Transcription profiling and functional analysis of spRNAs and their corresponding asRNAs in Methanosarcina mazei

Small proteins (sPs) encoded by small RNAs (sRNAs), the so-called small protein RNAs (spRNAs), and their corresponding antisense RNAs (asRNAs) have emerged as important regulatory elements in microbial stress adaptation, yet remain poorly characterized in archaea. In this study, we identified and characterized five sRNA/asRNA pairs in the methanoarchaeon Methanosarcina mazei. Expression analysis revealed condition-specific regulation of two of those pairs, spRNA23/asRNA93 and spRNA24/asRNA94, under oxidative, temperature, and osmotic stress. Overexpression of the corresponding small proteins, sP23 and sP24, revealed distinct physiological effects: both enhanced growth under high-salt conditions, while sP24 in addition supported cell size maintenance during osmotic stress, as confirmed by transmission electron microscopy. Consistently, overexpression of asRNA94 let to impaired growth under salt stress, suggesting its negative regulatory role towards sP24. The results also imply that the antisense RNA might be crucial for controlling sP24 expression under non-stress conditions. Bioinformatic analysis predicted one transmembrane domain in sP24. Membrane-association of sP24 was experimentally validated in vitro using a cell-free expression system, demonstrating sP24s integration into lipid bilayers. Conservation analysis showed that spRNA24 appears specific for M. mazei strains potentially reflecting niche adaptation, while spRNA23 is widespread within Methanosarcina. These findings demonstrate that archaeal sRNAs can encode functional small proteins, often encoded together with their respective regulatory asRNA, that contribute to environmental stress responses, overall offering new insights into the role of sRNA-derived small proteins in archaea.