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Venter JC, Glass JI, Hutchison CA, Vashee S. Synthetic chromosomes, genomes, viruses, and cells. Cell 2022; 185:2708-2724. [DOI: 10.1016/j.cell.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 10/17/2022]
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2
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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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3
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Creating custom synthetic genomes in Escherichia coli with REXER and GENESIS. Nat Protoc 2021; 16:2345-2380. [PMID: 33903757 DOI: 10.1038/s41596-020-00464-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 11/16/2020] [Indexed: 11/08/2022]
Abstract
We previously developed REXER (Replicon EXcision Enhanced Recombination); this method enables the replacement of >100 kb of the Escherichia coli genome with synthetic DNA in a single step and allows the rapid identification of non-viable or otherwise problematic sequences with nucleotide resolution. Iterative repetition of REXER (GENESIS, GENomE Stepwise Interchange Synthesis) enables stepwise replacement of longer contiguous sections of genomic DNA with synthetic DNA, and even the replacement of the entire E. coli genome with synthetic DNA. Here we detail protocols for REXER and GENESIS. A standard REXER protocol typically takes 7-10 days to complete. Our description encompasses (i) synthetic DNA design, (ii) assembly of synthetic DNA constructs, (iii) utilization of CRISPR-Cas9 coupled to lambda-red recombination and positive/negative selection to enable the high-fidelity replacement of genomic DNA with synthetic DNA (or insertion of synthetic DNA), (iv) evaluation of the success of the integration and replacement and (v) identification of non-tolerated synthetic DNA sequences with nucleotide resolution. This protocol provides a set of precise genome engineering methods to create custom synthetic E. coli genomes.
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Abstract
Recent studies have renewed interest in developing novel antiviral therapeutics and vaccines based on defective interfering particles (DIPs)—a subset of viral deletion mutants that conditionally replicate. Identifying and engineering DIPs require that viral cis- and trans-acting elements be accurately mapped. It has long been known that noncoding genomic regions can be obligate cis elements acted upon in trans by gene products. In viruses, cis elements regulate gene expression, encapsidation, and other maturation processes, but mapping these elements relies on targeted iterative deletion or laborious prospecting for rare spontaneously occurring mutants. Here, we introduce a method to comprehensively map viral cis and trans elements at single-nucleotide resolution by high-throughput random deletion. Variable-size deletions are randomly generated by transposon integration, excision, and exonuclease chewback and then barcoded for tracking via sequencing (i.e., random deletion library sequencing [RanDeL-seq]). Using RanDeL-seq, we generated and screened >23,000 HIV-1 variants to generate a single-base resolution map of HIV-1’s cis and trans elements. The resulting landscape recapitulated HIV-1’s known cis-acting elements (i.e., long terminal repeat [LTR], Ψ, and Rev response element [RRE]) and, surprisingly, indicated that HIV-1’s central DNA flap (i.e., central polypurine tract [cPPT] to central termination sequence [CTS]) is as critical as the LTR, Ψ, and RRE for long-term passage. Strikingly, RanDeL-seq identified a previously unreported ∼300-bp region downstream of RRE extending to splice acceptor 7 that is equally critical for sustained viral passage. RanDeL-seq was also used to construct and screen a library of >90,000 variants of Zika virus (ZIKV). Unexpectedly, RanDeL-seq indicated that ZIKV’s cis-acting regions are larger than the untranscribed (UTR) termini, encompassing a large fraction of the nonstructural genes. Collectively, RanDeL-seq provides a versatile framework for generating viral deletion mutants, enabling discovery of replication mechanisms and development of novel antiviral therapeutics, particularly for emerging viral infections.
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Abstract
The encoded biosynthesis of proteins provides the ultimate paradigm for high-fidelity synthesis of long polymers of defined sequence and composition, but it is limited to polymerizing the canonical amino acids. Recent advances have built on genetic code expansion - which commonly permits the cellular incorporation of one type of non-canonical amino acid into a protein - to enable the encoded incorporation of several distinct non-canonical amino acids. Developments include strategies to read quadruplet codons, use non-natural DNA base pairs, synthesize completely recoded genomes and create orthogonal translational components with reprogrammed specificities. These advances may enable the genetically encoded synthesis of non-canonical biopolymers and provide a platform for transforming the discovery and evolution of new materials and therapeutics.
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Affiliation(s)
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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6
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Garcia-Morales L, Ruiz E, Gourgues G, Rideau F, Piñero-Lambea C, Lluch-Senar M, Blanchard A, Lartigue C. A RAGE Based Strategy for the Genome Engineering of the Human Respiratory Pathogen Mycoplasma pneumoniae. ACS Synth Biol 2020; 9:2737-2748. [PMID: 33017534 DOI: 10.1021/acssynbio.0c00263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genome engineering of microorganisms has become a standard in microbial biotechnologies. Several efficient tools are available for the genetic manipulation of model bacteria such as Escherichia coli and Bacillus subtilis, or the yeast Saccharomyces cerevisiae. Difficulties arise when transferring these tools to nonmodel organisms. Synthetic biology strategies relying on genome transplantation (GT) aim at using yeast cells for engineering bacterial genomes cloned as artificial chromosomes. However, these strategies remain unsuccessful for many bacteria, including Mycoplasma pneumoniae (MPN), a human pathogen infecting the respiratory tract that has been extensively studied as a model for systems biology of simple unicellular organisms. Here, we have designed a novel strategy for genome engineering based on the recombinase-assisted genomic engineering (RAGE) technology for editing the MPN genome. Using this strategy, we have introduced a 15 kbp fragment at a specific locus of the MPN genome and replaced 38 kbp from its genome by engineered versions modified either in yeast or in E. coli. A strain harboring a synthetic version of this fragment cleared of 13 nonessential genes could also be built and propagated in vitro. These strains were depleted of known virulence factors aiming at creating an avirulent chassis for SynBio applications. Such a chassis and technology are a step forward to build vaccines or deliver therapeutic compounds in the lungs to prevent or cure respiratory diseases in humans.
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Affiliation(s)
- Luis Garcia-Morales
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Estelle Ruiz
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Géraldine Gourgues
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Fabien Rideau
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Alain Blanchard
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Carole Lartigue
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
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Mariscal AM, Kakizawa S, Hsu JY, Tanaka K, González-González L, Broto A, Querol E, Lluch-Senar M, Piñero-Lambea C, Sun L, Weyman PD, Wise KS, Merryman C, Tse G, Moore AJ, Hutchison CA, Smith HO, Tomita M, Venter JC, Glass JI, Piñol J, Suzuki Y. Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells. ACS Synth Biol 2018; 7:1538-1552. [PMID: 29786424 DOI: 10.1021/acssynbio.8b00028] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functional genomics studies in minimal mycoplasma cells enable unobstructed access to some of the most fundamental processes in biology. Conventional transposon bombardment and gene knockout approaches often fail to reveal functions of genes that are essential for viability, where lethality precludes phenotypic characterization. Conditional inactivation of genes is effective for characterizing functions central to cell growth and division, but tools are limited for this purpose in mycoplasmas. Here we demonstrate systems for inducible repression of gene expression based on clustered regularly interspaced short palindromic repeats-mediated interference (CRISPRi) in Mycoplasma pneumoniae and synthetic Mycoplasma mycoides, two organisms with reduced genomes actively used in systems biology studies. In the synthetic cell, we also demonstrate inducible gene expression for the first time. Time-course data suggest rapid kinetics and reversible engagement of CRISPRi. Targeting of six selected endogenous genes with this system results in lowered transcript levels or reduced growth rates that agree with lack or shortage of data in previous transposon bombardment studies, and now produces actual cells to analyze. The ksgA gene encodes a methylase that modifies 16S rRNA, rendering it vulnerable to inhibition by the antibiotic kasugamycin. Targeting the ksgA gene with CRISPRi removes the lethal effect of kasugamycin and enables cell growth, thereby establishing specific and effective gene modulation with our system. The facile methods for conditional gene activation and inactivation in mycoplasmas open the door to systematic dissection of genetic programs at the core of cellular life.
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Affiliation(s)
- Ana M Mariscal
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina , Universitat Autònoma de Barcelona , Cerdanyola del Vallès, Barcelona 08193 , Spain
| | - Shigeyuki Kakizawa
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- National Institute of Advanced Industrial Science and Technology , Tsukuba , Ibaraki 305-8560 , Japan
| | - Jonathan Y Hsu
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- Department of Bioengineering , University of California, San Diego , La Jolla , California 92093 , United States
| | - Kazuki Tanaka
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- Institute for Advanced Biosciences , Keio University , Tsuruoka , Yamagata 997-0035 , Japan
- Faculty of Environment and Information Studies , Keio University , Fujisawa , Kanagawa 252-0882 , Japan
| | - Luis González-González
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina , Universitat Autònoma de Barcelona , Cerdanyola del Vallès, Barcelona 08193 , Spain
| | - Alicia Broto
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) , The Barcelona Institute of Science and Technology , Barcelona 08036 , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona 08002 , Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina , Universitat Autònoma de Barcelona , Cerdanyola del Vallès, Barcelona 08193 , Spain
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) , The Barcelona Institute of Science and Technology , Barcelona 08036 , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona 08002 , Spain
| | - Carlos Piñero-Lambea
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) , The Barcelona Institute of Science and Technology , Barcelona 08036 , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona 08002 , Spain
| | - Lijie Sun
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Philip D Weyman
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Kim S Wise
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Chuck Merryman
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Gavin Tse
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- Department of Bioengineering , University of California, San Diego , La Jolla , California 92093 , United States
| | - Adam J Moore
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- Department of Bioengineering , University of California, San Diego , La Jolla , California 92093 , United States
| | - Clyde A Hutchison
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Hamilton O Smith
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Masaru Tomita
- Institute for Advanced Biosciences , Keio University , Tsuruoka , Yamagata 997-0035 , Japan
| | - J Craig Venter
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - John I Glass
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina , Universitat Autònoma de Barcelona , Cerdanyola del Vallès, Barcelona 08193 , Spain
| | - Yo Suzuki
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
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Balikó G, Vernyik V, Karcagi I, Györfy Z, Draskovits G, Fehér T, Pósfai G. Rational Efforts to Streamline the Escherichia coliGenome. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Gabriella Balikó
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Viktor Vernyik
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Ildikó Karcagi
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Zsuzsanna Györfy
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Gábor Draskovits
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Tamás Fehér
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - György Pósfai
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
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Xin Y, Guo T, Mu Y, Kong J. Coupling the recombineering to Cre-lox system enables simplified large-scale genome deletion in Lactobacillus casei. Microb Cell Fact 2018; 17:21. [PMID: 29433512 PMCID: PMC5808424 DOI: 10.1186/s12934-018-0872-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
Background Lactobacillus casei is widely used in the dairy and pharmaceutical industries and a promising candidate for use as cell factories. Recently, genome sequencing and functional genomics provide the possibility for reducing L. casei genome. However, it was still limited by the inefficient and laborious genome deletion methods. Results Here, we proposed a genome minimization strategy based on LCABL_13040-50-60 recombineering and Cre-lox site-specific recombination system in L. casei. The LCABL_13040-50-60 recombineering system was used to introduce two lox sites (lox66 and lox71) into 5′ and 3′ ends of the targeted region. Subsequently, the targeted region was excised by Cre recombinase. The robustness of the strategy was demonstrated by single-deletion of a nonessential ~ 39.3 kb or an important ~ 12.8 kb region and simultaneous deletion of two non-continuous genome regions (5.2 and 6.6 kb) with 100% efficiency. Furthermore, a cyclical application of this strategy generated a double-deletion mutant of which 1.68% of the chromosome was sequentially excised. Moreover, biological features (including growth rate, electroporation efficiency, cell morphology or heterologous protein productivity) of these mutants were characterized. Conclusions To our knowledge, this strategy is the first instance of sequential deletion of large-scale genome regions in L. casei. We expected this efficient and inexpensive tool can help for rapid genome streamlining and generation restructured L. casei strains used as cell factories. Electronic supplementary material The online version of this article (10.1186/s12934-018-0872-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yongping Xin
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, 250100, People's Republic of China
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, 250100, People's Republic of China
| | - Yingli Mu
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, 250100, People's Republic of China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, 250100, People's Republic of China.
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10
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Genome reprogramming for synthetic biology. Front Chem Sci Eng 2017. [DOI: 10.1007/s11705-017-1618-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zheng X, Li SY, Zhao GP, Wang J. An efficient system for deletion of large DNA fragments in Escherichia coli via introduction of both Cas9 and the non-homologous end joining system from Mycobacterium smegmatis. Biochem Biophys Res Commun 2017; 485:768-774. [PMID: 28257845 DOI: 10.1016/j.bbrc.2017.02.129] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/25/2017] [Indexed: 12/24/2022]
Abstract
Accompanied with the internal non-homologous end joining (NHEJ) system, Cas9 can be used to easily inactivate a gene or delete a fragment through introduction of DNA double-stranded breaks (DSBs) in eukaryotic cells. While in most prokaryotes (e.g. Escherichia coli), due to the lack of NHEJ, homologous recombination (HR) is required for repair of DSBs, which is less convenient. Here, a markerless system was developed for rapid gene inactivation or fragment deletion in E. coli via introduction of both Cas9 and a bacterial NHEJ system. Three bacterial NHEJ systems, i.e. Mycobacterium smegmatis (Msm), Mycobacterium tuberculosis (Mtb) and Bacillus subtilis (Bs), were tested in E. coli, and the MsmNHEJ system showed the best efficiency. With the employment of Cas9 and MsmNHEJ, we efficiently mutated lacZ gene, deleted glnALG operon and two large DNA fragments (67 kb and 123 kb) in E. coli, respectively. Moreover, the system was further designed to allow for continuous inactivation of genes or deletion of DNA fragments in E. coli. We envision this system can be extended to other bacteria, especially those with low HR efficiency.
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Affiliation(s)
- Xuan Zheng
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science, Henan University, Kaifeng 475004, China
| | - Shi-Yuan Li
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guo-Ping Zhao
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Microbiology and Li KaShing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Jin Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Bott M, Eggeling L. Novel Technologies for Optimal Strain Breeding. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:227-254. [PMID: 27872965 DOI: 10.1007/10_2016_33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The implementation of a knowledge-based bioeconomy requires the rapid development of highly efficient microbial production strains that are able to convert renewable carbon sources to value-added products, such as bulk and fine chemicals, pharmaceuticals, or proteins at industrial scale. Starting from classical strain breeding by random mutagenesis and screening in the 1950s via rational design by metabolic engineering initiated in the 1970s, a range of powerful new technologies have been developed in the past two decades that can revolutionize future strain engineering. In particular, next-generation sequencing technologies combined with new methods of genome engineering and high-throughput screening based on genetically encoded biosensors have allowed for new concepts. In this chapter, selected new technologies relevant for breeding microbial production strains with a special emphasis on amino acid producers will be summarized.
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Affiliation(s)
- Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany.
| | - Lothar Eggeling
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany
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13
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Defining synonymous codon compression schemes by genome recoding. Nature 2016; 539:59-64. [PMID: 27776354 DOI: 10.1038/nature20124] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 09/26/2016] [Indexed: 12/24/2022]
Abstract
Synthetic recoding of genomes, to remove targeted sense codons, may facilitate the encoded cellular synthesis of unnatural polymers by orthogonal translation systems. However, our limited understanding of allowed synonymous codon substitutions, and the absence of methods that enable the stepwise replacement of the Escherichia coli genome with long synthetic DNA and provide feedback on allowed and disallowed design features in synthetic genomes, have restricted progress towards this goal. Here we endow E. coli with a system for efficient, programmable replacement of genomic DNA with long (>100-kb) synthetic DNA, through the in vivo excision of double-stranded DNA from an episomal replicon by CRISPR/Cas9, coupled to lambda-red-mediated recombination and simultaneous positive and negative selection. We iterate the approach, providing a basis for stepwise whole-genome replacement. We attempt systematic recoding in an essential operon using eight synonymous recoding schemes. Each scheme systematically replaces target codons with defined synonyms and is compatible with codon reassignment. Our results define allowed and disallowed synonymous recoding schemes, and enable the identification and repair of recoding at idiosyncratic positions in the genome.
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Abstract
Bacillus subtilis is one of the best-studied organisms. Due to the broad knowledge and annotation and the well-developed genetic system, this bacterium is an excellent starting point for genome minimization with the aim of constructing a minimal cell. We have analyzed the genome of B. subtilis and selected all genes that are required to allow life in complex medium at 37°C. This selection is based on the known information on essential genes and functions as well as on gene and protein expression data and gene conservation. The list presented here includes 523 and 119 genes coding for proteins and RNAs, respectively. These proteins and RNAs are required for the basic functions of life in information processing (replication and chromosome maintenance, transcription, translation, protein folding, and secretion), metabolism, cell division, and the integrity of the minimal cell. The completeness of the selected metabolic pathways, reactions, and enzymes was verified by the development of a model of metabolism of the minimal cell. A comparison of the MiniBacillus genome to the recently reported designed minimal genome of Mycoplasma mycoides JCVI-syn3.0 indicates excellent agreement in the information-processing pathways, whereas each species has a metabolism that reflects specific evolution and adaptation. The blueprint of MiniBacillus presented here serves as the starting point for a successive reduction of the B. subtilis genome.
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15
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Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P. CART-a chemical annotation retrieval toolkit. Bioinformatics 2016; 32:2869-71. [PMID: 27256313 PMCID: PMC5018367 DOI: 10.1093/bioinformatics/btw233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 04/18/2016] [Indexed: 12/01/2022] Open
Abstract
Motivation: Data on bioactivities of drug-like chemicals are rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to prevailing ambiguity between chemical names and identifiers and a lack of cross-references between databases. Results: To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality, it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data. Availability and Implementation: CART is available as a Galaxy web service (cart.embl.de). Source code and an easy-to-install command line tool can also be obtained from the web site. Contact: bork@embl.de Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Samy Deghou
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Murat Iskar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marja Driessen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mercedes Castillo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vera van Noort
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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16
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Abstract
The fields of molecular genetics, biotechnology and synthetic biology are demanding ever more sophisticated molecular tools for programmed precise modification of cell genomic DNA and other DNA sequences. This review presents the current state of knowledge and development of one important group of DNA-modifying enzymes, the site-specific recombinases (SSRs). SSRs are Nature's 'molecular machines' for cut-and-paste editing of DNA molecules by inserting, deleting or inverting precisely defined DNA segments. We survey the SSRs that have been put to use, and the types of applications for which they are suitable. We also discuss problems associated with uses of SSRs, how these problems can be minimized, and how recombinases are being re-engineered for improved performance and novel applications.
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17
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Karas BJ, Suzuki Y, Weyman PD. Strategies for cloning and manipulating natural and synthetic chromosomes. Chromosome Res 2015; 23:57-68. [PMID: 25596826 DOI: 10.1007/s10577-014-9455-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Advances in synthetic biology methods to assemble and edit DNA are enabling genome engineering at a previously impracticable scale and scope. The synthesis of the Mycoplasma mycoides genome followed by its transplantation to convert a related cell into M. mycoides has transformed strain engineering. This approach exemplifies the combination of newly emerging chromosome-scale genome editing strategies that can be defined in three main steps: (1) chromosome acquisition into a microbial engineering platform, (2) alteration and improvement of the acquired chromosome, and (3) installation of the modified chromosome into the original or alternative organism. In this review, we outline recent progress in methods for acquiring chromosomes and chromosome-scale DNA molecules in the workhorse organisms Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae. We present overviews of important genetic strategies and tools for each of the three organisms, point out their respective strengths and weaknesses, and highlight how the host systems can be used in combination to facilitate chromosome assembly or engineering. Finally, we highlight efforts for the installation of the cloned/altered chromosomes or fragments into the target organism and present remaining challenges in expanding this powerful experimental approach to a wider range of target organisms.
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Affiliation(s)
- Bogumil J Karas
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
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18
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Standage-Beier K, Zhang Q, Wang X. Targeted Large-Scale Deletion of Bacterial Genomes Using CRISPR-Nickases. ACS Synth Biol 2015; 4:1217-25. [PMID: 26451892 PMCID: PMC4655420 DOI: 10.1021/acssynbio.5b00132] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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Programmable
CRISPR-Cas systems have augmented our ability to produce
precise genome manipulations. Here we demonstrate and characterize
the ability of CRISPR-Cas derived nickases to direct targeted recombination
of both small and large genomic regions flanked by repetitive elements
in Escherichia coli. While CRISPR directed double-stranded DNA breaks are highly lethal
in many bacteria, we show that CRISPR-guided nickase systems can be
programmed to make precise, nonlethal, single-stranded incisions in
targeted genomic regions. This induces recombination events and leads
to targeted deletion. We demonstrate that dual-targeted nicking enables
deletion of 36 and 97 Kb of the genome. Furthermore, multiplex targeting
enables deletion of 133 Kb, accounting for approximately 3% of the
entire E. coli genome. This technology provides a
framework for methods to manipulate bacterial genomes using CRISPR-nickase
systems. We envision this system working synergistically with preexisting
bacterial genome engineering methods.
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Affiliation(s)
- Kylie Standage-Beier
- School of Life Sciences, ‡School of Biological
and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Qi Zhang
- School of Life Sciences, ‡School of Biological
and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiao Wang
- School of Life Sciences, ‡School of Biological
and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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19
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Krishnamurthy VV, Khamo JS, Cho E, Schornak C, Zhang K. Multiplex gene removal by two-step polymerase chain reactions. Anal Biochem 2015; 481:7-9. [DOI: 10.1016/j.ab.2015.03.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 11/29/2022]
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20
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Noskov VN, Ma L, Chen S, Chuang RY. Recombinase-mediated cassette exchange (RMCE) system for functional genomics studies in Mycoplasma mycoides. Biol Proced Online 2015; 17:6. [PMID: 25774095 PMCID: PMC4359775 DOI: 10.1186/s12575-015-0016-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/17/2015] [Indexed: 02/04/2023] Open
Abstract
Background We have previously established technologies enabling us to engineer the Mycoplasma mycoides genome while cloned in the yeast Saccharomyces cerevisiae, followed by genome transplantation into Mycoplasma capricolum recipient cells to produce M. mycoides with an altered genome. To expand the toolbox for genomic modifications, we designed a strategy based on the Cre/loxP-based Recombinase-Mediated Cassette Exchange (RMCE) system for functional genomics analyses. Results In this paper, we demonstrated replacement of an approximately 100 kb DNA segment of the M. mycoides genome with a synthetic DNA counterpart in two orientations. The function of the altered genomes was then validated by genome transplantation and phenotypic characterization of the transplanted cells. Conclusion This method offers an easy and efficient way to manipulate the M. mycoides genome and will be a valuable tool for functional genomic studies, such as genome organization and minimization. Electronic supplementary material The online version of this article (doi:10.1186/s12575-015-0016-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vladimir N Noskov
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD USA
| | - Li Ma
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD USA
| | - Stephen Chen
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD USA
| | - Ray-Yuan Chuang
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD USA
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21
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Suzuki Y, Assad-Garcia N, Kostylev M, Noskov VN, Wise KS, Karas BJ, Stam J, Montague MG, Hanly TJ, Enriquez NJ, Ramon A, Goldgof GM, Richter RA, Vashee S, Chuang RY, Winzeler EA, Hutchison CA, Gibson DG, Smith HO, Glass JI, Venter JC. Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling. Genome Res 2015; 25:435-44. [PMID: 25654978 PMCID: PMC4352883 DOI: 10.1101/gr.182477.114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding of basic biological processes. Mycoplasma bacteria, with the smallest known genomes among free-living cellular organisms, are ideal models for this purpose, but the natural versions of these cells have genome complexities still too great to offer a comprehensive view of a fundamental life form. Here we describe an efficient method for reducing genomes from these organisms by identifying individually deletable regions using transposon mutagenesis and progressively clustering deleted genomic segments using meiotic recombination between the bacterial genomes harbored in yeast. Mycoplasmal genomes subjected to this process and transplanted into recipient cells yielded two mycoplasma strains. The first simultaneously lacked eight singly deletable regions of the genome, representing a total of 91 genes and ∼10% of the original genome. The second strain lacked seven of the eight regions, representing 84 genes. Growth assay data revealed an absence of genetic interactions among the 91 genes under tested conditions. Despite predicted effects of the deletions on sugar metabolism and the proteome, growth rates were unaffected by the gene deletions in the seven-deletion strain. These results support the feasibility of using single-gene disruption data to design and construct viable genomes lacking multiple genes, paving the way toward genome minimization. The progressive clustering method is expected to be effective for the reorganization of any mega-sized DNA molecules cloned in yeast, facilitating the construction of designer genomes in microbes as well as genomic fragments for genetic engineering of higher eukaryotes.
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Affiliation(s)
- Yo Suzuki
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA;
| | - Nacyra Assad-Garcia
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Maxim Kostylev
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Vladimir N Noskov
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Kim S Wise
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65212, USA
| | - Bogumil J Karas
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Jason Stam
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Michael G Montague
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Timothy J Hanly
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Nico J Enriquez
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Adi Ramon
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Gregory M Goldgof
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; University of California, San Diego, School of Medicine, La Jolla, California 92093, USA
| | - R Alexander Richter
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Sanjay Vashee
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Ray-Yuan Chuang
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Elizabeth A Winzeler
- University of California, San Diego, School of Medicine, La Jolla, California 92093, USA
| | - Clyde A Hutchison
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Daniel G Gibson
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Hamilton O Smith
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - John I Glass
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - J Craig Venter
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
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