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Garcia-Lopez E, Ruiz-Blas F, Sanchez-Casanova S, Peña Perez S, Martin-Cerezo ML, Cid C. Microbial Communities in Volcanic Glacier Ecosystems. Front Microbiol 2022; 13:825632. [PMID: 35547132 PMCID: PMC9084427 DOI: 10.3389/fmicb.2022.825632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Glaciers constitute a polyextremophilic environment characterized by low temperatures, high solar radiation, a lack of nutrients, and low water availability. However, glaciers located in volcanic regions have special characteristics, since the volcanic foci provide them with heat and nutrients that allow the growth of microbial communities highly adapted to this environment. Most of the studies on these glacial ecosystems have been carried out in volcanic environments in the northern hemisphere, including Iceland and the Pacific Northwest. To better know, the microbial diversity of the underexplored glacial ecosystems and to check what their specific characteristics were, we studied the structure of bacterial communities living in volcanic glaciers in Deception Island, Antarctica, and in the Kamchatka peninsula. In addition to geographic coordinates, many other glacier environmental factors (like volcanic activity, altitude, temperature, pH, or ice chemical composition) that can influence the diversity and distribution of microbial communities were considered in this study. Finally, using their taxonomic assignments, an attempt was made to compare how different or similar are the biogeochemical cycles in which these microbiomes are involved.
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Affiliation(s)
- Eva Garcia-Lopez
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
| | - Fatima Ruiz-Blas
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - Sonia Peña Perez
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - Cristina Cid
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
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Zhang LS, Xiong QP, Perez SP, Liu C, Wei J, Le C, Zhang L, Harada BT, Dai Q, Feng X, Hao Z, Wang Y, Dong X, Hu L, Wang ED, Pan T, Klungland A, Liu RJ, He C. ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing. Nat Cell Biol 2021; 23:684-691. [PMID: 34253897 PMCID: PMC8716185 DOI: 10.1038/s41556-021-00709-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Members of the mammalian AlkB family are known to mediate nucleic acid demethylation1,2. ALKBH7, a mammalian AlkB homologue, localizes in mitochondria and affects metabolism3, but its function and mechanism of action are unknown. Here we report an approach to site-specifically detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) modifications simultaneously within all cellular RNAs, and discovered that human ALKBH7 demethylates m22G and m1A within mitochondrial Ile and Leu1 pre-tRNA regions, respectively, in nascent polycistronic mitochondrial RNA4-6. We further show that ALKBH7 regulates the processing and structural dynamics of polycistronic mitochondrial RNAs. Depletion of ALKBH7 leads to increased polycistronic mitochondrial RNA processing, reduced steady-state mitochondria-encoded tRNA levels and protein translation, and notably decreased mitochondrial activity. Thus, we identify ALKBH7 as an RNA demethylase that controls nascent mitochondrial RNA processing and mitochondrial activity.
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Affiliation(s)
- Li-Sheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China
| | - Sonia Peña Perez
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Chang Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Cassy Le
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Linda Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Bryan T. Harada
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xinran Feng
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Ziyang Hao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuru Wang
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Xueyang Dong
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Lulu Hu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, PR China
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ru-Juan Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, PR China
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
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Li M, Zhao X, Wang W, Shi H, Pan Q, Lu Z, Perez SP, Suganthan R, He C, Bjørås M, Klungland A. Ythdf2-mediated m 6A mRNA clearance modulates neural development in mice. Genome Biol 2018; 19:69. [PMID: 29855337 PMCID: PMC5984442 DOI: 10.1186/s13059-018-1436-y] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND N 6 -methyladenosine (m6A) modification in mRNAs was recently shown to be dynamically regulated, indicating a pivotal role in multiple developmental processes. Most recently, it was shown that the Mettl3-Mettl14 writer complex of this mark is required for the temporal control of cortical neurogenesis. The m6A reader protein Ythdf2 promotes mRNA degradation by recognizing m6A and recruiting the mRNA decay machinery. RESULTS We show that the conditional depletion of the m6A reader protein Ythdf2 in mice causes lethality at late embryonic developmental stages, with embryos characterized by compromised neural development. We demonstrate that neural stem/progenitor cell (NSPC) self-renewal and spatiotemporal generation of neurons and other cell types are severely impacted by the loss of Ythdf2 in embryonic neocortex. Combining in vivo and in vitro assays, we show that the proliferation and differentiation capabilities of NSPCs decrease significantly in Ythdf2 -/- embryos. The Ythdf2 -/- neurons are unable to produce normally functioning neurites, leading to failure in recovery upon reactive oxygen species stimulation. Consistently, expression of genes enriched in neural development pathways is significantly disturbed. Detailed analysis of the m6A-methylomes of Ythdf2 -/- NSPCs identifies that the JAK-STAT cascade inhibitory genes contribute to neuroprotection and neurite outgrowths show increased expression and m6A enrichment. In agreement with the function of Ythdf2, delayed degradation of neuron differentiation-related m6A-containing mRNAs is seen in Ythdf2 -/- NSPCs. CONCLUSIONS We show that the m6A reader protein Ythdf2 modulates neural development by promoting m6A-dependent degradation of neural development-related mRNA targets.
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Affiliation(s)
- Miaomiao Li
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, NO-0317, Oslo, Norway
| | - Xu Zhao
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway.
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, NO-0317, Oslo, Norway.
| | - Wei Wang
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hailing Shi
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Qingfei Pan
- Department of Computational Biology, St. Jude Children's Hospital, Memphis, TN, 38105, USA
| | - Zhike Lu
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Sonia Peña Perez
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway
| | - Rajikala Suganthan
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway
| | - Chuan He
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway.
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway.
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, NO-0317, Oslo, Norway.
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