Comparative Genomic Insights into MatE Transporter Diversity and Habitat Adaptation of Archaea

Archaea comprise deeply rooted and phylogenetically diverse lineages that inhabit a wide range of environments and play essential roles in global biogeochemical cycles. However, the diversity of MATE (Multidrug and Toxic Compound Extrusion) family transporters in archaea, which are presumably involved in habitat adaptation, remains poorly understood. Here, we systematically analyzed archaeal MatE transporters using large-scale phylogenetic and comparative genomic analyses, combined with structure-based clustering and molecular docking. Our results show that MatE transporters are significantly enriched in archaea from host-associated and hypersaline environments compared with those from other habitats. Specific MatE transporters are strongly associated with particular habitats, and their copy numbers are positively correlated with genome size. Moreover, MatE transporters in archaea exhibit structural diversity and can be classified into four structural classes, among which Class I is predominant in both abundance and phylogenetic distribution compared with Classes II, III, and IV. Overall, these findings indicate that the successful adaptation of archaea to specific habitats is related to the acquisition and maintenance of MatE transporters, which may be critical for their survival in these environments.