METACONE:一种可扩展的框架,用于探索代谢网络的转换
Álvaro Altamirano1, Ignacio Tapia1, Vicente Acuña2
1Departamento de Ingeniería Química y Bioprocesos, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago de Chile, 7820436, Región Metropolitana, Chile.
Computational biology and chemistry
|August 12, 2025
概括
METACONE是一个新的算法,可以有效计算大型生物网络中代谢转化模式的代表性基础. 该工具有助于理解微生物代谢和复杂微生物群落内的相互作用.
科学领域:
- 系统生物学 系统生物学
- 代谢工程是代谢工程.
- 计算生物学 计算生物学
背景情况:
- 初级转换模式 (ECM) 提供了对代谢网络潜力的实用视图,但在基因组规模上计算起来具有挑战性.
- 现有的方法在基因组规模模型中难以处理大量的ECM,这限制了它们的应用.
- 可扩展性是分析复杂代谢相互作用的关键瓶.
研究的目的:
- 开发一个可扩展的算法,METACONE,用于计算代谢转化的代表性线性基础.
- 为探索微生物系统中的代谢能力和相互作用提供一个实用的工具.
- 为了克服在大型代谢网络中计算基本转换模式 (ECM) 的计算局限性.
主要方法:
- 开发了METACONE (METAbolic Conversion cOne for Network Exploration),这是一个用于计算转换圆的代表线性基础的新算法.
- 实现了METACONE的两个变体,使用基于解决一系列线性程序的不同启发式.
- 在不同尺寸的代谢模型上评估算法性能和可扩展性.
主要成果:
- 证明了METACONE在各种代谢模型上的可扩展性,证实了它对基因组规模网络的效率.
- 分析了计算的基础,以探索Escherichia coli在各种环境条件下的代谢能力,确定已知的代谢模式.
- 成功地将METACONE应用于一个微生物联盟 (*Phocaeicola dorei*和 *Lachnoclostridium symbiosum*),回顾了已知的交叉养,并表明了新的相互作用.
结论:
- METACONE为分析代谢转换模式提供了一个可扩展的解决方案,解决了详尽的ECM清单的局限性.
- 该算法有助于探索单个生物体和复杂微生物联盟中的代谢潜力和相互作用.
- 在系统生物学和合成生物学应用中,METACONE是促进对微生物新陈代谢的理解的宝贵工具.
相关概念视频
01:40Overview of Metabolism
31.9K
Living cells constantly carry out various chemical reactions which are necessary for their proper functioning. These reactions are interlinked to one another via multiple pathways. The collection of these chemical reactions is known as metabolism.
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...
31.9K
01:30Introduction to Metabolism
395
Metabolism encompasses all biochemical reactions in a living organism, facilitating both the breakdown and synthesis of biomolecules. These metabolic processes are categorized into catabolic and anabolic pathways, which operate in a coordinated manner to ensure energy balance and cellular function.Catabolic Pathways and Energy ReleaseCatabolic pathways involve the breakdown of complex macromolecules such as carbohydrates, lipids, and proteins into smaller structures like monosaccharides, fatty...
395
01:15Metabolism of Chemolithotrophs
168
Chemolithotrophs are microorganisms that obtain energy by oxidizing inorganic molecules such as hydrogen gas (H₂), ammonia (NH₃), reduced sulfur compounds (H₂S, S²⁻), and ferrous iron (Fe²⁺). Unlike heterotrophic organisms that rely on organic carbon, chemolithotrophs transfer electrons from these inorganic donors to the electron transport chain (ETC), generating a proton motive force (PMF) that drives ATP synthesis through oxidative phosphorylation.
168
01:21Overview of Protein Metabolism
1.8K
Proteins are broken down into amino acids during digestion. Unlike fats and carbohydrates, which are stored for later use, proteins are not. Instead, amino acids are either used to produce ATP through oxidation or contribute to the creation of new proteins for the growth and repair of the body. Any surplus amino acids from the diet are converted into glucose or triglycerides rather than excreted.
Amino acids play various roles in the body once they are absorbed into cells. They are restructured...
Amino acids play various roles in the body once they are absorbed into cells. They are restructured...
1.8K
00:52What is Metabolism?
117.5K
Overview
117.5K
01:19Overview of Carbohydrate Metabolism
1.8K
Carbohydrate metabolism is a fundamental biochemical process that ensures a constant supply of energy to living cells. The most important carbohydrate is glucose, which can be broken down via glycolysis to enter into the Krebs cycle and eventually lead to the production of ATP through oxidative phosphorylation.
Glucose transport into cells is facilitated by a family of transport proteins called GLUT (Glucose Transporters). GLUT4 is the primary glucose transporter for insulin-stimulated glucose...
Glucose transport into cells is facilitated by a family of transport proteins called GLUT (Glucose Transporters). GLUT4 is the primary glucose transporter for insulin-stimulated glucose...
1.8K