Dataset Information

The lactococcal phage p2 protein ORF47 impedes Lactococcus lactis MG1363 resistance to phage infection

ABSTRACT: The lactococcal phage p2 is a model for studying the Skunavirus genus, the most prevalent group of phages in cheese factories worldwide. It infects L. lactis MG1363, a model strain for the study of Gram-positive bacteria. The structural proteins of phage p2 have been thoroughly described. However, most of its non-structural proteins are still uncharacterized. Here, we developed an integrative approach, making use of structural biology, genomics, physiology, and proteomics to provide insights into the function of ORF47, the most conserved non-structural protein of unknown function among the Skunavirus genus. We found this small phage protein to have a major impact on the bacterial proteome and to be important to prevent bacterial resistance to phage infection.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Lactococcus Phage Lactococcus Lactis Subsp. Cremoris Mg1363

SUBMITTER: Sandra Maass

LAB HEAD: Doete Becher

PROVIDER: PXD013186 | Pride | 2020-07-30

REPOSITORIES: Pride

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Publications

A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection.

Lemay Marie-Laurence ML Maaß Sandra S Otto Andreas A Hamel Jérémie J Plante Pier-Luc PL Rousseau Geneviève M GM Tremblay Denise M DM Shi Rong R Corbeil Jacques J Gagné Stéphane M SM Becher Dörte D Moineau Sylvain S

Viruses 20200724 8

The lactococcal virulent phage p2 is a model for studying the <i>Skunavirus</i> genus, the most prevalent group of phages causing milk fermentation failures in cheese factories worldwide. This siphophage infects <i>Lactococcus lactis</i> MG1363, a model strain used to study Gram-positive lactic acid bacteria. The structural proteins of phage p2 have been thoroughly described, while most of its non-structural proteins remain uncharacterized. Here, we developed an integrative approach, making use ...[more]

PMID: 32722163

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Project description:Background Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. In aCGH data, systematic errors are comparable to those occurring in transcriptome data. However, especially for microbes, an additional source of variation exists: differences in hybridization due to gene sequence divergence between the strains hybridized. Current normalization methods do not take this source of variation into consideration. Results We present Supervised Lowess, or S-Lowess, an application of the subset Lowess normalization method that does take difference in genomic content into account. The performance of S-Lowess was assessed on aCGH experiments in which differentially labeled genomic DNA fragments of Lactococcus lactis IL1403 and L. lactis MG1363 strains were hybridized to IL1403 microarrays. Since both genome sequences are known (they have only on average 85 % sequence identity), the success rate in detecting deletions in the MG1363 genome of different aCGH normalization methods can be compared. S-Lowess detects 97% of the deletions, whereas other aCGH normalization methods detect up to only 60% of the deletions. Conclusions S-Lowess removes systematic errors from dual-dye aCGH data in two steps: (i) determination of likely homologous genes (LHG); and (ii) estimation of correction factors for systematic errors from spots of LHG and subset Lowess normalization of the remaining spots using these correction factors. It is implemented in a user-friendly web-tool accessible from http://bioinformatics.biol.rug.nl/websoftware/s-lowess. We demonstrate that it outperforms existing normalization methods and maximizes the number of detectable genomic deletions or duplications from microbial aCGH data. Keywords: comparative genome hybridisation In this study, 4 aCGH comparisons (slides) between L. lactis MG1363 and L. lactis IL1403 were performed (including dye swap with biological replicates; see also supplementary materials). The resulting aCGH slide signals were normalized using the different 'likely homologous gene' (LHG) sets (see above) yielding ratios of signals of labelled DNA of MG1363 over those of IL1403. A maximum of 8 ratios per amplicon (gene) were obtained for the 4 hybridized slides (each with 2 replicate spots per amplicon). Only genes with at least 5 measurements were used in this study. The normalization methods evaluated in this study are: a) no normalization, b) total signal normalization, c) grid-based Lowess (implemented in PreP; f = 0.7) [GarcM-CM--a de la Nava, J et al. 2003. Bioinformatics 19:2328-2329], and d) S-Lowess using different subsets of conserved lactococcal genes (for details see above). Results with the MANOR R package (spatial normalization; standard parameters) [Neuvial P, et al. 2006. BMC Bioinformatics 7:264; Liva S, et al. 2006. Nucleic Acids Res 34:W477-W481] are shown in our supplementary materials.

Dataset Information

The lactococcal phage p2 protein ORF47 impedes Lactococcus lactis MG1363 resistance to phage infection

Publications

A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection.

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