Comparative genome sequence analysis of two Lactobacillus curvatus strains

TERÁN, L; ARISTIMUÑO FICOSECO, C; HÉBERT, E.M,; SESMA, F; FADDA S

Rosario

Congreso; 4to. Congreso Argentino de Bioinformática y Biología Computacional (4CAB2C) y 4ta. Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (SolBio); 2013

Terán, L.C.; Aristimuño, C.; Hébert, E.; Sesma, F.; Fadda, S. & Raya, R. ?Comparative genome sequence analysis of two Lactobacillus curvatus strains?. 4to. Congreso Argentino de Bioinformática y Biología Computacional (4CAB2C) y 4ta. Conferencia Internaci

Background Lactobacillus curvatus involves microorganisms associated with fermented meat products, vacuum-packaged refrigerated meat and fish. This species possess interesting technological features to be applied as starter and bioprotective cultures for meat and meat products. L. curvatus is phylogenetically closely related to Lactobacillus sakei, Lactobaillus fuchuensis and Lactobacillus graminis. Until today, only the genome of L. sakei (strain 23K) has been completely sequenced and annotated. Comparative genome analysis of L. curvatus CRL705 with the closely related L. sakei 23K strain revealed that they are highly similar. However, 52 protein-encoding genes were unique in L. curvatus CRL705 [1]. In the present work, the genomes of two strains, L. curvatus strain CRL 705 isolated from an Argentinean artisanal fermented sausage and the neotype[S1]  strain CRL 1000 were analyzed.   Materials and methods The Genome annotation was performed according to standard operating procedures (SOPs) for prokaryotic annotation from ISGA, the RAST annotation server, Glimmer 3.02 modeling software package, tRNAscan-SE 1.21, and RNAmmer 1.2. The comparative analysis between the genome of L. curvatus CRL 705 and the available, non-published genome of L. curvatus CRL 1000 (188 contigs) was performed with BLAST and in a manual way.   Results The L. curvatus CRL705 genome was sequenced (23-fold coverage) by using a whole-genome shotgun (WGS) strategy (198,804 total reads; 80 Mb) with a 454 GS Titanium pyrosequencer at INDEAR, Argentina. The assembly was performed using a 454 Newbler 2.5.3 assembler, giving 128 large contigs. The draft genome of the strain CRL705 is a single circular chromosome of 1,833,251 bases, with a mean GC content of 41.9%, and two circular plasmids, pRC12 (12,342 bp) and pRC18 (18,664 bp; accession number AF200347.3), which have GC contents of 43.9 and 34.4%, respectively. The genome of the neotype strain CRL 1000 counts with 188 contigs. The alignments of sequences between both strains, CRL 705 and CRL 1000, were highly similar (agregar que en crl 1000 phage sequences were detected, but not crisprs[S2] .   Conclusions The similarity of both genome sequences will allow completing them with primer design, PCR reactions and new sequencing. These data would be very useful to predict unknown metabolic/technological potential of these strains, such as the existence of a specialized gene catalog related to the ability to survive and compete in meat environments or to overcoming harsh conditions of meat processing. In addition, experimentally proven functions by means of proteomic studies could corroborate them thereby confirming the predicting value of genome data mining.   Reference 1.     Hebert E, Saavedra L, Taranto MP, Mozzi F, Magni C, Nader ME, Font de Valdez G, Sesma F, Vignolo G, Raya RR: Genome sequence of the bacteriocin-producing Lactobacillus curvatus strain CRL705. J Bacteriol. 2011, 194:538-539.    [S1]Neotype ya implica que es una cepa derivada de la anterior??  [S2]Quizas agregar si se encontraron diferencias relacionadas a sus diferencias fenotípicas?.