Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins

Abstract

Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of TRs in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently, and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg–host associations and possibly cospeciation.

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

“…All Borg genomes harbor pervasive nucleotide TR that are located in intergenic regions and within open reading frames (Extended Data Table 1). Approximately half of these TRs occur in genes, where they essentially always introduce amino acid repeats that generally confer local intrinsic disorder, as reported by us previously 5 . Representative examples in Amber and Amethyst Borg are TRs located in multiheme cytochromes (MHC) (Supplementary Figure 3), which often harbor aaTRs 5 .…”

“…Approximately half of these TRs occur in genes, where they essentially always introduce amino acid repeats that generally confer local intrinsic disorder, as reported by us previously 5 . Representative examples in Amber and Amethyst Borg are TRs located in multiheme cytochromes (MHC) (Supplementary Figure 3), which often harbor aaTRs 5 . These regions may provide sites for post translational modifications, mediate complex formation or bind small molecules 5,6 .…”

“…The majority of previously reported Borg genomes derived from soil sampled from a seasonal wetland in Lake County, northern California, and all were reconstructed using Illumina sequences 1,5 . We performed long read nanopore sequencing on a subset of the same samples to evaluate the accuracy of the manually curated Illumina-based complete genomes reconstructed from these samples and to recover new Borg genomes.…”

“…This is unsurprising, as some TR regions are longer than the Illumina read lengths. However, the number of TR units in TR regions is often variable within populations 5 , so a combination of deep Illumina and some longer nanopore reads may be best used to define the TR regions.…”

Deep Learning Enhanced Tandem Repeat Variation Identification via Multi-Modal Conversion of Nanopore Reads Alignment

“…3) Unique k-mer counting methods, which leverage the overrepresentation of specific k-mers to locate TR regions. Tandem Repeats Database (TRDB) [18], GMATo [19], and IDR [20] are commonly used tools for seed-and-extend strategies in TR identification. 4) Graph-based methods, which construct graphs to capture the repetitive structure and identify TRs through graph analysis.…”