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Exploration of the core metabolism of symbiotic bacteria

Cecilia Coimbra Klein 1, 2, * Ludovic Cottret * Janice Kielbassa 1, 3, * Hubert Charles 1, * Christian Gautier 1, 3 Ana Tereza Ribeiro de Vasconcelos 1, 3, * Vincent Lacroix 1, 3, * Marie-France Sagot 1, 3, * 
* Corresponding author
1 BAMBOO - An algorithmic view on genomes, cells, and environments
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
3 Baobab
PEGASE - Département PEGASE [LBBE]
Abstract : Background
A 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.
We 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.
Even 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.
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Cecilia Coimbra Klein, Ludovic Cottret, Janice Kielbassa, Hubert Charles, Christian Gautier, et al.. Exploration of the core metabolism of symbiotic bacteria. BMC Genomics, BioMed Central, 2012, 13 (1), pp.438. ⟨10.1186/1471-2164-13-438⟩. ⟨hal-00784396⟩



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