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

Area of Science:

• Genomics
• Molecular Evolution
• Bioinformatics

Background:

• Simple sequence repeats (SSRs) are crucial for genome organization and evolution.
• Methanogens possess A+T-rich genomes, influencing their genomic characteristics.

Purpose of the Study:

• To investigate the prevalence, relative abundance (RA), and relative density (RD) of long SSRs in various methanogens.
• To uncover the evolutionary relevance and potential functional implications of SSRs in methanogen genomes.

Main Methods:

• Comparative genomic analysis of SSRs across different methanogen species.
• Statistical analysis of SSR distribution in genic and intergenic regions.
• 3D structural modeling of SSR-containing proteins to predict functional impacts.

Main Results:

• Methanococcus aeolicus showed the highest RA and RD for SSRs, while M. abyssi had the lowest.
• A positive correlation (r=0.380) was observed between SSR frequency and genome AT content.
• SSRs were predominantly found in genic regions (67.4%) compared to intergenic regions (32.4%).

Conclusions:

• SSRs are unevenly distributed in methanogen genomes, favoring genic regions.
• SSR insertions in proteins, like the 4Fe-4S domain, may affect protein structure, active site accessibility, and flexibility.
• These structuralmodulations could contribute to protein adaptation under stress and influence methane production efficiency.