Integrating high-throughput and computational data elucidates bacterial networks

Abstract

The flood of high-throughput biological data has led to the expectation that computational (or in silico) models can be used to direct biological discovery, enabling biologists to reconcile heterogeneous data types, find inconsistencies and systematically generate hypotheses1,2,3. Such a process is fundamentally iterative, where each iteration involves making model predictions, obtaining experimental data, reconciling the predicted outcomes with experimental ones, and using discrepancies to update the in silico model. Here we have reconstructed, on the basis of information derived from literature and databases, the first integrated genome-scale computational model of a transcriptional regulatory and metabolic network. The model accounts for 1,010 genes in Escherichia coli, including 104 regulatory genes whose products together with other stimuli regulate the expression of 479 of the 906 genes in the reconstructed metabolic network. This model is able not only to predict the outcomes of high-throughput growth phenotyping and gene expression experiments, but also to indicate knowledge gaps and identify previously unknown components and interactions in the regulatory and metabolic networks. We find that a systems biology approach that combines genome-scale experimentation and computation can systematically generate hypotheses on the basis of disparate data sources.

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Figure 1: Growth phenotype study.
Figure 2: Characterization of the regulatory network related to the aerobic–anaerobic shift.
Figure 3: Biological network elucidation by a model-centric approach.

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Acknowledgements

We thank K. Stadsklev and A. Fleming for assistance with computation; Z. Zhang and A. Raghunathan for experimental assistance; the Perna and Blattner laboratories for access to the high-throughput phenotyping data in the ASAP database; and the NIH for funding and support. M.W.C. and B.O.P. designed the project and were involved in all phases of the study; E.M.K. carried out experiments; J.L.R. reconstructed the model, ran simulations and did the phenotyping analysis; M.J.H. did the statistical analysis of the gene expression data.

Author information

Correspondence to Bernhard O. Palsson.

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Competing interests

UCSD has licensed patent applications to a spin-off company, Genomatica, that may relate to the present paper. UCSD and some of the authors hold shares in Genomatica.

Supplementary information

Suppplementary Notes

Text describing the contents of all the supplementary Excel files in more detail, together with a case-by-case study of inconsistent environments and strains from Figure 1 in the main text, and a completed MIAME checklist. (DOC 118 kb)

Supplementary Data 1

Regulatory Model Rules (iMC1010v1). A list of the genes accounted for by the model, together with the regulatory rules, if any. (XLS 126 kb)

Supplementary Data 2

Simulation Parameters. A detailed list of all parameters used to run the simulations described in the manuscript. (XLS 47 kb)

Supplementary Data 3

Regulatory Model Abbreviations. Abbreviations used in the model to represent metabolites or metabolic reactions. (XLS 81 kb)

Supplementary Data 4

Phenotype-Model Comparison. A more detailed version of the phenotype model comparison shown in Figure 1 of the main text. (XLS 220 kb)

Supplementary Data 5

Phenotype sensitivity analysis. Sensitivity analysis of the phenotype cutoff parameter. (XLS 19 kb)

Supplementary Data 6

Anaerobic-aerobic culture data. Growth, substrate uptake and by-product secretion of wild-type and 6 knockout E. coli strains under aerobic and anaerobic conditions. (XLS 18 kb)

Supplementary Data 7

Normalized Array Data. A table with all the dChip-normalized array data from our experiments. (XLS 9871 kb)

Supplementary Data 8

Detailed hypothesis list. A detailed list of the regulatory interaction hypotheses generated by this study. Includes new regulatory rules implemented in iMC1010v2. (XLS 54 kb)

Supplementary Data 9

qPCR cross-validation. Results of qPCR validation of various changes in gene expression from the microarray data set. (XLS 17 kb)

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