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Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes
Garza, D.R.; von Meijenfeldt, F. A.B.; van Dijk, B.; Boleij, A.; Huynen, M.A.; Dutilh, B.E. (2022). Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes. BMC Ecology and Evolution 22(1). https://dx.doi.org/10.1186/s12862-022-02052-3

Bijhorende data:
In: BMC Ecology and Evolution. BioMed Central Ltd.: London. ISSN 2730-7182, meer
Peer reviewed article  

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Author keywords
    Pan-genome evolution; Reactomes; Genome-scale metabolic models; Prokaryote evolution; Gene frequency distribution

Auteurs  Top 
  • Garza, D.R.
  • von Meijenfeldt, F. A.B., meer
  • van Dijk, B.
  • Boleij, A.
  • Huynen, M.A.
  • Dutilh, B.E.

Abstract
    Background: Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces.Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of gene products with each other and with the organism’s external environment. However, to date, conceptual models of pan-genome dynamics often represent genes as independent unitsand provide limited information about their mechanistic interactions.Results: We simulated the stochastic process of gene-loss using the pooled genome-scale metabolic reaction networks of 46 taxonomically diverse bacterial and archaeal families as proxies for their pan-genomes. The frequency bywhich reactions are retained in functional networks when stochastic gene loss is simulated in diverse environmentsallowed us to disentangle the metabolic reactions whose presence depends on the metabolite composition of theexternal environment (constrained by “nutrition”) from those that are independent of the environment (constrainedby “nature”). By comparing the frequency of reactions from the frst group with their observed frequencies in bacterialand archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages.Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diversebiomes as assessed by global environmental sequencing datasets.Conclusion: We introduce a computational framework for analyzing and interpreting pan-reactomes that providesnovel insights into the ecological and evolutionary drivers of pan-genome dynamics.

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