Genomes, living styles, and pathogenicity of five <i>Mycobacterium</i> species.

<p>GI: gastrointestinal tract.</p

Recent studies of polymorphic single nucleotides in the human genome that are significantly associated with risk for or protection against leprosy.

<p>Note: the alleles and frequencies were from uninfected controls. For consistency, the odds ratios for the infected and uninfected were aligned by the major allele. SNP: single nucleotide polymorphism; Chr: chromosome. Ref. <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002544#pntd.0002544-Ali1" target="_blank">[47]</a> study: the haplotypes of four SNPs of rs2853694 (C), rs2853697 (A), rs3181216 (A), and rs3181225 (C) with a frequency of 0.34 were compared with their alternate three haplotypes, which had a combined frequency of 0.67.</p

Phylogenetic tree of several <i>Mycobacterium</i> species based on the amino acid sequences of rpoB protein.

<p>Adapted from <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002544#pntd.0002544-GomezValero1" target="_blank">[15]</a><b>.</b></p

Preferential inactivation of the PE/PPE family genes during the reductive evolution of <i>M. leprae</i>.

<p><i>M. leprae</i> vs <i>M. tuberculosis</i>: % PE/PPE genes, 9 of 1,604 versus 167 of 3,974, odds ratio = 0.13, χ² = 49.6, p<0.0001; % all PE/PPE genes and pseudogenes, 39 of 2,720 versus 167 of 3,974, odds ratio = 0.33, χ² = 41.5, p<0.0001.</p><p>Data from <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002544#pntd.0002544-Cole1" target="_blank">[7]</a> and <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002544#pntd.0002544-Cole2" target="_blank">[9]</a>.</p

Results of reductive evolution simulations under nutrient-limited and nutrient-rich conditions.

<p>Results of reductive evolution simulations under nutrient-limited and nutrient-rich conditions.</p

Network reconstruction protocol.

<p>Schematic representation of the reconstruction of ancestral and extant genome-scale metabolic networks of <i>S. glossinidius</i>. For a detailed explanation of the protocol, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030652#pone.0030652.s009" target="_blank">Methods S1</a>.</p

Comparison of the genome characteristics and <i>in silico</i> metabolic networks of <i>S. glossinidius</i>, <i>B. aphidicola</i> APS and <i>E. coli</i> K12.

<p>Comparison of the genome characteristics and <i>in silico</i> metabolic networks of <i>S. glossinidius</i>, <i>B. aphidicola</i> APS and <i>E. coli</i> K12.</p

Robustness analysis on <i>E. coli</i> K12, <i>S. glossinidius</i> and <i>B. aphidicola</i> BAp and <i>B. aphidicola</i> BCc metabolic networks.

<p>The fraction of essential and non-essential genes in single knockout simulations on different genome-scale metabolic networks is represented. Essential genes are defined as those genes whose deletion results in a decrease of more than 99% of the original biomass production.</p

Phosphoenolpyruvate carboxylase (PPC reaction) inactivation effect in <i>E. coli</i> K12 iJR904 and <i>S. glossinidius</i> metabolic networks.

<p>Reactions of glycolysis, TCA cycle, and transport and metabolization of external L-arginine are represented together with their corresponding reaction fluxes in FBA simulations. Red metabolites are included in the biomass equation. Black values correspond to reaction fluxes in the <i>E. coli</i> K12 iJR904 network with glucose as sole external carbon source. Red values correspond to reaction fluxes in the <i>E. coli</i> K12 iJR904 network under the same conditions but removing the PPC reaction. Green values correspond to reaction fluxes in the <i>S. glossinidius</i> ancestral network, with glucose as sole external carbon source. Purple values correspond to reaction fluxes in the <i>S. glossinidius</i> extant network with glucose and L-arginine as external metabolites. Reaction fluxes are represented in mmol gr DryWeight⁻¹ hr⁻¹.</p