Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

Metabolic flux analysis (MFA) is
considered to be the gold standard
for determining the intracellular flux distribution of biological
systems. The majority of work using MFA has been limited to core models
of metabolism due to challenges in implementing genome-scale MFA and
the undesirable trade-off between increased scope and decreased precision
in flux estimations. This work presents a tunable workflow for expanding
the scope of MFA to the genome-scale without trade-offs in flux precision.
The genome-scale MFA model presented here, iDM2014, accounts for 537
net reactions, which includes the core pathways of traditional MFA
models and also covers the additional pathways of purine, pyrimidine,
isoprenoid, methionine, riboflavin, coenzyme A, and folate, as well
as other biosynthetic pathways. When evaluating the iDM2014 using
a set of measured intracellular intermediate and cofactor mass isotopomer
distributions (MIDs), it was found that
a total of 232 net fluxes of central and peripheral metabolism could
be resolved in the E. coli network. The increase
in scope was shown to cover the full biosynthetic route to an expanded
set of bioproduction pathways, which should facilitate applications
such as the design of more complex bioprocessing strains and aid in
identifying new antimicrobials. Importantly, it was found that there
was no loss in precision of core fluxes when compared to a traditional
core model, and additionally there was an overall increase in precision
when considering all observable reactions.

代谢流分析（Metabolic flux analysis, MFA）被认为是确定生物系统胞内代谢流分布的金标准。由于基因组规模代谢流分析（genome-scale MFA）的实施存在技术挑战，且流估计过程中存在研究范围扩大与精度降低之间的不尽如人意的权衡，绝大多数基于MFA的研究仅局限于代谢核心模型。本研究提出了一种可调工作流，可在不牺牲代谢流估计精度的前提下，将MFA的研究范围拓展至基因组规模。本文提出的基因组规模MFA模型iDM2014共涵盖537个净反应，既包含传统MFA模型的核心代谢途径，同时覆盖了嘌呤、嘧啶、类异戊二烯、甲硫氨酸、核黄素、辅酶A、叶酸以及其他生物合成途径。利用一组实测的胞内中间代谢物与辅因子质量同位素分布（mass isotopomer distributions, MIDs）对iDM2014进行评估时，发现大肠杆菌（E. coli）代谢网络中可解析得到中央与外周代谢共232个净流。该模型的范围拓展可覆盖一套扩展的生物生产途径的完整生物合成路线，这将助力更复杂生物加工菌株的设计，同时有助于新型抗菌剂的筛选与发现。值得注意的是，相较于传统核心模型，核心代谢流的精度并未出现任何损失；而在纳入所有可观测反应进行分析时，整体精度还实现了提升。