Stringent response of Escherichia coli: revisiting the bibliome using literature mining.

Microbial Informatics and Experimentation
Sónia CarneiroIsabel Rocha

Abstract

Understanding the mechanisms responsible for cellular responses depends on the systematic collection and analysis of information on the main biological concepts involved. Indeed, the identification of biologically relevant concepts in free text, namely genes, tRNAs, mRNAs, gene products and small molecules, is crucial to capture the structure and functioning of different responses. In this work, we review literature reports on the study of the stringent response in Escherichia coli. Rather than undertaking the development of a highly specialised literature mining approach, we investigate the suitability of concept recognition and statistical analysis of concept occurrence as means to highlight the concepts that are most likely to be biologically engaged during this response. The co-occurrence analysis of core concepts in this stringent response, i.e. the (p)ppGpp nucleotides with gene products was also inspected and suggest that besides the enzymes RelA and SpoT that control the basal levels of (p)ppGpp nucleotides, many other proteins have a key role in this response. Functional enrichment analysis revealed that basic cellular processes such as metabolism, transcriptional and translational regulation are central, but other str...Continue Reading

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Citations

Dec 21, 2012·Briefings in Bioinformatics·Mariana Neves, Ulf Leser
Nov 29, 2017·Applied and Environmental Microbiology·Nathan G WalworthDavid A Hutchins
Mar 7, 2020·Current Biology : CB·Hugo C BarretoIsabel Gordo
Dec 18, 2016·Metabolic Engineering·Zachary A KingBernhard O Palsson

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Methods Mentioned

BETA
GTPase
immunoprecipitation
PCR
array technology
x-ray
scintillation
electrophoresis
GTPases

Software Mentioned

Cytoscape viewer
Excel
EcoCyc
MultiFun
MI
PSI

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