A widespread group of large plasmids in methanotrophic Methanoperedens archaea

Abstract

Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane, yet their extrachromosomal genetic elements are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments. By manual curation we show that two of the plasmids are large (155,605 bp and 191,912 bp), circular, and may replicate bidirectionally. The plasmids occur in the same copy number as the main chromosome, and plasmid genes are actively transcribed. One of the plasmids encodes three tRNAs, ribosomal protein uL16 and elongation factor eEF2; these genes appear to be missing in the host Methanoperedens genome, suggesting an obligate interdependence between plasmid and host. Our work opens the way for the development of genetic vectors to shed light on the physiology and biochemistry of Methanoperedens, and potentially genetically edit them to enhance growth and accelerate methane oxidation rates.

Acetate and Acetyl-CoA Metabolism of ANME-2 Anaerobic Archaeal Methanotrophs

“…Analysis of the metagenome-assembled genome (MAG) from the in-house "Ca. Methanoperedens BLZ2" strain revealed the presence of one putative ACS-encoding gene and one ACD-encoding gene (16,33). For a MAG from ANME-2a, three putative ACS-encoding genes were found.…”

“…Transcriptome analysis of the "Ca. Methanoperedens BLZ2" biomass grown in bioreactors fed with nitrate and methane (33) showed that ACS and ACD of ANME-2d were expressed at 20 and 40 transcripts per million (TPM), respectively, which are about one-half the values of the nitrate reductase genes narA (79 TPM) and narB (109 TPM) as well as the F 420 -dependent methylene-tetrahydromethanopterin (H 4 MPT) reductase gene mer (75 TPM) and the methenyl-H 4 MPT cyclohydrolase gene mch (65 TPM), which encode enzymes that are required for reverse methanogenesis. ACS and ACD of ANME-2d were also previously detected in the proteome of ANME-2d (9).…”

“…Cloning. Analysis of the metagenome-assembled genomes (MAGs) from ANME-2a and ANME-2d revealed the presence of putative ACS-and ACD-encoding genes (16,27,33,40). The ANME-2a MAG was obtained from enrichment cultures from the Captain Aryutinov Mud Volcano (Spain) (40), and the ANME-2d MAG was obtained from an in-house culture seeded with Ooijpolder (Netherlands) sediments (16,41,42).…”

Convergence and horizontal gene transfer drive the evolution of anaerobic methanotrophy in archaea

“…While these alone are larger than many typical plasmids and viral genomes, megaplasmids have been reported in Methanosarcinales (the taxonomic order containing the organisms in this study) and are common in Haloarchaea ( 83 ). Additionally, extrachromosomal elements up to 1 Mb known as borgs ( 56 ) and unusually large plasmids up to 200 kb ( 84 ) have recently been identified in Methanoperedens spp. (ANME-2d) and proposed to act as gene transfer agents, including of large MHCs.…”

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

“…Based on gene content and co-occurrence patterns, Borgs associate with several species of anaerobic methanotrophic (ANME) archaea of the Methanoperedens genus [ 3 ]. A search for other ECEs associated with these archaea also led to the recent discovery of large plasmids found in members of the same genus, yet a distinct clade of Methanoperedens species [ 4 ].…”