Structural Insights Reveal Long-SSRs May Affect 4Fe-4S Protein Flexibility and Function in Methanogenesis

Simple sequence repeats (SSRs) represent a fundamental component of an organism's genome and can play critical roles in genome organization and evolution. In this study, we examined the prevalence, relative abundance (RA), and relative density (RD) of long SSRs across various methanogens to uncover their evolutionary relevance and potential functional implications. Among the species analyzed, Methanococcus aeolicus exhibited the highest RA and RD values (110.0 and 1844.5, respectively), followed by Methanococcus liminatans (86.6 and 1087.0). In contrast, the lowest values were observed in Methanococcus abyssi (20.6 and 277.0). Notably, methanogens are generally characterized by A + T-rich genomes, and a positive correlation (r = 0.380) was found between SSR frequency and AT content. SSRs were distributed unevenly between genic and intergenic regions: on average, 65.4 SSRs (67.4% of total) were located in genic regions, while 31.6 SSRs (32.4%) occurred in intergenic regions. To explore potential functional effects of SSRs, we performed 3D structural modelling of a long-SSR-containing 4Fe-4S domain protein from Methanococcus maripaludis. The model revealed that SSR insertions may influence domain-domain interactions and modulate the accessibility and flexibility of the active site, potentially contributing to protein adaptation under stress conditions and during methane production.