Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants

Abstract

Helicobacter pylori is a human gastric pathogen infecting almost half of the world population. Herein, we present an updated version of the metabolic reconstruction of H. pylori strain 26695 based on the revised genome annotation and new experimental data. This reconstruction, iIT341 GSM/GPR, represents a detailed review of the current literature about H. pylori as it integrates biochemical and genomic data in a comprehensive framework. In total, it accounts for 341 metabolic genes, 476 intracellular reactions, 78 exchange reactions, and 485 metabolites. Novel features of iIT341 GSM/GPR include (i) gene-protein-reaction associations, (ii) elementally and charge-balanced reactions, (iii) more accurate descriptions of isoprenoid and lipopolysaccharide metabolism, and (iv) quantitative assessments of the supporting data for each reaction. This metabolic reconstruction was used to carry out in silico deletion studies to identify essential and conditionally essential genes in H. pylori. A total of 128 essential and 75 conditionally essential metabolic genes were identified. Predicted growth phenotypes of single knockouts were validated using published experimental data. In addition, in silico double-deletion studies identified a total of 47 synthetic lethal mutants involving 67 different metabolic genes in rich medium.

FIG. 1.

Distributions of genes (A) and reactions (B) over subsystems. The reactions of each subsystem in panel B are additionally subcategorized into gene-associated and non-gene-associated reactions. w/o, without.

FIG. 2.

Schematic representation of biotin biosynthesis. The dotted line represents the hypothetical downstream conversion of S-adenosyl-4-methylthio-2-oxobutanoate (amob) (43). Metabolites a and b represent 2-oxobut-3-enoate and 5′-methylthioadenosine, respectively. Reaction and metabolite abbreviations used here can be found in Table S2 in the supplemental data.

FIG. 3.

Results of the in silico single-deletion studies. The growth rate percentages of lethal and nonlethal deletions are shown for each medium. The reduced-growth section indicates the percentage of mutants displaying reduced growth compared to that of the wild type in the same medium. See Table 1, footnote a, for medium abbreviations.

FIG. 4.

Distributions of essential genes (A) and conditionally essential genes (B) over subsystems. The number of essential or conditionally essential genes per subsystem is shown in parentheses.

FIG. 5.

Variation in growth rate observed in single knockouts of nonessential genes. The percentage growth rate was calculated relative to that of the wild type under the same medium conditions. The reaction abbreviations used here can be found in Table S2 of the supplemental data at http://gcrg.ucsd.edu/organisms/hpylori.html). See Table 1, footnote a, for medium abbreviations.