Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera

Tom A. Mendum, Jane Newcombe (Collaborator), Ahmad A Mannan (Collaborator), Andrzej M Kierzek (Collaborator), Johnjoe McFadden (Corresponding Author)

Research output: Contribution to journalArticle

21 Citations (Scopus)
4 Downloads (Pure)

Abstract

Background
Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequences are available for several strains but our understanding of how these data relate to phenotype remains limited.

Results
To investigate the metabolism of N. meningitidis we generated and then selected a representative Tn5 library on rich medium, a minimal defined medium and in human serum to identify genes essential for growth under these conditions. To relate these data to a systems-wide understanding of the pathogen's biology we constructed a genome-scale metabolic network: Nmb_iTM560. This model was able to distinguish essential and non-essential genes as predicted by the global mutagenesis. These essentiality data, the library and the Nmb_iTM560 model are powerful and widely applicable resources for the study of meningococcal metabolism and physiology. We demonstrate the utility of these resources by predicting and demonstrating metabolic requirements on minimal medium, such as a requirement for phosphoenolpyruvate carboxylase, and by describing the nutritional and biochemical status of N. meningitidis when grown in serum, including a requirement for both the synthesis and transport of amino acids.

Conclusions
This study describes the application of a genome scale transposon library combined with an experimentally validated genome-scale metabolic network of N. meningitidis to identify essential genes and provide novel insight into the pathogen's metabolism both in vitro and during infection.
Original languageEnglish
Article numberR127
Number of pages15
JournalGenome Biology
Volume12
DOIs
Publication statusPublished - 30 Dec 2011

Fingerprint

Neisseria meningitidis
mutagenesis
Mutagenesis
serum
fitness
genome
pathogen
metabolism
Genome
Libraries
gene
pathogens
Essential Genes
Metabolic Networks and Pathways
Serum
Genes
genes
Phosphoenolpyruvate Carboxylase
commensal
phosphoenolpyruvate carboxylase

Keywords

  • neisseria-meningitidis
  • genome scale model
  • global mutagenesis

Cite this

Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera. / Mendum, Tom A.; Newcombe, Jane (Collaborator); Mannan, Ahmad A (Collaborator); Kierzek, Andrzej M (Collaborator); McFadden, Johnjoe (Corresponding Author).

In: Genome Biology, Vol. 12, R127, 30.12.2011.

Research output: Contribution to journalArticle

Mendum, Tom A. ; Newcombe, Jane ; Mannan, Ahmad A ; Kierzek, Andrzej M ; McFadden, Johnjoe. / Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera. In: Genome Biology. 2011 ; Vol. 12.
@article{aee0a1c29922499eb667f9b06be0489b,
title = "Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera",
abstract = "BackgroundNeisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequences are available for several strains but our understanding of how these data relate to phenotype remains limited.ResultsTo investigate the metabolism of N. meningitidis we generated and then selected a representative Tn5 library on rich medium, a minimal defined medium and in human serum to identify genes essential for growth under these conditions. To relate these data to a systems-wide understanding of the pathogen's biology we constructed a genome-scale metabolic network: Nmb_iTM560. This model was able to distinguish essential and non-essential genes as predicted by the global mutagenesis. These essentiality data, the library and the Nmb_iTM560 model are powerful and widely applicable resources for the study of meningococcal metabolism and physiology. We demonstrate the utility of these resources by predicting and demonstrating metabolic requirements on minimal medium, such as a requirement for phosphoenolpyruvate carboxylase, and by describing the nutritional and biochemical status of N. meningitidis when grown in serum, including a requirement for both the synthesis and transport of amino acids.ConclusionsThis study describes the application of a genome scale transposon library combined with an experimentally validated genome-scale metabolic network of N. meningitidis to identify essential genes and provide novel insight into the pathogen's metabolism both in vitro and during infection.",
keywords = "neisseria-meningitidis, genome scale model, global mutagenesis",
author = "Mendum, {Tom A.} and Jane Newcombe and Mannan, {Ahmad A} and Kierzek, {Andrzej M} and Johnjoe McFadden",
year = "2011",
month = "12",
day = "30",
doi = "10.1186/gb-2011-12-12-r127",
language = "English",
volume = "12",
journal = "Genome Biology",
issn = "1474-760X",
publisher = "BioMed Central",

}

TY - JOUR

T1 - Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera

AU - Mendum, Tom A.

AU - McFadden, Johnjoe

A2 - Newcombe, Jane

A2 - Mannan, Ahmad A

A2 - Kierzek, Andrzej M

PY - 2011/12/30

Y1 - 2011/12/30

N2 - BackgroundNeisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequences are available for several strains but our understanding of how these data relate to phenotype remains limited.ResultsTo investigate the metabolism of N. meningitidis we generated and then selected a representative Tn5 library on rich medium, a minimal defined medium and in human serum to identify genes essential for growth under these conditions. To relate these data to a systems-wide understanding of the pathogen's biology we constructed a genome-scale metabolic network: Nmb_iTM560. This model was able to distinguish essential and non-essential genes as predicted by the global mutagenesis. These essentiality data, the library and the Nmb_iTM560 model are powerful and widely applicable resources for the study of meningococcal metabolism and physiology. We demonstrate the utility of these resources by predicting and demonstrating metabolic requirements on minimal medium, such as a requirement for phosphoenolpyruvate carboxylase, and by describing the nutritional and biochemical status of N. meningitidis when grown in serum, including a requirement for both the synthesis and transport of amino acids.ConclusionsThis study describes the application of a genome scale transposon library combined with an experimentally validated genome-scale metabolic network of N. meningitidis to identify essential genes and provide novel insight into the pathogen's metabolism both in vitro and during infection.

AB - BackgroundNeisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequences are available for several strains but our understanding of how these data relate to phenotype remains limited.ResultsTo investigate the metabolism of N. meningitidis we generated and then selected a representative Tn5 library on rich medium, a minimal defined medium and in human serum to identify genes essential for growth under these conditions. To relate these data to a systems-wide understanding of the pathogen's biology we constructed a genome-scale metabolic network: Nmb_iTM560. This model was able to distinguish essential and non-essential genes as predicted by the global mutagenesis. These essentiality data, the library and the Nmb_iTM560 model are powerful and widely applicable resources for the study of meningococcal metabolism and physiology. We demonstrate the utility of these resources by predicting and demonstrating metabolic requirements on minimal medium, such as a requirement for phosphoenolpyruvate carboxylase, and by describing the nutritional and biochemical status of N. meningitidis when grown in serum, including a requirement for both the synthesis and transport of amino acids.ConclusionsThis study describes the application of a genome scale transposon library combined with an experimentally validated genome-scale metabolic network of N. meningitidis to identify essential genes and provide novel insight into the pathogen's metabolism both in vitro and during infection.

KW - neisseria-meningitidis

KW - genome scale model

KW - global mutagenesis

U2 - 10.1186/gb-2011-12-12-r127

DO - 10.1186/gb-2011-12-12-r127

M3 - Article

VL - 12

JO - Genome Biology

JF - Genome Biology

SN - 1474-760X

M1 - R127

ER -