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Fujita H, Osaku A, Sakane Y, Yoshida K, Yamada K, Nara S, Mukai T, Su’etsugu M. Enzymatic Supercoiling of Bacterial Chromosomes Facilitates Genome Manipulation. ACS Synth Biol 2022; 11:3088-3099. [PMID: 35998348 PMCID: PMC9486964 DOI: 10.1021/acssynbio.2c00353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The physical stability of bacterial chromosomes is important for their in vitro manipulation, while genetic stability is important in vivo. However, extracted naked chromosomes in the open circular form are fragile due to nicks and gaps. Using a nick/gap repair and negative supercoiling reaction (named SCR), we first achieved the negative supercoiling of the whole genomes extracted from Escherichia coli and Vibrio natriegens cells. Supercoiled chromosomes of 0.2-4.6 megabase (Mb) were separated by size using a conventional agarose gel electrophoresis and served as DNA size markers. We also achieved the enzymatic replication of 1-2 Mb chromosomes using the reconstituted E. coli replication-cycle reaction (RCR). Electroporation-ready 1 Mb chromosomes were prepared by a modified SCR performed at a low salt concentration (L-SCR) and directly introduced into commercial electrocompetent E. coli cells. Since successful electroporation relies on the genetic stability of a chromosome in cells, genetically stable 1 Mb chromosomes were developed according to a portable chromosome format (PCF). Using physically and genetically stabilized chromosomes, the democratization of genome synthetic biology will be greatly accelerated.
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2
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Abstract
Approximately 10% of bacterial strains contain more than one chromosome; however, in contrast to the primary chromosomes, the mechanisms underlying the formation of the second chromosomes and the significance of their existence remain unclear. Species of the genus Flammeovirga are typical polysaccharide-degrading bacteria, and herein, we report complete genome maps of this genus. These genomes all had multireplicons and second chromosomes. The second chromosome, much larger than plasmids and even megaplasmids, had rRNA and a disparity of 1% relative to the main chromosome in guanine-cytosine (GC) content. The largest chromosomes carried core genes for cellular processes, while the second chromosomes were enriched with genes involved in the transport and metabolism of inorganic ions and carbohydrates, particularly genes encoding glycoside hydrolases and polysaccharide lyases, which constituted the genetic basis for the strains’ excellent capabilities to utilize polysaccharides. The second chromosomal evolution had a higher mutation rate than the primary chromosomes. Furthermore, the second chromosomes were also enriched in horizontal transfer genes and duplicated genes. The primary chromosomes were more evolutionarily conserved, while the second chromosomes were more plastic, which might be related to their different roles in the bacterial survival process. This study can be used as an example to explain possible formation mechanisms and functions of the second chromosomes, providing a reference for peer research on the second chromosomes. In particular, the second chromosomes were enriched in polysaccharide-degrading enzymes, which will provide theoretical support for using genomic data to mine tool-type carbohydrase resources. IMPORTANCE For decades, the typical bacterial genome has been thought to contain a single chromosome and a few small plasmids carrying nonessential genes. However, an increasing number of secondary chromosomes have been identified in various bacteria (e.g., plant symbiotic bacteria and human pathogens). This study reported three complete genomes of the polysaccharide-degrading marine bacterial genus Flammeovirga, revealed that they harbor two chromosomes, and further identified that the presence of a multireplicon system is a characteristic of complete Flammeovirga genomes. These sequences will add to our knowledge on secondary chromosomes, especially within Bacteroidetes. This study indicated that the second chromosomes of the genus Flammeovirga initially originated from an ancestral plasmid and subsequently expanded by gene duplication or by obtaining heterologous genes with functions, thus promoting host strains to adapt to complex living environments (e.g., to degrade more diverse polysaccharides from marine environments). These findings will promote the understanding of the evolution and function of bacteria with multireplicon systems.
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Yoneji T, Fujita H, Mukai T, Su'etsugu M. Grand scale genome manipulation via chromosome swapping in Escherichia coli programmed by three one megabase chromosomes. Nucleic Acids Res 2021; 49:8407-8418. [PMID: 33907814 PMCID: PMC8421210 DOI: 10.1093/nar/gkab298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/10/2021] [Indexed: 11/30/2022] Open
Abstract
In bacterial synthetic biology, whole genome transplantation has been achieved only in mycoplasmas that contain a small genome and are competent for foreign genome uptake. In this study, we developed Escherichia coli strains programmed by three 1-megabase (Mb) chromosomes by splitting the 3-Mb chromosome of a genome-reduced strain. The first split-chromosome retains the original replication origin (oriC) and partitioning (par) system. The second one has an oriC and the par locus from the F plasmid, while the third one has the ori and par locus of the Vibrio tubiashii secondary chromosome. The tripartite-genome cells maintained the rod-shaped form and grew only twice as slowly as their parent, allowing their further genetic engineering. A proportion of these 1-Mb chromosomes were purified as covalently closed supercoiled molecules with a conventional alkaline lysis method and anion exchange columns. Furthermore, the second and third chromosomes could be individually electroporated into competent cells. In contrast, the first split-chromosome was not able to coexist with another chromosome carrying the same origin region. However, it was exchangeable via conjugation between tripartite-genome strains by using different selection markers. We believe that this E. coli-based technology has the potential to greatly accelerate synthetic biology and synthetic genomics.
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Affiliation(s)
- Tatsuya Yoneji
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Hironobu Fujita
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Takahito Mukai
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Masayuki Su'etsugu
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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4
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Mukai T, Yoneji T, Yamada K, Fujita H, Nara S, Su'etsugu M. Overcoming the Challenges of Megabase-Sized Plasmid Construction in Escherichia coli. ACS Synth Biol 2020; 9:1315-1327. [PMID: 32459960 DOI: 10.1021/acssynbio.0c00008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although Escherichia coli has been a popular tool for plasmid construction, this bacterium was believed to be "unsuitable" for constructing a large plasmid whose size exceeds 500 kilobases. We assumed that traditional plasmid vectors may lack some regulatory DNA elements required for the stable replication and segregation of such a large plasmid. In addition, the use of a few site-specific recombination systems may facilitate cloning of large DNA segments. Here we show two strategies for constructing 1-megabase (1-Mb) secondary chromosomes by using new bacterial artificial chromosome (BAC) vectors. First, the 3-Mb genome of a genome-reduced E. coli strain was split into two chromosomes (2-Mb and 1-Mb), of which the smaller one has the origin of replication and the partitioning locus of the Vibrio tubiashii secondary chromosome. This chromosome fission method (Flp-POP cloning) works via flippase-mediated excision, which coincides with the reassembly of a split chloramphenicol resistance gene, allowing chloramphenicol selection. Next, we developed a new cloning method (oriT-POP cloning) and a fully equipped BAC vector (pMegaBAC1H) for developing a 1-Mb plasmid. Two 0.5-Mb genomic regions were sequentially transferred from two donor strains to a recipient strain via conjugation and captured by pMegaBAC1H in the recipient strain to produce a 1-Mb plasmid. This 1-Mb plasmid was transmissible to another E. coli strain via conjugation. Furthermore, these 1-Mb secondary chromosomes were amplifiable in vitro by using the reconstituted E. coli chromosome replication cycle reaction (RCR). These strategies and technologies would make popular E. coli cells a productive factory for designer chromosome engineering.
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Affiliation(s)
- Takahito Mukai
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Tatsuya Yoneji
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Kayoko Yamada
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Hironobu Fujita
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Seia Nara
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Masayuki Su'etsugu
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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Abstract
TelN and tos are a unique DNA linearization unit isolated from bacteriophage N15. While being transferable, the TelN cleaving-rejoining activities remained stable to function on tos in both bacterial and mammalian environments. However, TelN contribution in linear plasmid replication in mammalian cells remains unknown. Herein, we investigated the association of TelN in linear tos-containing DNA (tos-DNA) replication in mammalian cells. Additionally, the mammalian origin of replication (ori) that is well-known to initiate the replication event of plasmid vectors was also studied. In doing so, we identified that both TelN and mammalian initiation sites were essential for the replication of linear tos-DNA, determined by using methylation sensitive DpnI/MboI digestion and polymerase chain reaction (PCR) amplification approaches. Furthermore, we engineered the linear tos-DNA to be able to retain in mammalian cells using S/MAR technology. The resulting S/MAR containing tos-DNA was robust for at least 15 days, with (1) continuous tos-DNA replication, (2) correct splicing of gene transcripts, and (3) stable exogenous gene expression that was statistically comparable to the endogenous gene expression level. Understanding the activities of TelN and tos in mammalian cells can potentially provide insights for adapting this simple DNA linearization unit in developing novel genetic engineering tools, especially to the eukaryotic telomere/telomerase study.
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Affiliation(s)
- Pei Sheng Liew
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Tze Hao Tan
- Faculty of Science, Kyushu University, Ito campus, Fukuoka 819-0395, Japan
| | - Yin Cheng Wong
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Edmund Ui Hang Sim
- Faculty of Resource Sciences and Technology, University Malaysia Sarawak, 94300 Kota Samarahan, Malaysia
| | - Choon Weng Lee
- Institute of Biological Science, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kumaran Narayanan
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
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Sozhamannan S, Waldminghaus T. Exception to the exception rule: synthetic and naturally occurring single chromosome Vibrio cholerae. Environ Microbiol 2020; 22:4123-4132. [PMID: 32237026 DOI: 10.1111/1462-2920.15002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/25/2020] [Indexed: 12/26/2022]
Abstract
The genome of Vibrio cholerae, the etiological agent of cholera, is an exception to the single chromosome rule found in the vast majority of bacteria and has its genome partitioned between two unequally sized chromosomes. This unusual two-chromosome arrangement in V. cholerae has sparked considerable research interest since its discovery. It was demonstrated that the two chromosomes could be fused by deliberate genome engineering or forced to fuse spontaneously by blocking the replication of Chr2, the secondary chromosome. Recently, natural isolates of V. cholerae with chromosomal fusion have been found. Here, we summarize the pertinent findings on this exception to the exception rule and discuss the potential utility of single-chromosome V. cholerae to address fundamental questions on chromosome biology in general and DNA replication in particular.
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Affiliation(s)
- Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, CBRND-Enabling Biotechnologies, 110 Thomas Johnson Drive, Frederick, MD, 21702, USA.,Logistics Management Institute, Tysons, VA, 22102, USA
| | - Torsten Waldminghaus
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
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7
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Wang K, de la Torre D, Robertson WE, Chin JW. Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly. Science 2020; 365:922-926. [PMID: 31467221 DOI: 10.1126/science.aay0737] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/02/2019] [Indexed: 12/26/2022]
Abstract
The design and creation of synthetic genomes provide a powerful approach to understanding and engineering biology. However, it is often limited by the paucity of methods for precise genome manipulation. Here, we demonstrate the programmed fission of the Escherichia coli genome into diverse pairs of synthetic chromosomes and the programmed fusion of synthetic chromosomes to generate genomes with user-defined inversions and translocations. We further combine genome fission, chromosome transplant, and chromosome fusion to assemble genomic regions from different strains into a single genome. Thus, we program the scarless assembly of new genomes with nucleotide precision, a key step in the convergent synthesis of genomes from diverse progenitors. This work provides a set of precise, rapid, large-scale (megabase) genome-engineering operations for creating diverse synthetic genomes.
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Affiliation(s)
- Kaihang Wang
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Daniel de la Torre
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Wesley E Robertson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK.
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8
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Liew PS, Chen Q, Ng AWR, Chew YC, Ravin NV, Sim EUH, Lee CW, Narayanan K. Phage N15 protelomerase resolves its tos recognition site into hairpin telomeres within mammalian cells. Anal Biochem 2019; 583:113361. [DOI: 10.1016/j.ab.2019.113361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022]
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Luo H, Quan CL, Peng C, Gao F. Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform 2018; 20:1114-1124. [DOI: 10.1093/bib/bbx174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Indexed: 01/28/2023] Open
Abstract
Abstract
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.
Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.
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10
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Establishing a System for Testing Replication Inhibition of the Vibrio cholerae Secondary Chromosome in Escherichia coli. Antibiotics (Basel) 2017; 7:antibiotics7010003. [PMID: 29295515 PMCID: PMC5872114 DOI: 10.3390/antibiotics7010003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/05/2017] [Accepted: 12/20/2017] [Indexed: 12/29/2022] Open
Abstract
Regulators of DNA replication in bacteria are an attractive target for new antibiotics, as not only is replication essential for cell viability, but its underlying mechanisms also differ from those operating in eukaryotes. The genetic information of most bacteria is encoded on a single chromosome, but about 10% of species carry a split genome spanning multiple chromosomes. The best studied bacterium in this context is the human pathogen Vibrio cholerae, with a primary chromosome (Chr1) of 3 M bps, and a secondary one (Chr2) of about 1 M bps. Replication of Chr2 is under control of a unique mechanism, presenting a potential target in the development of V. cholerae-specific antibiotics. A common challenge in such endeavors is whether the effects of candidate chemicals can be focused on specific mechanisms, such as DNA replication. To test the specificity of antimicrobial substances independent of other features of the V. cholerae cell for the replication mechanism of the V. cholerae secondary chromosome, we establish the replication machinery in the heterologous E. coli system. We characterize an E. coli strain in which chromosomal replication is driven by the replication origin of V. cholerae Chr2. Surprisingly, the E. coli ori2 strain was not inhibited by vibrepin, previously found to inhibit ori2-based replication.
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11
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diCenzo GC, Finan TM. The Divided Bacterial Genome: Structure, Function, and Evolution. Microbiol Mol Biol Rev 2017; 81:e00019-17. [PMID: 28794225 PMCID: PMC5584315 DOI: 10.1128/mmbr.00019-17] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.
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Affiliation(s)
- George C diCenzo
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Turlough M Finan
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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12
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Döhlemann J, Wagner M, Happel C, Carrillo M, Sobetzko P, Erb TJ, Thanbichler M, Becker A. A Family of Single Copy repABC-Type Shuttle Vectors Stably Maintained in the Alpha-Proteobacterium Sinorhizobium meliloti. ACS Synth Biol 2017; 6:968-984. [PMID: 28264559 PMCID: PMC7610768 DOI: 10.1021/acssynbio.6b00320] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
A considerable
share of bacterial species maintains segmented genomes.
Plant symbiotic α-proteobacterial rhizobia contain up to six repABC-type replicons in addition to the primary chromosome.
These low or unit-copy replicons, classified as secondary chromosomes,
chromids, or megaplasmids, are exclusively found in α-proteobacteria.
Replication and faithful partitioning of these replicons to the daughter
cells is mediated by the repABC region. The importance
of α-rhizobial symbiotic nitrogen fixation for sustainable agriculture
and Agrobacterium-mediated plant transformation as
a tool in plant sciences has increasingly moved biological engineering
of these organisms into focus. Plasmids are ideal DNA-carrying vectors
for these engineering efforts. On the basis of repABC regions collected from α-rhizobial secondary replicons, and
origins of replication derived from traditional cloning vectors, we
devised the versatile family of pABC shuttle vectors propagating in Sinorhizobium meliloti, related members of the Rhizobiales, and Escherichia coli. A modular plasmid library
providing the elemental parts for pABC vector assembly was founded.
The standardized design of these vectors involves five basic modules:
(1) repABC cassette, (2) plasmid-derived origin of
replication, (3) RK2/RP4 mobilization site (optional), (4) antibiotic
resistance gene, and (5) multiple cloning site flanked by transcription
terminators. In S. meliloti, pABC vectors showed
high propagation stability and unit-copy number. We demonstrated stable
coexistence of three pABC vectors in addition to the two indigenous
megaplasmids in S. meliloti, suggesting combinability
of multiple compatible pABC plasmids. We further devised an in vivo cloning strategy involving Cre/lox-mediated translocation of large DNA fragments to an autonomously
replicating repABC-based vector, followed by conjugation-mediated
transfer either to compatible rhizobia or E. coli.
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Affiliation(s)
- Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Marcel Wagner
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Carina Happel
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Martina Carrillo
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
| | - Tobias J. Erb
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Martin Thanbichler
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
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Messerschmidt SJ, Schindler D, Zumkeller CM, Kemter FS, Schallopp N, Waldminghaus T. Optimization and Characterization of the Synthetic Secondary Chromosome synVicII in Escherichia coli. Front Bioeng Biotechnol 2016; 4:96. [PMID: 28066763 PMCID: PMC5179572 DOI: 10.3389/fbioe.2016.00096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/09/2016] [Indexed: 11/15/2022] Open
Abstract
Learning by building is one of the core ideas of synthetic biology research. Consequently, building synthetic chromosomes is the way to fully understand chromosome characteristics. The last years have seen exciting synthetic chromosome studies. We had previously introduced the synthetic secondary chromosome synVicII in Escherichia coli. It is based on the replication mechanism of the secondary chromosome in Vibrio cholerae. Here, we present a detailed analysis of its genetic characteristics and a selection approach to optimize replicon stability. We probe the origin diversity of secondary chromosomes from Vibrionaceae by construction of several new respective replicons. Finally, we present a synVicII version 2.0 with several innovations including its full compatibility with the popular modular cloning (MoClo) assembly system.
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Affiliation(s)
- Sonja J Messerschmidt
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Daniel Schindler
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Celine M Zumkeller
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Franziska S Kemter
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Nadine Schallopp
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
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14
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Milbredt S, Farmani N, Sobetzko P, Waldminghaus T. DNA Replication in Engineered Escherichia coli Genomes with Extra Replication Origins. ACS Synth Biol 2016; 5:1167-1176. [PMID: 27268399 DOI: 10.1021/acssynbio.6b00064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The standard outline of bacterial genomes is a single circular chromosome with a single replication origin. From the bioengineering perspective, it appears attractive to extend this basic setup. Bacteria with split chromosomes or multiple replication origins have been successfully constructed in the last few years. The characteristics of these engineered strains will largely depend on the respective DNA replication patterns. However, the DNA replication has not been investigated systematically in engineered bacteria with multiple origins or split replicons. Here we fill this gap by studying a set of strains consisting of (i) E. coli strains with an extra copy of the native replication origin (oriC), (ii) E. coli strains with an extra copy of the replication origin from the secondary chromosome of Vibrio cholerae (oriII), and (iii) a strain in which the E. coli chromosome is split into two linear replicons. A combination of flow cytometry, microarray-based comparative genomic hybridization (CGH), and modeling revealed silencing of extra oriC copies and differential timing of ectopic oriII copies compared to the native oriC. The results were used to derive construction rules for future multiorigin and multireplicon projects.
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Affiliation(s)
- Sarah Milbredt
- LOEWE Center for Synthetic
Microbiology, SYNMIKRO, Philipps-University, Marburg, Hans-Meerwein-Strasse 6, D-35043 Marburg, Germany
| | - Neda Farmani
- LOEWE Center for Synthetic
Microbiology, SYNMIKRO, Philipps-University, Marburg, Hans-Meerwein-Strasse 6, D-35043 Marburg, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic
Microbiology, SYNMIKRO, Philipps-University, Marburg, Hans-Meerwein-Strasse 6, D-35043 Marburg, Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic
Microbiology, SYNMIKRO, Philipps-University, Marburg, Hans-Meerwein-Strasse 6, D-35043 Marburg, Germany
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15
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Touchon M, Rocha EPC. Coevolution of the Organization and Structure of Prokaryotic Genomes. Cold Spring Harb Perspect Biol 2016; 8:a018168. [PMID: 26729648 DOI: 10.1101/cshperspect.a018168] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The cytoplasm of prokaryotes contains many molecular machines interacting directly with the chromosome. These vital interactions depend on the chromosome structure, as a molecule, and on the genome organization, as a unit of genetic information. Strong selection for the organization of the genetic elements implicated in these interactions drives replicon ploidy, gene distribution, operon conservation, and the formation of replication-associated traits. The genomes of prokaryotes are also very plastic with high rates of horizontal gene transfer and gene loss. The evolutionary conflicts between plasticity and organization lead to the formation of regions with high genetic diversity whose impact on chromosome structure is poorly understood. Prokaryotic genomes are remarkable documents of natural history because they carry the imprint of all of these selective and mutational forces. Their study allows a better understanding of molecular mechanisms, their impact on microbial evolution, and how they can be tinkered in synthetic biology.
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Affiliation(s)
- Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 75015 Paris, France CNRS, UMR3525, 75015 Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 75015 Paris, France CNRS, UMR3525, 75015 Paris, France
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16
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Schindler D, Waldminghaus T. Synthetic chromosomes. FEMS Microbiol Rev 2015; 39:871-91. [DOI: 10.1093/femsre/fuv030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
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17
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Gao F. Bacteria may have multiple replication origins. Front Microbiol 2015; 6:324. [PMID: 25941523 PMCID: PMC4403523 DOI: 10.3389/fmicb.2015.00324] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/31/2015] [Indexed: 01/15/2023] Open
Affiliation(s)
- Feng Gao
- Department of Physics, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China
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Messerschmidt SJ, Kemter FS, Schindler D, Waldminghaus T. Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae. Biotechnol J 2014; 10:302-14. [PMID: 25359671 DOI: 10.1002/biot.201400031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/02/2014] [Accepted: 10/30/2014] [Indexed: 01/25/2023]
Abstract
Recent developments in DNA-assembly methods make the synthesis of synthetic chromosomes a reachable goal. However, the redesign of primary chromosomes bears high risks and still requires enormous resources. An alternative approach is the addition of synthetic chromosomes to the cell. The natural secondary chromosome of Vibrio cholerae could potentially serve as template for a synthetic secondary chromosome in Escherichia coli. To test this assumption we constructed a replicon named synVicII based on the replication module of V. cholerae chromosome II (oriII). A new assay for the assessment of replicon stability was developed based on flow-cytometric analysis of unstable GFP variants. Application of this assay to cells carrying synVicII revealed an improved stability compared to a secondary replicon based on E. coli oriC. Cell cycle analysis and determination of cellular copy numbers of synVicII indicate that replication timing of the synthetic replicon in E. coli is comparable to the natural chromosome II (ChrII) in V. cholerae. The presented synthetic biology work provides the basis to use secondary chromosomes in E. coli to answer basic research questions as well as for several biotechnological applications.
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Affiliation(s)
- Sonja J Messerschmidt
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Germany
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