1
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Kim K, Choe D, Cho S, Palsson B, Cho BK. Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology. Trends Biotechnol 2024; 42:1048-1063. [PMID: 38423803 DOI: 10.1016/j.tibtech.2024.02.008] [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: 12/14/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
Advances in systems and synthetic biology have propelled the construction of reduced bacterial genomes. Genome reduction was initially focused on exploring properties of minimal genomes, but more recently it has been deployed as an engineering strategy to enhance strain performance. This review provides the latest updates on reduced genomes, focusing on dual-track approaches of top-down reduction and bottom-up synthesis for their construction. Using cases from studies that are based on established industrial workhorse strains, we discuss the construction of a series of synthetic phenotypes that are candidates for biotechnological applications. Finally, we address the possible uses of reduced genomes for biotechnological applications and the needed future research directions that may ultimately lead to the total synthesis of rationally designed genomes.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghui Choe
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Suhyung Cho
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kongens, Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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2
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Nyerges A, Chiappino-Pepe A, Budnik B, Baas-Thomas M, Flynn R, Yan S, Ostrov N, Liu M, Wang M, Zheng Q, Hu F, Chen K, Rudolph A, Chen D, Ahn J, Spencer O, Ayalavarapu V, Tarver A, Harmon-Smith M, Hamilton M, Blaby I, Yoshikuni Y, Hajian B, Jin A, Kintses B, Szamel M, Seregi V, Shen Y, Li Z, Church GM. Synthetic genomes unveil the effects of synonymous recoding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.16.599206. [PMID: 38915524 PMCID: PMC11195188 DOI: 10.1101/2024.06.16.599206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Engineering the genetic code of an organism provides the basis for (i) making any organism safely resistant to natural viruses and (ii) preventing genetic information flow into and out of genetically modified organisms while (iii) allowing the biosynthesis of genetically encoded unnatural polymers1-4. Achieving these three goals requires the reassignment of multiple of the 64 codons nature uses to encode proteins. However, synonymous codon replacement-recoding-is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using whole-genome synthesis, multiplexed directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple recoded genomes. Using this information, we assemble a synthetic Escherichia coli genome in seven sections using only 57 codons to encode proteins. By discovering the rules responsible for the lethality of synonymous recoding and developing a data-driven multi-omics-based genome construction workflow that troubleshoots synthetic genomes, we overcome the lethal effects of 62,007 synonymous codon swaps and 11,108 additional genomic edits. We show that synonymous recoding induces transcriptional noise including new antisense RNAs, leading to drastic transcriptome and proteome perturbation. As the elimination of select codons from an organism's genetic code results in the widespread appearance of cryptic promoters, we show that synonymous codon choice may naturally evolve to minimize transcriptional noise. Our work provides the first genome-scale description of how synonymous codon changes influence organismal fitness and paves the way for the construction of functional genomes that provide genetic firewalls from natural ecosystems and safely produce biopolymers, drugs, and enzymes with an expanded chemistry.
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Affiliation(s)
- Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Bogdan Budnik
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | | | - Regan Flynn
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shirui Yan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- BGI Research, Shenzhen 518083, China
| | - Nili Ostrov
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Min Liu
- GenScript USA Inc., Piscataway, NJ 08854, USA
| | | | | | | | | | - Alexandra Rudolph
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dawn Chen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jenny Ahn
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Owen Spencer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Angela Tarver
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miranda Harmon-Smith
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew Hamilton
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian Blaby
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yasuo Yoshikuni
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Behnoush Hajian
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adeline Jin
- GenScript USA Inc., Piscataway, NJ 08854, USA
| | - Balint Kintses
- Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, 6726, Hungary
| | - Monika Szamel
- Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, 6726, Hungary
| | - Viktoria Seregi
- Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, 6726, Hungary
| | - Yue Shen
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China
| | - Zilong Li
- GenScript USA Inc., Piscataway, NJ 08854, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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3
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Jones EM, Marken JP, Silver PA. Synthetic microbiology in sustainability applications. Nat Rev Microbiol 2024; 22:345-359. [PMID: 38253793 DOI: 10.1038/s41579-023-01007-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.
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Affiliation(s)
- Ethan M Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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4
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Synthetic moss. NATURE PLANTS 2024; 10:831-832. [PMID: 38906995 DOI: 10.1038/s41477-024-01733-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
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5
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Chen XR, Cui YZ, Li BZ, Yuan YJ. Genome engineering on size reduction and complexity simplification: A review. J Adv Res 2024; 60:159-171. [PMID: 37442424 PMCID: PMC11156615 DOI: 10.1016/j.jare.2023.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/25/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Genome simplification is an important topic in the field of life sciences that has attracted attention from its conception to the present day. It can help uncover the essential components of the genome and, in turn, shed light on the underlying operating principles of complex biological systems. This has made it a central focus of both basic and applied research in the life sciences. With the recent advancements in related technologies and our increasing knowledge of the genome, now is an opportune time to delve into this topic. AIM OF REVIEW Our review investigates the progress of genome simplification from two perspectives: genome size reduction and complexity simplification. In addition, we provide insights into the future development trends of genome simplification. KEY SCIENTIFIC CONCEPTS OF REVIEW Reducing genome size requires eliminating non-essential elements as much as possible. This process has been facilitated by advances in genome manipulation and synthesis techniques. However, we still need a better and clearer understanding of living systems to reduce genome complexity. As there is a lack of quantitative and clearly defined standards for this task, we have opted to approach the topic from various perspectives and present our findings accordingly.
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Affiliation(s)
- Xiang-Rong Chen
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - You-Zhi Cui
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
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6
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Yi M, Ashton-Rickardt G, Tan W, Liu Z, He H, Hsieh JT, Xu B. Accelerating Cellular Uptake with Unnatural Amino Acid for Inhibiting Immunosuppressive Cancer Cells. Chemistry 2024; 30:e202400691. [PMID: 38527252 PMCID: PMC11132931 DOI: 10.1002/chem.202400691] [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: 02/20/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Targeting immunosuppressive metastatic cancer cells is a key challenge in therapy. We recently have shown that a rigid-rod aromatic, pBP-NBD, that responds to enzymes and kill immunosuppressive metastatic osteosarcoma (mOS) and castration resistant prostate cancer (CRPC) cells in mimetic bone microenvironment. However, pBP-NBD demonstrated moderate efficacy against CRPC cells. To enhance activity, we incorporated the unnatural amino acid L- or D-4,4'-biphenylalanine (L- or D-BiP) into pBP-NBD, drastically increasing cellular uptake and CRPC inhibition. Specifically, we inserted BiP into pBP-NBD to target mOS (Saos2 and SJSA1) and CRPC (VCaP and PC3) cells with overexpressed phosphatases. Our results show that the D-peptide backbone with an aspartate methyl diester at the C-terminal offers the highest activity against these immunosuppressive mOS and CRPC cells. Importantly, imaging shows that the peptide assemblies almost instantly enter the cells and accumulate primarily within the endoplasmic reticulum of Saos2, SJSA1, and PC3 cells and at the lysosomes of VCaP cells. By using BiP to boost cellular uptake and self-assembly within cancer cells, this work illustrates an unnatural hydrophobic amino acid as a versatile and effective residue to boost endocytosis of synthetic peptides for intracellular self-assembly.
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Affiliation(s)
- Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | | | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Zhiyu Liu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Jer-Tsong Hsieh
- Department of Urology, Southwestern Medical Center, University of Texas, Dallas, TX 75235, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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7
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Fu X, Shen Y. Synthetic Genomics: Repurposing Biological Systems for Applications in Engineering Biology. ACS Synth Biol 2024; 13:1394-1399. [PMID: 38757697 PMCID: PMC11106769 DOI: 10.1021/acssynbio.4c00006] [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: 01/02/2024] [Indexed: 05/18/2024]
Abstract
Substantial improvements in DNA sequencing and synthesis technologies and increased understanding of genome biology have empowered the development of synthetic genomics. The ability to design and construct engineered living cells boosted up by synthetic chromosomes provides opportunities to tackle enormous current and future challenges faced by humanity and the planet. Here we review the progresses, considerations, challenges, and future direction of the "design-build-test-learn" cycle used in synthetic genomics. We also discuss future applications enabled by synthetic genomics as this emerging field shapes and revolutionizes biomanufacturing and biomedicine.
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Affiliation(s)
- Xian Fu
- BGI
Research, Changzhou 213299, China
- BGI
Research, Shenzhen 518083, China
- Guangdong
Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China
| | - Yue Shen
- BGI
Research, Changzhou 213299, China
- BGI
Research, Shenzhen 518083, China
- Guangdong
Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China
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8
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Fujino T, Sonoda R, Higashinagata T, Mishiro-Sato E, Kano K, Murakami H. Ser/Leu-swapped cell-free translation system constructed with natural/in vitro transcribed-hybrid tRNA set. Nat Commun 2024; 15:4143. [PMID: 38755134 PMCID: PMC11099018 DOI: 10.1038/s41467-024-48056-z] [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: 08/22/2023] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
The Ser/Leu-swapped genetic code can act as a genetic firewall, mitigating biohazard risks arising from horizontal gene transfer in genetically modified organisms. Our prior work demonstrated the orthogonality of this swapped code to the standard genetic code using a cell-free translation system comprised of 21 in vitro transcribed tRNAs. In this study, to advance this system for protein engineering, we introduce a natural/in vitro transcribed-hybrid tRNA set. This set combines natural tRNAs from Escherichia coli (excluding Ser, Leu, and Tyr) and in vitro transcribed tRNAs, encompassing anticodon-swapped tRNASerGAG and tRNALeuGGA. This approach reduces the number of in vitro transcribed tRNAs required from 21 to only 4. In this optimized system, the production of a model protein, superfolder green fluorescent protein, increases to 3.5-fold. With this hybrid tRNA set, the Ser/Leu-swapped cell-free translation system will stand as a potent tool for protein production with reduced biohazard concerns in future biological endeavors.
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MESH Headings
- Cell-Free System
- Protein Biosynthesis
- Escherichia coli/genetics
- Escherichia coli/metabolism
- RNA, Transfer, Leu/genetics
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Ser/metabolism
- RNA, Transfer, Ser/genetics
- Genetic Code
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Green Fluorescent Proteins/metabolism
- Green Fluorescent Proteins/genetics
- Protein Engineering/methods
- Transcription, Genetic
- Anticodon/genetics
- Anticodon/metabolism
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Affiliation(s)
- Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Ryogo Sonoda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Taito Higashinagata
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Emi Mishiro-Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Keiko Kano
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan.
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9
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Grybchuk D, Galan A, Klocek D, Macedo DH, Wolf YI, Votýpka J, Butenko A, Lukeš J, Neri U, Záhonová K, Kostygov AY, Koonin EV, Yurchenko V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol 2024; 10:veae037. [PMID: 38774311 PMCID: PMC11108086 DOI: 10.1093/ve/veae037] [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: 10/26/2023] [Revised: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 05/24/2024] Open
Abstract
Trypanosomatids (Euglenozoa) are a diverse group of unicellular flagellates predominately infecting insects (monoxenous species) or circulating between insects and vertebrates or plants (dixenous species). Monoxenous trypanosomatids harbor a wide range of RNA viruses belonging to the families Narnaviridae, Totiviridae, Qinviridae, Leishbuviridae, and a putative group of tombus-like viruses. Here, we focus on the subfamily Blastocrithidiinae, a previously unexplored divergent group of monoxenous trypanosomatids comprising two related genera: Obscuromonas and Blastocrithidia. Members of the genus Blastocrithidia employ a unique genetic code, in which all three stop codons are repurposed to encode amino acids, with TAA also used to terminate translation. Obscuromonas isolates studied here bear viruses of three families: Narnaviridae, Qinviridae, and Mitoviridae. The latter viral group is documented in trypanosomatid flagellates for the first time. While other known mitoviruses replicate in the mitochondria, those of trypanosomatids appear to reside in the cytoplasm. Although no RNA viruses were detected in Blastocrithidia spp., we identified an endogenous viral element in the genome of B. triatomae indicating its past encounter(s) with tombus-like viruses.
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Affiliation(s)
- Danyil Grybchuk
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czechia
| | - Arnau Galan
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Donnamae Klocek
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Diego H Macedo
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Yuri I Wolf
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda 20894, USA
| | - Jan Votýpka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Department of Parasitology, Faculty of Science, Charles University, Prague 128 00, Czechia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czechia
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 39040, Israel
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec 252 50, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Alexei Yu Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Zoological Institute of the Ruian Academy of Sciences, St. Petersburg 199034, Russia
| | - Eugene V Koonin
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda 20894, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
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10
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Gómez-Márquez J. The Lithbea Domain. Adv Biol (Weinh) 2024; 8:e2300679. [PMID: 38386280 DOI: 10.1002/adbi.202300679] [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: 12/11/2023] [Revised: 02/09/2024] [Indexed: 02/23/2024]
Abstract
The tree of life is the evolutionary metaphor for the past and present connections of all cellular organisms. Today, to speak of biodiversity is not only to speak of archaea, bacteria, and eukaryotes, but they should also consider the "new biodiversity" that includes viruses and synthetic organisms, which represent the new forms of life created in laboratories. There is even a third group of artificial entities that, although not living systems, pretend to imitate the living. To embrace and organize all this new biodiversity, I propose the creation of a new domain, with the name Lithbea (from life-on-the-border entites) The criteria for inclusion as members of Lithbea are: i) the acellular nature of the living system, ii) its origin in laboratory manipulation, iii) showing new biological traits, iv) the presence of exogenous genetic elements, v) artificial or inorganic nature. Within Lithbea there are two subdomains: Virworld (from virus world) which includes all viruses, regarded as lifeless living systems, and classified according to the International Committee on Taxonomy of Viruses (ICTV), and ii) Humade (from human-made) which includes all synthetic organisms and artificial entities. The relationships of Lithbea members to the three classical woesian domains and their implications are briefly discussed.
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Affiliation(s)
- Jaime Gómez-Márquez
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Santiago de Compostela, Galicia, 15782, Spain
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11
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Rothschild LJ, Averesch NJH, Strychalski EA, Moser F, Glass JI, Cruz Perez R, Yekinni IO, Rothschild-Mancinelli B, Roberts Kingman GA, Wu F, Waeterschoot J, Ioannou IA, Jewett MC, Liu AP, Noireaux V, Sorenson C, Adamala KP. Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol 2024; 13:974-997. [PMID: 38530077 PMCID: PMC11037263 DOI: 10.1021/acssynbio.3c00724] [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: 12/01/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.
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Affiliation(s)
- Lynn J. Rothschild
- Space Science
& Astrobiology Division, NASA Ames Research
Center, Moffett
Field, California 94035-1000, United States
- Department
of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Nils J. H. Averesch
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Felix Moser
- Synlife, One Kendall Square, Cambridge, Massachusetts 02139-1661, United States
| | - John I. Glass
- J.
Craig
Venter Institute, La Jolla, California 92037, United States
| | - Rolando Cruz Perez
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Blue
Marble
Space Institute of Science at NASA Ames Research Center, Moffett Field, California 94035-1000, United
States
| | - Ibrahim O. Yekinni
- Department
of Biomedical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brooke Rothschild-Mancinelli
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0150, United States
| | | | - Feilun Wu
- J. Craig
Venter Institute, Rockville, Maryland 20850, United States
| | - Jorik Waeterschoot
- Mechatronics,
Biostatistics and Sensors (MeBioS), KU Leuven, 3000 Leuven Belgium
| | - Ion A. Ioannou
- Department
of Chemistry, MSRH, Imperial College London, London W12 0BZ, U.K.
| | - Michael C. Jewett
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Allen P. Liu
- Mechanical
Engineering & Biomedical Engineering, Cellular and Molecular Biology,
Biophysics, Applied Physics, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent Noireaux
- Physics
and Nanotechnology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlise Sorenson
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
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12
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Lomeli‐Ortega CO, Balcázar JL. Why tRNA acquisition could be relevant to bacteriophages? Microb Biotechnol 2024; 17:e14464. [PMID: 38635123 PMCID: PMC11025619 DOI: 10.1111/1751-7915.14464] [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: 09/25/2023] [Revised: 02/09/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
In this opinion, we discuss the role of tRNAs in phage biology and their importance in DNA replication and phage-host interactions. Phages are a diverse group of obligate bacterial viruses that possess genomes with a wide range of sizes. Among them, we find phages with few genes that depend entirely on their host's translational machinery for replication. However, some phages carry genes for all replication steps and even contain genes for their own translational synthesis. In these cases, the integration of tRNA genes in their genomes is not completely understood, generating different theories about their presence and function during the replication cycle. Although different studies have attempted to elucidate their role, additional studies are needed to clarify the presence and significance of tRNA genes in phages. Moreover, we highlight the importance of tRNA genes in phages from both ecological and therapeutic perspectives.
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Affiliation(s)
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA‐CERCA)GironaSpain
- University of GironaGironaSpain
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13
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Goold HD, Moseley JL, Lauersen KJ. The synthetic future of algal genomes. CELL GENOMICS 2024; 4:100505. [PMID: 38395701 PMCID: PMC10943592 DOI: 10.1016/j.xgen.2024.100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/18/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Algae are diverse organisms with significant biotechnological potential for resource circularity. Taking inspiration from fermentative microbes, engineering algal genomes holds promise to broadly expand their application ranges. Advances in genome sequencing with improvements in DNA synthesis and delivery techniques are enabling customized molecular tool development to confer advanced traits to algae. Efforts to redesign and rebuild entire genomes to create fit-for-purpose organisms currently being explored in heterotrophic prokaryotes and eukaryotic microbes could also be applied to photosynthetic algae. Future algal genome engineering will enhance yields of native products and permit the expression of complex biochemical pathways to produce novel metabolites from sustainable inputs. We present a historical perspective on advances in engineering algae, discuss the requisite genetic traits to enable algal genome optimization, take inspiration from whole-genome engineering efforts in other microbes for algal systems, and present candidate algal species in the context of these engineering goals.
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Affiliation(s)
- Hugh D Goold
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia; ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia; School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeffrey L Moseley
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Phycoil Biotechnology International, Inc., Fremont, CA 94538, USA
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
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14
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Kienbeck K, Malfertheiner L, Zelger-Paulus S, Johannsen S, von Mering C, Sigel RKO. Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages. Nat Commun 2024; 15:1559. [PMID: 38378708 PMCID: PMC10879173 DOI: 10.1038/s41467-024-45653-w] [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: 07/25/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Trillions of microorganisms, collectively known as the microbiome, inhabit our bodies with the gut microbiome being of particular interest in biomedical research. Bacteriophages, the dominant virome constituents, can utilize suppressor tRNAs to switch to alternative genetic codes (e.g., the UAG stop-codon is reassigned to glutamine) while infecting hosts with the standard bacterial code. However, what triggers this switch and how the bacteriophage manipulates its host is poorly understood. Here, we report the discovery of a subgroup of minimal hepatitis delta virus (HDV)-like ribozymes - theta ribozymes - potentially involved in the code switch leading to the expression of recoded lysis and structural phage genes. We demonstrate their HDV-like self-scission behavior in vitro and find them in an unreported context often located with their cleavage site adjacent to tRNAs, indicating a role in viral tRNA maturation and/or regulation. Every fifth associated tRNA is a suppressor tRNA, further strengthening our hypothesis. The vast abundance of tRNA-associated theta ribozymes - we provide 1753 unique examples - highlights the importance of small ribozymes as an alternative to large enzymes that usually process tRNA 3'-ends. Our discovery expands the short list of biological functions of small HDV-like ribozymes and introduces a previously unknown player likely involved in the code switch of certain recoded gut bacteriophages.
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Affiliation(s)
- Kasimir Kienbeck
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland
| | | | - Silke Johannsen
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland.
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15
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Matteau D, Duval A, Baby V, Rodrigue S. Mesoplasma florum: a near-minimal model organism for systems and synthetic biology. Front Genet 2024; 15:1346707. [PMID: 38404664 PMCID: PMC10884336 DOI: 10.3389/fgene.2024.1346707] [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: 11/29/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
Mesoplasma florum is an emerging model organism for systems and synthetic biology due to its small genome (∼800 kb) and fast growth rate. While M. florum was isolated and first described almost 40 years ago, many important aspects of its biology have long remained uncharacterized due to technological limitations, the absence of dedicated molecular tools, and since this bacterial species has not been associated with any disease. However, the publication of the first M. florum genome in 2004 paved the way for a new era of research fueled by the rise of systems and synthetic biology. Some of the most important studies included the characterization and heterologous use of M. florum regulatory elements, the development of the first replicable plasmids, comparative genomics and transposon mutagenesis, whole-genome cloning in yeast, genome transplantation, in-depth characterization of the M. florum cell, as well as the development of a high-quality genome-scale metabolic model. The acquired data, knowledge, and tools will greatly facilitate future genome engineering efforts in M. florum, which could next be exploited to rationally design and create synthetic cells to advance fundamental knowledge or for specific applications.
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Affiliation(s)
- Dominick Matteau
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Anthony Duval
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Vincent Baby
- Centre de diagnostic vétérinaire de l'Université de Montréal, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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16
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Zalatan JG, Petrini L, Geiger R. Engineering bacteria for cancer immunotherapy. Curr Opin Biotechnol 2024; 85:103061. [PMID: 38219524 PMCID: PMC10922846 DOI: 10.1016/j.copbio.2023.103061] [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: 06/02/2023] [Revised: 10/30/2023] [Accepted: 12/16/2023] [Indexed: 01/16/2024]
Abstract
Bacterial therapeutics have emerged as promising delivery systems to target tumors. These engineered live therapeutics can be harnessed to modulate the tumor microenvironment or to deliver and selectively release therapeutic payloads to tumors. A major challenge is to deliver bacteria systemically without causing widespread inflammation, which is critical for the many tumors that are not accessible to direct intratumoral injection. We describe potential strategies to address this challenge, along with approaches for specific payload delivery and biocontainment to ensure safety. These strategies will pave the way for the development of cost-effective, widely applicable next-generation cancer therapeutics.
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Affiliation(s)
- Jesse G Zalatan
- Department of Chemistry, University of Washington, Seattle, WA, United States.
| | - Lorenzo Petrini
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland; Institute of Oncology Research, Università della Svizzera italiana, Bellinzona, Switzerland.
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17
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Seydel C. DNA writing technologies moving toward synthetic genomes. Nat Biotechnol 2023; 41:1504-1509. [PMID: 37884745 DOI: 10.1038/s41587-023-02006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
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18
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Fooladi S, Rabiee N, Iravani S. Genetically engineered bacteria: a new frontier in targeted drug delivery. J Mater Chem B 2023; 11:10072-10087. [PMID: 37873584 DOI: 10.1039/d3tb01805a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Genetically engineered bacteria (GEB) have shown significant promise to revolutionize modern medicine. These engineered bacteria with unique properties such as enhanced targeting, versatility, biofilm disruption, reduced drug resistance, self-amplification capabilities, and biodegradability represent a highly promising approach for targeted drug delivery and cancer theranostics. This innovative approach involves modifying bacterial strains to function as drug carriers, capable of delivering therapeutic agents directly to specific cells or tissues. Unlike synthetic drug delivery systems, GEB are inherently biodegradable and can be naturally eliminated from the body, reducing potential long-term side effects or complications associated with residual foreign constituents. However, several pivotal challenges such as safety and controllability need to be addressed. Researchers have explored novel tactics to improve their capabilities and overcome existing challenges, including synthetic biology tools (e.g., clustered regularly interspaced short palindromic repeats (CRISPR) and bioinformatics-driven design), microbiome engineering, combination therapies, immune system interaction, and biocontainment strategies. Because of the remarkable advantages and tangible progress in this field, GEB may emerge as vital tools in personalized medicine, providing precise and controlled drug delivery for various diseases (especially cancer). In this context, future directions include the integration of nanotechnology with GEB, the focus on microbiota-targeted therapies, the incorporation of programmable behaviors, the enhancement in immunotherapy treatments, and the discovery of non-medical applications. In this way, careful ethical considerations and regulatory frameworks are necessary for developing GEB-based systems for targeted drug delivery. By addressing safety concerns, ensuring informed consent, promoting equitable access, understanding long-term effects, mitigating dual-use risks, and fostering public engagement, these engineered bacteria can be employed as promising delivery vehicles in bio- and nanomedicine. In this review, recent advances related to the application of GEB in targeted drug delivery and cancer therapy are discussed, covering crucial challenging issues and future perspectives.
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Affiliation(s)
- Saba Fooladi
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA
| | - Navid Rabiee
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia.
- School of Engineering, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Siavash Iravani
- Independent Researcher, W Nazar ST, Boostan Ave, Isfahan, Iran.
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19
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Chang T, Ding W, Yan S, Wang Y, Zhang H, Zhang Y, Ping Z, Zhang H, Huang Y, Zhang J, Wang D, Zhang W, Xu X, Shen Y, Fu X. A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid. Nat Commun 2023; 14:6487. [PMID: 37838746 PMCID: PMC10576815 DOI: 10.1038/s41467-023-42358-4] [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: 05/27/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023] Open
Abstract
Synthetic auxotrophy in which cell viability depends on the presence of an unnatural amino acid (unAA) provides a powerful strategy to restrict unwanted propagation of genetically modified organisms (GMOs) in open environments and potentially prevent industrial espionage. Here, we describe a generic approach for robust biocontainment of budding yeast dependent on unAA. By understanding escape mechanisms, we specifically optimize our strategies by introducing designed "immunity" to the generation of amber-suppressor tRNAs and developing the transcriptional- and translational-based biocontainment switch. We further develop a fitness-oriented screening method to easily obtain multiplex safeguard strains that exhibit robust growth and undetectable escape frequency (<~10-9) on solid media for 14 days. Finally, we show that employing our multiplex safeguard system could restrict the proliferation of strains of interest in a real fermentation scenario, highlighting the great potential of our yeast biocontainment strategy to protect the industrial proprietary strains.
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Affiliation(s)
- Tiantian Chang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Weichao Ding
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Shirui Yan
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Yun Wang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Haoling Zhang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Yu Zhang
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Zhi Ping
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Huiming Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Yijian Huang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Jiahui Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Dan Wang
- Guangdong Provincial Key Laboratory of Interdisciplinary Research and Application for Data Science, BNU-HKBU United International College, Zhuhai, 519087, China
- BNU-HKBU United International College, Zhuhai, 519087, China
| | - Wenwei Zhang
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Yue Shen
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Changzhou, 213299, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China.
| | - Xian Fu
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Changzhou, 213299, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China.
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20
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Rudolph A, Nyerges A, Chiappino-Pepe A, Landon M, Baas-Thomas M, Church G. Strategies to identify and edit improvements in synthetic genome segments episomally. Nucleic Acids Res 2023; 51:10094-10106. [PMID: 37615546 PMCID: PMC10570025 DOI: 10.1093/nar/gkad692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/30/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Genome engineering projects often utilize bacterial artificial chromosomes (BACs) to carry multi-kilobase DNA segments at low copy number. However, all stages of whole-genome engineering have the potential to impose mutations on the synthetic genome that can reduce or eliminate the fitness of the final strain. Here, we describe improvements to a multiplex automated genome engineering (MAGE) protocol to improve recombineering frequency and multiplexability. This protocol was applied to recoding an Escherichia coli strain to replace seven codons with synonymous alternatives genome wide. Ten 44 402-47 179 bp de novo synthesized DNA segments contained in a BAC from the recoded strain were unable to complement deletion of the corresponding 33-61 wild-type genes using a single antibiotic resistance marker. Next-generation sequencing (NGS) was used to identify 1-7 non-recoding mutations in essential genes per segment, and MAGE in turn proved a useful strategy to repair these mutations on the recoded segment contained in the BAC when both the recoded and wild-type copies of the mutated genes had to exist by necessity during the repair process. Finally, two web-based tools were used to predict the impact of a subset of non-recoding missense mutations on strain fitness using protein structure and function calls.
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Affiliation(s)
- Alexandra Rudolph
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anush Chiappino-Pepe
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - Matthieu Landon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
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21
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Zürcher JF, Kleefeldt AA, Funke LFH, Birnbaum J, Fredens J, Grazioli S, Liu KC, Spinck M, Petris G, Murat P, Rehm FBH, Sale JE, Chin JW. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature 2023; 619:555-562. [PMID: 37380776 PMCID: PMC7614783 DOI: 10.1038/s41586-023-06268-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Whole-genome synthesis provides a powerful approach for understanding and expanding organism function1-3. To build large genomes rapidly, scalably and in parallel, we need (1) methods for assembling megabases of DNA from shorter precursors and (2) strategies for rapidly and scalably replacing the genomic DNA of organisms with synthetic DNA. Here we develop bacterial artificial chromosome (BAC) stepwise insertion synthesis (BASIS)-a method for megabase-scale assembly of DNA in Escherichia coli episomes. We used BASIS to assemble 1.1 Mb of human DNA containing numerous exons, introns, repetitive sequences, G-quadruplexes, and long and short interspersed nuclear elements (LINEs and SINEs). BASIS provides a powerful platform for building synthetic genomes for diverse organisms. We also developed continuous genome synthesis (CGS)-a method for continuously replacing sequential 100 kb stretches of the E. coli genome with synthetic DNA; CGS minimizes crossovers1,4 between the synthetic DNA and the genome such that the output for each 100 kb replacement provides, without sequencing, the input for the next 100 kb replacement. Using CGS, we synthesized a 0.5 Mb section of the E. coli genome-a key intermediate in its total synthesis1-from five episomes in 10 days. By parallelizing CGS and combining it with rapid oligonucleotide synthesis and episome assembly5,6, along with rapid methods for compiling a single genome from strains bearing distinct synthetic genome sections1,7,8, we anticipate that it will be possible to synthesize entire E. coli genomes from functional designs in less than 2 months.
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Affiliation(s)
- Jérôme F Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Askar A Kleefeldt
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Louise F H Funke
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Jakob Birnbaum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julius Fredens
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Synthetic Biology for Clinical and Technological Innovation, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Simona Grazioli
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martin Spinck
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Pierre Murat
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fabian B H Rehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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22
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23
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Truong DM. An artificial protein translation language makes bacteria resistant to viruses. Synth Biol (Oxf) 2023; 8:ysad011. [PMID: 37305737 PMCID: PMC10256184 DOI: 10.1093/synbio/ysad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/13/2023] Open
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24
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Blount BA. Synthetic bacterial genome upgraded for viral defence and biocontainment. Nature 2023; 615:592-594. [PMID: 36922657 DOI: 10.1038/d41586-023-00702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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