Modeling leucine's metabolic pathway and knockout prediction improving the production of surfactin, a biosurfactant from Bacillus subtilis

Abstract

A Bacillus subtilis mutant strain overexpressing surfactin biosynthetic genes was previously constructed. In order to further increase the production of this biosurfactant, our hypothesis is that the surfactin precursors, especially leucine, must be overproduced. We present a three step approach for leucine overproduction directed by methods from computational biology. Firstly, we develop a new algorithm for gene knockout prediction based on abstract interpretation, which applies to a recent modeling language for reaction networks with partial kinetic information. Secondly, we model the leucine metabolic pathway as a reaction network in this language, and apply the knockout prediction algorithm with the target of leucine overproduction. Out of the 21 reactions corresponding to potential gene knockouts, the prediction algorithm selects 12 reactions. Six knockouts were introduced in B. subtilis 168 derivatives strains to verify their effects on surfactin production. For all generated mutants, the specific surfactin production is increased from 1.6-to 20.9-fold during the exponential growth phase, depending on the medium composition. These results show the effectiveness of the knockout prediction approach based on formal models for metabolic reaction networks with partial kinetic information, and confirms our hypothesis that precursors supply is one of the main parameters to optimize surfactin overproduction. Keywords: Abstract interpretation · Bacillus subtilis · Knockout prediction · Modeling language · SurfactinCorresponding author: Dr. François Coutte, Research Institute for Food and Biotechnology -Charles Viollette, Polytech-Lille, Université de Lille, Sciences et Technologies, 59655 Villeneuve d'Ascq, France. E-mail: francois.coutte@polytech-lille.fr Abbreviations: Acyl-CoA, acyl coenzyme A; Akb, L-2-amino-acetoacetate; BCAA, branched chain amino acid; Glu, glutamate; Gtp, guanosine triphosphate; Ile, isoleucine; Ket a , 2-keto-3-methylvalerate;Ket b , 2-keto-isovalerate; Ket c , 2-keto-isocaproate; Leu, leucine; NRPS, nonribosomal peptide synthetase; OxoGlu, oxoglutarate; P Ilv-Leu , ilv-leu operon promoter; Pyr, pyruvate; Thr, threonine; Val, valine; XML, eXtensible Markup Language; XSLT, eXtensible Stylesheet Language Transformations Biotechnology JournalSupporting information available online * These authors contributed equally to this work. Biotechnol. J. 2015Biotechnol. J. , 10, 1216Biotechnol. J. -1234 surfactin is composed of a ring of seven amino acid residues connected to a β-hydroxylated fatty acid chain of different length and isomery [1,2]. The peptide moiety contains four leucines (Fig. 1). Genetic engineering of B. subtilis has already been made in order to increase the lipopeptide production. In previous work [3], the overproduction of surfactin was obtained by replacing the native promoter of the surfactin operon (srfA) by a constitutive one and disrupted the plipastatin operon (ppsA) to save the precursor availability. The same approach was recently developed for the mycosubtilin producti...

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