensis NRRL18488, FK506 biosynthesis is encoded by a gene cluster that spans 83.5 (kb). A whole transcriptome differential shotgun sequencing (dRNA-seq) of S. tsukubaensis was performed to analyze transcription at 2 different time points; before and during active FK506 production. In total, 8,914 transcription start sites were identified in either condition, which enabled precise determination of the 5'-UTR length of the corresponding transcripts as well as the identification of 2 consensus sequence motifs in the promoter regions. The transcription start sites of all gene operons within the FK506 cluster were identified, including 3 examples of leaderless RNA transcripts. These data provide detailed insight into the transcription of the FK506 biosynthetic gene cluster to support future regulatory studies, genetic manipulation, and industrial production.
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Affiliation(s)
- Judith S Bauer
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany.,b German Centre for Infection Research (DZIF), Partner Site Tübingen , Tübingen , Germany
| | - Sven Fillinger
- c Integrative Transcriptomics, Center for Bioinformatics Tübingen, University of Tübingen , Germany
| | - Konrad Förstner
- e Research Center for Infectious Diseases , University of Würzburg , Würzburg , Germany , Core Unit Systems Medicine , Institute for Molecular Infection Biology, University of Würzburg , Würzburg , Germany
| | - Alexander Herbig
- d Max Planck Institute for the Science of Human History , Jena , Germany
| | - Adam C Jones
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany
| | - Katrin Flinspach
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany
| | - Cynthia Sharma
- e Research Center for Infectious Diseases , University of Würzburg , Würzburg , Germany , Core Unit Systems Medicine , Institute for Molecular Infection Biology, University of Würzburg , Würzburg , Germany
| | - Harald Gross
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany.,b German Centre for Infection Research (DZIF), Partner Site Tübingen , Tübingen , Germany
| | - Kay Nieselt
- c Integrative Transcriptomics, Center for Bioinformatics Tübingen, University of Tübingen , Germany
| | - Alexander K Apel
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany.,b German Centre for Infection Research (DZIF), Partner Site Tübingen , Tübingen , Germany
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Abstract
About 2,500 papers dated 2014–2016 were recovered by searching the PubMed database for
Streptomyces, which are the richest known source of antibiotics. This review integrates around 100 of these papers in sections dealing with evolution, ecology, pathogenicity, growth and development, stress responses and secondary metabolism, gene expression, and technical advances. Genomic approaches have greatly accelerated progress. For example, it has been definitively shown that interspecies recombination of conserved genes has occurred during evolution, in addition to exchanges of some of the tens of thousands of non-conserved accessory genes. The closeness of the association of
Streptomyces with plants, fungi, and insects has become clear and is reflected in the importance of regulators of cellulose and chitin utilisation in overall
Streptomyces biology. Interestingly, endogenous cellulose-like glycans are also proving important in hyphal growth and in the clumping that affects industrial fermentations. Nucleotide secondary messengers, including cyclic di-GMP, have been shown to provide key input into developmental processes such as germination and reproductive growth, while late morphological changes during sporulation involve control by phosphorylation. The discovery that nitric oxide is produced endogenously puts a new face on speculative models in which regulatory Wbl proteins (peculiar to actinobacteria) respond to nitric oxide produced in stressful physiological transitions. Some dramatic insights have come from a new model system for
Streptomyces developmental biology,
Streptomyces venezuelae, including molecular evidence of very close interplay in each of two pairs of regulatory proteins. An extra dimension has been added to the many complexities of the regulation of secondary metabolism by findings of regulatory crosstalk within and between pathways, and even between species, mediated by end products. Among many outcomes from the application of chromosome immunoprecipitation sequencing (ChIP-seq) analysis and other methods based on “next-generation sequencing” has been the finding that 21% of
Streptomyces mRNA species lack leader sequences and conventional ribosome binding sites. Further technical advances now emerging should lead to continued acceleration of knowledge, and more effective exploitation, of these astonishing and critically important organisms.
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Affiliation(s)
- Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
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Bekiesch P, Basitta P, Apel AK. Challenges in the Heterologous Production of Antibiotics inStreptomyces. Arch Pharm (Weinheim) 2016; 349:594-601. [DOI: 10.1002/ardp.201600058] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/27/2016] [Accepted: 05/06/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Paulina Bekiesch
- Pharmaceutical Biology; Pharmaceutical Institute; Eberhard-Karls-Universität Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Patrick Basitta
- Pharmaceutical Biology; Pharmaceutical Institute; Eberhard-Karls-Universität Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Alexander K. Apel
- Pharmaceutical Biology; Pharmaceutical Institute; Eberhard-Karls-Universität Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
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Bekiesch P, Forchhammer K, Apel AK. Characterization of DNA Binding Sites of RokB, a ROK-Family Regulator from Streptomyces coelicolor Reveals the RokB Regulon. PLoS One 2016; 11:e0153249. [PMID: 27145180 PMCID: PMC4856308 DOI: 10.1371/journal.pone.0153249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/27/2016] [Indexed: 12/27/2022] Open
Abstract
ROK-family proteins have been described to act either as sugar kinases or as transcriptional regulators. Few ROK-family regulators have been characterized so far and most of them are involved in carbon catabolite repression. RokB (Sco6115) has originally been identified in a DNA-affinity capturing approach as a possible regulator of the heterologously expressed novobiocin biosynthetic gene cluster in Streptomyces coelicolor M512. Interestingly, both, the rokB deletion mutants as well as its overexpressing mutants showed significantly reduced novobiocin production in the host strain S.coelicolor M512. We identified the DNA-binding site for RokB in the promoter region of the novobiocin biosynthetic genes novH-novW. It overlaps with the novH start codon which may explain the reduction of novobiocin production caused by overexpression of rokB. Bioinformatic screening coupled with surface plasmon resonance based interaction studies resulted in the discovery of five RokB binding sites within the genome of S. coelicolor. Using the genomic binding sites, a consensus motif for RokB was calculated, which differs slightly from previously determined binding motifs for ROK-family regulators. The annotations of the possible members of the so defined RokB regulon gave hints that RokB might be involved in amino acid metabolism and transport. This hypothesis was supported by feeding experiments with casamino acids and L-tyrosine, which could also explain the reduced novobiocin production in the deletion mutants.
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Affiliation(s)
- Paulina Bekiesch
- Pharmaceutical Biology, Pharmaceutical Institute, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen, 72076, Tübingen, Germany
| | - Karl Forchhammer
- Microbiology/Department of Organismic Interactions, Interfaculty Institute of Microbiology and Infection, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Alexander Kristian Apel
- Pharmaceutical Biology, Pharmaceutical Institute, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen, 72076, Tübingen, Germany
- * E-mail:
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