1
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Xiao H, Hu H, Guo Y, Li J, Zeng WB, Luo MH, Wang M, Hu Z. Efficient Strategy for Synthesizing Vector-Free and Oncolytic Herpes Simplex Type 1 Viruses. ACS Synth Biol 2024. [PMID: 39358309 DOI: 10.1021/acssynbio.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Synthesizing viral genomes plays an important role in fundamental virology research and in the development of vaccines and antiviral drugs. Herpes simplex virus type 1 (HSV-1) is a large DNA virus widely used in oncolytic virotherapy. Although de novo synthesis of the HSV-1 genome has been previously reported, the synthetic procedure is still far from efficient, and the synthesized genome contains a vector sequence that may affect its replication and application. In the present study, we developed an efficient vector-free strategy for synthesis and rescue of synthetic HSV-1. In contrast to the conventional method of transfecting mammalian cells with a completely synthesized genome containing a vector, overlapping HSV-1 fragments synthesized by transformation-associated recombination (TAR) in yeast were linearized and cotransfected into mammalian cells to rescue the synthetic virus. Using this strategy, a synthetic virus, F-Syn, comprising the complete genome of the HSV-1 F strain, was generated. The growth curve and electron microscopy of F-Syn confirmed that its replication dynamics and morphogenesis are similar to those of the parental virus. In addition, by combining TAR with in vitro CRISPR/Cas9 editing, an oncolytic virus, F-Syn-O, with deleted viral genes ICP6, ICP34.5, and ICP47 was generated. The antitumor effect of F-Syn-O was tested in vitro. F-Syn-O established a successful infection and induced dose-dependent cytotoxic effects in various human tumor cell lines. These strategies will facilitate convenient and systemic manipulation of HSV-1 genomes and could be further applied to the design and construction of oncolytic herpesviruses.
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Affiliation(s)
- Han Xiao
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hengrui Hu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Yijia Guo
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Li
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Wen-Bo Zeng
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Min-Hua Luo
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Manli Wang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihong Hu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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2
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Ye H, Luo G, Zheng Z, Li X, Cao J, Liu J, Dai J. Plant synthetic genomics: Big lessons from the little yeast. Cell Chem Biol 2024:S2451-9456(24)00321-0. [PMID: 39214084 DOI: 10.1016/j.chembiol.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/11/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Yeast has been extensively studied and engineered due to its genetic amenability. Projects like Sc2.0 and Sc3.0 have demonstrated the feasibility of constructing synthetic yeast genomes, yielding promising results in both research and industrial applications. In contrast, plant synthetic genomics has faced challenges due to the complexity of plant genomes. However, recent advancements of the project SynMoss, utilizing the model moss plant Physcomitrium patens, offer opportunities for plant synthetic genomics. The shared characteristics between P. patens and yeast, such as high homologous recombination rates and dominant haploid life cycle, enable researchers to manipulate P. patens genomes similarly, opening promising avenues for research and application in plant synthetic biology. In conclusion, harnessing insights from yeast synthetic genomics and applying them to plants, with P. patens as a breakthrough, shows great potential for revolutionizing plant synthetic genomics.
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Affiliation(s)
- Hao Ye
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Guangyu Luo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhenwu Zheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaofang Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Jie Cao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Jia Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Junbiao Dai
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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3
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Galli A, Bellè F, Fargnoli A, Caligo MA, Cervelli T. Functional Characterization of the Human BRCA1 ∆11 Splicing Isoforms in Yeast. Int J Mol Sci 2024; 25:7511. [PMID: 39062754 PMCID: PMC11276823 DOI: 10.3390/ijms25147511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
BRCA1, a crucial tumor suppressor gene, has several splicing isoforms, including Δ9-11, Δ11, and Δ11q, which lack exon 11, coding for significant portions of the protein. These isoforms are naturally present in both normal and cancerous cells, exhibiting altered activity compared to the full-length BRCA1. Despite this, the impact on cancer risk of the germline intronic variants promoting the exclusive expression of these Δ11 isoforms remains uncertain. Consequently, they are classified as variants of uncertain significance (VUS), posing challenges for traditional genetic classification methods due to their rarity and complexity. Our research utilizes a yeast-based functional assay, previously validated for assessing missense BRCA1 variants, to compare the activity of the Δ11 splicing isoforms with known pathogenic missense variants. This approach allows us to elucidate the functional implications of these isoforms and determine whether their exclusive expression could contribute to increased cancer risk. By doing so, we aim to provide insights into the pathogenic potential of intronic VUS-generating BRCA1 splicing isoforms and improve the classification of BRCA1 variants.
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Affiliation(s)
- Alvaro Galli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy; (A.G.); (F.B.); (A.F.)
| | - Francesca Bellè
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy; (A.G.); (F.B.); (A.F.)
| | - Arcangelo Fargnoli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy; (A.G.); (F.B.); (A.F.)
| | - Maria Adelaide Caligo
- Molecular Genetics Unit, Department of Oncology, University Hospital of Pisa, 56126 Pisa, Italy;
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy; (A.G.); (F.B.); (A.F.)
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4
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Kim JH, Nagaraja R, Ogurtsov AY, Noskov VN, Liskovykh M, Lee HS, Hori Y, Kobayashi T, Hunter K, Schlessinger D, Kouprina N, Shabalina SA, Larionov V. Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability. NAR Genom Bioinform 2024; 6:lqae070. [PMID: 38881577 PMCID: PMC11177557 DOI: 10.1093/nargab/lqae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/20/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
Ribosomal DNA (rDNA) repeat units are organized into tandem clusters in eukaryotic cells. In mice, these clusters are located on at least eight chromosomes and show extensive variation in the number of repeats between mouse genomes. To analyze intra- and inter-genomic variation of mouse rDNA repeats, we selectively isolated 25 individual rDNA units using Transformation-Associated Recombination (TAR) cloning. Long-read sequencing and subsequent comparative sequence analysis revealed that each full-length unit comprises an intergenic spacer (IGS) and a ∼13.4 kb long transcribed region encoding the three rRNAs, but with substantial variability in rDNA unit size, ranging from ∼35 to ∼46 kb. Within the transcribed regions of rDNA units, we found 209 variants, 70 of which are in external transcribed spacers (ETSs); but the rDNA size differences are driven primarily by IGS size heterogeneity, due to indels containing repetitive elements and some functional signals such as enhancers. Further evolutionary analysis categorized rDNA units into distinct clusters with characteristic IGS lengths; numbers of enhancers; and presence/absence of two common SNPs in promoter regions, one of which is located within promoter (p)RNA and may influence pRNA folding stability. These characteristic features of IGSs also correlated significantly with 5'ETS variant patterns described previously and associated with differential expression of rDNA units. Our results suggest that variant rDNA units are differentially regulated and open a route to investigate the role of rDNA variation on nucleolar formation and possible associations with pathology.
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Affiliation(s)
- Jung-Hyun Kim
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Ramaiah Nagaraja
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Alexey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir N Noskov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Mikhail Liskovykh
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Hee-Sheung Lee
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Yutaro Hori
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Takehiko Kobayashi
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Kent Hunter
- National Cancer Institute, Laboratory of Cancer Biology and Genetics, Bethesda, MD, USA
| | - David Schlessinger
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Natalay Kouprina
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir Larionov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
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5
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Han SW, Won HS. Advancements in the Application of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs). Biomolecules 2024; 14:479. [PMID: 38672495 PMCID: PMC11048544 DOI: 10.3390/biom14040479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a significant potential for novel therapeutic applications because of their bioactive properties, stability, and specificity. RiPPs are synthesized on ribosomes, followed by intricate post-translational modifications (PTMs), crucial for their diverse structures and functions. PTMs, such as cyclization, methylation, and proteolysis, play crucial roles in enhancing RiPP stability and bioactivity. Advances in synthetic biology and bioinformatics have significantly advanced the field, introducing new methods for RiPP production and engineering. These methods encompass strategies for heterologous expression, genetic refactoring, and exploiting the substrate tolerance of tailoring enzymes to create novel RiPP analogs with improved or entirely new functions. Furthermore, the introduction and implementation of cutting-edge screening methods, including mRNA display, surface display, and two-hybrid systems, have expedited the identification of RiPPs with significant pharmaceutical potential. This comprehensive review not only discusses the current advancements in RiPP research but also the promising opportunities that leveraging these bioactive peptides for therapeutic applications presents, illustrating the synergy between traditional biochemistry and contemporary synthetic biology and genetic engineering approaches.
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Affiliation(s)
- Sang-Woo Han
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
- BK21 Project Team, Department of Applied Life Science, Graduate School, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea
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6
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Gambogi CW, Birchak GJ, Mer E, Brown DM, Yankson G, Kixmoeller K, Gavade JN, Espinoza JL, Kashyap P, Dupont CL, Logsdon GA, Heun P, Glass JI, Black BE. Efficient formation of single-copy human artificial chromosomes. Science 2024; 383:1344-1349. [PMID: 38513017 PMCID: PMC11059994 DOI: 10.1126/science.adj3566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/23/2024] [Indexed: 03/23/2024]
Abstract
Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125-base pair DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. We describe an approach that efficiently forms single-copy HACs. It employs a ~750-kilobase construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Gabriel J. Birchak
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Graduate Program in Cell and Molecular Biology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Elie Mer
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - George Yankson
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Janardan N. Gavade
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - Prakriti Kashyap
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - Glennis A. Logsdon
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Patrick Heun
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - Ben E. Black
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
- Graduate Program in Cell and Molecular Biology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
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7
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Liu X, Li K, Yu J, Ma C, Che Q, Zhu T, Li D, Pfeifer BA, Zhang G. Cyclo-diphenylalanine production in Aspergillus nidulans through stepwise metabolic engineering. Metab Eng 2024; 82:147-156. [PMID: 38382797 DOI: 10.1016/j.ymben.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
Cyclo-diphenylalanine (cFF) is a symmetrical aromatic diketopiperazine (DKP) found wide-spread in microbes, plants, and resulting food products. As different bioactivities continue being discovered and relevant food and pharmaceutical applications gradually emerge for cFF, there is a growing need for establishing convenient and efficient methods to access this type of compound. Here, we present a robust cFF production system which entailed stepwise engineering of the filamentous fungal strain Aspergillus nidulans A1145 as a heterologous expression host. We first established a preliminary cFF producing strain by introducing the heterologous nonribosomal peptide synthetase (NRPS) gene penP1 to A. nidulans A1145. Key metabolic pathways involving shikimate and aromatic amino acid biosynthetic support were then engineered through a combination of gene deletions of competitive pathway steps, over-expressing feedback-insensitive enzymes in phenylalanine biosynthesis, and introducing a phosphoketolase-based pathway, which diverted glycolytic flux toward the formation of erythrose 4-phosphate (E4P). Through the stepwise engineering of A. nidulans A1145 outlined above, involving both heterologous pathway addition and native pathway metabolic engineering, we were able to produce cFF with titers reaching 611 mg/L in shake flask culture and 2.5 g/L in bench-scale fed-batch bioreactor culture. Our study establishes a production platform for cFF biosynthesis and successfully demonstrates engineering of phenylalanine derived diketopiperazines in a filamentous fungal host.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Kang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jing Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Chuanteng Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Department for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, 14260, United States.
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Department for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China; Lab of Marine Medicinal Resources Discovery, Marine Biomedical Research Institute of Qingdao, Qingdao, 266075, China.
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8
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Kouprina N, Larionov V. Transformation-associated recombination (TAR) cloning and its applications for gene function; genome architecture and evolution; biotechnology and biomedicine. Oncotarget 2023; 14:1009-1033. [PMID: 38147065 PMCID: PMC10750837 DOI: 10.18632/oncotarget.28546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
Transformation-associated recombination (TAR) cloning represents a unique tool to selectively and efficiently recover a given chromosomal segment up to several hundred kb in length from complex genomes (such as animals and plants) and simple genomes (such as bacteria and viruses). The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. In this review, we summarize multiple applications of the pioneering TAR cloning technique, developed previously for complex genomes, for functional, evolutionary, and structural studies, and extended the modified TAR versions to isolate biosynthetic gene clusters (BGCs) from microbes, which are the major source of pharmacological agents and industrial compounds, and to engineer synthetic viruses with novel properties to design a new generation of vaccines. TAR cloning was adapted as a reliable method for the assembly of synthetic microbe genomes for fundamental research. In this review, we also discuss how the TAR cloning in combination with HAC (human artificial chromosome)- and CRISPR-based technologies may contribute to the future.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
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9
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Guesdon G, Gourgues G, Rideau F, Ipoutcha T, Manso-Silván L, Jules M, Sirand-Pugnet P, Blanchard A, Lartigue C. Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast. ACS Synth Biol 2023; 12:3252-3266. [PMID: 37843014 PMCID: PMC10662353 DOI: 10.1021/acssynbio.3c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Indexed: 10/17/2023]
Abstract
The genetic engineering of genome fragments larger than 100 kbp is challenging and requires both specific methods and cloning hosts. The yeast Saccharomyces cerevisiae is considered as a host of choice for cloning and engineering whole or partial genomes from viruses, bacteria, and algae. Several methods are now available to perform these manipulations, each with its own limitations. In order to extend the range of yeast cloning strategies, a new approach combining two already described methods, Fusion cloning and CReasPy-Cloning, was developed. The CReasPy-Fusion method allows the simultaneous cloning and engineering of megabase-sized genomes in yeast by the fusion of bacterial cells with yeast spheroplasts carrying the CRISPR-Cas9 system. With this new approach, we demonstrate the feasibility of cloning and editing whole genomes from several Mycoplasma species belonging to different phylogenetic groups. We also show that CReasPy-Fusion allows the capture of large genome fragments with high efficacy, resulting in the successful cloning of selected loci in yeast. We finally identify bacterial nuclease encoding genes as barriers for CReasPy-Fusion by showing that their removal from the donor genome improves the cloning efficacy.
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Affiliation(s)
- Gabrielle Guesdon
- 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
| | - Thomas Ipoutcha
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Lucía Manso-Silván
- CIRAD,
UMR ASTRE, F-34398 Montpellier, France
- ASTRE,
Univ. Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Matthieu Jules
- Université
Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, F-78350 Jouy-en-Josas, France
| | - Pascal Sirand-Pugnet
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - 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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10
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Heo KT, Lee B, Hwang GJ, Park B, Jang JP, Hwang BY, Jang JH, Hong YS. A unique dual acyltransferase system shared in the polyketide chain initiation of kidamycinone and rubiflavinone biosynthesis. Front Microbiol 2023; 14:1274358. [PMID: 38029143 PMCID: PMC10646177 DOI: 10.3389/fmicb.2023.1274358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
The pluramycin family of natural products has diverse substituents at the C2 position, which are closely related to their biological activity. Therefore, it is important to understand the biosynthesis of C2 substituents. In this study, we describe the biosynthesis of C2 moieties in Streptomyces sp. W2061, which produces kidamycin and rubiflavinone C-1, containing anthrapyran aglycones. Sequence analysis of the loading module (Kid13) of the PKS responsible for the synthesis of these anthrapyran aglycones is useful for confirming the incorporation of atypical primer units into the corresponding products. Kid13 is a ketosynthase-like decarboxylase (KSQ)-type loading module with unusual dual acyltransferase (AT) domains (AT1-1 and AT1-2). The AT1-2 domain primarily loads ethylmalonyl-CoA and malonyl-CoA for rubiflavinone and kidamycinone and rubiflavinone, respectively; however, the AT1-1 domain contributed to the functioning of the AT1-2 domain to efficiently load ethylmalonyl-CoA for rubiflavinone. We found that the dual AT system was involved in the production of kidamycinone, an aglycone of kidamycin, and rubiflavinone C-1 by other shared biosynthetic genes in Streptomyces sp. W2061. This study broadens our understanding of the incorporation of atypical primer units into polyketide products.
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Affiliation(s)
- Kyung Taek Heo
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Byeongsan Lee
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Gwi Ja Hwang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Beomcheol Park
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Bang Yeon Hwang
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
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11
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Sakuta K, Uchida K, Fukuhara T, Komatsu K, Okada R, Moriyama H. Successful full-length genomic cloning and characterization of site-specific nick structures of Phytophthora endornaviruses 2 and 3 in yeast, Saccharomyces cerevisiae. Front Microbiol 2023; 14:1243068. [PMID: 37771702 PMCID: PMC10523305 DOI: 10.3389/fmicb.2023.1243068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Two endornaviruses, Phytophthora endornavirus 2 (PEV2) and Phytophthora endornavirus 3 (PEV3), have been discovered in pathogens targeting asparagus. In this study, we analyzed the nick structure in the RNA genomes of PEV2 and PEV3 in the host oomycetes. Northern blot hybridization using positive and negative strand-specific RNA probes targeting the 5' and 3' regions of PEV2 and PEV3 RNA genomes revealed approximately 1.0 kilobase (kb) RNA fragments located in the 5' regions of the two genomes. 3' RACE analysis determined that the size of the RNA fragments were 958 nucleotides (nt) for PEV2 and 968 nt for PEV3. We have successfully constructed full-length cDNA clones of the entire RNA genomes of PEV2 and PEV3 using a homologous recombination system in the yeast, Saccharomyces cerevisiae. These full-length cDNA sequences were ligated downstream of a constitutive expression promoter (TDH3) or a galactose-inducing promoter (GAL1) in the shuttle vector to enable the production of the full-length RNA transcripts of PEV2 and PEV3 in yeast cells. Interestingly, a 1.0 kb RNA fragment from the PEV3 positive-strand transcript was also detected with a 5'-region RNA probe, indicating that site-specific cleavage also occurred in yeast cells. Further, when PEV2 or PEV3 mRNA was overexpressed under the GAL1 promoter, yeast cell growth was suppressed. A fusion protein combining EGFP to the N-terminus of the full-length PEV2 ORF or C-terminus of the full-length PEV3 ORF was expressed, and allowed PEV2 and PEV3 ORFs to be successfully visualized in yeast cells. Expression of the fusion protein also revealed presence of heterogeneous bodies in the cells.
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Affiliation(s)
- Kohei Sakuta
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Keiko Uchida
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Toshiyuki Fukuhara
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Ryo Okada
- Horticultural Research Institute, Agricultural Center, Kasama, Ibaraki, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
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12
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Awal RP, Lefevre CT, Schüler D. Functional expression of foreign magnetosome genes in the alphaproteobacterium Magnetospirillum gryphiswaldense. mBio 2023; 14:e0328222. [PMID: 37318230 PMCID: PMC10470508 DOI: 10.1128/mbio.03282-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/03/2023] [Indexed: 06/16/2023] Open
Abstract
Magnetosomes of magnetotactic bacteria (MTB) consist of structurally perfect, nano-sized magnetic crystals enclosed within vesicles of a proteo-lipid membrane. In species of Magnetospirillum, biosynthesis of their cubo-octahedral-shaped magnetosomes was recently demonstrated to be a complex process, governed by about 30 specific genes that are comprised within compact magnetosome gene clusters (MGCs). Similar, yet distinct gene clusters were also identified in diverse MTB that biomineralize magnetosome crystals with different, genetically encoded morphologies. However, since most representatives of these groups are inaccessible by genetic and biochemical approaches, their analysis will require the functional expression of magnetosome genes in foreign hosts. Here, we studied whether conserved essential magnetosome genes from closely and remotely related MTB can be functionally expressed by rescue of their respective mutants in the tractable model Magnetospirillum gryphiswaldense of the Alphaproteobacteria. Upon chromosomal integration, single orthologues from other magnetotactic Alphaproteobacteria restored magnetosome biosynthesis to different degrees, while orthologues from distantly related Magnetococcia and Deltaproteobacteria were found to be expressed but failed to re-induce magnetosome biosynthesis, possibly due to poor interaction with their cognate partners within multiprotein magnetosome organelle of the host. Indeed, co-expression of the known interactors MamB and MamM from the alphaproteobacterium Magnetovibrio blakemorei increased functional complementation. Furthermore, a compact and portable version of the entire MGCs of M. magneticum was assembled by transformation-associated recombination cloning, and it restored the ability to biomineralize magnetite both in deletion mutants of the native donor and M. gryphiswaldense, while co-expression of gene clusters from both M. gryphiswaldense and M. magneticum resulted in overproduction of magnetosomes. IMPORTANCE We provide proof of principle that Magnetospirillum gryphiswaldense is a suitable surrogate host for the functional expression of foreign magnetosome genes and extended the transformation-associated recombination cloning platform for the assembly of entire large magnetosome gene cluster, which could then be transplanted to different magnetotactic bacteria. The reconstruction, transfer, and analysis of gene sets or entire magnetosome clusters will be also promising for engineering the biomineralization of magnetite crystals with different morphologies that would be valuable for biotechnical applications.
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Affiliation(s)
- Ram Prasad Awal
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Christopher T. Lefevre
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
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13
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de Melo GD, Perraud V, Alvarez F, Vieites-Prado A, Kim S, Kergoat L, Coleon A, Trüeb BS, Tichit M, Piazza A, Thierry A, Hardy D, Wolff N, Munier S, Koszul R, Simon-Lorière E, Thiel V, Lecuit M, Lledo PM, Renier N, Larrous F, Bourhy H. Neuroinvasion and anosmia are independent phenomena upon infection with SARS-CoV-2 and its variants. Nat Commun 2023; 14:4485. [PMID: 37495586 PMCID: PMC10372078 DOI: 10.1038/s41467-023-40228-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
Anosmia was identified as a hallmark of COVID-19 early in the pandemic, however, with the emergence of variants of concern, the clinical profile induced by SARS-CoV-2 infection has changed, with anosmia being less frequent. Here, we assessed the clinical, olfactory and neuroinflammatory conditions of golden hamsters infected with the original Wuhan SARS-CoV-2 strain, its isogenic ORF7-deletion mutant and three variants: Gamma, Delta, and Omicron/BA.1. We show that infected animals develop a variant-dependent clinical disease including anosmia, and that the ORF7 of SARS-CoV-2 contributes to the induction of olfactory dysfunction. Conversely, all SARS-CoV-2 variants are neuroinvasive, regardless of the clinical presentation they induce. Taken together, this confirms that neuroinvasion and anosmia are independent phenomena upon SARS-CoV-2 infection. Using newly generated nanoluciferase-expressing SARS-CoV-2, we validate the olfactory pathway as a major entry point into the brain in vivo and demonstrate in vitro that SARS-CoV-2 travels retrogradely and anterogradely along axons in microfluidic neuron-epithelial networks.
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Affiliation(s)
- Guilherme Dias de Melo
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France
| | - Victoire Perraud
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France
| | - Flavio Alvarez
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, F-75015, Paris, France
- Sorbonne Université, Collège Doctoral, F-75005, Paris, France
| | - Alba Vieites-Prado
- Institut du Cerveau et de la Moelle Épinière, Laboratoire de Plasticité Structurale, , Sorbonne Université, INSERM U1127, CNRS UMR7225, 75013, Paris, France
| | - Seonhee Kim
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France
| | - Anthony Coleon
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France
| | - Bettina Salome Trüeb
- Institute of Virology and Immunology (IVI), Bern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Magali Tichit
- Institut Pasteur, Université Paris Cité, Histopathology Platform, F-75015, Paris, France
| | - Aurèle Piazza
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Laboratory, F-75015, Paris, France
| | - Agnès Thierry
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Laboratory, F-75015, Paris, France
| | - David Hardy
- Institut Pasteur, Université Paris Cité, Histopathology Platform, F-75015, Paris, France
| | - Nicolas Wolff
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, F-75015, Paris, France
| | - Sandie Munier
- Institut Pasteur, Université Paris Cité, Molecular Genetics of RNA viruses Unit, F-75015, Paris, France
| | - Romain Koszul
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Laboratory, F-75015, Paris, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, Evolutionary Genomics of RNA Viruses Group, F-75015, Paris, France
| | - Volker Thiel
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Marc Lecuit
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015, Paris, France
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, 75006, Paris, France
| | - Pierre-Marie Lledo
- Institut Pasteur, Université Paris Cité, Perception and Memory Unit, F-75015 Paris, France; CNRS UMR3571, 75015, Paris, France
| | - Nicolas Renier
- Institut du Cerveau et de la Moelle Épinière, Laboratoire de Plasticité Structurale, , Sorbonne Université, INSERM U1127, CNRS UMR7225, 75013, Paris, France
| | - Florence Larrous
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France.
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14
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Gambogi CW, Mer E, Brown DM, Yankson G, Gavade JN, Logsdon GA, Heun P, Glass JI, Black BE. Efficient Formation of Single-copy Human Artificial Chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547284. [PMID: 37546784 PMCID: PMC10402137 DOI: 10.1101/2023.06.30.547284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125 bp DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. Here, we describe an approach that efficiently forms single-copy HACs. It employs a ~750 kb construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Elie Mer
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | | | - George Yankson
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Janardan N. Gavade
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Glennis A. Logsdon
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Patrick Heun
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - Ben E. Black
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
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15
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Wu G, Zhou J, Zheng J, Abdalmegeed D, Tian J, Wang M, Sun S, Sedjoah RCAA, Shao Y, Sun S, Xin Z. Construction of lipopeptide mono-producing Bacillus strains and comparison of their antimicrobial activity. FOOD BIOSCI 2023; 53:102813. [DOI: 10.1016/j.fbio.2023.102813] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
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16
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Zhu MC, Cui YZ, Wang JY, Xu H, Li BZ, Yuan YJ. Cross-species microbial genome transfer: a Review. Front Bioeng Biotechnol 2023; 11:1183354. [PMID: 37214278 PMCID: PMC10194841 DOI: 10.3389/fbioe.2023.1183354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Synthetic biology combines the disciplines of biology, chemistry, information science, and engineering, and has multiple applications in biomedicine, bioenergy, environmental studies, and other fields. Synthetic genomics is an important area of synthetic biology, and mainly includes genome design, synthesis, assembly, and transfer. Genome transfer technology has played an enormous role in the development of synthetic genomics, allowing the transfer of natural or synthetic genomes into cellular environments where the genome can be easily modified. A more comprehensive understanding of genome transfer technology can help to extend its applications to other microorganisms. Here, we summarize the three host platforms for microbial genome transfer, review the recent advances that have been made in genome transfer technology, and discuss the obstacles and prospects for the development of genome transfer.
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17
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Liskovykh M, Petrov NS, Noskov VN, Masumoto H, Earnshaw WC, Schlessinger D, Shabalina SA, Larionov V, Kouprina N. Actively transcribed rDNA and distal junction (DJ) sequence are involved in association of NORs with nucleoli. Cell Mol Life Sci 2023; 80:121. [PMID: 37043028 PMCID: PMC10097779 DOI: 10.1007/s00018-023-04770-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
Although they are organelles without a limiting membrane, nucleoli have an exclusive structure, built upon the rDNA-rich acrocentric short arms of five human chromosomes (nucleolar organizer regions or NORs). This has raised the question: what are the structural features of a chromosome required for its inclusion in a nucleolus? Previous work has suggested that sequences adjacent to the tandemly repeated rDNA repeat units (DJ, distal junction sequence) may be involved, and we have extended such studies by addressing several issues related to the requirements for the association of NORs with nucleoli. We exploited both a set of somatic cell hybrids containing individual human acrocentric chromosomes and a set of Human Artificial Chromosomes (HACs) carrying different parts of a NOR, including an rDNA unit or DJ or PJ (proximal junction) sequence. Association of NORs with nucleoli was increased when constituent rDNA was transcribed and may be also affected by the status of heterochromatin blocks formed next to the rDNA arrays. Furthermore, our data suggest that a relatively small size DJ region, highly conserved in evolution, is also involved, along with the rDNA repeats, in the localization of p-arms of acrocentric chromosomes in nucleoli. Thus, we infer a cooperative action of rDNA sequence-stimulated by its activity-and sequences distal to rDNA contributing to incorporation into nucleoli. Analysis of NOR sequences also identified LncRNA_038958 in the DJ, a candidate transcript with the region of the suggested promoter that is located close to the DJ/rDNA boundary and contains CTCF binding sites. This LncRNA may affect RNA Polymerase I and/or nucleolar activity. Our findings provide the basis for future studies to determine which RNAs and proteins interact critically with NOR sequences to organize the higher-order structure of nucleoli and their function in normal cells and pathological states.
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Affiliation(s)
- Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Nikolai S Petrov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Vladimir N Noskov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, Scotland, UK
| | - David Schlessinger
- National Institute on Aging, Laboratory of Genetics and Genomics, NIH, Baltimore, MD, 21224, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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18
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Mining an O-methyltransferase for de novo biosynthesis of physcion in Aspergillus nidulans. Appl Microbiol Biotechnol 2023; 107:1177-1188. [PMID: 36648527 DOI: 10.1007/s00253-023-12373-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/18/2023]
Abstract
Physcion is one of natural anthraquinones, registered as a novel plant-derived fungicide due to its excellent prevention of plant disease. However, the current production of physcion via plant extraction limits its yield promotion and application. Here, a pair of polyketide synthases (PKS) in emodin biosynthesis were used as probes to mining the potential O-methyltransferase (OMT) responsible for physcion biosynthesis. Further refinement using the phylogenetic analysis of the mined OMTs revealed a distinct OMT (AcOMT) with the ability of transferring a methyl group to C-6 hydroxyl of emodin to form physcion. Through introducing AcOMT, we successfully obtained the de novo production of physcion in Aspergillus nidulans. The physcion biosynthetic pathway was further rationally engineered by expressing the decarboxylase genes from different fungi. Finally, the titer of physcion reached to 64.6 mg/L in shake-flask fermentation through enhancing S-adenosylmethionine supply. Our work provides a native O-methyltransferase for physcion biosynthesis and lays the foundation for further improving the production of physcion via a sustainable route. KEY POINTS: • Genome mining of the native O-methyltransferase responsible for physcion biosynthesis • De novo biosynthesis of physcion in the engineered Aspergillus nidulans • Providing an alternative way to produce plant-derived fungicide physcion.
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19
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Nozaki S. Rapid and Accurate Assembly of Large DNA Assisted by In Vitro Packaging of Bacteriophage. ACS Synth Biol 2022; 11:4113-4122. [PMID: 36446634 PMCID: PMC9764419 DOI: 10.1021/acssynbio.2c00419] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Development of DNA assembly methods made it possible to construct large DNA. However, achieving a large DNA assembly easily, accurately, and at a low cost remains a challenge. This study shows that DNA assembled only by annealing of overlapping single-stranded DNA ends, which are generated by exonuclease treatment, without ligation can be packaged in phage particles and can also be transduced into bacterial cells. Based on this, I developed a simple method to construct long DNA of about 40-50 kb from five to ten PCR fragments using the bacteriophage in vitro packaging system. This method, namely, iPac (in vitro Packaging-assisted DNA assembly), allowed accurate and rapid construction of large plasmids and phage genomes. This simple method will accelerate research in molecular and synthetic biology, including the construction of gene circuits or the engineering of metabolic pathways.
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Affiliation(s)
- Shingo Nozaki
- Department
of Life Science, College of Science, Rikkyo
University, Tokyo 171-8501, Japan,Graduate
School of Advanced Science and Engineering, Hiroshima University, Hiroshima 739-8527, Japan,
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20
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Park HS, Park JH, Kim HJ, Kang SH, Choi SS, Kim ES. BAC cloning and heterologous expression of a giant biosynthetic gene cluster encoding antifungal neotetrafibricin in streptomyces rubrisoli. Front Bioeng Biotechnol 2022; 10:964765. [PMID: 36046673 PMCID: PMC9421130 DOI: 10.3389/fbioe.2022.964765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Polyene natural products including nystatin A1, amphotericin B, ECO-02301, and mediomycin belong to a large family of valuable antifungal polyketide compounds typically produced by soil actinomycetes. A previous study (Park et al., Front. Bioeng. Biotechnol., 2021, 9, 692340) isolated Streptomyces rubrisoli Inha501 with strong antifungal activity and analyzed a large-sized biosynthetic gene cluster (BGC) of a linear polyene compound named Inha-neotetrafibricin (I-NTF) using whole genome sequencing and bioinformatics. In the present study, an entire I-NTF BGC (∼167 kb) was isolated through construction and screening of Streptomyces BAC library. Overexpression of the cloned I-NTF BGC in the wild-type S. rubrisoli Inha501 and its heterologous expression in S. lividans led to 2.6-fold and 2.8-fold increase in I-NTF yields, respectively. The qRT-PCR confirmed that the transcription levels of I-NTF BGC were significantly increased in both homologous and heterologous hosts containing the BAC integration of I-NTF BGC. In addition, the I-NTF aglycone-producing strains were constructed by a target-specific deletion of glycosyltransferase gene present in I-NTF BGC. A comparison of the in vitro biological activities of I-NTF and I-NTF aglycone confirmed that the rhamnose sugar motif of I-NTF plays a critical role in both antifungal and antibacterial activities. These results suggest that the Streptomyces BAC cloning of a large-sized natural product BGC is a valuable approach for natural product titer improvement and biological activity screening of natural product in actinomycetes.
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21
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Ponomartsev SV, Sinenko SA, Tomilin AN. Human Artificial Chromosomes and Their Transfer to Target Cells. Acta Naturae 2022; 14:35-45. [PMID: 36348716 PMCID: PMC9611860 DOI: 10.32607/actanaturae.11670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 07/12/2022] [Indexed: 11/02/2023] Open
Abstract
Human artificial chromosomes (HACs) have been developed as genetic vectors with the capacity to carry large transgenic constructs or entire gene loci. HACs represent either truncated native chromosomes or de novo synthesized genetic constructs. The important features of HACs are their ultra-high capacity and ability to self-maintain as independent genetic elements, without integrating into host chromosomes. In this review, we discuss the development and construction methods, structural and functional features, as well as the areas of application of the main HAC types. Also, we address one of the most technically challenging and time-consuming steps in this technology - the transfer of HACs from donor to recipient cells.
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Affiliation(s)
- S. V. Ponomartsev
- Institute of Cytology Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - S. A. Sinenko
- Institute of Cytology Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - A. N. Tomilin
- Institute of Cytology Russian Academy of Sciences, St. Petersburg, 194064 Russia
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199034 Russia
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22
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Galkin SO, Anisenko AN, Shadrina OA, Gottikh MB. Genetic Engineering Systems to Study Human Viral Pathogens from the Coronaviridae Family. Mol Biol 2022; 56:72-89. [PMID: 35194246 PMCID: PMC8853348 DOI: 10.1134/s0026893322010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 12/02/2022]
Abstract
The COVID-19 pandemic caused by the previously unknown SARS-CoV-2 Betacoronavirus made it extremely important to develop simple and safe cellular systems which allow manipulation of the viral genome and high-throughput screening of its potential inhibitors. In this review, we made an attempt at summarizing the currently existing data on genetic engineering systems used to study not only SARS-CoV-2, but also other viruses from the Coronaviridae family. In addition, the review covers the basic knowledge about the structure and the life cycle of coronaviruses.
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Affiliation(s)
- S. O. Galkin
- Bioengineering and Bioinformatics Department, Moscow State University, 119991 Moscow, Russia
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
| | - A. N. Anisenko
- Bioengineering and Bioinformatics Department, Moscow State University, 119991 Moscow, Russia
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
| | - O. A. Shadrina
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
| | - M. B. Gottikh
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
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23
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Yang L, Tian L, Li L, Liu Q, Guo X, Zhou Y, Pei R, Chen X, Wang Y. Efficient assembly of a large fragment of monkeypox virus genome as a qPCR template using dual-selection based transformation-associated recombination. Virol Sin 2022; 37:341-347. [PMID: 35393265 PMCID: PMC9243609 DOI: 10.1016/j.virs.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/23/2022] [Indexed: 11/05/2022] Open
Abstract
Transformation-associated recombination (TAR) has been widely used to assemble large DNA constructs. One of the significant obstacles hindering assembly efficiency is the presence of error-prone DNA repair pathways in yeast, which results in vector backbone recircularization or illegitimate recombination products. To increase TAR assembly efficiency, we prepared a dual-selective TAR vector, pGFCS, by adding a PADH1-URA3 cassette to a previously described yeast-bacteria shuttle vector, pGF, harboring a PHIS3–HIS3 cassette as a positive selection marker. This new cassette works as a negative selection marker to ensure that yeast harboring a recircularized vector cannot propagate in the presence of 5-fluoroorotic acid. To prevent pGFCS bearing ura3 from recombining with endogenous ura3-52 in the yeast genome, a highly transformable Saccharomyces cerevisiae strain, VL6-48B, was prepared by chromosomal substitution of ura3-52 with a transgene conferring resistance to blasticidin. A 55-kb genomic fragment of monkeypox virus encompassing primary detection targets for quantitative PCR was assembled by TAR using pGFCS in VL6-48B. The pGFCS-mediated TAR assembly showed a zero rate of vector recircularization and an average correct assembly yield of 79% indicating that the dual-selection strategy provides an efficient approach to optimizing TAR assembly. The first TAR assembly system using dual-selection markers. Highly efficient TAR assembly system with a zero rate of vector recircularization. Assembly of an MPXV genomic fragment containing multiple qPCR detection targets.
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24
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Potapova NA, Kondrashov AS, Mirkin SM. Characteristics and possible mechanisms of formation of microinversions distinguishing human and chimpanzee genomes. Sci Rep 2022; 12:591. [PMID: 35022450 PMCID: PMC8755829 DOI: 10.1038/s41598-021-04621-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/28/2021] [Indexed: 12/02/2022] Open
Abstract
Genomic inversions come in various sizes. While long inversions are relatively easy to identify by aligning high-quality genome sequences, unambiguous identification of microinversions is more problematic. Here, using a set of extra stringent criteria to distinguish microinversions from other mutational events, we describe microinversions that occurred after the divergence of humans and chimpanzees. In total, we found 59 definite microinversions that range from 17 to 33 nucleotides in length. In majority of them, human genome sequences matched exactly the reverse-complemented chimpanzee genome sequences, implying that the inverted DNA segment was copied precisely. All these microinversions were flanked by perfect or nearly perfect inverted repeats pointing to their key role in their formation. Template switching at inverted repeats during DNA replication was previously discussed as a possible mechanism for the microinversion formation. However, many of definite microinversions found by us cannot be easily explained via template switching owing to the combination of the short length and imperfect nature of their flanking inverted repeats. We propose a novel, alternative mechanism that involves repair of a double-stranded break within the inverting segment via microhomology-mediated break-induced replication, which can consistently explain all definite microinversion events.
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Affiliation(s)
- Nadezhda A Potapova
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia, 127051.
| | - Alexey S Kondrashov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
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25
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Nielsen MR, Sørensen JL. Investigating Fungal Biosynthetic Pathways Using Heterologous Gene Expression: Fusarium sp. as a Heterologous Host. Methods Mol Biol 2022; 2489:53-74. [PMID: 35524045 DOI: 10.1007/978-1-0716-2273-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Heterologous expression of uncharacterized biosynthetic gene clusters is a popular strategy for exploring the chemical potential of filamentous fungi. Here, we describe the process of PCR-amplifying fungal gene clusters and re-assembling them in a cloning vector via target-associated recombination in Saccharomyces cerevisiae . The gene cluster-carrying construct is validated and used to transform protoplasts of Fusarium graminearum , a well-studied host that is able to express the gene cluster. Chemical analysis of transformants expressing biosynthetic genes can lead to the detection and isolation of novel compounds, such as polyketides.
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Affiliation(s)
- Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Esbjerg, Denmark.
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Esbjerg, Denmark
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26
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Yao Y, Wang W, Shi W, Yan R, Zhang J, Wei G, Liu L, Che Y, An C, Gao SS. Overproduction of medicinal ergot alkaloids based on a fungal platform. Metab Eng 2021; 69:198-208. [PMID: 34902590 DOI: 10.1016/j.ymben.2021.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/17/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022]
Abstract
Privileged ergot alkaloids (EAs) produced by the fungal genus Claviceps are used to treat a wide range of diseases. However, their use and research have been hampered by the challenging genetic engineering of Claviceps. Here we systematically refactored and rationally engineered the EA biosynthetic pathway in heterologous host Aspergillus nidulans by using a Fungal-Yeast-Shuttle-Vector protocol. The obtained strains allowed the production of diverse EAs and related intermediates, including prechanoclavine (PCC, 333.8 mg/L), chanoclavine (CC, 241.0 mg/L), agroclavine (AC, 78.7 mg/L), and festuclavine (FC, 99.2 mg/L), etc. This fungal platform also enabled the access to the methyl-oxidized EAs (MOEAs), including elymoclavine (EC), lysergic acid (LA), dihydroelysergol (DHLG), and dihydrolysergic acid (DHLA), by overexpressing a P450 enzyme CloA. Furthermore, by optimizing the P450 electron transfer (ET) pathway and using multi-copy of cloA, the titers of EC and DHLG have been improved by 17.3- and 9.4-fold, respectively. Beyond our demonstration of A. nidulans as a robust platform for EA overproduction, our study offers a proof of concept for engineering the eukaryotic P450s-contained biosynthetic pathways in a filamentous fungal host.
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Affiliation(s)
- Yongpeng Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Wei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Rui Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Jun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Guangzheng Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ling Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Yongsheng Che
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, PR China
| | - Chunyan An
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.
| | - Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.
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27
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Ricardo-Lax I, Luna JM, Thao TTN, Le Pen J, Yu Y, Hoffmann HH, Schneider WM, Razooky BS, Fernandez-Martinez J, Schmidt F, Weisblum Y, Trüeb BS, Berenguer Veiga I, Schmied K, Ebert N, Michailidis E, Peace A, Sánchez-Rivera FJ, Lowe SW, Rout MP, Hatziioannou T, Bieniasz PD, Poirier JT, MacDonald MR, Thiel V, Rice CM. Replication and single-cycle delivery of SARS-CoV-2 replicons. Science 2021; 374:1099-1106. [PMID: 34648371 PMCID: PMC9007107 DOI: 10.1126/science.abj8430] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/06/2021] [Indexed: 01/16/2023]
Abstract
Molecular virology tools are critical for basic studies of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and for developing new therapeutics. Experimental systems that do not rely on viruses capable of spread are needed for potential use in lower-containment settings. In this work, we use a yeast-based reverse genetics system to develop spike-deleted SARS-CoV-2 self-replicating RNAs. These noninfectious self-replicating RNAs, or replicons, can be trans-complemented with viral glycoproteins to generate replicon delivery particles for single-cycle delivery into a range of cell types. This SARS-CoV-2 replicon system represents a convenient and versatile platform for antiviral drug screening, neutralization assays, host factor validation, and viral variant characterization.
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Affiliation(s)
- Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Joseph M. Luna
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Tran Thi Nhu Thao
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Yingpu Yu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - H.-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - William M. Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Brandon S. Razooky
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | | | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Bettina Salome Trüeb
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Inês Berenguer Veiga
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Kimberly Schmied
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Avery Peace
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | | | - Scott W. Lowe
- Cancer Biology and Genetics, MSKCC, New York, NY 10065, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - John T. Poirier
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Margaret R. MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
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28
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Kouprina N, Kim J, Larionov V. Highly Selective, CRISPR/Cas9-Mediated Isolation of Genes and Genomic Loci from Complex Genomes by TAR Cloning in Yeast. Curr Protoc 2021; 1:e207. [PMID: 34370406 PMCID: PMC8363120 DOI: 10.1002/cpz1.207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Here we describe an updated TAR cloning protocol for the selective and efficient isolation of any genomic fragment or gene of interest up to 280 kb in size from genomic DNA. The method exploits the special recombination machinery of the yeast Saccharomyces cerevisiae. TAR cloning is based on the high level of in vivo recombination that occurs between a specific genomic DNA fragment of interest and targeting sequences (hooks) in a TAR vector that are homologous to the 5' and 3' ends of the targeted region. Upon co-transformation into yeast, this results in the isolation of the chromosomal region of interest as a circular YAC molecule, which then propagates and segregates in yeast cells and can be selected for. In the updated TAR cloning protocol described here, the fraction of region-positive clones typically obtained is increased from 1% up to 35% by pre-treatment of the genomic DNA with specifically designed CRISPR/Cas9 endonucleases that create double-strand breaks (DSBs) bracketing the target genomic DNA sequence, thereby making the ends of the chromosomal region of interest highly recombinogenic. In addition, a new TAR vector was constructed that contains YAC and BAC cassettes, permitting direct transfer of a TAR-cloned DNA from yeast to bacterial cells. Once the TAR vector with the hooks is constructed and genomic DNA is prepared, the entire procedure takes 3 weeks to complete. The updated TAR protocol does not require significant yeast experience or extensively time-consuming yeast work because screening only about a dozen yeast transformants is typically enough to find a clone with the region of interest. TAR cloning of chromosomal fragments, individual genes, or gene families can be used for functional, structural, and population studies, for comparative genomics, and for long-range haplotyping, and has potential for gene therapy. Published 2021. This article is a U.S. Government work and is in the public domain in the USA. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of CRISPR/Cas9-treated genomic DNA for TAR cloning Basic Protocol 2: Isolation of a gene or genomic locus by TAR cloning Basic Protocol 3: Transfer of TAR/YAC/BAC isolates from yeast to E. coli.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer InstituteNIHBethesdaMaryland
| | - Jung‐Hyun Kim
- Developmental Therapeutics Branch, National Cancer InstituteNIHBethesdaMaryland
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer InstituteNIHBethesdaMaryland
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29
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Dhakal D, Chen M, Luesch H, Ding Y. Heterologous production of cyanobacterial compounds. J Ind Microbiol Biotechnol 2021; 48:6119914. [PMID: 33928376 PMCID: PMC8210676 DOI: 10.1093/jimb/kuab003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
Abstract
Cyanobacteria produce a plethora of compounds with unique chemical structures and diverse biological activities. Importantly, the increasing availability of cyanobacterial genome sequences and the rapid development of bioinformatics tools have unraveled the tremendous potential of cyanobacteria in producing new natural products. However, the discovery of these compounds based on cyanobacterial genomes has progressed slowly as the majority of their corresponding biosynthetic gene clusters (BGCs) are silent. In addition, cyanobacterial strains are often slow-growing, difficult for genetic engineering, or cannot be cultivated yet, limiting the use of host genetic engineering approaches for discovery. On the other hand, genetically tractable hosts such as Escherichia coli, Actinobacteria, and yeast have been developed for the heterologous expression of cyanobacterial BGCs. More recently, there have been increased interests in developing model cyanobacterial strains as heterologous production platforms. Herein, we present recent advances in the heterologous production of cyanobacterial compounds in both cyanobacterial and noncyanobacterial hosts. Emerging strategies for BGC assembly, host engineering, and optimization of BGC expression are included for fostering the broader applications of synthetic biology tools in the discovery of new cyanobacterial natural products.
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Affiliation(s)
- Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
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30
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Wang W, Zheng G, Lu Y. Recent Advances in Strategies for the Cloning of Natural Product Biosynthetic Gene Clusters. Front Bioeng Biotechnol 2021; 9:692797. [PMID: 34327194 PMCID: PMC8314000 DOI: 10.3389/fbioe.2021.692797] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial natural products (NPs) are a major source of pharmacological agents. Most NPs are synthesized from specific biosynthetic gene clusters (BGCs). With the rapid increase of sequenced microbial genomes, large numbers of NP BGCs have been discovered, regarded as a treasure trove of novel bioactive compounds. However, many NP BGCs are silent in native hosts under laboratory conditions. In order to explore their therapeutic potential, a main route is to activate these silent NP BGCs in heterologous hosts. To this end, the first step is to accurately and efficiently capture these BGCs. In the past decades, a large number of effective technologies for cloning NP BGCs have been established, which has greatly promoted drug discovery research. Herein, we describe recent advances in strategies for BGC cloning, with a focus on the preparation of high-molecular-weight DNA fragment, selection and optimization of vectors used for carrying large-size DNA, and methods for assembling targeted DNA fragment and appropriate vector. The future direction into novel, universal, and high-efficiency methods for cloning NP BGCs is also prospected.
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Affiliation(s)
- Wenfang Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guosong Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, China.,Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
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31
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The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes. Essays Biochem 2021; 65:261-275. [PMID: 33956071 DOI: 10.1042/ebc20200132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023]
Abstract
Streptomycetes are producers of a wide range of specialized metabolites of great medicinal and industrial importance, such as antibiotics, antifungals, or pesticides. Having been the drivers of the golden age of antibiotics in the 1950s and 1960s, technological advancements over the last two decades have revealed that very little of their biosynthetic potential has been exploited so far. Given the great need for new antibiotics due to the emerging antimicrobial resistance crisis, as well as the urgent need for sustainable biobased production of complex molecules, there is a great renewed interest in exploring and engineering the biosynthetic potential of streptomycetes. Here, we describe the Design-Build-Test-Learn (DBTL) cycle for metabolic engineering experiments in streptomycetes and how it can be used for the discovery and production of novel specialized metabolites.
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32
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Alam K, Hao J, Zhang Y, Li A. Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways. Biotechnol Adv 2021; 49:107759. [PMID: 33930523 DOI: 10.1016/j.biotechadv.2021.107759] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Microbial-derived natural products (NPs) and their derivative products are of great importance and used widely in many fields, especially in pharmaceutical industries. However, there is an immediate need to establish innovative approaches, strategies, and techniques to discover new NPs with novel or enhanced biological properties, due to the less productivity and higher cost on traditional drug discovery pipelines from natural bioresources. Revealing of untapped microbial cryptic biosynthetic gene clusters (BGCs) using DNA sequencing technology and bioinformatics tools makes genome mining possible for NP discovery from microorganisms. Meanwhile, new approaches and strategies in the area of synthetic biology offer great potentials for generation of new NPs by engineering or creating synthetic systems with improved and desired functions. Development of approaches, strategies and tools in synthetic biology can facilitate not only exploration and enhancement in supply, and also in the structural diversification of NPs. Here, we discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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33
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Grazioli S, Petris G. Synthetic genomics for curing genetic diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:477-520. [PMID: 34175051 DOI: 10.1016/bs.pmbts.2021.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
From the beginning of the genome sequencing era, it has become increasingly evident that genetics plays a role in all diseases, of which only a minority are single-gene disorders, the most common target of current gene therapies. However, the majority of people have some kind of health problems resulting from congenital genetic mutations (over 6000 diseases have been associated to genes, https://www.omim.org/statistics/geneMap) and most genetic disorders are rare and only incompletely understood. The vision and techniques applied to the synthesis of genomes may help to address unmet medical needs from a chromosome and genome-scale perspective. In this chapter, we address the potential therapy of genetic diseases from a different outlook, in which we no longer focus on small gene corrections but on higher-order tools for genome manipulation. These will play a crucial role in the next years, as they prelude to a much deeper understanding of the architecture of the human genome and a more accurate modeling of human diseases, offering new therapeutic opportunities.
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Affiliation(s)
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology (MRC LMB), Cambridge, United Kingdom.
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34
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Rescue of Infectious Sindbis Virus by Yeast Spheroplast-Mammalian Cell Fusion. Viruses 2021; 13:v13040603. [PMID: 33916100 PMCID: PMC8066160 DOI: 10.3390/v13040603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022] Open
Abstract
Sindbis virus (SINV), a positive-sense single stranded RNA virus that causes mild symptoms in humans, is transmitted by mosquito bites. SINV reverse genetics have many implications, not only in understanding alphavirus transmission, replication cycle, and virus-host interactions, but also in biotechnology and biomedical applications. The rescue of SINV infectious particles is usually achieved by transfecting susceptible cells (BHK-21) with SINV-infectious mRNA genomes generated from cDNA constructed via in vitro translation (IVT). That procedure is time consuming, costly, and relies heavily on reagent quality. Here, we constructed a novel infectious SINV cDNA construct that expresses its genomic RNA in yeast cells controlled by galactose induction. Using spheroplasts made from this yeast, we established a robust polyethylene glycol-mediated yeast: BHK-21 fusion protocol to rescue infectious SINV particles. Our approach is timesaving and utilizes common lab reagents for SINV rescue. It could be a useful tool for the rescue of large single strand RNA viruses, such as SARS-CoV-2.
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35
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Oberortner E, Evans R, Meng X, Nath S, Plahar H, Simirenko L, Tarver A, Deutsch S, Hillson NJ, Cheng JF. An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology. Methods Mol Biol 2021; 2205:3-18. [PMID: 32809190 DOI: 10.1007/978-1-0716-0908-8_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Biological computer-aided design and manufacturing (bioCAD/CAM) tools facilitate the design and build processes of engineering biological systems using iterative design-build-test-learn (DBTL) cycles. In this book chapter, we highlight some of the bioCAD/CAM tools developed and used at the US Department of Energy (DOE) Joint Genome Institute (JGI), Joint BioEnergy Institute (JBEI), and Agile BioFoundry (ABF). We demonstrate the use of these bioCAD/CAM tools on a common workflow for designing and building a multigene pathway in a hierarchical fashion. Each tool presented in this book chapter is specifically tailored to support one or more specific steps in a workflow, can be integrated with the others into design and build workflows, and can be deployed at academic, government, or commercial entities.
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Affiliation(s)
- Ernst Oberortner
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA. .,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Robert Evans
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xianwei Meng
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sangeeta Nath
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hector Plahar
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Technology Division, DOE Joint BioEnergy Institute (JBEI), Emeryville, CA, USA
| | - Lisa Simirenko
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Angela Tarver
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Samuel Deutsch
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nathan J Hillson
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Technology Division, DOE Joint BioEnergy Institute (JBEI), Emeryville, CA, USA.,DOE Agile BioFoundry, Emeryville, CA, USA.,TeselaGen Biotechnology, Inc., San Francisco, CA, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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36
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Groß S, Schnell B, Haack PA, Auerbach D, Müller R. In vivo and in vitro reconstitution of unique key steps in cystobactamid antibiotic biosynthesis. Nat Commun 2021; 12:1696. [PMID: 33727542 PMCID: PMC7966384 DOI: 10.1038/s41467-021-21848-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/13/2021] [Indexed: 01/31/2023] Open
Abstract
Cystobactamids are myxobacteria-derived topoisomerase inhibitors with potent anti-Gram-negative activity. They are formed by a non-ribosomal peptide synthetase (NRPS) and consist of tailored para-aminobenzoic acids, connected by a unique α-methoxy-L-isoasparagine or a β-methoxy-L-asparagine linker moiety. We describe the heterologous expression of the cystobactamid biosynthetic gene cluster (BGC) in Myxococcus xanthus. Targeted gene deletions produce several unnatural cystobactamids. Using in vitro experiments, we reconstitute the key biosynthetic steps of linker formation and shuttling via CysB to the NRPS. The biosynthetic logic involves a previously uncharacterized bifunctional domain found in the stand-alone NRPS module CysH, albicidin biosynthesis and numerous BGCs of unknown natural products. This domain performs either an aminomutase (AM) or an amide dehydratase (DH) type of reaction, depending on the activity of CysJ which hydroxylates CysH-bound L-asparagine. Furthermore, CysQ O-methylates hydroxyl-L-(iso)asparagine only in the presence of the AMDH domain. Taken together, these findings provide direct evidence for unique steps in cystobactamid biosynthesis.
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Affiliation(s)
- Sebastian Groß
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Bastien Schnell
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Patrick A. Haack
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - David Auerbach
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
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37
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Belda I, Williams TC, de Celis M, Paulsen IT, Pretorius IS. Seeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell. Nat Commun 2021; 12:1599. [PMID: 33707418 PMCID: PMC7952416 DOI: 10.1038/s41467-021-21877-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Synthetic metagenomics could potentially unravel the complexities of microbial ecosystems by revealing the simplicity of microbial communities captured in a single cell. Conceptionally, a yeast cell carrying a representative synthetic metagenome could uncover the complexity of multi-species interactions, illustrated here with wine ferments.
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Affiliation(s)
- Ignacio Belda
- grid.4795.f0000 0001 2157 7667Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Thomas C. Williams
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Miguel de Celis
- grid.4795.f0000 0001 2157 7667Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Ian T. Paulsen
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Isak S. Pretorius
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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38
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Liu Z, Zhao Y, Huang C, Luo Y. Recent Advances in Silent Gene Cluster Activation in Streptomyces. Front Bioeng Biotechnol 2021; 9:632230. [PMID: 33681170 PMCID: PMC7930741 DOI: 10.3389/fbioe.2021.632230] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Natural products (NPs) are critical sources of drug molecules for decades. About two-thirds of natural antibiotics are produced by Streptomyces. Streptomyces have a large number of secondary metabolite biosynthetic gene clusters (SM-BGCs) that may encode NPs. However, most of these BGCs are silent under standard laboratory conditions. Hence, activation of these silent BGCs is essential to current natural products discovery research. In this review, we described the commonly used strategies for silent BGC activation in Streptomyces from two aspects. One focused on the strategies applied in heterologous host, including methods to clone and reconstruct BGCs along with advances in chassis engineering; the other focused on methods applied in native host which includes engineering of promoters, regulatory factors, and ribosomes. With the metabolic network being elucidated more comprehensively and methods optimized more high-thoroughly, the discovery of NPs will be greatly accelerated.
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Affiliation(s)
- Zhenyu Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yatong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Chaoqun Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yunzi Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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39
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The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning. Sci Rep 2021; 11:2997. [PMID: 33542373 PMCID: PMC7862453 DOI: 10.1038/s41598-021-82565-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
The rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.
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40
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Sinenko SA, Ponomartsev SV, Tomilin AN. Pluripotent stem cell-based gene therapy approach: human de novo synthesized chromosomes. Cell Mol Life Sci 2021; 78:1207-1220. [PMID: 33011821 PMCID: PMC11072874 DOI: 10.1007/s00018-020-03653-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023]
Abstract
A novel approach in gene therapy was introduced 20 years ago since artificial non-integrative chromosome-based vectors containing gene loci size inserts were engineered. To date, different human artificial chromosomes (HAC) were generated with the use of de novo construction or "top-down" engineering approaches. The HAC-based therapeutic approach includes ex vivo gene transferring and correction of pluripotent stem cells (PSCs) or highly proliferative modified stem cells. The current progress in the technology of induced PSCs, integrating with the HAC technology, resulted in a novel platform of stem cell-based tissue replacement therapy for the treatment of genetic disease. Nowadays, the sophisticated and laborious HAC technology has significantly improved and is now closer to clinical studies. In here, we reviewed the achievements in the technology of de novo synthesized HACs for a chromosome transfer for developing gene therapy tissue replacement models of monogenic human diseases.
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Affiliation(s)
- Sergey A Sinenko
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave, St-Petersburg, 194064, Russia.
| | - Sergey V Ponomartsev
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave, St-Petersburg, 194064, Russia
| | - Alexey N Tomilin
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave, St-Petersburg, 194064, Russia.
- Institute of Translational Biomedicine, St-Petersburg State University, 7-9, Universitetskaya Emb, St-Petersburg, 199034, Russia.
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41
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Goldberg GW, Spencer JM, Giganti DO, Camellato BR, Agmon N, Ichikawa DM, Boeke JD, Noyes MB. Engineered dual selection for directed evolution of SpCas9 PAM specificity. Nat Commun 2021; 12:349. [PMID: 33441553 PMCID: PMC7807044 DOI: 10.1038/s41467-020-20650-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
The widely used Streptococcus pyogenes Cas9 (SpCas9) nuclease derives its DNA targeting specificity from protein-DNA contacts with protospacer adjacent motif (PAM) sequences, in addition to base-pairing interactions between its guide RNA and target DNA. Previous reports have established that the PAM specificity of SpCas9 can be altered via positive selection procedures for directed evolution or other protein engineering strategies. Here we exploit in vivo directed evolution systems that incorporate simultaneous positive and negative selection to evolve SpCas9 variants with commensurate or improved activity on NAG PAMs relative to wild type and reduced activity on NGG PAMs, particularly YGG PAMs. We also show that the PAM preferences of available evolutionary intermediates effectively determine whether similar counterselection PAMs elicit different selection stringencies, and demonstrate that negative selection can be specifically increased in a yeast selection system through the fusion of compensatory zinc fingers to SpCas9.
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Affiliation(s)
- Gregory W Goldberg
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA.
| | - Jeffrey M Spencer
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - David O Giganti
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - Brendan R Camellato
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - Neta Agmon
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
- Neochromosome, Inc., Alexandria Center for Life Science, New York, NY, 10016, USA
| | - David M Ichikawa
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
| | - Marcus B Noyes
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA.
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42
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Kang HS, Kim ES. Recent advances in heterologous expression of natural product biosynthetic gene clusters in Streptomyces hosts. Curr Opin Biotechnol 2021; 69:118-127. [PMID: 33445072 DOI: 10.1016/j.copbio.2020.12.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 01/09/2023]
Abstract
The heterologous expression of natural product biosynthetic gene clusters (BGCs) has traditionally been used as a genetic platform to link various natural product chemotypes to their corresponding genotypes. In recent years, heterologous expression has played an increasing role in natural products research with the advances in sequencing technologies and bioinformatics tools that allow for the rapid and systematic identification of known and cryptic BGCs from a large number of microbial genome sequences. The advances in synthetic biology have also facilitated the process of heterologous expression by providing tools for rapid cloning and engineering of BGCs to improve production yield or to activate silent BGCs. This paper summarizes the recent progress in the cloning and engineering of natural product BGCs and highlights recent examples of the heterologous expression of both known and cryptic BGCs in Streptomyces hosts, which will continue to play a pivotal role in genomics-driven natural product research.
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Affiliation(s)
- Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea.
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43
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Lü J, Long Q, Zhao Z, Chen L, He W, Hong J, Liu K, Wang Y, Pang X, Deng Z, Tao M. Engineering the Erythromycin-Producing Strain Saccharopolyspora erythraea HOE107 for the Heterologous Production of Polyketide Antibiotics. Front Microbiol 2020; 11:593217. [PMID: 33363524 PMCID: PMC7752772 DOI: 10.3389/fmicb.2020.593217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/10/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteria of the genus Saccharopolyspora produce important polyketide antibiotics, including erythromycin A (Sac. erythraea) and spinosad (Sac. spinosa). We herein report the development of an industrial erythromycin-producing strain, Sac. erythraea HOE107, into a host for the heterologous expression of polyketide biosynthetic gene clusters (BGCs) from other Saccharopolyspora species and related actinomycetes. To facilitate the integration of natural product BGCs and auxiliary genes beneficial for the production of natural products, the erythromycin polyketide synthase (ery) genes were replaced with two bacterial attB genomic integration sites associated with bacteriophages ϕC31 and ϕBT1. We also established a highly efficient conjugation protocol for the introduction of large bacterial artificial chromosome (BAC) clones into Sac. erythraea strains. Based on this optimized protocol, an arrayed BAC library was effectively transferred into Sac. erythraea. The large spinosad gene cluster from Sac. spinosa and the actinorhodin gene cluster from Streptomyces coelicolor were successfully expressed in the ery deletion mutant. Deletion of the endogenous giant polyketide synthase genes pkeA1-pkeA4, the product of which is not known, and the flaviolin gene cluster (rpp) from the bacterium increased the heterologous production of spinosad and actinorhodin. Furthermore, integration of pJTU6728 carrying additional beneficial genes dramatically improved the yield of actinorhodin in the engineered Sac. erythraea strains. Our study demonstrated that the engineered Sac. erythraea strains SLQ185, LJ161, and LJ162 are good hosts for the expression of heterologous antibiotics and should aid in expression-based genome-mining approaches for the discovery of new and cryptic antibiotics from Streptomyces and rare actinomycetes.
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Affiliation(s)
- Jin Lü
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingshan Long
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhilong Zhao
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Lu Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weijun He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiali Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yemin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuhua Pang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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44
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Gao S, Xu X, Zeng W, Xu S, Lyv Y, Feng Y, Kai G, Zhou J, Chen J. Efficient Biosynthesis of (2 S)-Eriodictyol from (2 S)-Naringenin in Saccharomyces cerevisiae through a Combination of Promoter Adjustment and Directed Evolution. ACS Synth Biol 2020; 9:3288-3297. [PMID: 33226782 DOI: 10.1021/acssynbio.0c00346] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The compound (2S)-eriodictyol is an important flavonoid that can be derived from (2S)-naringenin through flavonoid 3'-hydroxylase (F3'H) catalyzation. F3'H is a cytochrome P450 enzyme that requires a cytochrome P450 reductase (CPR) to function. However, P450s have limited applications in industrial scale biosynthesis, owing to their low activity. Here, an efficient SmF3'H and a matched SmCPR were identified from Silybum marianum. To improve the efficiency of SmF3'H, we established a high-throughput detection method for (2S)-eriodictyol, in which the promoter combination of SmF3'H and SmCPR were optimized in Saccharomyces cerevisiae. The results revealed that SmF3'H/SmCPR should be expressed by using promoters with similar and strong expression levels. Furthermore, directed evolution was applied to further improve the efficiency of SmF3'H/SmCPR. With the optimized promoter and mutated combinations SmF3'HD285N/SmCPRI453V, the (2S)-eriodictyol titer was improved to 3.3 g/L, the highest titer in currently available reports. These results indicated that S. cerevisiae is an ideal platform for functional expression of flavonoid related P450 enzymes.
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Affiliation(s)
- Song Gao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xiaoyu Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yunbin Lyv
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yue Feng
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Guoyin Kai
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
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45
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Young R, Haines M, Storch M, Freemont PS. Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly. Metab Eng 2020; 63:81-101. [PMID: 33301873 DOI: 10.1016/j.ymben.2020.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.
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Affiliation(s)
- Rosanna Young
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Matthew Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK
| | - Paul S Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK; UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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46
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Coradini ALV, Hull CB, Ehrenreich IM. Building genomes to understand biology. Nat Commun 2020; 11:6177. [PMID: 33268788 PMCID: PMC7710724 DOI: 10.1038/s41467-020-19753-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic manipulation is one of the central strategies that biologists use to investigate the molecular underpinnings of life and its diversity. Thus, advances in genetic manipulation usually lead to a deeper understanding of biological systems. During the last decade, the construction of chromosomes, known as synthetic genomics, has emerged as a novel approach to genetic manipulation. By facilitating complex modifications to chromosome content and structure, synthetic genomics opens new opportunities for studying biology through genetic manipulation. Here, we discuss different classes of genetic manipulation that are enabled by synthetic genomics, as well as biological problems they each can help solve.
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Affiliation(s)
- Alessandro L V Coradini
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Cara B Hull
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
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Vashee S, Arfi Y, Lartigue C. Budding yeast as a factory to engineer partial and complete microbial genomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2020; 24:1-8. [PMID: 33015421 PMCID: PMC7523139 DOI: 10.1016/j.coisb.2020.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Yeast cells have long been used as hosts to propagate exogenous DNA. Recent progress in genome editing opens new avenues in synthetic biology. These developments allow the efficient engineering of microbial genomes in Saccharomyces cerevisiae that can then be rescued to yield modified bacteria/viruses. Recent examples show that the ability to quickly synthesize, assemble, and/or modify viral and bacterial genomes may be a critical factor to respond to emerging pathogens. However, this process has some limitations. DNA molecules much larger than two megabase pairs are complex to clone, bacterial genomes have proven to be difficult to rescue, and the dual-use potential of these technologies must be carefully considered. Regardless, the use of yeast as a factory has enormous appeal for biological applications.
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Affiliation(s)
| | - Yonathan Arfi
- 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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48
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Malcı K, Walls LE, Rios-Solis L. Multiplex Genome Engineering Methods for Yeast Cell Factory Development. Front Bioeng Biotechnol 2020; 8:589468. [PMID: 33195154 PMCID: PMC7658401 DOI: 10.3389/fbioe.2020.589468] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
As biotechnological applications of synthetic biology tools including multiplex genome engineering are expanding rapidly, the construction of strategically designed yeast cell factories becomes increasingly possible. This is largely due to recent advancements in genome editing methods like CRISPR/Cas tech and high-throughput omics tools. The model organism, baker's yeast (Saccharomyces cerevisiae) is an important synthetic biology chassis for high-value metabolite production. Multiplex genome engineering approaches can expedite the construction and fine tuning of effective heterologous pathways in yeast cell factories. Numerous multiplex genome editing techniques have emerged to capitalize on this recently. This review focuses on recent advancements in such tools, such as delta integration and rDNA cluster integration coupled with CRISPR-Cas tools to greatly enhance multi-integration efficiency. Examples of pre-placed gate systems which are an innovative alternative approach for multi-copy gene integration were also reviewed. In addition to multiple integration studies, multiplexing of alternative genome editing methods are also discussed. Finally, multiplex genome editing studies involving non-conventional yeasts and the importance of automation for efficient cell factory design and construction are considered. Coupling the CRISPR/Cas system with traditional yeast multiplex genome integration or donor DNA delivery methods expedites strain development through increased efficiency and accuracy. Novel approaches such as pre-placing synthetic sequences in the genome along with improved bioinformatics tools and automation technologies have the potential to further streamline the strain development process. In addition, the techniques discussed to engineer S. cerevisiae, can be adapted for use in other industrially important yeast species for cell factory development.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
| | - Laura E Walls
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
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49
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Blaby IK, Cheng JF. Building a custom high-throughput platform at the Joint Genome Institute for DNA construct design and assembly-present and future challenges. Synth Biol (Oxf) 2020; 5:ysaa023. [PMID: 34746437 PMCID: PMC7737003 DOI: 10.1093/synbio/ysaa023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 11/11/2023] Open
Abstract
The rapid design and assembly of synthetic DNA constructs have become a crucial component of biological engineering projects via iterative design-build-test-learn cycles. In this perspective, we provide an overview of the workflows used to generate the thousands of constructs and libraries produced each year at the U.S. Department of Energy Joint Genome Institute. Particular attention is paid to describing pipelines, tools used, types of scientific projects enabled by the platform and challenges faced in further scaling output.
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Affiliation(s)
- Ian K Blaby
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jan-Fang Cheng
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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50
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Naseri G, Mueller-Roeber B. A Step-by-Step Protocol for COMPASS, a Synthetic Biology Tool for Combinatorial Gene Assembly. Methods Mol Biol 2020; 2205:277-303. [PMID: 32809205 DOI: 10.1007/978-1-0716-0908-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
For industry-scale production of high-value chemicals in microbial cell factories, the elimination of metabolic flux imbalances is a critical aspect. However, a priori knowledge about the genetic design of optimal production pathways is typically not available. COMPASS, COMbinatorial Pathway ASSembly, is a rapid cloning method for the balanced expression of multiple genes in biochemical pathways. The method generates thousands of individual DNA constructs in modular, parallel, and high-throughput manner. COMPASS employs inducible artificial transcription factors derived from plant (Arabidopsis thaliana) regulators to control the expression of pathway genes in yeast (Saccharomyces cerevisiae). It utilizes homologous recombination for parts assembly and employs a positive selection scheme to identify correctly assembled pathway variants after both in vivo and in vitro recombination. Finally, COMPASS is equipped with a CRISPR/Cas9 genome modification system allowing for the one-step multilocus integration of genes. Although COMPASS was initially developed for pathway engineering, it can equally be employed for balancing gene expression in other synthetic biology projects.
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Affiliation(s)
- Gita Naseri
- Department of Molecular Biology, University of Potsdam, Potsdam, Germany
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, University of Potsdam, Potsdam, Germany. .,Plant Signalling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany. .,Department of Plant Development, Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
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