1
|
Jia P, Tian M, Zhang B, Wu X, He X, Zhang W. Habitat changes due to glacial freezing and melting reshape microbial networks. ENVIRONMENT INTERNATIONAL 2024; 189:108788. [PMID: 38838490 DOI: 10.1016/j.envint.2024.108788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/15/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
The phenomenon of glacial freezing and thawing involves microbial sequestration, release, and colonization, which has the potential to impact ecosystem functioning through changes in microbial diversity and interactions. In this study, we examined the structural features of microbial communities of the Dongkemadi glacier, including bacteria, fungi, and archaea, in four distinct glacial environments (snow, ice, meltwater, and frontier soil). The sequestration, release, and colonization of glacial microbes have been found to significantly impact the diversity and structure of glacial microbial communities, as well as the complexity of microbial networks. Specifically, the complexity of bacterial networks has been observed to increase in a sequential manner during these processes. Utilizing the Inter-Domain Ecological Network approach, researchers have further explored the cross-trophic interactions among bacteria, fungi, and archaea. The complexity of the bacteria-fungi-archaea network exhibited a sequential increase due to the processes of sequestration, release, and colonization of glacial microbes. The release and colonization of glacial microbes led to a shift in the role of archaea as key species within the network. Additionally, our findings suggest that the hierarchical interactions among various microorganisms contributed to the heightened complexity of the bacteria-fungi-archaea network. The primary constituents of the glacial microbial ecosystem are unclassified species associated with the Polaromonas. It is noteworthy that various key species in glacial ecosystems are influenced by the distinct environmental factors. Moreover, our findings suggest that key species are not significantly depleted in response to abrupt alterations in individual environmental factors, shedding light on the dynamics of microbial cross-trophic interactions within glacial ecosystems.
Collapse
Affiliation(s)
- Puchao Jia
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mao Tian
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Cryospheric Sciences and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Cryospheric Sciences and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiukun Wu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiaobo He
- Key Laboratory of Cryospheric Sciences and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Tanggula Mountain Cryosphere and Environment Observation and Research Station of Tibet Autonomous Region, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
| |
Collapse
|
2
|
Recio M, de la Torre J, Daddaoua A, Udaondo Z, Duque E, Gavira JA, López‐Sánchez C, Ramos JL. Characterization of an extremophile bacterial acid phosphatase derived from metagenomics analysis. Microb Biotechnol 2024; 17:e14404. [PMID: 38588312 PMCID: PMC11001196 DOI: 10.1111/1751-7915.14404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 04/10/2024] Open
Abstract
Acid phosphatases are enzymes that play a crucial role in the hydrolysis of various organophosphorous molecules. A putative acid phosphatase called FS6 was identified using genetic profiles and sequences from different environments. FS6 showed high sequence similarity to type C acid phosphatases and retained more than 30% of consensus residues in its protein sequence. A histidine-tagged recombinant FS6 produced in Escherichia coli exhibited extremophile properties, functioning effectively in a broad pH range between 3.5 and 8.5. The enzyme demonstrated optimal activity at temperatures between 25 and 50°C, with a melting temperature of 51.6°C. Kinetic parameters were determined using various substrates, and the reaction catalysed by FS6 with physiological substrates was at least 100-fold more efficient than with p-nitrophenyl phosphate. Furthermore, FS6 was found to be a decamer in solution, unlike the dimeric forms of crystallized proteins in its family.
Collapse
Affiliation(s)
- Maria‐Isabel Recio
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental ProtectionGranadaSpain
| | - Jesús de la Torre
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental ProtectionGranadaSpain
| | - Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, Pharmacy SchoolGranada UniversityGranadaSpain
| | - Zulema Udaondo
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Estrella Duque
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental ProtectionGranadaSpain
| | - José Antonio Gavira
- Consejo Superior de Investigaciones Científicas, Instituto de Ciencias de la TierraGranadaSpain
| | - Carmen López‐Sánchez
- Consejo Superior de Investigaciones Científicas, Instituto de Ciencias de la TierraGranadaSpain
| | - Juan L. Ramos
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental ProtectionGranadaSpain
| |
Collapse
|
3
|
Lisitskaya L, Shin Y, Agapov A, Olina A, Kropocheva E, Ryazansky S, Aravin AA, Esyunina D, Murakami KS, Kulbachinskiy A. Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity. Nat Commun 2022; 13:4624. [PMID: 35941106 PMCID: PMC9360449 DOI: 10.1038/s41467-022-32079-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 12/26/2022] Open
Abstract
Argonaute proteins are programmable nucleases that have defense and regulatory functions in both eukaryotes and prokaryotes. All known prokaryotic Argonautes (pAgos) characterized so far act on DNA targets. Here, we describe a new class of pAgos that uniquely use DNA guides to process RNA targets. The biochemical and structural analysis of Pseudooceanicola lipolyticus pAgo (PliAgo) reveals an unusual organization of the guide binding pocket that does not rely on divalent cations and the canonical set of contacts for 5'-end interactions. Unconventional interactions of PliAgo with the 5'-phosphate of guide DNA define its new position within pAgo and shift the site of target RNA cleavage in comparison with known Argonautes. The specificity for RNA over DNA is defined by ribonucleotide residues at the cleavage site. The analysed pAgos sense mismatches and modifications in the RNA target. The results broaden our understanding of prokaryotic defense systems and extend the spectrum of programmable nucleases with potential use in RNA technology.
Collapse
Affiliation(s)
- Lidiya Lisitskaya
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Ekaterina Kropocheva
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
4
|
Abstract
Mg2+ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg2+, bacteria adopt two main strategies: They increase the abundance and activity of Mg2+ importers and decrease the abundance of Mg2+-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5' leader region of some mRNAs responds to low cytoplasmic Mg2+ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg2+ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg2+ despite relying on different genes to do so.
Collapse
Affiliation(s)
- Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA; .,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
| | - Carissa Chan
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA;
| |
Collapse
|
5
|
Wang B, Svetlov D, Artsimovitch I. NMPylation and de-NMPylation of SARS-CoV-2 nsp9 by the NiRAN domain. Nucleic Acids Res 2021; 49:8822-8835. [PMID: 34352100 PMCID: PMC8385902 DOI: 10.1093/nar/gkab677] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
The catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) contains two active sites that catalyze nucleotidyl-monophosphate transfer (NMPylation). Mechanistic studies and drug discovery have focused on RNA synthesis by the highly conserved RdRp. The second active site, which resides in a Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain, is poorly characterized, but both catalytic reactions are essential for viral replication. One study showed that NiRAN transfers NMP to the first residue of RNA-binding protein nsp9; another reported a structure of nsp9 containing two additional N-terminal residues bound to the NiRAN active site but observed NMP transfer to RNA instead. We show that SARS-CoV-2 RdRp NMPylates the native but not the extended nsp9. Substitutions of the invariant NiRAN residues abolish NMPylation, whereas substitution of a catalytic RdRp Asp residue does not. NMPylation can utilize diverse nucleotide triphosphates, including remdesivir triphosphate, is reversible in the presence of pyrophosphate, and is inhibited by nucleotide analogs and bisphosphonates, suggesting a path for rational design of NiRAN inhibitors. We reconcile these and existing findings using a new model in which nsp9 remodels both active sites to alternately support initiation of RNA synthesis by RdRp or subsequent capping of the product RNA by the NiRAN domain.
Collapse
Affiliation(s)
- Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
6
|
Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases. Cells 2021; 10:cells10071591. [PMID: 34202661 PMCID: PMC8307549 DOI: 10.3390/cells10071591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022] Open
Abstract
It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites and deaminated residues, and enzymes catalyzing the direct reversal of UV and alkylation damage. The absence of uracil–DNA N-glycosylases in some Archaea, together with the presence of an AP endonuclease, which can cleave uracil-containing DNA, suggests that the AP endonuclease-initiated nucleotide incision repair (NIR) pathway evolved independently from DNA glycosylase-mediated base excision repair. NIR may be a relic that appeared in an early thermophilic ancestor to counteract spontaneous DNA damage. We hypothesize that a rise in the oxygen level in the Earth’s atmosphere ~2 Ga triggered the narrow specialization of AP endonucleases and DNA glycosylases to cope efficiently with a widened array of oxidative base damage and complex DNA lesions.
Collapse
|