Abstract :
[en] Archaea, one of the three domains of life, exhibit remarkable physiological diversity and occupy a wide spectrum of ecological niches, ranging from extreme environments such as hypersaline lakes, hot springs, and acidic or alkaline habitats to moderate ecosystems including marine, freshwater, terrestrial, oilfield and host-associated environments. Among them, methanogenic archaea are obligate anaerobes that produce methane through distinct methanogenic pathways, traditionally utilizing simple substrates
such as H2/CO2, acetate, methanol, and methylated compounds. The recent discovery that
Methermicoccus shengliensis can metabolize methoxylated aromatic compounds (MACs)
has expanded the known substrate spectrum of methanogens. However, the molecular
mechanisms underlying the transport of these structurally complex compounds into
archaeal cells remain unknown. In this study, we investigated the substrate transport system of M. shengliensis ZC-1 cultivated with methanol and 2-methoxybenzoate. Transcriptomic analysis identified two highly expressed genes, matE and tlp, potentially involved in substrate uptake. Integrating bioinformatic analyses, protein-protein interaction, and structural modeling assays, we propose a transport model comprising three sequential steps: the transduction like protein Tlp first recognizes the 2-methoxybenzoate extracellularly, then interacts with the transmembrane MATE family transporter MatE, and finally MatE mediates the translocation of the substrate into the cell. Deletion of MatE markedly impairs cell
growth and methane production under methoxylated aromatic conditions, underscoring its critical role in methoxydotrophic methanogenesis. To further elucidate the diversity and habitat adaptation of archaeal MatE transporters, we performed large-scale comparative genomic phylogenetic analyses, combined with structural classification and molecular docking. Our results reveal that MatE transporters are widely distributed but unevenly represented across archaeal lineages, exhibiting structural diversity that can be classified into four major classes. Class I MatE is the most conserved and phylogenetically prevalent, whereas Classes II, III, and IV are comparatively rare. Notably, compared with MatE-negative genomes, MatE-positive archaeal genomes are significantly enriched in host-associated and hypersaline environments, as well as in heterotrophic lineages. Furthermore, specific
MatE transporters exhibit strong associations with particular habitats, and their copy numbers are positively correlated with genome size. This non-random distribution indicates that the presence of MatE transporters is closely linked to specific ecological
niches and metabolic strategies. Overall, this work uncovers a previously uncharacterized transport mechanism for methoxylated aromatic compounds in methanogenic archaea and provides a comprehensive framework for understanding the diversity and habitat adaptation of the archaeal MATE transporter family. These findings advance our understanding of
substrate acquisition strategies and methane metabolism in archaea, provide new insights
into their ecological distribution, and elucidate their adaptation to extreme environments, highlighting their biological importance and deepening our understanding of life on Earth.
