Identifying Hop Resistance Genes

Genes coding for proteins related to stress resistance were identified using annotation algorithms, including the KEGG database. Putative bacteriocin clusters were identified using BAGEL4 [36 (link)]. Comparative genomic analysis was used to predict the functionality of the annotated proteins involved in hop resistance. More specifically, Uniprot was searched for registered sequences of genes horA, horC and hitA, which were previously shown to be involved in the manifestation of hop resistance [3 (link),37 (link),38 (link)]. These sequences were queried against the WGS of the two novel strains. The alignment of sequences showing the higher sequence identity was performed with ClustalW [39 (link)]. Visualization of alignments was performed with Jalview [40 (link)]. Gene matrices for predicted proteins conferring resistance to stress and hop were constructed using GENE-E (GENE-E, Matrix visualization tool. Available online: https://software.broadinstitute.org/GENE-E/index.html (accessed on 1 November 2022)).

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Kiousi D.E., Bucka-Kolendo J., Wojtczak A., Sokołowska B., Doulgeraki A.I, & Galanis A. (2023). Genomic Analysis and In Vitro Investigation of the Hop Resistance Phenotype of Two Novel Loigolactobacillus backii Strains, Isolated from Spoiled Beer. Microorganisms, 11(2), 280.

Publication 2023

Bacteriocin Comparative genomic analysis Gene Gene proteins Proteins Sequences alignment Strains

Corresponding Organization : Democritus University of Thrace

Other organizations : Institute of Agricultural and Food Biotechnology

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Variable analysis

independent variables

Genes coding for proteins related to stress resistance
Putative bacteriocin clusters

dependent variables

Functionality of the annotated proteins involved in hop resistance

control variables

Registered sequences of genes horA, horC and hitA, which were previously shown to be involved in the manifestation of hop resistance

controls

Positive control: Previously known hop resistance genes (horA, horC, hitA)
Negative control: Not explicitly mentioned

Annotations

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