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Meijer WJJ, Miguel-Arribas A. Genetic Engineering of Bacillus subtilis Using Competence-Induced Homologous Recombination Techniques. Methods Mol Biol 2024; 2819:241-260. [PMID: 39028510 DOI: 10.1007/978-1-0716-3930-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Bacillus subtilis is one of the best-studied bacteria and serves as a Gram-positive model system to address fundamental biological processes. Depending on conditions, a B. subtilis cell can initiate one out of various distinct differentiation processes to cope with changing environmental conditions. One of these differentiation processes is natural competence that allows cells to adsorb exogenous DNA and subsequently incorporate it into its chromosome by homologous recombination. Due to competence development, the genome of B. subtilis can be easily manipulated, and this has contributed to B. subtilis being a model system. In this chapter, we describe some of the most common genetic tools that can be used in combination with natural competence to tailor the genome of B. subtilis.
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Affiliation(s)
- Wilfried J J Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Andrés Miguel-Arribas
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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2
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Miguel-Arribas A, Martín-María A, Alaerds ECW, Val-Calvo J, Yuste L, Rojo F, Abia D, Wu L, Meijer WJJ. Extraordinary long-stem confers resistance of intrinsic terminators to processive antitermination. Nucleic Acids Res 2023; 51:6073-6086. [PMID: 37125647 PMCID: PMC10325885 DOI: 10.1093/nar/gkad333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/14/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023] Open
Abstract
Many prokaryotic operons encode a processive antitermination (P-AT) system. Transcription complexes associated with an antitermination factor can bypass multiple transcription termination signals regardless of their sequences. However, to avoid compromising transcriptional regulation of downstream regions, the terminator at the end of the operon needs to be resistant to antitermination. So far, no studies on the mechanism of resistance to antitermination have been reported. The recently discovered conAn P-AT system is composed of two components that are encoded at the start of many conjugation operons on plasmids of Gram-positive bacteria. Here we report the identification of a conAn-resistant terminator, named TerR, in the conjugation operon of the Bacillus subtilis plasmid pLS20, re-defining the end of the conjugation operon. We investigated the various characteristics of TerR and show that its extraordinary long stem is the determining feature for resistance to antitermination. This is the first P-AT resistance mechanism to be reported.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Ana Martín-María
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Eef C W Alaerds
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, C. Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, C. Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa”, (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Bernardo N, Crespo I, Cuppari A, Meijer WJJ, Boer DR. A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53. Acta Crystallogr D Struct Biol 2023; 79:259-267. [PMID: 36876435 PMCID: PMC9986798 DOI: 10.1107/s2059798323001298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
Transcriptional regulation usually requires the action of several proteins that either repress or activate a promotor of an open reading frame. These proteins can counteract each other, thus allowing tight regulation of the transcription of the corresponding genes, where tight repression is often linked to DNA looping or cross-linking. Here, the tetramerization domain of the bacterial gene repressor Rco from Bacillus subtilis plasmid pLS20 (RcopLS20) has been identified and its structure is shown to share high similarity to the tetramerization domain of the well known p53 family of human tumor suppressors, despite lacking clear sequence homology. In RcopLS20, this tetramerization domain is responsible for inducing DNA looping, a process that involves multiple tetramers. In accordance, it is shown that RcopLS20 can form octamers. This domain was named TetDloop and its occurrence was identified in other Bacillus species. The TetDloop fold was also found in the structure of a transcriptional repressor from Salmonella phage SPC32H. It is proposed that the TetDloop fold has evolved through divergent evolution and that the TetDloop originates from a common ancestor predating the occurrence of multicellular life.
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Affiliation(s)
- Nerea Bernardo
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Vallès, Catalunya, Spain
| | - Isidro Crespo
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Vallès, Catalunya, Spain
| | - Anna Cuppari
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Vallès, Catalunya, Spain
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC–UAM), Universidad Autónoma de Madrid, Calle Nicolás Cabrera 1, Canto Blanco, 28049 Madrid, Spain
| | - D. Roeland Boer
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Vallès, Catalunya, Spain
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Val-Calvo J, Miguel-Arribas A, Abia D, Wu LJ, Meijer WJJ. pLS20 is the archetype of a new family of conjugative plasmids harboured by Bacillus species. NAR Genom Bioinform 2021; 3:lqab096. [PMID: 34729475 PMCID: PMC8557374 DOI: 10.1093/nargab/lqab096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/03/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Conjugation plays important roles in genome plasticity, adaptation and evolution but is also the major horizontal gene-transfer route responsible for spreading toxin, virulence and antibiotic resistance genes. A better understanding of the conjugation process is required for developing drugs and strategies to impede the conjugation-mediated spread of these genes. So far, only a limited number of conjugative elements have been studied. For most of them, it is not known whether they represent a group of conjugative elements, nor about their distribution patterns. Here we show that pLS20 from the Gram-positive bacterium Bacillus subtilis is the prototype conjugative plasmid of a family of at least 35 members that can be divided into four clades, and which are harboured by different Bacillus species found in different global locations and environmental niches. Analyses of their phylogenetic relationship and their conjugation operons have expanded our understanding of a family of conjugative plasmids of Gram-positive origin.
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Affiliation(s)
- Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
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Mori K, Verrone V, Amatsu R, Fukui K, Meijer WJJ, Ishikawa S, Wipat A, Yoshida KI. Assessment of Bacillus subtilis Plasmid pLS20 Conjugation in the Absence of Quorum Sensing Repression. Microorganisms 2021; 9:microorganisms9091931. [PMID: 34576826 PMCID: PMC8470214 DOI: 10.3390/microorganisms9091931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
Bacillus subtilis conjugative plasmid pLS20 uses a quorum-sensing mechanism to control expression levels of its conjugation genes, involving the repressor RcopLS20, the anti-repressor RappLS20, and the signaling peptide Phr*pLS20. In previous studies, artificial overexpression of rappLS20 in the donor cells was shown to enhance conjugation efficiency. However, we found that the overexpression of rappLS20 led to various phenotypic traits, including cell aggregation and death, which might have affected the correct determination of the conjugation efficiency when determined by colony formation assay. In the current study, conjugation efficiencies were determined under different conditions using a two-color fluorescence-activated flow cytometry method and measuring a single-round of pLS20-mediated transfer of a mobilizable plasmid. Under standard conditions, the conjugation efficiency obtained by fluorescence-activated flow cytometry was 23-fold higher than that obtained by colony formation. Furthermore, the efficiency difference increased to 45-fold when rappLS20 was overexpressed.
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Affiliation(s)
- Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Valeria Verrone
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne NE4 5TG, UK; (V.V.); (A.W.)
| | - Ryotaro Amatsu
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Kaho Fukui
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Anil Wipat
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne NE4 5TG, UK; (V.V.); (A.W.)
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
- Correspondence: ; Tel.: +81-78-803-5891
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Miguel-Arribas A, Val-Calvo J, Gago-Córdoba C, Izquierdo JM, Abia D, Wu LJ, Errington J, Meijer WJJ. A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria. Nucleic Acids Res 2021; 49:5553-5567. [PMID: 33999173 PMCID: PMC8191782 DOI: 10.1093/nar/gkab360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/09/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulation allows adaptive and coordinated gene expression, and is essential for life. Processive antitermination systems alter the transcription elongation complex to allow the RNA polymerase to read through multiple terminators in an operon. Here, we describe the discovery of a novel bipartite antitermination system that is widespread among conjugative elements from Gram-positive bacteria, which we named conAn. This system is composed of a large RNA element that exerts antitermination, and a protein that functions as a processivity factor. Besides allowing coordinated expression of very long operons, we show that these systems allow differential expression of genes within an operon, and probably contribute to strict regulation of the conjugation genes by minimizing the effects of spurious transcription. Mechanistic features of the conAn system are likely to decisively influence its host range, with important implications for the spread of antibiotic resistance and virulence genes.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Córdoba
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - José M Izquierdo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular "Severo Ochoa", (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
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A native conjugative plasmid confers potential selective advantages to plant growth-promoting Bacillus velezensis strain GH1-13. Commun Biol 2021; 4:582. [PMID: 33990691 PMCID: PMC8121941 DOI: 10.1038/s42003-021-02107-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
The conjugative plasmid (pBV71) possibly confers a selective advantage to Bacillus velezensis strain GH1-13, although a selective marker gene is yet to be identified. Here we show that few non-mucoid wild-type GH1-13 cells are spontaneously converted to mucoid variants with or without the loss of pBV71. Mucoid phenotypes, which contain or lack the plasmid, become sensitive to bacitracin, gramicidin, selenite, and tellurite. Using the differences in antibiotic resistance and phenotype, we isolated a reverse complement (COM) and a transconjugant of strain FZB42 with the native pBV71. Transformed COM and FZB42p cells were similar to the wild-type strain GH1-13 with high antibiotic resistance and slow growth rates on lactose compared to those of mucoid phenotypes. RT-PCR analysis revealed that the expression of plasmid-encoded orphan aspartate phosphatase (pRapD) was coordinated with a new quorum-sensing (QS) cassette of RapF2-PhrF2 present in the chromosome of strain GH1-13, but not in strain FZB42. Multi-omics analysis on wild-type and plasmid-cured cells of strain GH1-13 suggested that the conjugative plasmid expression has a crucial role in induction of early envelope stress response that promotes cell morphogenesis, biofilm formation, catabolite repression, and biosynthesis of extracellular-matrix components and antibiotics for protection of host cell during exponential phase.
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Meijer WJJ, Boer DR, Ares S, Alfonso C, Rojo F, Luque-Ortega JR, Wu LJ. Multiple Layered Control of the Conjugation Process of the Bacillus subtilis Plasmid pLS20. Front Mol Biosci 2021; 8:648468. [PMID: 33816561 PMCID: PMC8014075 DOI: 10.3389/fmolb.2021.648468] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/08/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial conjugation is the main horizontal gene transfer route responsible for the spread of antibiotic resistance, virulence and toxin genes. During conjugation, DNA is transferred from a donor to a recipient cell via a sophisticated channel connecting the two cells. Conjugation not only affects many different aspects of the plasmid and the host, ranging from the properties of the membrane and the cell surface of the donor, to other developmental processes such as competence, it probably also poses a burden on the donor cell due to the expression of the large number of genes involved in the conjugation process. Therefore, expression of the conjugation genes must be strictly controlled. Over the past decade, the regulation of the conjugation genes present on the conjugative Bacillus subtilis plasmid pLS20 has been studied using a variety of methods including genetic, biochemical, biophysical and structural approaches. This review focuses on the interplay between RcopLS20, RappLS20 and Phr*pLS20, the proteins that control the activity of the main conjugation promoter Pc located upstream of the conjugation operon. Proper expression of the conjugation genes requires the following two fundamental elements. First, conjugation is repressed by default and an intercellular quorum-signaling system is used to sense conditions favorable for conjugation. Second, different layers of regulation act together to repress the Pc promoter in a strict manner but allowing rapid activation. During conjugation, ssDNA is exported from the cell by a membrane-embedded DNA translocation machine. Another membrane-embedded DNA translocation machine imports ssDNA in competent cells. Evidences are reviewed indicating that conjugation and competence are probably mutually exclusive processes. Some of the questions that remain unanswered are discussed.
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Affiliation(s)
- Wilfried J J Meijer
- Laboratory 402, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | | | - Saúl Ares
- Laboratory 35, C. Grupo Interdisciplinar de Sistemas Complejos and Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Carlos Alfonso
- Laboratory B08, Systems Biochemistry of Bacterial Division Lab, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Fernando Rojo
- Laboratory 216, Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Juan R Luque-Ortega
- Laboratory S07, Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
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Gago-Córdoba C, Val-Calvo J, Abia D, Díaz-Talavera A, Miguel-Arribas A, Aguilar Suárez R, van Dijl JM, Wu LJ, Meijer WJJ. A Conserved Class II Type Thioester Domain-Containing Adhesin Is Required for Efficient Conjugation in Bacillus subtilis. mBio 2021; 12:e00104-21. [PMID: 33727345 PMCID: PMC8092201 DOI: 10.1128/mbio.00104-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
Conjugation, the process by which a DNA element is transferred from a donor to a recipient cell, is the main horizontal gene transfer route responsible for the spread of antibiotic resistance and virulence genes. Contact between a donor and a recipient cell is a prerequisite for conjugation, because conjugative DNA is transferred into the recipient via a channel connecting the two cells. Conjugative elements encode proteins dedicated to facilitating the recognition and attachment to recipient cells, also known as mating pair formation. A subgroup of the conjugative elements is able to mediate efficient conjugation during planktonic growth, and mechanisms facilitating mating pair formation will be particularly important in these cases. Conjugative elements of Gram-negative bacteria encode conjugative pili, also known as sex pili, some of which are retractile. Far less is known about mechanisms that promote mating pair formation in Gram-positive bacteria. The conjugative plasmid pLS20 of the Gram-positive bacterium Bacillus subtilis allows efficient conjugation in liquid medium. Here, we report the identification of an adhesin gene in the pLS20 conjugation operon. The N-terminal region of the adhesin contains a class II type thioester domain (TED) that is essential for efficient conjugation, particularly in liquid medium. We show that TED-containing adhesins are widely conserved in Gram-positive bacteria, including pathogens where they often play crucial roles in pathogenesis. Our study is the first to demonstrate the involvement of a class II type TED-containing adhesin in conjugation.IMPORTANCE Bacterial resistance to antibiotics has become a serious health care problem. The spread of antibiotic resistance genes between bacteria of the same or different species is often mediated by a process named conjugation, where a donor cell transfers DNA to a recipient cell through a connecting channel. The first step in conjugation is recognition and attachment of the donor to a recipient cell. Little is known about this first step, particularly in Gram-positive bacteria. Here, we show that the conjugative plasmid pLS20 of Bacillus subtilis encodes an adhesin protein that is essential for effective conjugation. This adhesin protein has a structural organization similar to adhesins produced by other Gram-positive bacteria, including major pathogens, where the adhesins serve in attachment to host tissues during colonization and infection. Our findings may thus also open novel avenues to design drugs that inhibit the spread of antibiotic resistance by blocking the first recipient-attachment step in conjugation.
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Affiliation(s)
- César Gago-Córdoba
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - David Abia
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Alberto Díaz-Talavera
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Rocío Aguilar Suárez
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wilfried J J Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
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Crespo I, Bernardo N, Miguel-Arribas A, Singh PK, Luque-Ortega JR, Alfonso C, Malfois M, Meijer WJJ, Boer DR. Inactivation of the dimeric RappLS20 anti-repressor of the conjugation operon is mediated by peptide-induced tetramerization. Nucleic Acids Res 2020; 48:8113-8127. [PMID: 32658272 PMCID: PMC7430634 DOI: 10.1093/nar/gkaa540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 12/21/2022] Open
Abstract
Quorum sensing allows bacterial cells to communicate through the release of soluble signaling molecules into the surrounding medium. It plays a pivotal role in controlling bacterial conjugation in Gram-positive cells, a process that has tremendous impact on health. Intracellular regulatory proteins of the RRNPP family are common targets of these signaling molecules. The RRNPP family of gene regulators bind signaling molecules at their C-terminal domain (CTD), but have highly divergent functionalities at their N-terminal effector domains (NTD). This divergence is also reflected in the functional states of the proteins, and is highly interesting from an evolutionary perspective. RappLS20 is an RRNPP encoded on the Bacillus subtilis plasmid pLS20. It relieves the gene repression effectuated by RcopLS20 in the absence of the mature pLS20 signaling peptide Phr*pLS20. We report here an in-depth structural study of apo and Phr*pLS20-bound states of RappLS20 at various levels of atomic detail. We show that apo-RappLS20 is dimeric and that Phr*pLS20-bound Rap forms NTD-mediated tetramers. In addition, we show that RappLS20 binds RcopLS20 directly in the absence of Phr*pLS20 and that addition of Phr*pLS20 releases RcopLS20 from RappLS20. This allows RcopLS20 to bind the promotor region of crucial conjugation genes blocking their expression.
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Affiliation(s)
- Isidro Crespo
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Nerea Bernardo
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Praveen K Singh
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Juan R Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carlos Alfonso
- Systems Biochemistry of Bacterial Division Lab, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Marc Malfois
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Wilfried J J Meijer
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Dirk Roeland Boer
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
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Singh PK, Serrano E, Ramachandran G, Miguel-Arribas A, Gago-Cordoba C, Val-Calvo J, López-Pérez A, Alfonso C, Wu LJ, Luque-Ortega JR, Meijer WJJ. Reversible regulation of conjugation of Bacillus subtilis plasmid pLS20 by the quorum sensing peptide responsive anti-repressor RappLS20. Nucleic Acids Res 2020; 48:10785-10801. [PMID: 33045732 PMCID: PMC7641744 DOI: 10.1093/nar/gkaa797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/02/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Quorum sensing plays crucial roles in bacterial communication including in the process of conjugation, which has large economical and health-related impacts by spreading antibiotic resistance. The conjugative Bacillus subtilis plasmid pLS20 uses quorum sensing to determine when to activate the conjugation genes. The main conjugation promoter, Pc, is by default repressed by a regulator RcopLS20 involving DNA looping. A plasmid-encoded signalling peptide, Phr*pLS20, inactivates the anti-repressor of RcopLS20, named RappLS20, which belongs to the large group of RRNPP family of regulatory proteins. Here we show that DNA looping occurs through interactions between two RcopLS20 tetramers, each bound to an operator site. We determined the relative promoter strengths for all the promoters involved in synthesizing the regulatory proteins of the conjugation genes, and constructed an in vivo system uncoupling these regulatory genes to show that RappLS20 is sufficient for activating conjugation in vivo. We also show that RappLS20 actively detaches RcopLS20 from DNA by preferentially acting on the RcopLS20 molecules involved in DNA looping, resulting in sequestration but not inactivation of RcopLS20. Finally, results presented here in combination with our previous results show that activation of conjugation inhibits competence and competence development inhibits conjugation, indicating that both processes are mutually exclusive.
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Affiliation(s)
- Praveen K Singh
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Ester Serrano
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Gayetri Ramachandran
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Cordoba
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Arancha López-Pérez
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Juan R Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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12
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Tsigkinopoulou A, Takano E, Breitling R. Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling. PLoS Comput Biol 2020; 16:e1008039. [PMID: 32649676 PMCID: PMC7384680 DOI: 10.1371/journal.pcbi.1008039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 07/27/2020] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
Antibiotic production is coordinated in the Streptomyces coelicolor population through the use of diffusible signaling molecules of the γ-butyrolactone (GBL) family. The GBL regulatory system involves a small, and not completely defined two-gene network which governs a potentially bi-stable switch between the “on” and “off” states of antibiotic production. The use of this circuit as a tool for synthetic biology has been hampered by a lack of mechanistic understanding of its functionality. We here present the creation and analysis of a versatile and adaptable ensemble model of the Streptomyces GBL system (detailed information on all model mechanisms and parameters is documented in http://www.systemsbiology.ls.manchester.ac.uk/wiki/index.php/Main_Page). We use the model to explore a range of previously proposed mechanistic hypotheses, including transcriptional interference, antisense RNA interactions between the mRNAs of the two genes, and various alternative regulatory activities. Our results suggest that transcriptional interference alone is not sufficient to explain the system’s behavior. Instead, antisense RNA interactions seem to be the system's driving force, combined with an aggressive scbR promoter. The computational model can be used to further challenge and refine our understanding of the system’s activity and guide future experimentation. Streptomyces species are Gram-positive soil-dwelling bacteria, which are known as a prolific source of secondary metabolites, such as antibiotics. Antibiotic production is coordinated in the bacterial population through the use of diffusible signalling molecules of the γ-butyrolactone (GBL) family. The GBL regulatory system involves a small, yet complex two-gene network, the mechanism of which has not yet been completely defined. The complete elucidation of this system could potentially lead to the ability to design reliable and sensitive engineered cellular switches. We therefore designed a versatile model of the GBL system in order to investigate the feasibility of various hypothesized mechanisms. The ensemble modelling analysis that we performed revealed that antisense RNA interactions seem to be the system’s driving force, together with an aggressive scbR promoter. Transcriptional interference is also significant; however, it is not sufficient to explain the system’s behavior by itself. Finally, the model indicates key experiments, which could completely elucidate the role of the system and the interactions of its components and potentially lead to the design of reliable and sensitive systems with significant applications as orthologous regulatory circuits in synthetic biology and biotechnology.
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Affiliation(s)
- Areti Tsigkinopoulou
- DTU Biosustain, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Manchester Institute of Biotechnology, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
| | - Eriko Takano
- Manchester Institute of Biotechnology, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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13
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Gago-Córdoba C, Val-Calvo J, Miguel-Arribas A, Serrano E, Singh PK, Abia D, Wu LJ, Meijer WJJ. Surface Exclusion Revisited: Function Related to Differential Expression of the Surface Exclusion System of Bacillus subtilis Plasmid pLS20. Front Microbiol 2019; 10:1502. [PMID: 31354647 PMCID: PMC6635565 DOI: 10.3389/fmicb.2019.01502] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/14/2019] [Indexed: 11/17/2022] Open
Abstract
During conjugation a genetic element is transferred from a bacterial donor to a recipient cell via a connecting channel. It is the major route responsible for the spread of antibiotic resistance. Conjugative elements can contain exclusion system(s) that inhibit its transfer to a cell already harboring the element. Our limited knowledge on exclusion systems is mainly based on plasmids of Gram-negative bacteria. Here we studied the conjugative plasmid pLS20 of the Gram-positive Bacillus subtilis. We demonstrate that pLS20 contains an exclusion system and identified the single gene responsible for exclusion, named sespLS20 , which is embedded in the conjugation operon. SespLS20 is the founding member of a novel family of surface exclusion proteins encoded by conjugative elements of Gram-positive origin. We show that the extent of surface exclusion correlates with the level of sespLS20 expression, and that sespLS20 is expressed at basal low-levels in all donor cells but becomes highly expressed in conjugating cells. Accordingly, the transfer of pLS20 from a conjugation-primed donor cell to an un-primed or conjugation-primed donor is inhibited moderately and very efficiently, respectively. The consequences of this differential regulation, which appears to be a conserved feature of surface exclusion systems of Gram-positive and Gram-negative origin, are discussed.
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Affiliation(s)
- César Gago-Córdoba
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Jorge Val-Calvo
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Andrés Miguel-Arribas
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Ester Serrano
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Praveen K. Singh
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - David Abia
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wilfried J. J. Meijer
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
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14
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Kohler V, Keller W, Grohmann E. Regulation of Gram-Positive Conjugation. Front Microbiol 2019; 10:1134. [PMID: 31191478 PMCID: PMC6540685 DOI: 10.3389/fmicb.2019.01134] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/03/2019] [Indexed: 12/20/2022] Open
Abstract
Type IV Secretion Systems (T4SSs) are membrane-spanning multiprotein complexes dedicated to protein secretion or conjugative DNA transport (conjugation systems) in bacteria. The prototype and best-characterized T4SS is that of the Gram-negative soil bacterium Agrobacterium tumefaciens. For Gram-positive bacteria, only conjugative T4SSs have been characterized in some biochemical, structural, and mechanistic details. These conjugation systems are predominantly encoded by self-transmissible plasmids but are also increasingly detected on integrative and conjugative elements (ICEs) and transposons. Here, we report regulatory details of conjugation systems from Enterococcus model plasmids pIP501 and pCF10, Bacillus plasmid pLS1, Clostridium plasmid pCW3, and staphylococcal plasmid pSK41. In addition, regulation of conjugative processes of ICEs (ICEBs1, ICESt1, ICESt3) by master regulators belonging to diverse repressor families will be discussed. A special focus of this review lies on the comparison of regulatory mechanisms executed by proteins belonging to the RRNPP family. These regulators share a common fold and govern several essential bacterial processes, including conjugative transfer.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, BioTechMed Graz, University of Graz, Graz, Austria
| | - Walter Keller
- Institute of Molecular Biosciences, BioTechMed Graz, University of Graz, Graz, Austria
| | - Elisabeth Grohmann
- Life Sciences and Technology, Beuth University of Applied Sciences Berlin, Berlin, Germany
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15
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Miyano M, Tanaka K, Ishikawa S, Mori K, Miguel-Arribas A, Meijer WJJ, Yoshida KI. A novel method for transforming the thermophilic bacterium Geobacillus kaustophilus. Microb Cell Fact 2018; 17:127. [PMID: 30119674 PMCID: PMC6098629 DOI: 10.1186/s12934-018-0969-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial strains of the genus Geobacillus grow at high temperatures of 50-75 °C and could thus be useful for biotechnological applications. However, genetic manipulation of these species is difficult because the current techniques for transforming Geobacillus species are not efficient. In this study, we developed an easy and efficient method for transforming Geobacillus kaustophilus using the conjugative plasmid pLS20cat. RESULTS We constructed a transformation system comprising (i) a mobilizable Bacillus subtilis-G. kaustophilus shuttle plasmid named pGK1 that carries the elements for selection and replication in Geobacillus, and (ii) a pLS20cat-harboring B. subtilis donor strain expressing the dam methylase gene of Escherichia coli and the conjugation-stimulating rapLS20 gene of pLS20cat. This system can be used to efficiently introduce pGK1 into G. kaustophilus by mobilization in a pLS20cat-dependent way. Whereas the thermostable kanamycin marker and Geobacillus replication origin of pGK1 as well as expression of dam methylase in the donor were indispensable for mobilization, ectopic expression of rapLS20 increased its efficiency. In addition, the conditions of the recipient influenced mobilization efficiency: the highest mobilization efficiencies were obtained using recipient cells that were in the exponential growth phase. Furthermore, elimination of the origin of transfer from pLS20cat enhanced the mobilization. CONCLUSIONS We describe a novel method of plasmid mobilization into G. kaustophilus recipient from B. subtilis donor depending on the helper function of pLS20cat, which enables simple, rapid, and easy transformation of the thermophilic Gram-positive bacterium.
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Grants
- 17K19237 Ministry of Education, Culture, Sports, Science and Technology
- 18H02128 Ministry of Education, Culture, Sports, Science and Technology
- Bio2013-41489-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO2016-77883-C2-1-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
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Affiliation(s)
- Megumi Miyano
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kosei Tanaka
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
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16
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Fang X, Liu Q, Bohrer C, Hensel Z, Han W, Wang J, Xiao J. Cell fate potentials and switching kinetics uncovered in a classic bistable genetic switch. Nat Commun 2018; 9:2787. [PMID: 30018349 PMCID: PMC6050291 DOI: 10.1038/s41467-018-05071-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/17/2018] [Indexed: 11/13/2022] Open
Abstract
Bistable switches are common gene regulatory motifs directing two mutually exclusive cell fates. Theoretical studies suggest that bistable switches are sufficient to encode more than two cell fates without rewiring the circuitry due to the non-equilibrium, heterogeneous cellular environment. However, such a scenario has not been experimentally observed. Here by developing a new, dual single-molecule gene-expression reporting system, we find that for the two mutually repressing transcription factors CI and Cro in the classic bistable bacteriophage λ switch, there exist two new production states, in which neither CI nor Cro is produced, or both CI and Cro are produced. We construct the corresponding potential landscape and map the transition kinetics among the four production states. These findings uncover cell fate potentials beyond the classical picture of bistable switches, and open a new window to explore the genetic and environmental origins of the cell fate decision-making process in gene regulatory networks.
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Affiliation(s)
- Xiaona Fang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, 130022, China
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- College of Physics, Jilin University, Changchun, 130012, China
- Department of Chemistry and Physics, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Qiong Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, 130022, China
| | - Christopher Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Zach Hensel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Wei Han
- College of Physics, Jilin University, Changchun, 130012, China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, 130022, China.
- College of Physics, Jilin University, Changchun, 130012, China.
- Department of Chemistry and Physics, Stony Brook University, Stony Brook, NY, 11790, USA.
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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17
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Rapid conjugative mobilization of a 100 kb segment of Bacillus subtilis chromosomal DNA is mediated by a helper plasmid with no ability for self-transfer. Microb Cell Fact 2018; 17:13. [PMID: 29374463 PMCID: PMC5787278 DOI: 10.1186/s12934-017-0855-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/20/2017] [Indexed: 11/14/2022] Open
Abstract
Background The conjugative plasmid, pLS20, isolated from Bacillus subtilis natto, has an outstanding capacity for rapid self-transfer. In addition, it can function as a helper plasmid, mediating the mobilization of an independently replicating co-resident plasmid. Results In this study, the oriT sequence of pLS20cat (oriTLS20) was eliminated to obtain the plasmid, pLS20catΔoriT. This resulted in the complete loss of the conjugative transfer of the plasmid but still allowed it to mobilize a co-resident mobilizable plasmid. Moreover, pLS20catΔoriT was able to mobilize longer DNA segments, up to 113 kb of chromosomal DNA containing oriTLS20, after mixing the liquid cultures of the donor and recipient for only 15 min. Conclusions The chromosomal DNA mobilization mediated by pLS20catΔoriT will allow us to develop a novel genetic tool for the rapid, easy, and repetitive mobilization of longer DNA segments into a recipient chromosome.
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18
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Miguel-Arribas A, Hao JA, Luque-Ortega JR, Ramachandran G, Val-Calvo J, Gago-Córdoba C, González-Álvarez D, Abia D, Alfonso C, Wu LJ, Meijer WJJ. The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation. Front Microbiol 2017; 8:2138. [PMID: 29163424 PMCID: PMC5675868 DOI: 10.3389/fmicb.2017.02138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/19/2017] [Indexed: 12/15/2022] Open
Abstract
Bacterial conjugation is the process by which a conjugative element (CE) is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer (oriT), where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host. The conjugative plasmid pLS20 replicates in the Gram-positive Firmicute bacterium Bacillus subtilis. We have recently identified the relaxase gene and the oriT of pLS20, which are separated by a region of almost 1 kb. Here we show that this region contains two auxiliary genes that we name aux1LS20 and aux2LS20 , and which we show are essential for conjugation. Both Aux1LS20 and Aux2LS20 are predicted to contain a Ribbon-Helix-Helix DNA binding motif near their N-terminus. Analyses of the purified proteins show that Aux1LS20 and Aux2LS20 form tetramers and hexamers in solution, respectively, and that they both bind preferentially to oriTLS20 , although with different characteristics and specificities. In silico analyses revealed that genes encoding homologs of Aux1LS20 and/or Aux2LS20 are located upstream of almost 400 relaxase genes of the RelLS20 family (MOBL) of relaxases. Thus, Aux1LS20 and Aux2LS20 of pLS20 constitute the founding member of the first two families of auxiliary proteins described for CEs of Gram-positive origin.
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Affiliation(s)
- Andrés Miguel-Arribas
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Jian-An Hao
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
- The Institute of Seawater Desalination and Multipurpose Utilization (SOA), Tianjin, China
| | | | - Gayetri Ramachandran
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Jorge Val-Calvo
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - César Gago-Córdoba
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Daniel González-Álvarez
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - David Abia
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Ling J. Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Wilfried J. J. Meijer
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
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19
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Chen Y, Bandyopadhyay A, Kozlowicz BK, Haemig HAH, Tai A, Hu W, Dunny GM. Mechanisms of peptide sex pheromone regulation of conjugation in Enterococcus faecalis. Microbiologyopen 2017; 6:e00492. [PMID: 28523739 PMCID: PMC5552905 DOI: 10.1002/mbo3.492] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/30/2017] [Accepted: 04/10/2017] [Indexed: 12/22/2022] Open
Abstract
In many gram positive bacteria, horizontal transfer and virulence are regulated by peptide-mediated cell-cell signaling. The heptapeptide cCF10 (C) activates conjugative transfer of the Enterococcus faecalis plasmid pCF10, whereas the iCF10 (I) peptide inhibits transfer. Both peptides bind to the same domain of the master transcription regulator PrgX, a repressor of transcription of the prgQ operon encoding conjugation genes. We show that repression of prgQ by PrgX tetramers requires formation of a pCF10 DNA loop where each of two PrgX DNA-binding sites is occupied by a dimer. I binding to PrgX enhances prgQ repression, while C binding has the opposite effect. Previous models suggested that differential effects of these two peptides on the PrgX oligomerization state accounted for their distinct functions. Our new results demonstrate that both peptides have similar, high-binding affinity for PrgX, and that both peptides actually promote formation of PrgX tetramers with higher DNA-binding affinity than Apo-PrgX. We propose that differences in repression ability of PrgX/peptide complexes result from subtle differences in the structures of DNA-bound PrgX/peptide complexes. Changes in the induction state of a donor cell likely results from replacement of one type of DNA-bound peptide/PrgX tetramer with the other.
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Affiliation(s)
- Yuqing Chen
- Department of Microbiology and ImmunologyUniversity of MinnesotaMinneapolisMNUSA
| | - Arpan Bandyopadhyay
- Department of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolisMNUSA
| | - Briana K. Kozlowicz
- Department of Microbiology and ImmunologyUniversity of MinnesotaMinneapolisMNUSA
- Present address:
Cargill Biotechnology R&DPlymouthMNUSA
| | - Heather A. H. Haemig
- Department of Microbiology and ImmunologyUniversity of MinnesotaMinneapolisMNUSA
- Present address:
Department of ChemistryGustavus Adolphus CollegeSt. PeterMNUSA
| | | | - Wei‐Shou Hu
- Department of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolisMNUSA
| | - Gary M. Dunny
- Department of Microbiology and ImmunologyUniversity of MinnesotaMinneapolisMNUSA
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20
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Ramachandran G, Miguel-Arribas A, Abia D, Singh PK, Crespo I, Gago-Córdoba C, Hao JA, Luque-Ortega JR, Alfonso C, Wu LJ, Boer DR, Meijer WJJ. Discovery of a new family of relaxases in Firmicutes bacteria. PLoS Genet 2017; 13:e1006586. [PMID: 28207825 PMCID: PMC5313138 DOI: 10.1371/journal.pgen.1006586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 01/16/2017] [Indexed: 11/19/2022] Open
Abstract
Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes. A critical step in the conjugation process is the relaxase-mediated site- and strand-specific nick in the oriT region of the conjugative element. This generates a single-stranded DNA molecule that is transferred from the donor to the recipient cell via a connecting channel. Here we identified and characterized the relaxosome components oriT and the relaxase of the conjugative plasmid pLS20 of the Firmicute Bacillus subtilis. We show that the relaxase gene, named relLS20, is essential for conjugation, that it can function in trans and provide evidence that Tyr26 constitutes the active site residue. In vivo and in vitro analyses revealed that the oriT is located far upstream of the relaxase gene and that the nick site within oriT is located on the template strand of the conjugation genes. Surprisingly, the RelLS20 shows very limited similarity to known relaxases. However, more than 800 genes to which no function had been attributed so far are predicted to encode proteins showing significant similarity to RelLS20. Interestingly, these putative relaxases are encoded almost exclusively in Firmicutes bacteria. Thus, RelLS20 constitutes the prototype of a new family of relaxases. The identification of this novel relaxase family will have an important impact in different aspects of future research in the field of HGT in Gram-positive bacteria in general, and specifically in the phylum of Firmicutes, and in gut microbiome research.
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Affiliation(s)
- Gayetri Ramachandran
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - David Abia
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Praveen K. Singh
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Isidro Crespo
- XALOC beamline, ALBA synchrotron Light Source, Cerdanyola del Vallès, Barcelona, Spain
| | - César Gago-Córdoba
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Jian An Hao
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | | | - Carlos Alfonso
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Ling J. Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - D. Roeland Boer
- XALOC beamline, ALBA synchrotron Light Source, Cerdanyola del Vallès, Barcelona, Spain
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
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Grohmann E, Keller W, Muth G. Mechanisms of Conjugative Transfer and Type IV Secretion-Mediated Effector Transport in Gram-Positive Bacteria. Curr Top Microbiol Immunol 2017. [PMID: 29536357 DOI: 10.1007/978-3-319-75241-9_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Conjugative DNA transfer is the most important means to transfer antibiotic resistance genes and virulence determinants encoded by plasmids, integrative conjugative elements (ICE), and pathogenicity islands among bacteria. In gram-positive bacteria, there exist two types of conjugative systems, (i) type IV secretion system (T4SS)-dependent ones, like those encoded by the Enterococcus, Streptococcus, Staphylococcus, Bacillus, and Clostridia mobile genetic elements and (ii) T4SS-independent ones, as those found on Streptomyces plasmids. Interestingly, very recently, on the Streptococcus suis genome, the first gram-positive T4SS not only involved in conjugative DNA transfer but also in effector translocation to the host was detected. Although no T4SS core complex structure from gram-positive bacteria is available, several structures from T4SS protein key factors from Enterococcus and Clostridia plasmids have been solved. In this chapter, we summarize the current knowledge on the molecular mechanisms and structure-function relationships of the diverse conjugation machineries and emerging research needs focused on combatting infections and spread of multiple resistant gram-positive pathogens.
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Affiliation(s)
- Elisabeth Grohmann
- Beuth University of Applied Sciences Berlin, Life Sciences and Technology, 13347, Berlin, Germany.
| | - Walter Keller
- Institute of Molecular Biosciences, BioTechMed, University of Graz, 8010, Graz, Austria
| | - Günther Muth
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University Tübingen, 72076, Tübingen, Germany
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22
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Rösch TC, Graumann PL. Induction of Plasmid Conjugation in Bacillus subtilis Is Bistable and Driven by a Direct Interaction of a Rap/Phr Quorum-sensing System with a Master Repressor. J Biol Chem 2015; 290:20221-32. [PMID: 26112413 DOI: 10.1074/jbc.m115.664110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Indexed: 12/23/2022] Open
Abstract
Conjugation of plasmid pLS20 from Bacillus subtilis is limited to a time window between early and late exponential growth. Genetic evidence has suggested that pLS20-encoded protein RcoLS20 represses expression of a large conjugation operon, whereas Rap protein RapLS20 relieves repression. We show that RapLS20 is a true antirepressor protein that forms dimers in vivo and in vitro and that it directly binds to the repressor protein RcoLS20 in a 1:1 stoichiometry. We provide evidence that RapLS20 binds to the helix-turn-helix-containing domain of RcoLS20 in vivo, probably obstructing DNA binding of RcoLS20, as seen in competitive DNA binding experiments. The activity of RapLS20 in turn is counteracted by the addition of the cognate PhrLS20 peptide, which directly binds to the Rap protein and presumably induces a conformational change of the antirepressor. Thus, a Rap protein acts directly as an antirepressor protein during regulation of plasmid conjugation, turning on conjugation, and is counteracted by the PhrLS20 peptide, which, by analogy to known Rap/Phr systems, is secreted and taken back up into the cells, mediating cell density-driven regulation. Finally, we show that this switchlike process establishes a population heterogeneity, where up to 30% of the cells induce transcription of the conjugation operon.
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Affiliation(s)
- Thomas C Rösch
- From the LOEWE Zentrum für synthetische Mikrobiologie (SYNMIKRO), 35043 Marburg, Germany, the Spemann Graduate School of Biology and Medicine (SGBM), 79104 Freiburg, Germany, and the Fachbereich für Chemie, Hans-Meerwein Strasse, Universität Marburg, 35043 Marburg, Germany
| | - Peter L Graumann
- From the LOEWE Zentrum für synthetische Mikrobiologie (SYNMIKRO), 35043 Marburg, Germany, the Fachbereich für Chemie, Hans-Meerwein Strasse, Universität Marburg, 35043 Marburg, Germany
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