bbc 2015

Recommendations

Info

BeNeLux Bioinformatics Conference – Antwerp, December 7-8 2015 Abstract ID: P Poster 10th Benelux Bioinformatics Conference bbc 2015 P64. THE COMPLETE GENOME SEQUENCE OF LACTOBACILLUS FERMENTUM IMDO 130101 AND ITS METABOLIC TRAITS RELATED TO THE SOURDOUGH FERMENTATION PROCESS Marko Verce, Koen Illeghems, Luc De Vuyst & Stefan Weckx * . Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium. * stefan.weckx@vub.ac.be The genome of the lactic acid bacterium species Lactobacillus fermentum IMDO 130101, capable of dominating sourdough fermentation processes, was sequenced, annotated, and curated. Further, this genome sequence of 2.09 Mbp was compared to other complete genomes of different strains of L. fermentum to elucidate the potential of L. fermentum IMDO 130101 as a sourdough starter culture strain. As opposed to the other strains, L. fermentum IMDO 130101 contained unique genes related to carbohydrate import and metabolism as well as a gene coding for a phenolic acid decarboxylase and a gene encoding a 4,6- -glucanotransferase. The latter enzyme activity may result in the production of isomalto/malto-polysaccharides. All these features make L. fermentum IMDO 130101 attractive for further study as a candidate sourdough starter culture strain. INTRODUCTION Lactobacillus fermentum is a heterofermentative lactic acid bacterium often found in fermented food products, including sourdough. Strain L. fermentum IMDO 130101, a dominant sourdough strain originally isolated from a rye sourdough (Weckx et al., 2010) and extensively described previously (e.g., Vrancken et al., 2008), was sequenced and compared to other L. fermentum strains with completed genomes to elucidate unique adaptations of the strain studied to the sourdough environment. METHODS High-quality genomic DNA was used to construct an 8-kb paired-end library for 454 pyrosequencing. The pyrosequencing reads were assembled using the GS De Novo Assembler version 2.5.3 with default parameters. Primers for gap closure were designed using CONSED 23.0, the gaps amplified with polymerase chain reaction (PCR) assays and the amplicons sequenced using Sanger sequencing. The sequences were imported into CONSED 23.0 and used to close the gaps. The genome was annotated using the automated genome annotation platform GenDB v2.2 (Meyer et al., 2003), followed by extensive manual curation. Publicly available genome sequences of L. fermentum F-6 (Sun et al., 2015), L. fermentum IFO 3956 (Morita et al., 2008), and L. fermentum CECT 5716 (Jiménez et al., 2010) were acquired from RefSeq. Whole-genome comparisons with the other three L. fermentum strains and ortholog findings were performed using the progressiveMauve algorithm (Darling et al., 2010). RESULTS & DISCUSSION The 2.09 Mbp genome was assembled from 403,466 reads, resulting in 74 contigs. No plasmids were found. The comparative genome analysis with other strains showed that 477 coding sequences were found in L. fermentum IMDO 130101 solely (Figure 1). L. fermentum IMDO 130101 was predicted to be able to import and utilise glucose, fructose, xylose, mannose, N- acetylglucosamine, maltose, sucrose, lactose and gluconic acid via the heterolactic fermentation pathway. Also, the ability to degrade raffinose and arabinose was predicted. Consumption of glucose, fructose, maltose and sucrose was shown in previous research, although growth with sucrose as the sole energy source was impaired (Vrancken et al., 2008). The strain possibly imports isomaltose and maltodextrins, hence elaborating glucose subunits. The -glucosidase-encoding gene was not found in the genomes of the other three strains considered, and neither were the putative maltodextrin import-related genes, the trehalose-6-phosphate phosphorylase-encoding gene and a putative -glucanase-encoding gene, which all may be adaptations of L. fermentum IMDO 130101 to the sourdough environment. The presence of the arginine deiminase gene cluster was confirmed. Also, L. fermentum IMDO 130101 contained a gene for a phenolic acid decarboxylase, which may have an impact on sourdough aroma. Further, a 4,6- -glucanotransferase-encoding gene was present in strain IMDO 130101 solely, which could result in isomalto/malto-polysaccharide production, a soluble dietary fibre with prebiotic properties. Overall, comparative genome analysis revealed metabolic traits that are of interest for the use of L. fermentum IMDO 130101 as a functional starter culture for sourdough fermentation processes. FIGURE 1. Venn diagram of shared coding sequences between four different strains of Lactobacillus fermentum. REFERENCES Darling et al. PLoS ONE 5, e11147 (2010). Jiménez E. et al. J. Bacteriol. 192, 4800-4800 (2010). Meyer et al. Nucleic Acids Res. 31, 2187-2195 (2003). Morita et al. DNA Res. 15: 151-161 (2008). Sun et al. J. Biotechnol. 194, 110-111 (2015). Vrancken et al. Int. J. Food Microbiol. 128, 58-66 (2008). Weckx et al. Food Microbiol. 27, 1000-1008 (2010). 108
BeNeLux Bioinformatics Conference – Antwerp, December 7-8 2015 Abstract ID: P Poster 10th Benelux Bioinformatics Conference bbc 2015 P65. ORTHOLOGICAL ANALYSIS OF AN EBOLA VIRUS – HUMAN PPIN SUGGESTS REDUCED INTERFERENCE OF EBOLA VIRUS WITH EPIGENETIC PROCESSES IN ITS SUSPECTED BAT RESERVOIR HOST Ben Verhees 1* , Kris Laukens 1,2 , Stefan Naulaerts 1,2 , Pieter Meysman 1,2 & Xaveer Van Ostade 3 . Biomedical informatics research center Antwerpen (biomina) 1 ; Advanced Database Research and Modeling (ADReM), University of Antwerp 2 ; Laboratory of Protein Science, Proteomics and Epigenetic Signalling (PPES) and Centre for Proteomics and Mass spectrometry (CFP-CeProMa), University of Antwerp 3 . * ben.verhees@student.uantwerpen.be Ebola virus is a zoonosis, but its reservoir host has not yet been identified. Recent findings suggest however, that Mops condylurus, an insect-eating bat, is a likely candidate. Studying the interactions between Ebola virus and its reservoir host could prove highly informative, as reservoir hosts of zoonotic pathogens often appear to tolerate infections with these pathogens with little evidence of disease. In this study, a protein-protein interaction network (PPIN) was created between Ebola virus and human proteins. Orthology data in Myotis lucifugus – a model organism often used for bat studies – was employed to determine which of the human first neighbors of Ebola virus proteins do not possess an orthologue in M. lucifugus. Subsequent GO enrichment analysis suggested that these proteins are mostly involved in epigenetic processes, and thus we hypothesize that Ebola virus displays reduced interference with epigenetic processes in its reservoir host. INTRODUCTION The idea that bats serve as reservoirs for a wide range of zoonotic pathogens has been the topic of much recent research. Previous studies on human and bat orthology in this context have mainly focused on specific genes, important in fighting off viral infection. Our study is different however, in that it focuses on proteins the Ebola virus immediately interacts with in humans, and the existence of orthologues of these proteins in bats. METHODS Construction of an Ebola virus – human PPIN An Ebola virus – human PPIN was constructed from in silico data. All network analysis was done using Cytoscape v. 3.2.1. Orthology analysis Identification of orthologues was performed using the OMA orthology database, release: September 2015. Statistics For the statistical analysis, the hypergeometric test was performed. GO enrichment GO enrichment analysis was performed using ClueGO v. 1.2.7, a Cytoscape plug-in. Default settings were used, and all ontologies/pathways were examined. RESULTS & DISCUSSION Myotis lucifugus as a model for Mops condylurus In this study, Myotis lucifugus was used as a model to study interactions between Ebola virus and Mops condylurus, its suspected reservoir. Ebola virus – human PPIN and orthology in M. lucifugus An Ebola virus – human PPIN was created, and human first neighbors of Ebola virus proteins were examined for existence of orthologues in M. lucifugus. Statistical analysis revealed that there was an upregulation of human proteins with orthologues in M. lucifugus (p=0.019). GO enrichment suggests reduced interference of Ebola virus with epigenetic processes in its reservoir host Gene ontology (GO) enrichment analysis was performed of the human first neighbors of Ebola virus proteins which do not possess an orthologue in M. lucifugus. The analysis revealed that these proteins are mostly involved in epigenetic processes (Figure 1). FIGURE 1. GO enrichment analysis of human first neighbors of Ebola virus proteins which do not possess an orthologue in M. lucifugus. Discussion Using this novel approach, we have shown that Ebola virus is likely able to interfere with epigenetic processes in humans. Secondly, Ebola virus’ ability to interfere with host epigenetics is likely reduced or altered in its reservoir host. While the idea that viruses are able to interact with host epigenetic mechanisms is fairly recent, over the past few years significant research has been done exploring this topic. In a comprehensive review, Li et al. (2014) describe how specific viral proteins are able to modulate the activity of chromatin modification complexes, e.g. HATs, HDACs, HMTs, and HDMTs, and even directly bind histone proteins. These findings lend support to the results of our study, as these suggest that Ebola virus is also able to interact with HDACs, HMTs and several histone proteins in humans. REFERENCES Li S et al. Rev Med Virol 24, 223-241 (2014). 109
Page 1 and 2:
10 th Benelux Bioinformatics Confer
Page 3 and 4:
10th Benelux Bioinformatics Confere
Page 5 and 6:
Page 7 and 8:
Page 9 and 10:
Page 11 and 12:
Page 13 and 14:
Page 15 and 16:
Page 17 and 18:
Page 19 and 20:
BeNeLux Bioinformatics Conference -
Page 21 and 22:
Page 23 and 24:
Page 25 and 26:
Page 27 and 28:
Page 29 and 30:
Page 31 and 32:
Page 33 and 34:
Page 35 and 36:
Page 37 and 38:
Page 39 and 40:
Page 41 and 42:
Page 43 and 44:
Page 45 and 46:
Page 47 and 48:
Page 49 and 50:
Page 51 and 52:
Page 53 and 54:
Page 55 and 56:
Page 57 and 58: BeNeLux Bioinformatics Conference -
Page 107: BeNeLux Bioinformatics Conference -
Page 115: 10th Benelux Bioinformatics Confere
show all

bbc 2015

Create successful ePaper yourself

Delete template?

Save as template?