Identification and prioritization of macrolideresistance genes with hypothetical annotation in Streptococcus pneumoniae

Abstract

Macrolide resistant Streptococcus pneumoniae infections have limited treatment options. While some resistance mechanisms are well established, ample understanding is limited by incomplete genome annotation (hypothetical genes). Some hypothetical genes encode a domain of unknown function (DUF), a conserved protein domain with uncharacterized function. Here, we identify and confirm macrolide resistance genes. We further explore DUFs from macrolide resistance hypothetical genes to prioritize them for experimental characterization. We found gene similarities between two macrolide resistance gene signatures from untreated and either erythromycin- or spiramycin-treated resistant Streptococcus pneumoniae. We confirmed the association of these gene sets with macrolide resistance through comparison to gene signatures from (i) second erythromycin resistant Streptococcus pneumoniae strain, and (ii) erythromycin-treated sensitive Streptococcus pneumoniae strain, both from non-overlapping datasets. Examination into which cellular processes these macrolide resistance genes belong found connections to known resistance mechanisms such as increased amino acid biosynthesis and efflux genes, and decreased ribonucleotide biosynthesis genes, highlighting the predictive ability of the method used. 22 genes had hypothetical annotation with 10 DUFs associated with macrolide resistance. DUF characterization could uncover novel co-therapies that restore macrolide efficacy across multiple macrolide resistant species. Application of the methods to other antibiotic resistances could revolutionize treatment of resistant infections

An Educational Bioinformatics Project to Improve Genome Annotation

“…To overcome these limitations, GSEA considers all genes during analysis by removing the need for a statistical cut-off ( Tipney and Hunter, 2010 ). GSEA is extremely complex, and best for advanced educational projects such as a Master thesis, where the goal is to identify true HPs whose immediate experimental examination could directly enhance scientific understanding of a variety of biological mechanisms ( Goad and Harris, 2018 ).…”

“…If more than two experimental groups are available, HPs can be selected by gene enrichment analysis ( Goad and Harris, 2018 ). HPs can be selected by either singular enrichment analysis or gene set enrichment analysis ( Huang et al, 2009 ; Tipney and Hunter, 2010 ).…”

“…The record is easily retrievable via a unique identifier (i.e., locus tag) which is consistently used across knowledgebases (Brown et al, 2015;Tatusova et al, 2016;Coordinators, 2018). These public records are used for a wide variety of gene analyses, such as pathway enrichment, so having proper genome annotation is important to draw accurate and complete scientific conclusions (Goad and Harris, 2018;Smits, 2019).…”

Gene Expression Meta-Analysis Reveals Interferon-induced Genes

“…In a prior study to identify novel genes associated with macrolide resistance in Streptococcus pneumoniae , we demonstrated a GSEA-approach for gene identification that compared differential gene expression between mRNA expression datasets (Goad and Harris, 2018). This study successfully identified known and novel genes though it was limited due to incomplete genome annotation, a common problem for many microbial genomes (Kolker et al, 2004; Sivashankari and Shanmughavel, 2006; Mohan and Venugopal, 2012; Bharat Siva Varma et al, 2015; Ijaq et al, 2015; Islam et al, 2015; School et al, 2016; Omeershffudin and Kumar, 2019).…”

“…In a prior study to identify genes associated with macrolide resistance in Streptococcus pneumoniae, we demonstrated a GSEA-approach for gene identification that compared differential gene expression between mRNA expression datasets [42]. This study successfully identified known and novel genes though it was limited due to incomplete genome annotation, a common problem for many microbial genomes [43][44][45][46][47][48][49][50].…”