Annotation and metabolic network construction of the Probiotic Strain Lactobacillus acidophilus ATCC 4356. Visualization in XOMEQ platform

LEONARDO LUCIANNA; GERMÁN BURGUENER; EZEQUIEL SOSA; MARÍA MERCEDES PALOMINO; MARIANA ALLIEVI; SANDRA M RUZAL; ADRIÁN TURJANSKI; MARCELO MARTÍ; DARÍO FERNANDEZ DO PORTO

Bahía Blanca

Conferencia; VI Argentinian Conference on Bioinformatics and Computational Biology; 2015

A2B2C(Asociación Argentina de Bioinformática y Biología Computacional)

Annotation and metabolic network construction of the Probiotic Strain Lactobacillus acidophilus ATCC 4356.Visualization in XOMEQ platformLeonardo Lucianna 1 , Germán Burguener 1 , Ezequiel Sosa 1 , María Mercedes Palomino 2 , Mariana Allievi 2 , Sandra Ruzal 2 ,Adrián Turjanski 1,3 , Marcelo Martí 1,2 , Darío Fernández Do Porto 11 Plataforma de Bioinformática Argentina, Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, UBA2 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA IQUIBICEN,CONICET3 Instituto de Química, Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICETThe original Lactobacillus acidophilus strain ATCC 4356 was isolated in 1900 from human infant feces [1]. L.acidophilus ATCC 4356 is an important inhabitant of the gastrointestinal tract with reported probiotic properties[2?4]. The genome sequence was obtained using a wholegenomeshotgun strategy with a HiSeq 1500 Illuminaat Instituto de Agrobiotecnolgía de Rosario (INDEAR), Argentina. Assembly was done with Stampy v1.0.27 [5],using L. acidophilus La14as a template. This assembly generated 1 scaffold with 1,02% of gaps. The draftgenome is 1,991,579 bp in length, and the GC content is 34.64%. Genomic annotations were assignedautomatically by our own Annotation Pipeline [6]. The annotation predicted 1,882 coding sequences (CDSs)and 69 structural RNAs (61 tRNAs). A total of 17 CDSs (0.9%) were classified as hypothetical proteins and 407(21.6%) as uncharacterized proteins.Afterwards, we used Pathway tools [7] and manual revision to build a comprehensive metabolic network (MN)of the bacteria. The software automatically associates genes with reactions, based on enzyme code (EC)numbers and function descriptions contained in the GenBank file of the annotated genome. Curation includesdeleting inappropriate pathways, adding missing pathways with experimental evidence, or filling existingpathways (by using the hole filler tool of pathway tools). After MN construction, a Python script was written togenerate a list of all products and reactants involved in this network, and the metabolic network wasrepresented as a graph with Cytoscape 2.8.3 4 [8]. These allow us to analyze the uniqueness (I.e being achoke point) and centrality of the predicted reactions. As reported [9], there is significant coincidence betweenessential genes and genes associated to choke points and central reactions.As a last step in our procedure, the annotated genome was deployed in our server: XOMEQ platform( http://www.biargentina.com.ar/xomeq/ ). XomeQis an easytousewebbasedplatform which allows genomewide based data consolidation from diverse sources at different processing stages including assembly,annotation, comparative genomics, metabolic pathway recognition, and modeling of proteins? structure. All thisinformation can be easily navigated by position or by using keywords and different gene based annotations,including ontology (Figure 1) and cog terms, protein family and metabolic pathways.Figure 1 : Gene Ontology view for proteins, with cellular metabolic process annotations and its subcategoriesReferences1. Moro E: Ueber den Bacillus acidophilus. Jahrb Kinderheilk 1900, 52 : 38 ?55.2. Chen X, Xu J, Shuai J, Chen J, Zhang Z, Fang W: The Slayerproteins of Lactobacillus crispatus strainZJ001 is responsible for competitive exclusion against Escherichia coli O157:H7 and Salmonellatyphimurium. Int J Food Microbiol 2007, 115 :307?312.3. Foligne B, Nutten S, Grangette C, Dennin V, Goudercourt D, Poiret S, Dewulf J, Brassart D, Mercenier A, Pot B:Correlation between in vitro and in vivo immunomodulatory properties of lactic acid bacteria. World JGastroenterol 2007, 13 :236 ?243.4. RestaLenertS, Barrett KE: Live probiotics protect intestinal epithelial cells from the effects of infection withenteroinvasive Escherichia coli (EIEC). Gut 2003, 52 :988 997.5. Lunter G., Goodson M: S tampy: a statistical algorithm for sensitive and fast mapping of Illuminasequence reads. Genome Res. 2011, 21 :936939.6. Burguener GF, Maldonado MJ, Revale S, Fernández Do Porto D, Rascován N, Vázquez M, Farías ME, MartiMA, Turjanski AG: D raft genome sequence of the polyextremophilic H alorubrum sp. strain AJ67, i solatedfrom hyperarsenic lakes in the Argentinian Puna . Genome Announc. 2014 2(1) :e0109613.7. Karp P, Paley S, Romero P: The Pathway Tools Software. Bioinformatics 2002, 18 :S225322002.8. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T:Cytoscape: a software environment for integrated models of biomolecular interaction networks.Genome Res. 2003, 13(11) :2498504.9. Singh S, Joshi P, Chopade BA: C hoke point analysis of the metabolic pathways of Acinetobacter baylyi:A genomics approach to assess potential drug targets. Journal of Bioinformatics and Sequence Analysis2009, 1(3) : 041045.