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Płachetka M, Żyła-Uklejewicz D, Weigel C, Donczew R, Donczew M, Jakimowicz D, Zawilak-Pawlik A, Zakrzewska-Czerwinska J. Streptomycete origin of chromosomal replication with two putative unwinding elements. MICROBIOLOGY-SGM 2019; 165:1365-1375. [PMID: 31592764 DOI: 10.1099/mic.0.000859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA replication is controlled mostly at the initiation step. In bacteria, replication of the chromosome starts at a single origin of replication called oriC. The initiator protein, DnaA, binds to specific sequences (DnaA boxes) within oriC and assembles into a filament that promotes DNA double helix opening within the DNA unwinding element (DUE). This process has been thoroughly examined in model bacteria, including Escherichia coli and Bacillus subtilis, but we have a relatively limited understanding of chromosomal replication initiation in other species. Here, we reveal new details of DNA replication initiation in Streptomyces, a group of Gram-positive soil bacteria that possesses a long linear (8-10 Mbps) and GC-rich chromosome with a centrally positioned oriC. We used comprehensive in silico, in vitro and in vivo analyses to better characterize the structure of Streptomyces oriC. We identified 14 DnaA-binding motifs and determined the consensus sequence of the DnaA box. Unexpectedly, our in silico analysis using the WebSIDD algorithm revealed the presence of two putative Streptomyces DUEs (DUE1 and DUE2) located very near one another toward the 5' end of the oriC region. In vitro P1 nuclease assay revealed that DNA unwinding occurs at both of the proposed sites, but using an in vivo replication initiation point mapping, we were able to confirm only one of them (DUE2). The previously observed transcriptional activity of the Streptomyces oriC region may help explain the current results. We speculate that transcription itself could modulate oriC activity in Streptomyces by determining whether DNA unwinding occurs at DUE1 or DUE2.
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Affiliation(s)
- Małgorzata Płachetka
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Dorota Żyła-Uklejewicz
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Christoph Weigel
- Institute of Biotechnology, Faculty III, Technical University Berlin (TUB), Berlin, Germany
| | - Rafał Donczew
- Present address: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Magdalena Donczew
- Present address: Center for Infectious Disease, Seattle, WA, USA.,Department of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Dagmara Jakimowicz
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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Kemter FS, Messerschmidt SJ, Schallopp N, Sobetzko P, Lang E, Bunk B, Spröer C, Teschler JK, Yildiz FH, Overmann J, Waldminghaus T. Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae. PLoS Genet 2018; 14:e1007251. [PMID: 29505558 PMCID: PMC5854411 DOI: 10.1371/journal.pgen.1007251] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/15/2018] [Accepted: 02/13/2018] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae, the causative agent of the cholera disease, is commonly used as a model organism for the study of bacteria with multipartite genomes. Its two chromosomes of different sizes initiate their DNA replication at distinct time points in the cell cycle and terminate in synchrony. In this study, the time-delayed start of Chr2 was verified in a synchronized cell population. This replication pattern suggests two possible regulation mechanisms for other Vibrio species with different sized secondary chromosomes: Either all Chr2 start DNA replication with a fixed delay after Chr1 initiation, or the timepoint at which Chr2 initiates varies such that termination of chromosomal replication occurs in synchrony. We investigated these two models and revealed that the two chromosomes of various Vibrionaceae species terminate in synchrony while Chr2-initiation timing relative to Chr1 is variable. Moreover, the sequence and function of the Chr2-triggering crtS site recently discovered in V. cholerae were found to be conserved, explaining the observed timing mechanism. Our results suggest that it is beneficial for bacterial cells with multiple chromosomes to synchronize their replication termination, potentially to optimize chromosome related processes as dimer resolution or segregation.
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Affiliation(s)
- Franziska S. Kemter
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Sonja J. Messerschmidt
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Nadine Schallopp
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Elke Lang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jennifer K. Teschler
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States of America
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States of America
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Centre of Infection Research (DZIF), Partner Site Hannover–Braunschweig, Braunschweig, Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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Ruban-Ośmiałowska B, Jakimowicz D, Smulczyk-Krawczyszyn A, Chater KF, Zakrzewska-Czerwińska J. Replisome localization in vegetative and aerial hyphae of Streptomyces coelicolor. J Bacteriol 2006; 188:7311-6. [PMID: 17015671 PMCID: PMC1636232 DOI: 10.1128/jb.00940-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using a functional fusion of DnaN to enhanced green fluorescent protein, we examined the subcellular localization of the replisome machinery in the vegetative mycelium and aerial mycelium of the multinucleoid organism Streptomyces coelicolor. Chromosome replication took place in many compartments of both types of hypha, with the apical compartments of the aerial mycelium exhibiting the highest replication activity. Within a single compartment, the number of "current" ongoing DNA replications was lower than the expected chromosome number, and the appearance of fluorescent foci was often heterogeneous, indicating that this process is asynchronous within compartments and that only selected chromosomes undergo replication.
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Affiliation(s)
- Beata Ruban-Ośmiałowska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Weigla 12, 53-114, Wrocław, Poland.
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Huang CH, Chen CY, Tsai HH, Chen C, Lin YS, Chen CW. Linear plasmid SLP2 of Streptomyces lividans is a composite replicon. Mol Microbiol 2003; 47:1563-76. [PMID: 12622812 DOI: 10.1046/j.1365-2958.2003.03403.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SLP2 is a 50 kb linear plasmid in Streptomyces lividans that contains short (44 bp) terminal inverted repeats and covalently bound terminal proteins. The nucleotide sequence of SLP2 was determined. The rightmost 15.4 kb sequence is identical to that of the host chromosome, including the Tn4811 sequence at the border, which is interrupted by an insertion sequence (IS) element in SLP2. Examination of the flanking target sequences of Tn4811 suggests a previous recombinational event there. The 43 putative protein coding sequences contained many involved in replication (including two terminal protein homologues), partitioning, conjugal transfer and intramycelial spread. The terminally located helicase-like gene ttrA was necessary for conjugal transfer. The two telomeres diverge significantly in primary sequence, while preserving similar secondary structures. Mini-linear plasmids containing these telomeres replicated in S. lividans using the chromosomally encoded terminal protein. In addition, two pseudotelomere sequences are present near the left telomere. The G+C content and GC or AT skew profiles exhibit complex distributions. These, plus the inferred recombination at the right arm, indicate that SLP2 has evolved through rounds of exchanges involving at least three replicons.
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Affiliation(s)
- Chih-Hung Huang
- Institute of Genetics, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan
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Greendyke R, Rajagopalan M, Parish T, Madiraju MVVS. Conditional expression of Mycobacterium smegmatis dnaA, an essential DNA replication gene. MICROBIOLOGY (READING, ENGLAND) 2002; 148:3887-3900. [PMID: 12480893 DOI: 10.1099/00221287-148-12-3887] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To begin to understand the role of Mycobacterium smegmatis dnaA in DNA replication, the dnaA gene was characterized at the genetic level. Western analyses revealed that DnaA accounts for approximately 0.18% of the total cellular protein during both the active and stationary growth periods. Expression of antisense dnaA RNA reduced viability, indicating that dnaA is an essential gene in replication. To further understand the role(s) of dnaA in replication, a conditionally expressing strain was constructed in which expression of dnaA was controlled by acetamide. Growth in the presence of 0.2% acetamide elevated the intracellular levels of DnaA and increased cell length, but did not affect viability. Visualization of DNA by fluorescence microscopy revealed that DnaA-overproducing cells were multinucleoidal, indicating a loss of synchrony between the replication and cell-division cycles. Withdrawal of acetamide resulted in the depletion of the intracellular levels of DnaA, reduced viability and gradually blocked DNA synthesis. Acetamide-starved cells were very filamentous, several times the size of the parent cells and showed either abnormal or multi-nucleoid morphology, indicating a blockage in cell-division events. The addition of acetamide to the starved cells restored their viability and shortened the lengths of their filaments back to the size of the parent cells. Thus, both increasing and decreasing the levels of DnaA have an effect on the cells, indicating that the level of DnaA is critical to the maintenance of coordination between DNA replication and cell division. It is concluded that DNA replication and cell-division processes in M. smegmatis are linked, and it is proposed that DnaA has a role in both of these processes.
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Affiliation(s)
- Rebecca Greendyke
- Biomedical Research, 11937 US Hwy@271, The University of Texas Health Center at Tyler, Tyler, TX-75708-3154, USA1
| | - Malini Rajagopalan
- Biomedical Research, 11937 US Hwy@271, The University of Texas Health Center at Tyler, Tyler, TX-75708-3154, USA1
| | - Tanya Parish
- Department of Medical Microbiology, Barts and the London, Queen Mary's School of Medicine and Dentistry, Turner St, Whitechapel, London E1 2AD, UK2
| | - Murty V V S Madiraju
- Biomedical Research, 11937 US Hwy@271, The University of Texas Health Center at Tyler, Tyler, TX-75708-3154, USA1
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