Article
Cell Biology
Patrycja Szczupak, Malgorzata Sierant, Ewelina Wielgus, Ewa Radzikowska-Cieciura, Katarzyna Kulik, Agnieszka Krakowiak, Paulina Kuwerska, Grazyna Leszczynska, Barbara Nawrot
Summary: This study characterized the substrate requirements of the bacterial enzyme SelU, identified SelU-associated tRNAs and their specific modifications in the wobble position. It explained the sequence of steps in the selenation of tRNA and found that the recognition by SelU is influenced by the S2U position within the RNA chain, the flanking sequence of the modification, and the length of the RNA substrate.
Article
Biochemistry & Molecular Biology
Dallas R. Fonseca, Madison B. Loppnow, Leslie A. Day, Elisa L. Kelsey, Mohd Farid Abdul Halim, Kyle C. Costa
Summary: Natural transformation is an important evolutionary driver in microbial populations, but its mechanism is mainly characterized in bacteria. In this study, we identified a catalog of genes necessary for transformation in Methanococcus maripaludis, expanding our understanding of natural transformation in archaea. We found several transformation-associated candidate genes, including those encoding components of the type IV-like pilus, transcription/translation associated genes, putative membrane-bound transport proteins, and genes with unknown functions. Furthermore, we confirmed the importance of these genes for transformation using allelic replacement mutagenesis, and identified a conserved mechanism for DNA transfer in multiple archaea.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Biotechnology & Applied Microbiology
Qing Xu, Qing Du, Jian Gao, Lei Chen, Xiuzhu Dong, Jie Li
Summary: Researchers developed a genetic toolbox including libraries of promoters, ribosome binding sites, and neutral sites for precise gene expression in M. maripaludis. They successfully improved recombinant protein expression and modulated essential gene expression, establishing a solid foundation for further studies and biotechnological applications of M. maripaludis.
METABOLIC ENGINEERING
(2023)
Article
Microbiology
Hayk Palabikyan, Aquilla Ruddyard, Lara Pomper, David Novak, Barbara Reischl, Simon K. -M. R. Rittmann
Summary: This study provides a comprehensive revision and optimization of cultivation methods for Methanococcus maripaludis, a model organism for the production of methane biofuel. The research successfully achieved scale-up from serum bottles to a stainless steel bioreactor, contributing to the establishment of methanogens as essential organisms in large-scale biotechnology applications.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Jichen Bao, Enrique de Dios Mateos, Silvan Scheller
Summary: This study developed a genome-editing toolbox using LbCas12a and the endogenous homology-directed repair machinery in M. maripaludis, enabling reliable and efficient genome editing in methanogens. The toolbox demonstrated successful deletion and replacement of target genes, and was applicable for metabolic engineering and flux balancing studies. This CRISPR/LbCas12a toolbox provides a reliable and quick method for genome editing in methanogens.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Jichen Bao, Enrique de Dios Mateos, Silvan Scheller
Summary: A genome-editing toolbox using Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in combination with the endogenous homology-directed repair machinery of M. maripaludis has been designed, allowing reliable and quick genome editing in a methanogen.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Engineering, Chemical
Chi Hung Vo, Nishu Goyal, Markus Kraft, Iftekhar A. Karimi
Summary: Methanococcus maripaludis can use CO2 as the sole carbon source. The study found that N2 is a better nitrogen source for carbon conversion to CH4 in M. maripaludis. The revised metabolic model iMR557 was able to successfully replicate acetate dissimilation and provide insights into flux distributions under different conditions.
CHEMICAL ENGINEERING SCIENCE
(2023)
Article
Multidisciplinary Sciences
Zhirui Zeng, Huahui Chen, Huan Yang, Yufei Chen, Wei Yang, Xi Feng, Hongye Pei, Paula V. Welander
Summary: This study identified a protein involved in the synthesis of characteristic membrane lipids in archaea, which plays a crucial role and provides a competitive advantage in extreme environments.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Taiwo S. Akinyemi, Nana Shao, Zhe Lyu, Ian J. Drake, Yuchen Liu, William B. Whitman
Summary: A library of differentially regulated promoters was designed and characterized based on the pst promoter, enabling significant increases in gene expression when the medium phosphate drops to growth-limiting concentrations. This regulated system decouples growth from heterologous gene expression without requiring an inducer, offering a new approach for microbial cell factories.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biology
Devon Payne, Rachel L. Spietz, Dennis L. Newell, Paul Dijkstra, Eric S. Boyd
Summary: Iron, sulfur, and molybdenum availability affect the growth and metabolic characteristics of Methanococcus maripaludis, indicating that molybdenum nitrogenase may have originated in an iron-rich environment. Methanogens inhabit sulfide-rich or iron-rich environments, where transition metals precipitate as metal sulfides, reducing their availability. This study shows that methanogens can synthesize molybdenum nitrogenase metallocofactors from pyrite as a source of iron and sulfur, enabling nitrogen fixation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Matthew P. Holten, Dallas R. Fonseca, Kyle C. Costa
Summary: The study demonstrates the essential role of AgIB in surface growth of M. maripaludis JJ, with glycosylation of the cell surface layer enhancing anaerobic iron corrosion rates. These findings provide insights into the physiology of surface-associated methanogenic organisms and underscore the importance of surface association for anaerobic iron corrosion.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Eric Hernandez, Kyle C. Costa
Summary: This study demonstrates the use of FAST in combination with HMBR as a tool for live-cell fluorescence imaging of methanogenic archaea. FAST has potential applications in protein abundance analysis, subcellular localization analysis, and determination of protein-protein interactions.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Materials Science, Multidisciplinary
Shiqiang Chen, Ruizhi Hou, Xue Zhang, Mengyu Fu, Xin Cheng, Wenwen Dou, Guangzhou Liu, Jiarun Li
Summary: In this study, the riboflavin-mediated indirect electron transfer process during EH40 steel corrosion in Methanococcus maripaludis medium was investigated. The results showed that the presence of exogenous riboflavin promotes pitting corrosion of EH40 steel in the medium, but this trend is mitigated by increasing riboflavin concentrations. Additionally, both anodic and cathodic processes of EH40 steel corrosion are enhanced in the presence of riboflavin.
Article
Biochemistry & Molecular Biology
Lei Qi, Huan Liu, Jian Gao, Kai Deng, Xiaoyan Wang, Xiuzhu Dong, Jie Li
Summary: This study investigates the pathways of rRNA maturation in Methanococcus maripaludis, a representative archaeon lacking known 3'-5' exonucleases. The results demonstrate that endonucleolytic processing, particularly at the 10-nt A/U-rich motifs, plays an essential role in the pre-rRNA maturation of M. maripaludis, indicating diverse pathways of rRNA maturation in archaeal species.
Article
Biochemistry & Molecular Biology
Peter T. S. van der Gulik, Martijn Egas, Ken Kraaijeveld, Nina Dombrowski, Astrid T. Groot, Anja Spang, Wouter D. Hoff, Jenna Gallie
Summary: Automated genome annotation is crucial for extracting biological information from sequence data. However, there is a pervasive error in prokaryotic tRNA gene sets on GtRNAdb, where partial, non-canonical tRNA genes are mis-categorized as standard, canonical tRNA genes. We recommend using a combination of screening input sequences, activating the automated pseudogene detection function, and scrutinizing predicted tRNA genes with low isotype scores to improve predictions.
