1
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Wang J, Kan S, Liao X, Zhou J, Tembrock LR, Daniell H, Jin S, Wu Z. Plant organellar genomes: much done, much more to do. TRENDS IN PLANT SCIENCE 2024; 29:754-769. [PMID: 38220520 DOI: 10.1016/j.tplants.2023.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024]
Abstract
Plastids and mitochondria are the only organelles that possess genomes of endosymbiotic origin. In recent decades, advances in sequencing technologies have contributed to a meteoric rise in the number of published organellar genomes, and have revealed greatly divergent evolutionary trajectories. In this review, we quantify the abundance and distribution of sequenced plant organellar genomes across the plant tree of life. We compare numerous genomic features between the two organellar genomes, with an emphasis on evolutionary trajectories, transfers, the current state of organellar genome editing by transcriptional activator-like effector nucleases (TALENs), transcription activator-like effector (TALE)-mediated deaminase, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas), as well as genetic transformation. Finally, we propose future research to understand these different evolutionary trajectories, and genome-editing strategies to promote functional studies and eventually improve organellar genomes.
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Affiliation(s)
- Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6000-6999, Australia
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Marine College, Shandong University, Weihai, 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiawei Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Henry Daniell
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104-6030, USA.
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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2
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Secaira-Morocho H, Chede A, Gonzalez-de-Salceda L, Garcia-Pichel F, Zhu Q. An evolutionary optimum amid moderate heritability in prokaryotic cell size. Cell Rep 2024; 43:114268. [PMID: 38776226 DOI: 10.1016/j.celrep.2024.114268] [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: 01/04/2024] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
We investigate the distribution and evolution of prokaryotic cell size based on a compilation of 5,380 species. Size spans four orders of magnitude, from 100 nm (Mycoplasma) to more than 1 cm (Thiomargarita); however, most species congregate heavily around the mean. The distribution approximates but is distinct from log normality. Comparative phylogenetics suggests that size is heritable, yet the phylogenetic signal is moderate, and the degree of heritability is independent of taxonomic scale (i.e., fractal). Evolutionary modeling indicates the presence of an optimal cell size to which most species gravitate. The size is equivalent to a coccus of 0.70 μm in diameter. Analyses of 1,361 species with sequenced genomes show that genomic traits contribute to size evolution moderately and synergistically. Given our results, scaling theory, and empirical evidence, we discuss potential drivers that may expand or shrink cells around the optimum and propose a stability landscape model for prokaryotic cell size.
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Affiliation(s)
- Henry Secaira-Morocho
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Abhinav Chede
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Luis Gonzalez-de-Salceda
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Qiyun Zhu
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
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3
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Søgaard AB, Løvschall KB, Montasell MC, Cramer CB, Marcet PM, Pedersen AB, Jakobsen JH, Zelikin AN. Artificial Receptor in Synthetic Cells Performs Transmembrane Activation of Proteolysis. Adv Biol (Weinh) 2024:e2400053. [PMID: 38767247 DOI: 10.1002/adbi.202400053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/11/2024] [Indexed: 05/22/2024]
Abstract
The design of artificial, synthetic cells is a fundamentally important and fast-developing field of science. Of the diverse attributes of cellular life, artificial transmembrane signaling across the biomolecular barriers remains a high challenge with only a few documented successes. Herein, the study achieves signaling across lipid bilayers and connects an exofacial enzymatic receptor activation to an intracellular biochemical catalytic response using an artificial receptor. The mechanism of signal transduction for the artificial receptor relies on the triggered decomposition of a self-immolative linker. Receptor activation ensues its head-to-tail decomposition and the release of a secondary messenger molecule into the internal volume of the synthetic cell. Transmembrane signaling is demonstrated in synthetic cells based on liposomes and mammalian cell-sized giant unilamellar vesicles and illustrates receptor performance in cell mimics with a diverse size and composition of the lipid bilayer. In giant unilamellar vesicles, transmembrane signaling connects exofacial receptor activation with intracellular activation of proteolysis. Taken together, the results of this study take a step toward engineering receptor-mediated, responsive behavior in synthetic cells.
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Affiliation(s)
| | | | | | | | | | | | | | - Alexander N Zelikin
- iNano Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, 8000, Denmark
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
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4
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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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5
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Baverstock K. Responses to commentaries on "The gene: An appraisal". PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 188:31-42. [PMID: 38360273 DOI: 10.1016/j.pbiomolbio.2024.02.002] [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: 12/23/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
The central conclusions of "The Gene: An Appraisal" are that genetic variance does not underpin biological evolution, and, therefore, that genes are not Mendel's units of inheritance. In this response, I will address the criticisms I have received via commentaries on that paper by defending the following statements: 1. Epistasis does not explain the power-law fitness profile of the Long-Term Evolution Experiment (LTEE). The data from the evolution of natural systems displays the power-law form ubiquitously. Epistasis plays no role in evolution. 2. The common characteristics of living things (natural systems) are described by the principle of least action in de Maupertuis's original form, which is synonymous with the 2nd law of thermodynamics and Newton's 2nd law of motion in its complete form, i.e., F = dp/dt. Organisms strive to achieve free energy balance with their environments. 3. Based on an appraisal of the scientific environment between 1880 and 1911, I conclude that Johannsen's genotype conception was perhaps, the only option available to him. 4. The power-law fitness profile of the LTEE falsifies Fisher's Genetical Theory of Natural Selection, Johannsen's genotype conception, and the idea that 'Darwinian evolution' is an exception to the generic thermodynamic process of evolution in natural systems. 5. The use of the technique of genome-wide association to identify the causes and the likelihoods of inherited common diseases and behavioural traits is a 'wild goose chase' because genes are not the units of inheritance.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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6
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Hitomi K, Ishii Y, Ying BW. Experimental evolution for the recovery of growth loss due to genome reduction. eLife 2024; 13:RP93520. [PMID: 38690805 PMCID: PMC11062635 DOI: 10.7554/elife.93520] [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] [Indexed: 05/03/2024] Open
Abstract
As the genome encodes the information crucial for cell growth, a sizeable genomic deficiency often causes a significant decrease in growth fitness. Whether and how the decreased growth fitness caused by genome reduction could be compensated by evolution was investigated here. Experimental evolution with an Escherichia coli strain carrying a reduced genome was conducted in multiple lineages for approximately 1000 generations. The growth rate, which largely declined due to genome reduction, was considerably recovered, associated with the improved carrying capacity. Genome mutations accumulated during evolution were significantly varied across the evolutionary lineages and were randomly localized on the reduced genome. Transcriptome reorganization showed a common evolutionary direction and conserved the chromosomal periodicity, regardless of highly diversified gene categories, regulons, and pathways enriched in the differentially expressed genes. Genome mutations and transcriptome reorganization caused by evolution, which were found to be dissimilar to those caused by genome reduction, must have followed divergent mechanisms in individual evolutionary lineages. Gene network reconstruction successfully identified three gene modules functionally differentiated, which were responsible for the evolutionary changes of the reduced genome in growth fitness, genome mutation, and gene expression, respectively. The diversity in evolutionary approaches improved the growth fitness associated with the homeostatic transcriptome architecture as if the evolutionary compensation for genome reduction was like all roads leading to Rome.
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Affiliation(s)
- Kenya Hitomi
- School of Life and Environmental Sciences, University of TsukubaTsukubaJapan
| | - Yoichiro Ishii
- School of Life and Environmental Sciences, University of TsukubaTsukubaJapan
| | - Bei-Wen Ying
- School of Life and Environmental Sciences, University of TsukubaTsukubaJapan
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7
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Castle SD, Stock M, Gorochowski TE. Engineering is evolution: a perspective on design processes to engineer biology. Nat Commun 2024; 15:3640. [PMID: 38684714 PMCID: PMC11059173 DOI: 10.1038/s41467-024-48000-1] [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: 09/11/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Careful consideration of how we approach design is crucial to all areas of biotechnology. However, choosing or developing an effective design methodology is not always easy as biology, unlike most areas of engineering, is able to adapt and evolve. Here, we put forward that design and evolution follow a similar cyclic process and therefore all design methods, including traditional design, directed evolution, and even random trial and error, exist within an evolutionary design spectrum. This contrasts with conventional views that often place these methods at odds and provides a valuable framework for unifying engineering approaches for challenging biological design problems.
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Affiliation(s)
- Simeon D Castle
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, UK.
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, UK.
- BrisEngBio, School of Chemistry, University of Bristol, Cantock's Close, Bristol, UK.
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8
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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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9
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Bittencourt DDC, Brown DM, Assad-Garcia N, Romero MR, Sun L, Palhares de Melo LAM, Freire M, Glass JI. Minimal Bacterial Cell JCVI-syn3B as a Chassis to Investigate Interactions between Bacteria and Mammalian Cells. ACS Synth Biol 2024; 13:1128-1141. [PMID: 38507598 PMCID: PMC11036491 DOI: 10.1021/acssynbio.3c00513] [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: 08/21/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Mycoplasmas are atypical bacteria with small genomes that necessitate colonization of their respective animal or plant hosts as obligate parasites, whether as pathogens, or commensals. Some can grow axenically in specialized complex media yet show only host-cell-dependent growth in cell culture, where they can survive chronically and often through interactions involving surface colonization or internalization. To develop a mycoplasma-based system to identify genes mediating such interactions, we exploited genetically tractable strains of the goat pathogen Mycoplasma mycoides (Mmc) with synthetic designer genomes representing the complete natural organism (minus virulence factors; JCVI-syn1.0) or its reduced counterpart (JCVI-syn3B) containing only those genes supporting axenic growth. By measuring growth of surviving organisms, physical association with cultured human cells (HEK-293T, HeLa), and induction of phagocytosis by human myeloid cells (dHL-60), we determined that JCVI-syn1.0 contained a set of eight genes (MMSYN1-0179 to MMSYN1-0186, dispensable for axenic growth) conferring survival, attachment, and phagocytosis phenotypes. JCVI-syn3B lacked these phenotypes, but insertion of these genes restored cell attachment and phagocytosis, although not survival. These results indicate that JCVI-syn3B may be a powerful living platform to analyze the role of specific gene sets, from any organism, on the interaction with diverse mammalian cells in culture.
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Affiliation(s)
- Daniela
Matias de C. Bittencourt
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
- Embrapa
Genetic Resources and Biotechnology/National Institute of Science
and Technology − Synthetic Biology, Parque Estação
Biológica, PqEB, Av. W5 Norte (final), Brasília, DF 70770-917, Brazil
| | - David M. Brown
- The
J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, Maryland 20850, United States
| | - Nacyra Assad-Garcia
- The
J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, Maryland 20850, United States
| | - Michaela R. Romero
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - Lijie Sun
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - Luis Alberto M. Palhares de Melo
- Embrapa
Genetic Resources and Biotechnology/National Institute of Science
and Technology − Synthetic Biology, Parque Estação
Biológica, PqEB, Av. W5 Norte (final), Brasília, DF 70770-917, Brazil
| | - Marcelo Freire
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - John I. Glass
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
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10
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Wei X, Guo J, Geng X, Xue B, Huang S, Yuan Z. The Combination of Membrane Disruption and FtsZ Targeting by a Chemotherapeutic Hydrogel Synergistically Combats Pathogens Infections. Adv Healthc Mater 2024:e2304600. [PMID: 38491859 DOI: 10.1002/adhm.202304600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/23/2024] [Indexed: 03/18/2024]
Abstract
The emergence of multidrug-resistant (MDR) bacteria poses a significant challenge to global health. Due to a shortage of antibiotics, alternative therapeutic strategies are urgently needed. Unfortunately, colistin, the last-resort antibiotic, has unavoidable nephrotoxicity and hepatotoxicity, and its single killing mechanism is prone to drug resistance. To address this challenge, a promising combinatorial approach that includes colistin, a membrane-disrupting antimicrobial agent, and chelerythrine (CHE), a FtsZ protein inhibitor is proposed. This approach significantly reduces antibiotic dose and development of resistance, leading to almost complete inactivation of MDR pathogens in vitro. To address solubility issues and ensure transport, the antimicrobial hydrogel system LNP-CHE-CST@hydrogel, which induced reactive oxygen species (ROS) and apoptosis-like cell death by targeting the FtsZ protein, is used. In an in vivo mouse skin infection model, the combination therapy effectively eliminated MDR bacteria within 24 h, as monitored by fluorescence tracking. The findings demonstrate a promising approach for developing multifunctional hydrogels to combat MDR bacterial infections.
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Affiliation(s)
- Xianyuan Wei
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
| | - Jintong Guo
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
| | - Xiaorui Geng
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
| | - Bin Xue
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
- Shenzhen Key Laboratory of Ultraintense Laser and Advanced Material Technology, Center for Intense Laser Application Technology and College of Engineering Physics, Shenzhen Technology University, Shenzhen, 518118, China
| | - Shaohui Huang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101499, China
- LightEdge Technologies Limited, Zhongshan, Guangdong, 528403, China
| | - Zhen Yuan
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
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11
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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:S0167-7799(24)00037-4. [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] [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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12
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Gómez-Márquez C, Morales JA, Romero-Gutiérrez T, Paredes O, Borrayo E. Decoding semiotic minimal genome: a non-genocentric approach. Front Microbiol 2024; 15:1356050. [PMID: 38476952 PMCID: PMC10929006 DOI: 10.3389/fmicb.2024.1356050] [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: 12/14/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024] Open
Abstract
The search for the minimum information required for an organism to sustain a cellular system network has rendered both the identification of a fixed number of known genes and those genes whose function remains to be identified. The approaches used in such search generally focus their analysis on coding genomic regions, based on the genome to proteic-product perspective. Such approaches leave other fundamental processes aside, mainly those that include higher-level information management. To cope with this limitation, a non-genocentric approach based on genomic sequence analysis using language processing tools and gene ontology may prove an effective strategy for the identification of those fundamental genomic elements for life autonomy. Additionally, this approach will provide us with an integrative analysis of the information value present in all genomic elements, regardless of their coding status.
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Affiliation(s)
- Carolina Gómez-Márquez
- Biodigital Innovation Lab, Translational Bioengineering Department, Exact Sciences and Engineering University Center, Universidad de Guadalajara, Guadalajara, Mexico
| | - J. Alejandro Morales
- Biodigital Innovation Lab, Translational Bioengineering Department, Exact Sciences and Engineering University Center, Universidad de Guadalajara, Guadalajara, Mexico
| | - Teresa Romero-Gutiérrez
- Biodigital Innovation Lab, Translational Bioengineering Department, Exact Sciences and Engineering University Center, Universidad de Guadalajara, Guadalajara, Mexico
- Technological Innovation Department, Tlajomulco University Center, Universidad de Guadalajara, Guadalajara, Mexico
| | - Omar Paredes
- Biodigital Innovation Lab, Translational Bioengineering Department, Exact Sciences and Engineering University Center, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ernesto Borrayo
- Biodigital Innovation Lab, Translational Bioengineering Department, Exact Sciences and Engineering University Center, Universidad de Guadalajara, Guadalajara, Mexico
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Xu X, Chen M, Chen T, Ni X, Fang Z, Fang Y, Zhang L, Zhang X, Huang J. Ultra-high static magnetic field induces a change in the spectrum but not frequency of DNA spontaneous mutations in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1305069. [PMID: 38126008 PMCID: PMC10731980 DOI: 10.3389/fpls.2023.1305069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
Biological effects of magnetic fields have been extensively studied in plants, microorganisms and animals, and applications of magnetic fields in regulation of plant growth and phytoprotection is a promising field in sustainable agriculture. However, the effect of magnetic fields especially ultra-high static magnetic field (UHSMF) on genomic stability is largely unclear. Here, we investigated the mutagenicity of 24.5, 30.5 and 33.0 T UHSMFs with the gradient of 150, 95 and 0 T/m, respectively, via whole genome sequencing. Our results showed that 1 h exposure of Arabidopsis dried seeds to UHSMFs has no significant effect on the average rate of DNA mutations including single nucleotide variations and InDels (insertions and deletions) in comparison with the control, but 33.0 T and 24.5 T treatments lead to a significant change in the rate of nucleotide transitions and InDels longer than 3 bp, respectively, suggesting that both strength and gradient of UHSMF impact molecular spectrum of DNA mutations. We also found that the decreased transition rate in UHSMF groups is correlated with the upstream flanking sequences of G and C mutation sites. Furthermore, the germination rate of seeds exposed to 24.5 T SMF with -150 T/m gradient showed a significant decrease at 24 hours after sowing. Overall, our data lay a basis for precisely assessing the potential risk of UHSMF on DNA stability, and for elucidating molecular mechanism underlying gradient SMF-regulated biological processes in the future.
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Affiliation(s)
- Xiang Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Mengjiao Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Tianli Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xinda Ni
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhicai Fang
- Heye Health Industrial Research Institute of Heye Health Technology Co., Ltd., Huzhou, China
| | - Yanwen Fang
- Heye Health Industrial Research Institute of Heye Health Technology Co., Ltd., Huzhou, China
| | - Lei Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Xin Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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Typas D. Natural selection finds a way, even under heavy constraints. Nat Struct Mol Biol 2023; 30:1251. [PMID: 37696960 DOI: 10.1038/s41594-023-01106-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
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