Biology subjects

Mohd-Assaad, N.

Publications and source records attributed to Mohd-Assaad, N..

3 recordsLinked to original sources

bioRxiv2025

Integrative Transcriptomic and Network Analysis Reveals Small Open Reading Frames as Regulators of DNA Methylation-Linked Pathogenicity and Adaptability in Leptospira interrogans

Small open reading frames (sORFs) are increasingly recognized as crucial regulators in bacterial gene expression, yet their biological roles remain largely unexplored in pathogenic species. Here, we investigated the genome-wide regulatory landscape of sORFs in Leptospira interrogans serovar Manilae strain UP-MMC-NIID-LP using RNA-seq-based transcriptomic profiling integrated with weighted gene co-expression network analysis (WGCNA) following targeted disruption of lomA, a gene mediating 4-methylcytosine (4mC) DNA modification. Loss of 4mC was associated with broad transcriptional dysregulation and phenotypic impairments, including reduced motility, adhesion, and virulence. Analysis of 363 predicted sORFs identified 39 with significant differential expression (FDR < 0.05, |log2FC| [≥] 1) across wild-type, mutant, and complemented strains. Gene co-expression networks constructed using WGCNA and interrogated with Cytoscape tools (MCODE, CytoHubba, ClueGO) revealed ten differentially expressed sORFs (FDR-adjusted p < 0.05); eight upregulated and two downregulated, across the three pairwise comparisons of wild-type, mutant, and complemented strains. These sORFs were enriched in pathways related to flagellar assembly, DNA recombination, and transcriptional regulation, which are core processes supporting genome stability and adaptive stress responses. Several previously uncharacterized sORFs occupied hub-like positions within co-expression modules, highlighting their integrative roles in metabolic and regulatory networks. To our knowledge, this represents the first genome-wide integration of methylation-driven sORF regulation in Leptospira, revealing small proteins as central mediators that link epigenetic control with bacterial pathogenicity and adaptability. These findings provide a foundation for future antimicrobial and synthetic biology strategies targeting sORF-mediated regulation. ImportanceSmall open reading frames (sORFs) are emerging as important regulators of bacterial gene expression, yet their roles in pathogenic species remain largely unexplored. This study provides the first genome-wide framework linking methylation-driven sORF regulation to virulence and adaptive processes in Leptospira interrogans. We identify previously uncharacterized sORFs occupying central positions in regulatory networks, connecting epigenetic control to motility, adhesion, and stress adaptation. Understanding these mechanisms in a neglected tropical disease pathogen has implications for improving public health and informs future antimicrobial and synthetic biology strategies.

bioinformatics↗

bioRxiv2021

The population genetics of adaptation through copy-number variation in a fungal plant pathogen

Microbial pathogens can rapidly adapt to changing environments such as the application of pesticides or host resistance. Copy number variations (CNV) are a major source of adaptive genetic variation for recent adaptation. Here, we analyze how a major fungal pathogen of barley, Rhynchosporium commune, has adapted to host environment, fungicide and temperature challenges. We screen the genomes of 126 isolates sampled across a worldwide set of populations and identify a total of 7879 gene duplications and 116 gene deletions. Most gene duplications result from segmental chromosomal duplications. We find that genes showing recent gains or losses are enriched in functions related to host exploitation (i.e. effectors and cell wall degrading enzymes). We perform a phylogeny-informed genome-wide association study (GWAS) and identify 191 copy-number variants associated with different pathogenesis and temperature related traits, including a large segmental duplication of CYP51A that has contributed to the emergence of azole resistance. Additionally, we use a genome-wide SNP dataset to replicate the GWAS and contrast it with the CNV-focused analysis. We find that frequencies of adaptive CNV alleles show high variation among populations for traits under strong selection such as fungicide resistance. In contrast, adaptive CNV alleles underpinning temperature adaptation tend to be near fixation. Finally, we show that transposable elements are important drivers of recent gene copy-number variation. Loci showing signatures of recent positive selection are enriched in miniature inverted repeat transposons. Our findings show how extensive segmental duplications create the raw material for recent adaptation in global populations of a fungal pathogen.

evolutionary biology↗

bioRxiv2017

Genome-wide detection of genes under positive selection in worldwide populations of the barley scald pathogen

The coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect a specific host. Hence, heterogeneity in the host genotypes and abiotic factors leads to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. We analyzed global field populations of Rhynchosporium commune, the pathogen causing barley scald disease, to identify candidate genes for local adaptation. Whole genome sequencing data generated for 125 isolates showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded proteins with functions related to both biotic and abiotic stresses. We found that selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.

genomics↗