Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis

• Published in: PLoS computational biology Vol. 10; no. 9; p. e1003848
• Main Authors: Yang, Hong, Krumholz, Elias W., Brutinel, Evan D., Palani, Nagendra P., Sadowsky, Michael J., Odlyzko, Andrew M., Gralnick, Jeffrey A., Libourel, Igor G. L.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.09.2014; Public Library of Science (PLoS)
• Subjects: Agreements; Automation; Binding sites; Biology and Life Sciences; Deoxyribonucleic acid; DNA; DNA Transposable Elements - genetics; DNA, Bacterial - analysis; DNA, Bacterial - genetics; Gene mutations; Gene Regulatory Networks - genetics; Genes; Genetic aspects; Genetic testing; Genome, Bacterial - genetics; Genomes; Genomics; High-Throughput Nucleotide Sequencing - methods; Metabolic Networks and Pathways - genetics; Metabolism; Metabolites; Methods; Mutagenesis; Mutagenesis, Site-Directed; Mutation; Physiological aspects; Proteins; Shewanella; Shewanella - genetics; Shewanella - metabolism; Transposons; United States
• DOI: 10.1371/journal.pcbi.1003848
• ISSN: 1553-7358; 1553-734X

Transposon mutagenesis, in combination with parallel sequencing, is becoming a powerful tool for en-masse mutant analysis. A probability generating function was used to explain observed miniHimar transposon insertion patterns, and gene essentiality calls were made by transposon insertion frequency analysis (TIFA). TIFA incorporated the observed genome and sequence motif bias of the miniHimar transposon. The gene essentiality calls were compared to: 1) previous genome-wide direct gene-essentiality assignments; and, 2) flux balance analysis (FBA) predictions from an existing genome-scale metabolic model of Shewanella oneidensis MR-1. A three-way comparison between FBA, TIFA, and the direct essentiality calls was made to validate the TIFA approach. The refinement in the interpretation of observed transposon insertions demonstrated that genes without insertions are not necessarily essential, and that genes that contain insertions are not always nonessential. The TIFA calls were in reasonable agreement with direct essentiality calls for S. oneidensis, but agreed more closely with E. coli essentiality calls for orthologs. The TIFA gene essentiality calls were in good agreement with the MR-1 FBA essentiality predictions, and the agreement between TIFA and FBA predictions was substantially better than between the FBA and the direct gene essentiality predictions.