Structural analyses of a hypothetical minimal metabolism

Gabaldón, Toni; Peretó, Juli; Montero, Francisco; Gil, Rosario; Latorre, Amparo; Moya, Andrés

doi:10.1098/rstb.2007.2067

Cited by 40 publications

(50 citation statements)

References 44 publications

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“…This may be the reason, for example, that development is slow; complex programs, executed slowly, lead to a more robust outcome than simple processes proceeding quickly. Conversely, simulations of minimal metabolic networks suggest that they are more fragile than naturally evolved ones (Gabaldó n et al 2007). As engineered systems begin to achieve complexity comparable to biological ones, explorations of the tradeoff between complexity and robustness in natural and engineered biological systems may have lessons to teach engineers of complex mechanical and electronic systems too.…”

Section: Resultsmentioning

confidence: 99%

Synthetic Morphogenesis

Teague¹,

Guye

Weiss

2016

Cold Spring Harb Perspect Biol

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Throughout biology, function is intimately linked with form. Across scales ranging from subcellular to multiorganismal, the identity and organization of a biological structure's subunits dictate its properties. The field of molecular morphogenesis has traditionally been concerned with describing these links, decoding the molecular mechanisms that give rise to the shape and structure of cells, tissues, organs, and organisms. Recent advances in synthetic biology promise unprecedented control over these molecular mechanisms; this opens the path to not just probing morphogenesis but directing it. This review explores several frontiers in the nascent field of synthetic morphogenesis, including programmable tissues and organs, synthetic biomaterials and programmable matter, and engineering complex morphogenic systems de novo. We will discuss each frontier's objectives, current approaches, constraints and challenges, and future potential.

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Section: Resultsmentioning

confidence: 99%

Synthetic Morphogenesis

Teague¹,

Guye

Weiss

2016

Cold Spring Harb Perspect Biol

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“…Fortunately, genome-scale metabolic models exist that can be used to predict the set of metabolic functions required for a minimal organism to be viable in a specified chemical environment. Metabolic modeling has been applied to analyze the connectivity and behavior of the simple metabolic network included in Gill's minimal set of 206 genes [44]. This work found the simple network to function successfully as a concerted whole and behave similarly to natural metabolic networks.…”

Section: Model-driven Design Of a Minimal Metabolismmentioning

confidence: 99%

Building the blueprint of life

Henry

Overbeek²,

Stevens

2010

Biotechnology Journal

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With recent breakthroughs in experimental microbiology making it possible to synthesize and implant an entire genome to create a living cell, the challenge of constructing a working blueprint for the first truly minimal synthetic organism is more important than ever. Here we review the significant progress made in the design and creation of a minimal organism. We discuss how comparative genomics, gene essentiality data, naturally small genomes, and metabolic modeling are all being applied to produce a catalogue of the biological functions essential for life. We compare the minimal gene sets from three published sources with functions identified in 13 existing gene essentiality datasets. We examine how genome-scale metabolic models have been applied to design a minimal metabolism for growth in simple and complex media. Additionally, we survey the progress of efforts to construct a minimal organism, either through implementation of combinatorial deletions in Bacillus subtilis and Escherichia coli or through the synthesis and implantation of synthetic genomes.

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“…Using stoichiometric analysis of elementary flux modes (EFM), Gabaldón et al (2007) showed that 49 out of 50 enzymatic steps of a minimalist metabolism were essential for maintaining the stoichiometric coherence. Thus, this metabolic network had only one redundant chemical transformation revealing its true minimalist character.…”

Section: A Hierarchy Of Minimal Cells Based On Metabolic Complexitymentioning

confidence: 99%

“…However, from the metabolic point of view, our CMG defined just one of many possible minimal metabolic charts, which would depend on environmental conditions. Gabaldón et al (2007Gabaldón et al ( , 2008 further analyzed this particular minimalist metabolism, using graphtheory based methods and stoichiometric analysis.…”

Section: The Minimal Gene Set For Life Can Be Approached By Comparatimentioning

confidence: 99%

Small genomes and the difficulty to define minimal translation and metabolic machineries

Gil

Peretó

2015

Front. Ecol. Evol.

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Citation:Gil R and Peretó J (2015) Small genomes and the difficulty to define minimal translation and metabolic machineries. Front. Ecol. Evol. 3:123. doi: 10.3389/fevo.2015.00123 Small genomes and the difficulty to define minimal translation and metabolic machineries The notion of minimal life has sparked the interest of scientists in different fields, ranging from the origin-of-life research to biotechnology-oriented synthetic biology. Whether the interest is focused on the emergence of protocells out of prebiotic systems or the design of a cell chassis ready to incorporate new devices and functions, proposing minimal combinations of genes for life is not a trivial task. Using comparative genomics and biochemistry of endosymbionts (i.e., intracellular mutualistic symbionts) and intracellular parasites, we proposed a decade ago the core of a minimal gene set for a simple heterotrophic cell adapted to a chemically complex environment. In this work, we discuss the state-of-the-art of the definition of the minimal genome, based on our current knowledge about bacteria with naturally reduced genomes, including both endosymbionts and free-living cells. Any proposed minimal genome would be composed by a set of protein-coding and RNA genes involved in the flux of genetic information (from DNA to functional proteins) and a group of protein-coding sequences embodying a minimalist, stoichiometrically consistent metabolic network. Although the informational portion of the minimal genome is considered quasi-universal, previous proposals have not addressed the need of tRNA post-transcriptional modifications in order to perform their function. For this reason, we have focused on the essentiality of some enzymes involved in such modifications, in order to refine the set of informational genes. As for the metabolic aspect, an obvious difficulty is that there is no one minimal gene set for life but many, depending on the environment. Among cells with reduced genomes, we find a continuum of metabolic modes, from organic matter-dependent heterotrophy to the minimally demanding autotrophy. Both best-known cases of cells with small genomes, the endosymbionts and the ultra-small free-living bacteria, speak in favor of metabolic sharing as a strong force in genome reductive evolution. A hierarchy of minimal cells supported by different metabolic networks with a complexity inversely correlated with the chemical complexity of the environment can be postulated.

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Structural analyses of a hypothetical minimal metabolism

Cited by 40 publications

References 44 publications

Synthetic Morphogenesis

Synthetic Morphogenesis

Building the blueprint of life

Small genomes and the difficulty to define minimal translation and metabolic machineries

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