Exploration of the core metabolism of symbiotic bacteria

Cecilia Coimbra Klein,Christian Gautier,Hubert Charles,Janice Kielbassa,Ludovic Cottret,Ana Tereza Ribeiro De Vasconcelos,Marie-France Sagot,Vincent Lacroix

doi:10.1186/1471-2164-13-438

Abstract

BackgroundA large number of genome-scale metabolic networks is now available for many organisms, mostly bacteria. Previous works on minimal gene sets, when analysing host-dependent bacteria, found small common sets of metabolic genes. When such analyses are restricted to bacteria with similar lifestyles, larger portions of metabolism are expected to be shared and their composition is worth investigating. Here we report a comparative analysis of the small molecule metabolism of symbiotic bacteria, exploring common and variable portions as well as the contribution of different lifestyle groups to the reduction of a common set of metabolic capabilities.ResultsWe found no reaction shared by all the bacteria analysed. Disregarding those with the smallest genomes, we still do not find a reaction core, however we did find a core of biochemical capabilities. While obligate intracellular symbionts have no core of reactions within their group, extracellular and cell-associated symbionts do have a small core composed of disconnected fragments. In agreement with previous findings in Escherichia coli, their cores are enriched in biosynthetic processes whereas the variable metabolisms have similar ratios of biosynthetic and degradation reactions. Conversely, the variable metabolism of obligate intracellular symbionts is enriched in anabolism.ConclusionEven when removing the symbionts with the most reduced genomes, there is no core of reactions common to the analysed symbiotic bacteria. The main reason is the very high specialisation of obligate intracellular symbionts, however, host-dependence alone is not an explanation for such absence. The composition of the metabolism of cell-associated and extracellular bacteria shows that while they have similar needs in terms of the building blocks of their cells, they have to adapt to very distinct environments. On the other hand, in obligate intracellular bacteria, catabolism has largely disappeared, whereas synthetic routes appear to have been selected for depending on the nature of the symbiosis. As more genomes are added, we expect, based on our simulations, that the core of cell-associated and extracellular bacteria continues to diminish, converging to approximately 60 reactions.

Highlights

A large number of genome-scale metabolic networks is available for many organisms, mostly bacteria
Content and connectivity of the core metabolism of Cell Associated (CA) and EXTRA In the analyses of each lifestyle group, we did not find a core of reactions for the INTRA, we found it for the EXTRA and CA
Considering the proportion of biosynthesis and degradation reactions in the variable metabolism, we find that it is quite similar in E. coli (36% biosynthesis and 35% degradation) and the CA and EXTRA bacteria, but the numbers are quite different for obligate intracellular bacteria (62% biosynthesis and 24% degradation)

Summary

Introduction

A large number of genome-scale metabolic networks is available for many organisms, mostly bacteria. In comparative analyses of reaction sets instead of genes, NOGD has a reduced impact because different orthologous families encoding a single enzymatic capability are often represented by a same reaction Another possible explanation for incomplete pathways is the use of different alternative routes, which recently have been defined as alternologs (i.e., branches that proceed via different metabolites and converge to the same end product) [18]. Since metabolism is a core function expected to be required for sustaining life [19], and the core size may continue decreasing as more genome sequences appear [9,20], alternative approaches relaxing the requirement for ubiquity were proposed for analysing either prokaryotes [9,13,21,22] or species from the three domains of life [20,23,24] One such example is the search for proteins commonly present (persistent) instead of strictly conserved everywhere [20]. On the other hand, conserved portions of metabolism are found in lifestyle groups of bacteria [3]

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