Article
Biochemistry & Molecular Biology
Yancheng Liu, Yuko Takagi, Milyadi Sugijanto, Kieu Duong My Nguyen, Akira Hirata, Hiroyuki Hori, C. Kiong Ho
Summary: RNA ligases play crucial roles in repairing and circularizing RNAs post-transcriptionally. This study generated a mutation in the ATP-dependent RNA ligase in the hyperthermophilic archaeon Thermococcus kodakarensis and found that it is critical for circularization of C/D box sRNAs and ribosomal RNA processing.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Mason A. McCool, Amber F. Buhagiar, Carson J. Bryant, Lisa M. Ogawa, Laura Abriola, Yulia V. Surovtseva, Susan J. Baserga
Summary: This study shows that the nucleolar protein RSL24D1 and the PeBoW complex play important roles in multiple steps of ribosome biogenesis, including pre-ribosomal RNA transcription and mature 28S rRNA production. They regulate pre-ribosomal RNA transcription by modulating the steady-state levels of RNA polymerase I. Specifically, RSL24D1 is demonstrated to coimmunoprecipitate with the RNA polymerase I subunit, RPA194, and together regulate the process of ribosome biogenesis.
Article
Ecology
Anna N. Rasmussen, Julian Damashek, Emiley A. Eloe-Fadrosh, Christopher A. Francis
Summary: This study is the first in-depth spatiotemporal survey of microbial communities in San Francisco Bay, revealing specialization of planktonic microorganisms to different niches along the salinity gradient.
Article
Environmental Sciences
Ademir Sergio Ferreira Araujo, Arthur Prudencio de Araujo de Pereira, Jadson Emanuel Lopes Antunes, Louise Melo de Souza Oliveira, Wanderley Jose de Melo, Sandra Mara Barbosa Rocha, Marineide Rodrigues do Amorim, Fabio Fernando Araujo, Vania Maria Maciel Melo, Lucas William Mendes
Summary: The use of composting as a biological alternative to improve tannery sludge quality by microbial action has been proposed. This study assessed the responses of bacterial and archaeal communities during composting using 16S rRNA sequencing, revealing specific microbial community structures and dynamics at different stages of the composting process.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Review
Microbiology
Guillaume Tahon, Patricia Geesink, Thijs J. G. Ettema
Summary: The discovery and study of Archaea in the past few decades have greatly expanded our understanding of their cell biology, physiology, ecology, and diversity. However, due to computational limitations and the ongoing discovery of new lineages, a stable archaeal phylogeny has not yet been achieved. Therefore, obtaining consensus on the phylogenetic and taxonomic classification of Archaea should be a high priority for the research community.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021
(2021)
Article
Biochemistry & Molecular Biology
Victor G. Stepanov, George E. Fox
Summary: A comprehensive search identified 89 expanded 5S rRNAs of 15 structural types in 15 archaeal and 36 bacterial genomes, with expansion segments ranging from 13 to 109 residues distributed among 17 insertion sites. These expanded versions are mainly found in specific bacterial strains and can coexist with normal 5S rRNA genes in multiple copies.
Article
Environmental Sciences
Luana Agostini, Julio Cezar Fornazier Moreira, Amanda Goncalves Bendia, Maria Carolina Pezzo Kmit, Linda Gwen Waters, Marina Ferreira Mourao Santana, Paulo Yukio Gomes Sumida, Alexander Turra, Vivian Helena Pellizari
Summary: The study assessed the colonization of microbial communities on plastic substrates in deep-sea environments and found that the type of substrate strongly influenced microbial composition and structure. While some taxa were shared among different plastics, specific groups were also observed for each plastic type. The core microbiome identified was composed of low abundance taxa with known plastic-degradation capabilities. Additionally, bacterial strains with reported plastic-degradation abilities were isolated, suggesting the presence of potentially active microbial members involved in plastic degradation in the deep sea.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Multidisciplinary Sciences
Vanessa Grenier, Emmanuel Gonzalez, Nicholas J. B. Brereton, Frederic E. Pitre
Summary: Decomposing organic waste can contribute to greenhouse gas emissions. Composting can reduce these emissions and produce sustainable fertilizer. However, we still have limited understanding of the microbial communities involved in composting and their role in the process.
Article
Biochemistry & Molecular Biology
Sotaro Miyao, Kanako Saito, Renta Oshima, Kohichi Kawahara, Masami Nagahama
Summary: The study investigates the involvement of PICT1 in ribosome biogenesis and its interaction with MTR4 and the RNA exosome. PICT1 plays roles in two distinct pre-rRNA processing steps during the generation of 60S ribosomes, with recruitment of MTR4 and the exosome through the AIM sequence required only in the late processing step. Depletion of MTR4 and PICT1 stabilizes the tumor suppressor p53 protein, while depletion of the exosome catalytic subunits, RRP6 and DIS3, does not have the same effect.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Xiaoyu Kong, Huacai Wang, Mengting Zhang, Xiaoying Chen, Rongxiang Fang, Yongsheng Yan
Summary: A novel translation regulatory mechanism involving the SA-NPR1-SUNA1 signaling cascade was discovered in Arabidopsis, controlling pre-rRNA processing and translational efficiency of certain defense genes. This study demonstrates the importance of pre-rRNA processing in plant defense against pathogen infection.
Article
Microbiology
Brian P. Anton, Richard J. Roberts
Summary: Compared with bacteria, less is known about the restriction-modification systems of archaea. Through a survey of the restriction enzyme database, we discovered similarities between the RM systems of archaea and bacteria, including shared genetic pool and horizontal gene transfer. We also identified persistent DNA methyltransferases in archaeal taxa.
Article
Environmental Sciences
Jianxin Wang, Chunmiao Tian, Dongmei Wu, Rixin Wang
Summary: This study used high-throughput sequencing to explore the archaeal communities in the hypoxic and non-hypoxic zones of the Changjiang Estuary, revealing that Thaumarchaeota dominated in the hypoxic zones while Euryarchaeota were mainly distributed in the non-hypoxic zones. There was no significant difference in diversity and richness of the archaeal communities between the hypoxic and non-hypoxic zones. The archaeal communities were positively correlated with salinity, but negatively correlated with dissolved oxygen and temperature. The networks of archaeal communities showed a high proportion of positive interspecific interaction and indicated the distinct roles of Marine Group II species in both hypoxic and non-hypoxic zones.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Russell T. Sapio, Chelsea J. Burns, Dimitri G. Pestov
Summary: This study investigates the impact of oxidative stress on ribosome biogenesis by targeting redox-sensitive reporters and H2O2 scavengers to the nucleolus. The findings reveal increased oxidation and oxidative damage in the nucleolar environment in response to H2O2, leading to alterations in pre-rRNA maturation steps sensitive to H2O2 stress.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Ecology
Ademir Sergio Ferreira Araujo, Arthur Prudencio de Araujo Pereira, Vania Maria Maciel Melo, Erika Valente de Medeiros, Lucas William Mendes
Summary: Soils from the semiarid regions of Brazil are at high risk of desertification due to various factors. However, restoration strategies such as conservationist practices and grazing exclusion have shown potential in recovering the richness and diversity of soil bacterial and archaeal communities. These strategies also improve the connectivity and functionality of soil microorganisms over time.
Article
Biotechnology & Applied Microbiology
Na Yang, Chen Tian, Yongxin Lv, Jialin Hou, Zhifeng Yang, Xiang Xiao, Yu Zhang
Summary: This study designed specific primers to improve the detection resolution of unique microbial groups in oceanic trench sediments. Through high-throughput sequencing analysis, the V3-V4 hypervariable region was found to be the most informative and representative for oceanic trench microbial groups. Compared to universal primers, the newly designed primers were able to detect more microbial families, especially archaeal ones, resulting in the discovery of more species that were previously ignored in universal primer-based experiments.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Cell Biology
Kathleen L. McCann, J. Michael Charette, Nicholas G. Vincent, Susan J. Baserga
GENES & DEVELOPMENT
(2015)
