1
|
Winterhalter C, Pelliciari S, Stevens D, Fenyk S, Marchand E, Cronin N, Soultanas P, Costa TD, Ilangovan A, Murray H. The DNA replication initiation protein DnaD recognises a specific strand of the Bacillus subtilis chromosome origin. Nucleic Acids Res 2023; 51:4322-4340. [PMID: 37093985 PMCID: PMC10201434 DOI: 10.1093/nar/gkad277] [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: 04/18/2022] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
Genome replication is a fundamental biological activity shared by all organisms. Chromosomal replication proceeds bidirectionally from origins, requiring the loading of two helicases, one for each replisome. However, the molecular mechanisms underpinning helicase loading at bacterial chromosome origins (oriC) are unclear. Here we investigated the essential DNA replication initiation protein DnaD in the model organism Bacillus subtilis. A set of DnaD residues required for ssDNA binding was identified, and photo-crosslinking revealed that this ssDNA binding region interacts preferentially with one strand of oriC. Biochemical and genetic data support the model that DnaD recognizes a new single-stranded DNA (ssDNA) motif located in oriC, the DnaD Recognition Element (DRE). Considered with single particle cryo-electron microscopy (cryo-EM) imaging of DnaD, we propose that the location of the DRE within oriC orchestrates strand-specific recruitment of helicase during DNA replication initiation. These findings significantly advance our mechanistic understanding of bidirectional replication from a bacterial chromosome origin.
Collapse
Affiliation(s)
- Charles Winterhalter
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Simone Pelliciari
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Daniel Stevens
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Stepan Fenyk
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Elie Marchand
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Nora B Cronin
- LonCEM, London Consortium for Cryo-EM, The Francis Crick Institute, London NW1 1AT, UK
| | - Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Tiago R D Costa
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Aravindan Ilangovan
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| |
Collapse
|
2
|
Blaine HC, Simmons LA, Stallings CL. Diverse Mechanisms of Helicase Loading during DNA Replication Initiation in Bacteria. J Bacteriol 2023; 205:e0048722. [PMID: 36877032 PMCID: PMC10128896 DOI: 10.1128/jb.00487-22] [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] [Indexed: 03/07/2023] Open
Abstract
Initiation of DNA replication is required for cell viability and passage of genetic information to the next generation. Studies in Escherichia coli and Bacillus subtilis have established ATPases associated with diverse cellular activities (AAA+) as essential proteins required for loading of the replicative helicase at replication origins. AAA+ ATPases DnaC in E. coli and DnaI in B. subtilis have long been considered the paradigm for helicase loading during replication in bacteria. Recently, it has become increasingly clear that most bacteria lack DnaC/DnaI homologs. Instead, most bacteria express a protein homologous to the newly described DciA (dnaC/dnaI antecedent) protein. DciA is not an ATPase, and yet it serves as a helicase operator, providing a function analogous to that of DnaC and DnaI across diverse bacterial species. The recent discovery of DciA and of other alternative mechanisms of helicase loading in bacteria has changed our understanding of DNA replication initiation. In this review, we highlight recent discoveries, detailing what is currently known about the replicative helicase loading process across bacterial species, and we discuss the critical questions that remain to be investigated.
Collapse
Affiliation(s)
- Helen C. Blaine
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Christina L. Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| |
Collapse
|
3
|
Winterhalter C, Stevens D, Fenyk S, Pelliciari S, Marchand E, Soultanas P, Ilangovan A, Murray H. SirA inhibits the essential DnaA:DnaD interaction to block helicase recruitment during Bacillus subtilis sporulation. Nucleic Acids Res 2022; 51:4302-4321. [PMID: 36416272 DOI: 10.1093/nar/gkac1060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 10/04/2022] [Accepted: 10/24/2022] [Indexed: 11/24/2022] Open
Abstract
Bidirectional DNA replication from a chromosome origin requires the asymmetric loading of two helicases, one for each replisome. Our understanding of the molecular mechanisms underpinning helicase loading at bacterial chromosome origins is incomplete. Here we report both positive and negative mechanisms for directing helicase recruitment in the model organism Bacillus subtilis. Systematic characterization of the essential initiation protein DnaD revealed distinct protein interfaces required for homo-oligomerization, interaction with the master initiator protein DnaA, and interaction with the helicase co-loader protein DnaB. Informed by these properties of DnaD, we went on to find that the developmentally expressed repressor of DNA replication initiation, SirA, blocks the interaction between DnaD and DnaA, thereby restricting helicase recruitment from the origin during sporulation to inhibit further initiation events. These results advance our understanding of the mechanisms underpinning DNA replication initiation in B. subtilis, as well as guiding the search for essential cellular activities to target for antimicrobial drug design.
Collapse
Affiliation(s)
- Charles Winterhalter
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Daniel Stevens
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Stepan Fenyk
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Simone Pelliciari
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Elie Marchand
- Research Unit in Biology of Microorganisms, Department of Biology, Université de Namur, Namur, Belgium
| | - Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Aravindan Ilangovan
- Blizard Institute, School of Biological and Behavioural Sciences, Queen Mary University of London, Newark street, London E1 2AT, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| |
Collapse
|
4
|
Characterization of Streptococcus pneumoniae PriA helicase and its ATPase and unwinding activities in DNA replication restart. Biochem J 2021; 477:3911-3922. [PMID: 32985663 DOI: 10.1042/bcj20200269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022]
Abstract
DNA replication forks often encounter template DNA lesions that can stall their progression. The PriA-dependent pathway is the major replication restart mechanism in Gram-positive bacteria, and it requires several primosome proteins. Among them, PriA protein - a 3' to 5' superfamily-2 DNA helicase - is the key factor in recognizing DNA lesions and it also recruits other proteins. Here, we investigated the ATPase and helicase activities of Streptococcus pneumoniae PriA (SpPriA) through biochemical and kinetic analyses. By comparing various DNA substrates, we observed that SpPriA is unable to unwind duplex DNA with high GC content. We constructed a deletion mutant protein (SpPriAdeloop) from which the loop area of the DNA-binding domain of PriA had been removed. Functional assays on SpPriAdeloop revealed that the loop area is important in endowing DNA-binding properties on the helicase. We also show that the presence of DnaD loader protein is important for enhancing SpPriA ATPase and DNA unwinding activities.
Collapse
|
5
|
Regulation of DNA Binding and High-Order Oligomerization of the DnaB Helicase Loader. J Bacteriol 2020; 202:JB.00286-20. [PMID: 32817095 DOI: 10.1128/jb.00286-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022] Open
Abstract
DnaB is an essential primosomal protein that coloads the replicative helicase in many Gram-positive bacteria, including several human pathogens. Although DnaB is tetrameric in solution, it is from a protein family whose members can oligomerize into large complexes when exposed to DNA. It is currently unknown how DNA binding by DnaB is regulated or how these interactions induce changes in its oligomeric state. Here, we investigated DNA binding by DnaB from Bacillus subtilis and the critical human pathogen Staphylococcus aureus We found that B. subtilis DnaB binds double-stranded DNA as a tetramer; however, M13mp18 single-stranded DNA induces high-order oligomerization. Mutating a conserved motif at the C-terminal end of DnaB stimulates single-stranded DNA binding, suggesting that conformational changes in this region regulate DNA substrate preferences. S. aureus DnaB could also be induced to form high-order oligomers with either M13mp18 or PhiX174 single-stranded DNA. Therefore, oligomeric shifts in DnaB are tightly controlled and this activity is conserved between B. subtilis and a pathogenic species.IMPORTANCE DnaB is a replicative helicase loader involved in initiating DNA replication in many bacterial species. We investigated the binding preferences of DnaB for its DNA substrate and determined that the C-terminal end of the protein plays a critical role in controlling DNA interactions. Furthermore, we found that DNA binding in general did not trigger changes to the oligomeric state of DnaB, but rather, certain types of single-stranded DNA substrates specifically induced DnaB to self-assemble into a large complex. This indicates that the structure of DNA itself is an important regulatory element that influences the behavior of DnaB. Importantly, these observations held for both Bacillus subtilis and the pathogenic species Staphylococcus aureus, demonstrating conserved biochemical functions of DnaB in these species.
Collapse
|
6
|
Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Characterization of Bacteriophage Peptides of Pathogenic Streptococcus by LC-ESI-MS/MS: Bacteriophage Phylogenomics and Their Relationship to Their Host. Front Microbiol 2020; 11:1241. [PMID: 32582130 PMCID: PMC7296060 DOI: 10.3389/fmicb.2020.01241] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/14/2020] [Indexed: 01/21/2023] Open
Abstract
The present work focuses on LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analysis of phage-origin tryptic digestion peptides from mastitis-causing Streptococcus spp. isolated from milk. A total of 2,546 non-redundant peptides belonging to 1,890 proteins were identified and analyzed. Among them, 65 phage-origin peptides were determined as specific Streptococcus spp. peptides. These peptides belong to proteins such as phage repressors, phage endopeptidases, structural phage proteins, and uncharacterized phage proteins. Studies involving bacteriophage phylogeny and the relationship between phages encoding the peptides determined and the bacteria they infect were also performed. The results show how specific peptides are present in closely related phages, and a link exists between bacteriophage phylogeny and the Streptococcus spp. they infect. Moreover, the phage peptide M∗ATNLGQAYVQIM∗PSAK is unique and specific for Streptococcus agalactiae. These results revealed that diagnostic peptides, among others, could be useful for the identification and characterization of mastitis-causing Streptococcus spp., particularly peptides that belong to specific functional proteins, such as phage-origin proteins, because of their specificity to bacterial hosts.
Collapse
Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Jose L. R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| |
Collapse
|
7
|
Martin E, Williams HEL, Pitoulias M, Stevens D, Winterhalter C, Craggs TD, Murray H, Searle MS, Soultanas P. DNA replication initiation in Bacillus subtilis: structural and functional characterization of the essential DnaA-DnaD interaction. Nucleic Acids Res 2019; 47:2101-2112. [PMID: 30534966 PMCID: PMC6393240 DOI: 10.1093/nar/gky1220] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/15/2018] [Accepted: 11/22/2018] [Indexed: 02/06/2023] Open
Abstract
The homotetrameric DnaD protein is essential in low G+C content gram positive bacteria and is involved in replication initiation at oriC and re-start of collapsed replication forks. It interacts with the ubiquitously conserved bacterial master replication initiation protein DnaA at the oriC but structural and functional details of this interaction are lacking, thus contributing to our incomplete understanding of the molecular details that underpin replication initiation in bacteria. DnaD comprises N-terminal (DDBH1) and C-terminal (DDBH2) domains, with contradicting bacterial two-hybrid and yeast two-hybrid studies suggesting that either the former or the latter interact with DnaA, respectively. Using Nuclear Magnetic Resonance (NMR) we showed that both DDBH1 and DDBH2 interact with the N-terminal domain I of DnaA and studied the DDBH2 interaction in structural detail. We revealed two families of conformations for the DDBH2-DnaA domain I complex and showed that the DnaA-interaction patch of DnaD is distinct from the DNA-interaction patch, suggesting that DnaD can bind simultaneously DNA and DnaA. Using sensitive single-molecule FRET techniques we revealed that DnaD remodels DnaA-DNA filaments consistent with stretching and/or untwisting. Furthermore, the DNA binding activity of DnaD is redundant for this filament remodelling. This in turn suggests that DnaA and DnaD are working collaboratively in the oriC to locally melt the DNA duplex during replication initiation.
Collapse
Affiliation(s)
- Eleyna Martin
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Huw E L Williams
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Matthaios Pitoulias
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Daniel Stevens
- Centre for Bacterial Cell Biology, Medical School, Newcastle University, Newcastle NE2 4AX, UK
| | - Charles Winterhalter
- Centre for Bacterial Cell Biology, Medical School, Newcastle University, Newcastle NE2 4AX, UK
| | - Timothy D Craggs
- Sheffield Institute for Nucleic Acids, Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Medical School, Newcastle University, Newcastle NE2 4AX, UK
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
- Correspondence may also be addressed to Mark S. Searle. Tel: +44 115 9513567; Fax: +44 115 9513564;
| | - Panos Soultanas
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
- To whom correspondence should be addressed. Tel: +44 115 9513525; Fax: +44 115 9513564;
| |
Collapse
|
8
|
Matthews LA, Simmons LA. Cryptic protein interactions regulate DNA replication initiation. Mol Microbiol 2018; 111:118-130. [PMID: 30285297 DOI: 10.1111/mmi.14142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022]
Abstract
DNA replication is a fundamental biological process that is tightly regulated in all cells. In bacteria, DnaA controls when and where replication begins by building a step-wise complex that loads the replicative helicase onto chromosomal DNA. In many low-GC Gram-positive species, DnaA recruits the DnaD and DnaB proteins to function as adaptors to assist in helicase loading. How DnaA, its adaptors and the helicase form a complex at the origin is unclear. We addressed this question using the bacterial two-hybrid assay to determine how the initiation proteins from Bacillus subtilis interact with each other. We show that cryptic interaction sites play a key role in this process and we map these regions for the entire pathway. In addition, we found that the SirA regulator that blocks initiation in sporulating cells binds to a surface on DnaA that overlaps with DnaD. The interaction between DnaA and DnaD was also mapped to the same DnaA surface in the human pathogen Staphylococcus aureus, demonstrating the broad conservation of this surface. Therefore, our study has unveiled key protein interactions essential for initiation and our approach is widely applicable for mapping interactions in other signaling pathways that are governed by cryptic binding surfaces.
Collapse
Affiliation(s)
- Lindsay A Matthews
- Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Lyle A Simmons
- Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| |
Collapse
|
9
|
Jameson KH, Wilkinson AJ. Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli. Genes (Basel) 2017; 8:E22. [PMID: 28075389 PMCID: PMC5295017 DOI: 10.3390/genes8010022] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 01/21/2023] Open
Abstract
Initiation of DNA Replication is tightly regulated in all cells since imbalances in chromosomal copy number are deleterious and often lethal. In bacteria such as Bacillus subtilis and Escherichia coli, at the point of cytokinesis, there must be two complete copies of the chromosome to partition into the daughter cells following division at mid-cell during vegetative growth. Under conditions of rapid growth, when the time taken to replicate the chromosome exceeds the doubling time of the cells, there will be multiple initiations per cell cycle and daughter cells will inherit chromosomes that are already undergoing replication. In contrast, cells entering the sporulation pathway in B. subtilis can do so only during a short interval in the cell cycle when there are two, and only two, chromosomes per cell, one destined for the spore and one for the mother cell. Here, we briefly describe the overall process of DNA replication in bacteria before reviewing initiation of DNA replication in detail. The review covers DnaA-directed assembly of the replisome at oriC and the multitude of mechanisms of regulation of initiation, with a focus on the similarities and differences between E. coli and B. subtilis.
Collapse
Affiliation(s)
- Katie H Jameson
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
| | - Anthony J Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK.
| |
Collapse
|
10
|
Huang YH, Lien Y, Huang CC, Huang CY. Characterization of Staphylococcus aureus Primosomal DnaD Protein: Highly Conserved C-Terminal Region Is Crucial for ssDNA and PriA Helicase Binding but Not for DnaA Protein-Binding and Self-Tetramerization. PLoS One 2016; 11:e0157593. [PMID: 27304067 PMCID: PMC4909229 DOI: 10.1371/journal.pone.0157593] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 06/01/2016] [Indexed: 11/18/2022] Open
Abstract
The role of DnaD in the recruitment of replicative helicase has been identified. However, knowledge of the DNA, PriA, and DnaA binding mechanism of this protein for the DnaA- and PriA-directed replication primosome assemblies is limited. We characterized the DNA-binding properties of DnaD from Staphylococcus aureus (SaDnaD) and analyzed its interactions with SaPriA and SaDnaA. The gel filtration chromatography analysis of purified SaDnaD and its deletion mutant proteins (SaDnaD1-195, SaDnaD1-200 and SaDnaD1-204) showed a stable tetramer in solution. This finding indicates that the C-terminal region aa 196-228 is not crucial for SaDnaD oligomerization. SaDnaD forms distinct complexes with ssDNA of different lengths. In fluorescence titrations, SaDnaD bound to ssDNA with a binding-site size of approximately 32 nt. A stable complex of SaDnaD1-195, SaDnaD1-200, and SaDnaD1-204 with ssDNA dT40 was undetectable, indicating that the C-terminal region of SaDnaD (particularly aa 205-228) is crucial for ssDNA binding. The SPR results revealed that SaDnaD1-195 can interact with SaDnaA but not with SaPriA, which may indicate that DnaD has different binding sites for PriA and DnaA. Both SaDnaD and SaDnaDY176A mutant proteins, but not SaDnaD1-195, can significantly stimulate the ATPase activity of SaPriA. Hence, the stimulation effect mainly resulted from direct contact within the protein-protein interaction, not via the DNA-protein interaction. Kinetic studies revealed that the SaDnaD-SaPriA interaction increases the Vmax of the SaPriA ATPase fivefold without significantly affecting the Km. These results indicate that the conserved C-terminal region is crucial for ssDNA and PriA helicase binding, but not for DnaA protein-binding and self-tetramerization.
Collapse
Affiliation(s)
- Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
| | - Yi Lien
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
| | - Chien-Chih Huang
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
| | - Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
- * E-mail:
| |
Collapse
|
11
|
Abstract
From microbes to multicellular eukaryotic organisms, all cells contain pathways responsible for genome maintenance. DNA replication allows for the faithful duplication of the genome, whereas DNA repair pathways preserve DNA integrity in response to damage originating from endogenous and exogenous sources. The basic pathways important for DNA replication and repair are often conserved throughout biology. In bacteria, high-fidelity repair is balanced with low-fidelity repair and mutagenesis. Such a balance is important for maintaining viability while providing an opportunity for the advantageous selection of mutations when faced with a changing environment. Over the last decade, studies of DNA repair pathways in bacteria have demonstrated considerable differences between Gram-positive and Gram-negative organisms. Here we review and discuss the DNA repair, genome maintenance, and DNA damage checkpoint pathways of the Gram-positive bacterium Bacillus subtilis. We present their molecular mechanisms and compare the functions and regulation of several pathways with known information on other organisms. We also discuss DNA repair during different growth phases and the developmental program of sporulation. In summary, we present a review of the function, regulation, and molecular mechanisms of DNA repair and mutagenesis in Gram-positive bacteria, with a strong emphasis on B. subtilis.
Collapse
|
12
|
Abstract
Much of our knowledge of the initiation of DNA replication comes from studies in the gram-negative model organism Escherichia coli. However, the location and structure of the origin of replication within the E. coli genome and the identification and study of the proteins which constitute the E. coli initiation complex suggest that it might not be as universal as once thought. The archetypal low-G+C-content gram-positive Firmicutes initiate DNA replication via a unique primosomal machinery, quite distinct from that seen in E. coli, and an examination of oriC in the Firmicutes species Bacillus subtilis indicates that it might provide a better model for the ancestral bacterial origin of replication. Therefore, the study of replication initiation in organisms other than E. coli, such as B. subtilis, will greatly advance our knowledge and understanding of these processes as a whole. In this minireview, we highlight the structure-function relationships of the Firmicutes primosomal proteins, discuss the significance of their oriC architecture, and present a model for replication initiation at oriC.
Collapse
|
13
|
Collier C, Machón C, Briggs GS, Smits WK, Soultanas P. Untwisting of the DNA helix stimulates the endonuclease activity of Bacillus subtilis Nth at AP sites. Nucleic Acids Res 2011; 40:739-50. [PMID: 21954439 PMCID: PMC3258159 DOI: 10.1093/nar/gkr785] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Bacterial nucleoid associated proteins play a variety of roles in genome maintenance and dynamics. Their involvement in genome packaging, DNA replication and transcription are well documented but it is still unclear whether they play any specific roles in genome repair. We discovered that untwisting of the DNA double helix by bacterial non-specific DNA binding proteins stimulates the activity of a repair endonuclease of the Nth/MutY family involved in abasic site removal during base excision repair. The essential Bacillus subtilis primosomal gene dnaD, coding for a protein with DNA-untwisting activity, is in the same operon with nth and the promoter activity of this operon is transiently stimulated by H(2)O(2). Consequently, dnaD mRNA levels persist high upon treatment with H(2)O(2) compared to the reduced mRNA levels of the other essential primosomal genes dnaB and dnaI, suggesting that DnaD may play an important role in DNA repair in addition to its essential role in replication initiation. Homologous Nth repair endonucleases are found in nearly all organisms, including humans. Our data have wider implications for DNA repair as they suggest that genome associated proteins that alter the superhelicity of the DNA indirectly facilitate base excision repair mediated by repair endonucleases of the Nth/MutY family.
Collapse
Affiliation(s)
- Christopher Collier
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | | | | | | | | |
Collapse
|
14
|
AFM IMAGING AND SINGLE-MOLECULE FORCE SPECTROSCOPY STUDIES ON MACROMOLECULAR INTERACTIONS AT SINGLE-MOLECULE LEVEL. ACTA POLYM SIN 2011. [DOI: 10.3724/sp.j.1105.2011.11124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
15
|
Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis. J Bacteriol 2010; 193:640-8. [PMID: 21097613 DOI: 10.1128/jb.01253-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The initiation of DNA replication requires the binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. DnaA also binds to many sites around the chromosome, outside oriC, and acts as a transcription factor at several of these. In low-G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA. DnaD and DnaB also are required to load the replicative helicase outside oriC during replication restart, independently of DnaA. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in Bacillus subtilis. This association was dependent on DnaA, and the order of recruitment was the same as that at oriC, but it was independent of a functional oriC and suggests that DnaD and DnaB do not require open complex formation for the stable association with DNA. These secondary binding regions for DnaA could be serving as a reservoir for excess DnaA, DnaD, and DnaB to help properly regulate replication initiation and perhaps are analogous to the proposed function of the datA locus in Escherichia coli. Alternatively, DnaD and DnaB might modulate the activity of DnaA at the secondary binding regions. All three of these proteins are widely conserved and likely have similar functions in a range of organisms.
Collapse
|
16
|
Marston FY, Grainger WH, Smits WK, Hopcroft NH, Green M, Hounslow AM, Grossman AD, Craven CJ, Soultanas P. When simple sequence comparison fails: the cryptic case of the shared domains of the bacterial replication initiation proteins DnaB and DnaD. Nucleic Acids Res 2010; 38:6930-42. [PMID: 20587500 PMCID: PMC2978336 DOI: 10.1093/nar/gkq465] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB Homology 1 and 2). Despite strong sequence divergence, many of the DNA-binding and oligomerization properties of these domains have been conserved. Although eluding simple sequence comparisons, the DDBH2 domains share the only strong sequence motif; an extremely highly conserved YxxxIxxxW sequence that contributes to DNA binding. Sequence alignments of DnaD alone fail to identify another key part of the DNA-binding module, since it includes a poorly conserved sequence, a solvent-exposed and somewhat unstable helix and a mobile segment. We show by NMR, in vitro mutagenesis and in vivo complementation experiments that the DNA-binding module of Bacillus subtilis DnaD comprises the YxxxIxxxW motif, the unstable helix and a portion of the mobile region, the latter two being essential for viability. These structural insights lead us to a re-evaluation of the oligomerization and DNA-binding properties of the DnaD and DnaB proteins.
Collapse
Affiliation(s)
- Farhat Y Marston
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Chaurasiya KR, Paramanathan T, McCauley MJ, Williams MC. Biophysical characterization of DNA binding from single molecule force measurements. Phys Life Rev 2010; 7:299-341. [PMID: 20576476 DOI: 10.1016/j.plrev.2010.06.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/19/2010] [Accepted: 05/20/2010] [Indexed: 11/25/2022]
Abstract
Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.
Collapse
Affiliation(s)
- Kathy R Chaurasiya
- Department of Physics, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
| | | | | | | |
Collapse
|
18
|
Grainger WH, Machón C, Scott DJ, Soultanas P. DnaB proteolysis in vivo regulates oligomerization and its localization at oriC in Bacillus subtilis. Nucleic Acids Res 2010; 38:2851-64. [PMID: 20071750 PMCID: PMC2874997 DOI: 10.1093/nar/gkp1236] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Initiation of bacterial DNA replication at oriC is mediated by primosomal proteins that act cooperatively to melt an AT-rich region where the replicative helicase is loaded prior to the assembly of the replication fork. In Bacillus subtilis, the dnaD, dnaB and dnaI genes are essential for initiation of DNA replication. We established that their mRNAs are maintained in fast growing asynchronous cultures. DnaB is truncated at its C-terminus in a growth phase-dependent manner. Proteolysis is confined to cytosolic, not to membrane-associated DnaB, and affects oligomerization. Truncated DnaB is depleted at the oriC relative to the native protein. We propose that DNA-induced oligomerization is essential for its action at oriC and proteolysis regulates its localization at oriC. We show that DnaB has two separate ssDNA-binding sites one located within residues 1–300 and another between residues 365–428, and a dsDNA-binding site within residues 365–428. Tetramerization of DnaB is mediated within residues 1–300, and DNA-dependent oligomerization within residues 365–428. Finally, we show that association of DnaB with the oriC is asymmetric and extensive. It encompasses an area from the middle of dnaA to the end of yaaA that includes the AT-rich region melted during the initiation stage of DNA replication.
Collapse
Affiliation(s)
- William H Grainger
- Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | | | | | | |
Collapse
|
19
|
Intragenic and extragenic suppressors of temperature sensitive mutations in the replication initiation genes dnaD and dnaB of Bacillus subtilis. PLoS One 2009; 4:e6774. [PMID: 19707554 PMCID: PMC2727948 DOI: 10.1371/journal.pone.0006774] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 07/30/2009] [Indexed: 12/03/2022] Open
Abstract
Background The Bacillus subtilis genes dnaD and dnaB are essential for the initiation of DNA replication and are required for loading of the replicative helicase at the chromosomal origin of replication oriC. Wild type DnaD and DnaB interact weakly in vitro and this interaction has not been detected in vivo or in yeast two-hybrid assays. Methodology/Principal Findings We isolated second site suppressors of the temperature sensitive phenotypes caused by one dnaD mutation and two different dnaB mutations. Five different intragenic suppressors of the dnaD23ts mutation were identified. One intragenic suppressor was a deletion of two amino acids in DnaD. This deletion caused increased and detectable interaction between the mutant DnaD and wild type DnaB in a yeast two-hybrid assay, similar to the increased interaction caused by a missense mutation in dnaB that is an extragenic suppressor of dnaD23ts. We isolated both intragenic and extragenic suppressors of the two dnaBts alleles. Some of the extragenic suppressors were informational suppressors (missense suppressors) in tRNA genes. These suppressor mutations caused a change in the anticodon of an alanine tRNA so that it would recognize the mutant codon (threonine) in dnaB and likely insert the wild type amino acid (alanine). Conclusions/Significance The intragenic suppressors should provide insights into structure-function relationships in DnaD and DnaB, and interactions between DnaD and DnaB. The extragenic suppressors in the tRNA genes have important implications regarding the amount of wild type DnaB needed in the cell. Since missense suppressors are typically inefficient, these findings indicate that production of a small amount of wild type DnaB, in combination with the mutant protein, is sufficient to restore some DnaB function.
Collapse
|
20
|
Marbouty M, Saguez C, Chauvat F. The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domain. BMC STRUCTURAL BIOLOGY 2009; 9:54. [PMID: 19698108 PMCID: PMC2736966 DOI: 10.1186/1472-6807-9-54] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 08/21/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND DNA replication and cell cycle as well as their relationship have been extensively studied in the two model organisms E. coli and B. subtilis. By contrast, little is known about these processes in cyanobacteria, even though they are crucial to the biosphere, in utilizing solar energy to renew the oxygenic atmosphere and in producing the biomass for the food chain. Recent studies have allowed the identification of several cell division factors that are specifics to cyanobacteria. Among them, Ftn6 has been proposed to function in the recruitment of the crucial FtsZ proteins to the septum or the subsequent Z-ring assembly and possibly in chromosome segregation. RESULTS In this study, we identified an as yet undescribed domain located in the conserved N-terminal region of Ftn6. This 77 amino-acids-long domain, designated here as FND (Ftn6 N-Terminal Domain), exhibits striking sequence and structural similarities with the DNA-interacting module, listed in the PFAM database as the DnaD-like domain (pfam04271). We took advantage of the sequence similarities between FND and the DnaD-like domains to construct a homology 3D-model of the Ftn6 FND domain from the model cyanobacterium Synechocystis PCC6803. Mapping of the conserved residues exposed onto the FND surface allowed us to identify a highly conserved area that could be engaged in Ftn6-specific interactions. CONCLUSION Overall, similarities between FND and DnaD-like domains as well as previously reported observations on Ftn6 suggest that FND may function as a DNA-interacting module thereby providing an as yet missing link between DNA replication and cell division in cyanobacteria. Consistently, we also showed that Ftn6 is involved in tolerance to DNA damages generated by UV rays.
Collapse
Affiliation(s)
- Martial Marbouty
- CEA, iBiTec-S, SBIGeM, LBI, Bat 142 CEA-Saclay, F-91191 Gif sur Yvette CEDEX, France.
| | | | | |
Collapse
|
21
|
Huang CY, Chang YW, Chen WT. Crystal structure of the N-terminal domain of Geobacillus kaustophilus HTA426 DnaD protein. Biochem Biophys Res Commun 2008; 375:220-4. [DOI: 10.1016/j.bbrc.2008.07.160] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 07/30/2008] [Indexed: 11/25/2022]
|
22
|
Single-molecule atomic force spectroscopy reveals that DnaD forms scaffolds and enhances duplex melting. J Mol Biol 2008; 377:706-14. [PMID: 18291414 DOI: 10.1016/j.jmb.2008.01.067] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 01/18/2008] [Accepted: 01/22/2008] [Indexed: 11/23/2022]
Abstract
The Bacillus subtilis DnaD is an essential DNA-binding protein implicated in replication and DNA remodeling. Using single-molecule atomic force spectroscopy, we have studied the interaction of DnaD and its domains with DNA. Our data reveal that binding of DnaD to immobilized single molecules of duplex DNA causes a marked reduction in the 'end-to-end' distance of the DNA in a concentration-dependent manner, consistent with previously reported DnaD-induced looping by scaffold formation. Native DnaD enhances partial melting of the DNA strands. The C-terminal domain (Cd) of DnaD binds to DNA and enhances partial duplex melting but does not cause DNA looping. The Cd-mediated melting is not as efficient as that caused by native DnaD. The N-terminal domain (Nd) does not affect significantly the DNA. A mixture of Nd and Cd fails to recreate the DNA looping effect of native DnaD but produces exactly the same effects as Cd on its own, consistent with the previously reported failure of the separated domains to form DNA-interacting scaffolds.
Collapse
|
23
|
Schneider S, Zhang W, Soultanas P, Paoli M. Structure of the N-terminal oligomerization domain of DnaD reveals a unique tetramerization motif and provides insights into scaffold formation. J Mol Biol 2007; 376:1237-50. [PMID: 18206906 DOI: 10.1016/j.jmb.2007.12.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Revised: 12/18/2007] [Accepted: 12/20/2007] [Indexed: 02/05/2023]
Abstract
DnaD is a primosomal protein that remodels supercoiled plasmids. It binds to supercoiled forms and converts them to open forms without nicking. During this remodeling process, all the writhe is converted to twist and the plasmids are held around the periphery of large scaffolds made up of DnaD molecules. This DNA-remodeling function is the sum of a scaffold-forming activity on the N-terminal domain and a DNA-dependent oligomerization activity on the C-terminal domain. We have determined the crystal structure of the scaffold-forming N-terminal domain, which reveals a winged-helix architecture, with additional structural elements extending from both N- and C-termini. Four monomers form dimers that join into a tetramer. The N-terminal extension mediates dimerization and tetramerization, with extensive interactions and distinct interfaces. The wings and helices of the winged-helix domains remain exposed on the surface of the tetramer. Structure-guided mutagenesis and atomic force microscopy imaging indicate that these elements, together with the C-terminal extension, are involved in scaffold formation. Based upon our data, we propose a model for the DnaD-mediated scaffold formation.
Collapse
Affiliation(s)
- S Schneider
- Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | | | | | | |
Collapse
|
24
|
Zakrzewska-Czerwińska J, Jakimowicz D, Zawilak-Pawlik A, Messer W. Regulation of the initiation of chromosomal replication in bacteria. FEMS Microbiol Rev 2007; 31:378-87. [PMID: 17459114 DOI: 10.1111/j.1574-6976.2007.00070.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The initiation of chromosomal replication occurs only once during the cell cycle in both prokaryotes and eukaryotes. Initiation of chromosome replication is the first and tightly controlled step of a DNA synthesis. Bacterial chromosome replication is initiated at a single origin, oriC, by the initiator protein DnaA, which specifically interacts with 9-bp non-palindromic sequences (DnaA boxes) at oriC. In Escherichia coli, a model organism used to study the mechanism of DNA replication and its regulation, the control of initiation relies on a reduction of the availability and/or activity of the two key elements, DnaA and the oriC region. This review summarizes recent research into the regulatory mechanisms of the initiation of chromosomal replication in bacteria, with emphasis on organisms other than E. coli.
Collapse
|
25
|
Foster SR, Pearce A, Blake AJ, Welham MJ, Dowden J. Novel octavalent cross-linker displays efficient trapping of protein-protein interactions. Chem Commun (Camb) 2007:2512-4. [PMID: 17563813 PMCID: PMC2141736 DOI: 10.1039/b701542a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel octavalent, resorcin[4]arene derived, cross-linker designed to overcome some of the limitations of commercially available reagents is significantly more efficient for covalent stabilisation of protein–protein interactions.
A novel octavalent, resorcin[4]arene derived, cross-linker designed to overcome some of the limitations of commercially available reagents is significantly more efficient for covalent stabilisation of protein–protein interactions.
Collapse
Affiliation(s)
- Simon R. Foster
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK NG7 2RD. ; Fax: 0115 95135654; Tel: 0115 9513566
| | - Alice Pearce
- Department of Pharmacy and Pharmacology, University of Bath, Calverton Down, Bath, UK BA2 7AY
| | - Alexander J. Blake
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK NG7 2RD. ; Fax: 0115 95135654; Tel: 0115 9513566
| | - Melanie J. Welham
- Department of Pharmacy and Pharmacology, University of Bath, Calverton Down, Bath, UK BA2 7AY
| | - James Dowden
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK NG7 2RD. ; Fax: 0115 95135654; Tel: 0115 9513566
| |
Collapse
|
26
|
Schneider S, Carneiro MJVM, Ioannou C, Soultanas P, Paoli M. Crystallization and X-ray diffraction analysis of the DNA-remodelling protein DnaD from Bacillus subtilis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:110-3. [PMID: 17277452 PMCID: PMC2330131 DOI: 10.1107/s1744309107000474] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 01/05/2007] [Indexed: 11/17/2022]
Abstract
The DnaD protein is an essential component of the chromosome-replication machinery of the Gram-positive bacterium Bacillus subtilis and is part of the primosomal cascade that ultimately loads the replicative ring helicase DnaC onto DNA. Moreover, DnaD is a global regulator of DNA architecture, as it forms higher order nucleoprotein structures in order to open supercoiled DNA. Here, the crystallization and preliminary X-ray diffraction analysis of the two domains of DnaD from B. subtilis are reported. Crystals of the N-terminal domain are trigonal, with either P3(1)21 or P3(2)21 space-group symmetry, and diffracted X-rays to 2.0 A resolution; crystals of the C-terminal domain are hexagonal, with space group P6(1) or P6(5), and diffracted X-rays to 2.9 A resolution in-house. Determination of the structure of the DnaD domains will provide insight into how remodelling of the nucleoid is associated with priming of replication in the model Gram-positive organism B. subtilis.
Collapse
Affiliation(s)
- Sabine Schneider
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, England
| | | | - Charikleia Ioannou
- School of Chemistry and Centre for Biomolecular Sciences, University of Nottingham, England
| | - Panos Soultanas
- School of Chemistry and Centre for Biomolecular Sciences, University of Nottingham, England
| | - Max Paoli
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, England
| |
Collapse
|
27
|
Ioannou C, Schaeffer PM, Dixon NE, Soultanas P. Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading in Bacillus subtilis. Nucleic Acids Res 2006; 34:5247-58. [PMID: 17003052 PMCID: PMC1636449 DOI: 10.1093/nar/gkl690] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The Bacillus subtilis DnaI, DnaB and DnaD proteins load the replicative ring helicase DnaC onto DNA during priming of DNA replication. Here we show that DnaI consists of a C-terminal domain (Cd) with ATPase and DNA-binding activities and an N-terminal domain (Nd) that interacts with the replicative ring helicase. A Zn2+-binding module mediates the interaction with the helicase and C67, C70 and H84 are involved in the coordination of the Zn2+. DnaI binds ATP and exhibits ATPase activity that is not stimulated by ssDNA, because the DNA-binding site on Cd is masked by Nd. The ATPase activity resides on the Cd domain and when detached from the Nd domain, it becomes sensitive to stimulation by ssDNA because its cryptic DNA-binding site is exposed. Therefore, Nd acts as a molecular ‘switch’ regulating access to the ssDNA binding site on Cd, in response to binding of the helicase. DnaI is sufficient to load the replicative helicase from a complex with six DnaI molecules, so there is no requirement for a dual helicase loader system.
Collapse
Affiliation(s)
| | - Patrick M. Schaeffer
- Research School of Chemistry, Australian National UniversityCanberra ACT 0200, Australia
| | - Nicholas E. Dixon
- Research School of Chemistry, Australian National UniversityCanberra ACT 0200, Australia
| | - Panos Soultanas
- To whom correspondence should be addressed. Tel: +44 115 9513525; Fax: +44 115 8468002;
| |
Collapse
|
28
|
Zhang W, Allen S, Roberts CJ, Soultanas P. The Bacillus subtilis primosomal protein DnaD untwists supercoiled DNA. J Bacteriol 2006; 188:5487-93. [PMID: 16855238 PMCID: PMC1540042 DOI: 10.1128/jb.00339-06] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The essential Bacillus subtilis DnaD and DnaB proteins have been implicated in the initiation of DNA replication. Recently, DNA remodeling activities associated with both proteins were discovered that could provide a link between global or local nucleoid remodeling and initiation of replication. DnaD forms scaffolds and opens up supercoiled plasmids without nicking to form open circular complexes, while DnaB acts as a lateral compaction protein. Here we show that DnaD-mediated opening of supercoiled plasmids is accompanied by significant untwisting of DNA. The net result is the conversion of writhe (Wr) into negative twist (Tw), thus maintaining the linking number (Lk) constant. These changes in supercoiling will reduce the considerable energy required to open up closed circular plectonemic DNA and may be significant in the priming of DNA replication. By comparison, DnaB does not affect significantly the supercoiling of plasmids. Binding of the DnaD C-terminal domain (Cd) to DNA is not sufficient to convert Wr into negative Tw, implying that the formation of scaffolds is essential for duplex untwisting. Overall, our data suggest that the topological effects of the two proteins on supercoiled DNA are different; DnaD opens up, untwists and converts plectonemic DNA to a more paranemic form, whereas DnaB does not affect supercoiling significantly and condenses DNA only via its lateral compaction activity. The significance of these findings in the initiation of DNA replication is discussed.
Collapse
Affiliation(s)
- Wenke Zhang
- Centre for Biomolecular Sciences School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | | | | | | |
Collapse
|