Genome-wide identification and characterization of the PE/PPE gene family in Mycobacterium abscessus

Mycobacterium abscessus (Mab) is a rapidly growing non-tuberculous mycobacterium that causes opportunistic infections and exhibits extensive intrinsic antibiotic resistance. The proline-glutamate (PE) and proline-proline-glutamate (PPE) protein families are mycobacteria-specific virulence factors implicated in immune modulation, antigenic variation, and persistence. While Mycobacterium tuberculosis (Mtb) harbors approximately 170 PE/PPE members, the repertoire of PE/PPE genes in Mab remains largely uncharacterized. Here, we performed a genome-wide survey of PE/PPE genes in Mab ATCC 19,977 and identified 18 candidate family members, representing a relatively small fraction of the genome compared with slow-growing mycobacteria. Most predicted proteins harbor canonical PE or PPE domains and display acidic physicochemical properties. Phylogenetic analysis resolved the proteins into three subfamilies: PE, PPE, and PE-PPE, revealing moderate structural diversity but limited family expansion. Motif and gene structure analyses supported the evolutionary conservation. Notably, no PE_polymorphic GC-rich repetitive sequence (PE_PGRS) or PPE_major polymorphic tandem repeat (PPE_MPTR) members were detected, suggesting lineage-specific genomic reduction relative to other pathogenic mycobacteria. AlphaFold predictions revealed conserved N-terminal folds and variable C-terminal regions, which may contribute to functional diversification. Subcellular localization predictions indicated that most proteins are extracellular. Synteny analysis revealed no detectable collinearity among these genes. Transcriptomic analyses revealed condition-dependent expression of PE/PPE genes during amoeba and macrophage infection and under artificial sputum medium and metal ion stress, suggesting roles in environmental adaptation and host interaction. This study provides the first systematic overview of PE/PPE gene repertoire in Mab and lays the groundwork for elucidating their roles in intracellular survival, host interaction, and antimicrobial resistance.