Comparative genomics of Lactobacillus curvatus

Abstract

Lactobacillus curvatus is a lactic acid bacterium phylogenetically related to L. sakei, L. graminis and L. fuchuensis. L. curvatus has been strongly related with meat environments but also found in different types of fermented food (seafood, vegetables, and cereals). This study uses comparative analyses of 13 available genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species; the plasmid DNA content of strain CRL 705, a well-known bacteriocin-producer, is also analyzed. Phylogenomic analysis, based on a coalescent model of evolution, delineate two major groups within the L. curvatus core genome, with lineage 1 represented by strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food. The biotechnological potential of L. curvatus strains have often been associated with bacteriocin production, to be applied as a starter and a bioprotective culture for meat products. Strain CRL705 harbors two low-copy number and theta replicating plasmids, pRC12 and pRC18; their DNA sequences have been determined and analyzed. pRC12 is a pUCL287-like plasmid that possesses iterons and the repA and repB genes for replication while in pRC18 the pUCL287-like repA gene is disrupted by an 11 kb insertion, encompassing genes coding for a 168 amino acid replication protein (named RepB?), several transposases/IS elements, and the lactocin Lac705 operon. This replicon could be potentially useful to construct cloning vectors within Lactobacillus. A region that includes an integrase-toxin-antitoxin system is also well conserved among the plasmidome of L. curvatus CRL705. These results will contribute to study the functionality of different genes and gain knowledge about many beneficial properties of lactobacilli as probiotic properties or functions important for food fermentation or biopreservation.