TY - JOUR
T1 - A widespread group of large plasmids in methanotrophic Methanoperedens archaea
AU - Schoelmerich, Marie C.
AU - Ouboter, Heleen T.
AU - Sachdeva, Rohan
AU - Penev, Petar I.
AU - Amano, Yuki
AU - West-Roberts, Jacob
AU - Welte, Cornelia U.
AU - Banfield, Jillian F.
N1 - Funding Information:
Funding for this research was provided by a DFG fellowship for M.C.S. (Project Number: 447383558 to M.C.S.), the Soehngen Institute of Anaerobic Microbiology Gravitation program (grant 024.002.002 to C.U.W.) by the Dutch Science Foundation, and the Innovative Genomics Institute at UC Berkeley (IGI 52482 to J.F.B.). The Ministry of Economy, Trade, and Industry of Japan funded a part of the work as “The project for validating near-field system assessment methodology in geological disposal system” (2020 FY, Grant Number: JPJ007597). We thank Theo van Alen for technical support, Shufei Lei and Jordan Hoff for bioinformatics support, and Justin Smith, Luis Valentin Alvarado, Susan Mullen, Kenneth Williams, Karthik Anantharaman, and Basem Al-Shayeb for their contributions to fieldwork and generation of sequence datasets.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/11/18
Y1 - 2022/11/18
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/85142263660
U2 - 10.1038/s41467-022-34588-9
DO - 10.1038/s41467-022-34588-9
M3 - Article
C2 - 36400771
AN - SCOPUS:85142263660
SN - 2041-1723
VL - 13
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 7085
ER -