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Wang L, Maranas CD. MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes. ACS Synth Biol 2018; 7:462-473. [PMID: 29254336 DOI: 10.1021/acssynbio.7b00296] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Genome minimized strains offer advantages as production chassis by reducing transcriptional cost, eliminating competing functions and limiting unwanted regulatory interactions. Existing approaches for identifying stretches of DNA to remove are largely ad hoc based on information on presumably dispensable regions through experimentally determined nonessential genes and comparative genomics. Here we introduce a versatile genome reduction algorithm MinGenome that implements a mixed-integer linear programming (MILP) algorithm to identify in size descending order all dispensable contiguous sequences without affecting the organism's growth or other desirable traits. Known essential genes or genes that cause significant fitness or performance loss can be flagged and their deletion can be prohibited. MinGenome also preserves needed transcription factors and promoter regions ensuring that retained genes will be properly transcribed while also avoiding the simultaneous deletion of synthetic lethal pairs. The potential benefit of removing even larger contiguous stretches of DNA if only one or two essential genes (to be reinserted elsewhere) are within the deleted sequence is explored. We applied the algorithm to design a minimized E. coli strain and found that we were able to recapitulate the long deletions identified in previous experimental studies and discover alternative combinations of deletions that have not yet been explored in vivo.
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Affiliation(s)
- Lin Wang
- Department of Chemical
Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Costas D. Maranas
- Department of Chemical
Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Construction of a minimal genome as a chassis for synthetic biology. Essays Biochem 2016; 60:337-346. [DOI: 10.1042/ebc20160024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022]
Abstract
Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput ‘-omics’ research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300–500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis. Current size-reduced genomes are not perfect minimal genomes, but chemically synthesized genomes have just been constructed. Some minimal genomes provide various desirable functions for bioindustry, such as improved genome stability, increased transformation efficacy and improved production of biomaterials. The minimal genome as a chassis genome for synthetic biology can be used to construct custom-designed genomes for various practical and industrial applications.
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Gonchoroski T, Virginio VG, Thompson CE, Paes JA, Machado CX, Ferreira HB. Evolution and function of the Mycoplasma hyopneumoniae peroxiredoxin, a 2-Cys-like enzyme with a single Cys residue. Mol Genet Genomics 2016; 292:297-305. [PMID: 27858147 DOI: 10.1007/s00438-016-1272-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/05/2016] [Indexed: 10/20/2022]
Abstract
The minimal genome of the mollicute Mycoplasma hyopneumoniae, the etiological agent of porcine enzootic pneumonia, encodes a limited repertoire of antioxidant enzymes that include a single and atypical peroxiredoxin (MhPrx), whose evolution and function were studied here. MhPrx has only one catalytic cysteine, in contrast with some of its possible ancestors (2-Cys peroxiredoxins), which have two. Although it is more similar to 2-Cys orthologs, MhPrx can still function with a single peroxidatic cysteine (CysP), using non-thiolic electron donors to reduce it. Therefore, MhPrx could be a representative of a possible group of 2-Cys peroxiredoxins, which have lost the resolving cysteine (CysR) residue without losing their catalytic properties. To further investigate MhPrx evolution, we performed a comprehensive phylogenetic analysis in the context of several bacterial families, including Prxs belonging to Tpx and AhpE families, shedding light on the evolutionary history of Mycoplasmataceae Prxs and giving support to the hypothesis of a relatively recent loss of the CysR within this family. Moreover, mutational analyses provided insights into MhPrx function with one, two, or without catalytic cysteines. While removal of the MhPrx putative CysP caused complete activity loss, confirming its catalytic role, the introduction of a second cysteine in a site correspondent to that of the CysR of a 2-Cys orthologue, as in the MhPrx supposed ancestral form, was compatible with enzyme activity. Overall, our phylogenetic and mutational studies support that MhPrx recently diverged from a 2-Cys Prx ancestor and pave the way for future studies addressing structural, functional, and evolutive aspects of peroxiredoxin subfamilies in Mollicutes and other bacteria.
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Affiliation(s)
- Taylor Gonchoroski
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil.,Grupo de Pesquisa em Plasticidade Neuroglial, Departamento de Bioquímica, UFRGS, Porto Alegre, RS, Brazil
| | - Veridiana G Virginio
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil
| | - Claudia E Thompson
- Unidade de Biologia Teórica e Computacional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Jéssica A Paes
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Cláudio X Machado
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.,Departamento de Criminalística, Instituto Geral de Perícias do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Henrique B Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil. .,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil. .,Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, RS, Brazil.
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Choe D, Cho S, Kim SC, Cho BK. Minimal genome: Worthwhile or worthless efforts toward being smaller? Biotechnol J 2015; 11:199-211. [DOI: 10.1002/biot.201400838] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/08/2015] [Accepted: 07/27/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Donghui Choe
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
- Intelligent Synthetic Biology Center; Daejeon Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
- Intelligent Synthetic Biology Center; Daejeon Republic of Korea
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