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Zhang Y, Deng Y, Wang C, Li S, Lau FTK, Zhou J, Zhang T. Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants. mSystems 2024; 9:e0133323. [PMID: 38411061 PMCID: PMC10949511 DOI: 10.1128/msystems.01333-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Wastewater treatment plants (WWTPs) are indispensable biotechnology facilities for modern cities and play an essential role in modern urban infrastructure by employing microorganisms to remove pollutants in wastewater, thus protecting public health and the environment. This study conducted a 13-month bacterial community survey of six full-scale WWTPs in Hong Kong with samples of influent, activated sludge (AS), and effluent to explore their synchronism and asynchronism of bacterial community. Besides, we compared AS results of six Hong Kong WWTPs with data from 1,186 AS amplicon data in 269 global WWTPs and a 9-year metagenomic sequencing survey of a Hong Kong WWTP. Our results showed the compositions of bacterial communities varied and the bacterial community structure of AS had obvious differences across Hong Kong WWTPs. The co-occurrence analysis identified 40 pairs of relationships that existed among Hong Kong WWTPs to show solid associations between two species and stochastic processes took large proportions for the bacterial community assembly of six WWTPs. The abundance and distribution of the functional bacteria in worldwide and Hong Kong WWTPs were examined and compared, and we found that ammonia-oxidizing bacteria had more diversity than nitrite-oxidizing bacteria. Besides, Hong Kong WWTPs could make great contributions to the genome mining of microbial dark matter in the global "wanted list." Operational parameters had important effects on OTUs' abundance, such as the temperature to the genera of Tetrasphaera, Gordonia and Nitrospira. All these results obtained from this study can deepen our understanding of the microbial ecology in WWTPs and provide foundations for further studies. IMPORTANCE Wastewater treatment plants (WWTPs) are an indispensable component of modern cities, as they can remove pollutants in wastewater to prevent anthropogenic activities. Activated sludge (AS) is a fundamental wastewater treatment process and it harbors a highly complex microbial community that forms the main components and contains functional groups. Unveiling "who is there" is a long-term goal of the research on AS microbiology. High-throughput sequencing provides insights into the inventory diversity of microbial communities to an unprecedented level of detail. At present, the analysis of communities in WWTPs usually comes from a specific WWTP and lacks comparisons and verification among different WWTPs. The wide-scale and long-term sampling project and research in this study could help us evaluate the AS community more accurately to find the similarities and different results for different WWTPs in Hong Kong and other regions of the world.
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Affiliation(s)
- Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Frankie T. K. Lau
- Drainage Services Department, The Government of the Hong Kong Special Administrative Region of the People’s Republic of China, Wanchai, Hong Kong, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
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2
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Li M, Wu A, Li L, Li Z, Zang H. Three Stages of Dynamic Assembly Process of Dipeptide-Based Supramolecular Gel Revealed by In Situ Infrared Spectroscopy. ACS Biomater Sci Eng 2024; 10:863-874. [PMID: 38240580 DOI: 10.1021/acsbiomaterials.3c01609] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
The exploration of short peptide-based assembly is vital for understanding protein-misfolding-associated diseases and seeking strategies to attenuate aggregate formation. While, the molecular mechanism of their structural evolution remains poorly studied in view of the dynamic and unpredictable assembly process. Herein, infrared (IR) spectroscopy, which serves as an in situ and real-time analytical technique, was intelligently employed to investigate the mechanism of phase transition and aggregate formation during the dynamic assembly process of diphenylalanine. Combined with other spectroscopy and electron microscopy technologies, three stages of gel formation and the main driving forces in different stages were revealed. A variety of stoichiometric methods such as continuous wavelet transform, principal component analysis, and two-dimensional correlation spectroscopy techniques were conducted to analyze the original time-dependent IR spectra to obtain detailed information on the changes in the amide bands and hydration layer. The microenvironment of hydrogen bonding among amide bands was significantly changed with the addition of pyridine derivatives, resulting in great differences in the properties of co-assembled gels. This work not only provides a universal analytical way to reveal the dynamic assembly process of dipeptide-based supramolecular gel but also expands their applications in supramolecular regulation and high-throughput screens in situ.
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Affiliation(s)
- Meiqi Li
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Aoli Wu
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Lian Li
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Zibo Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Hengchang Zang
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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Xia J, Yu K, Yao Z, Sheng H, Mao L, Lu D, Gan H, Zhang S, Zhu DZ. Toward an intensive understanding of sewer sediment prokaryotic community assembly and function. Front Microbiol 2023; 14:1327523. [PMID: 38173681 PMCID: PMC10761402 DOI: 10.3389/fmicb.2023.1327523] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Prokaryotic communities play important roles in sewer sediment ecosystems, but the community composition, functional potential, and assembly mechanisms of sewer sediment prokaryotic communities are still poorly understood. Here, we studied the sediment prokaryotic communities in different urban functional areas (multifunctional, commercial, and residential areas) through 16S rRNA gene amplicon sequencing. Our results suggested that the compositions of prokaryotic communities varied significantly among functional areas. Desulfomicrobium, Desulfovibrio, and Desulfobacter involved in the sulfur cycle and some hydrolytic fermentation bacteria were enriched in multifunctional area, while Methanospirillum and Methanoregulaceae, which were related to methane metabolism were significantly discriminant taxa in the commercial area. Physicochemical properties were closely related to overall community changes (p < 0.001), especially the nutrient levels of sediments (i.e., total nitrogen and total phosphorus) and sediment pH. Network analysis revealed that the prokaryotic community network of the residential area sediment was more complex than the other functional areas, suggesting higher stability of the prokaryotic community in the residential area. Stochastic processes dominated the construction of the prokaryotic community. These results expand our understanding of the characteristics of prokaryotic communities in sewer sediment, providing a new perspective for studying sewer sediment prokaryotic community structure.
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Affiliation(s)
- Jingjing Xia
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Kai Yu
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Zhiyuan Yao
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Huafeng Sheng
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Lijuan Mao
- Zhenhai Urban Planning and Survey Research Institute of Ningbo, Ningbo, China
| | - Dingnan Lu
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - HuiHui Gan
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Shulin Zhang
- Zhenhai Urban Planning and Survey Research Institute of Ningbo, Ningbo, China
| | - David Z. Zhu
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB, Canada
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Liu H, Dai J, Fan Z, Yang B, Wang H, Hu Y, Shao K, Gao G, Tang X. Bacterial community assembly driven by temporal succession rather than spatial heterogeneity in Lake Bosten: a large lake suffering from eutrophication and salinization. Front Microbiol 2023; 14:1261079. [PMID: 37808304 PMCID: PMC10552925 DOI: 10.3389/fmicb.2023.1261079] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Oligosaline lakes in arid and semi-arid regions play a crucial role in providing essential water resources for local populations. However, limited research exists on the impact of the environment on bacterial community structure in these lakes, co-occurrence patterns and the mechanisms governing bacterial community assembly. This study aims to address this knowledge gap by examining samples collected from five areas of Lake Bosten over four seasons. Using the 16S rRNA gene sequencing method, we identified a total of 510 to 1,005 operational taxonomic units (OTUs) belonging to 37 phyla and 359 genera in Lake Bosten. The major bacterial phyla were Proteobacteria (46.5%), Actinobacteria (25.9%), Bacteroidetes (13.2%), and Cyanobacteria (5.7%), while the major genera were hgcI_clade (12.9%), Limnohabitans (6.2%), and Polynucleobacter (4.7%). Water temperature emerged as the primary driver of these community structure variations on global level. However, when considering only seasonal variations, pH and nitrate were identified as key factors influencing bacterial community structures. Summer differed from other seasons in aspects of seasonal symbiotic patterns of bacterial communities, community assembly and function are different from other seasons. There were notable variations in bacterial community structures between winter and summer. Deterministic processes dominated community assembly, but there was an increase in the proportion of stochastic processes during summer. In summer, the functions related to photosynthesis, nitrogen fixation, and decomposition of organic matter showed higher abundance. Our findings shed light on the response of bacterial communities to environmental changes and the underlying mechanisms of community assembly in oligosaline lakes in arid regions.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Taihu Basin Water Resources Management, Ministry of Water Resources, Nanjing Hydraulic Research Institute, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Jiangyu Dai
- Key Laboratory of Taihu Basin Water Resources Management, Ministry of Water Resources, Nanjing Hydraulic Research Institute, Nanjing, China
| | - Ziwu Fan
- Key Laboratory of Taihu Basin Water Resources Management, Ministry of Water Resources, Nanjing Hydraulic Research Institute, Nanjing, China
| | - Bei Yang
- Key Laboratory of Agricultural Environment of the Lower Reaches of the Yangtze River, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hang Wang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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Wang ZX, Liu B, Yang T, Yu D, Zhang C, Zheng L, Xie J, Liu B, Liu M, Peng H, Lai L, Ouyang Q, Ouyang S, Zhang YA. Structure of the Spring Viraemia of Carp Virus Ribonucleoprotein Complex Reveals Its Assembly Mechanism and Application in Antiviral Drug Screening. J Virol 2023; 97:e0182922. [PMID: 36943056 PMCID: PMC10134867 DOI: 10.1128/jvi.01829-22] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/03/2023] [Indexed: 03/23/2023] Open
Abstract
Spring viremia of carp virus (SVCV) is a highly pathogenic Vesiculovirus infecting the common carp, yet neither a vaccine nor effective therapies are available to treat spring viremia of carp (SVC). Like all negative-sense viruses, SVCV contains an RNA genome that is encapsidated by the nucleoprotein (N) in the form of a ribonucleoprotein (RNP) complex, which serves as the template for viral replication and transcription. Here, the three-dimensional (3D) structure of SVCV RNP was resolved through cryo-electron microscopy (cryo-EM) at a resolution of 3.7 Å. RNP assembly was stabilized by N and C loops; RNA was wrapped in the groove between the N and C lobes with 9 nt nucleotide per protomer. Combined with mutational analysis, our results elucidated the mechanism of RNP formation. The RNA binding groove of SVCV N was used as a target for drug virtual screening, and it was found suramin had a good antiviral effect. This study provided insights into RNP assembly, and anti-SVCV drug screening was performed on the basis of this structure, providing a theoretical basis and efficient drug screening method for the prevention and treatment of SVC. IMPORTANCE Aquaculture accounts for about 70% of global aquatic products, and viral diseases severely harm the development of aquaculture industry. Spring viremia of carp virus (SVCV) is the pathogen causing highly contagious spring viremia of carp (SVC) disease in cyprinids, especially common carp (Cyprinus carpio), yet neither a vaccine nor effective therapies are available to treat this disease. In this study, we have elucidated the mechanism of SVCV ribonucleoprotein complex (RNP) formation by resolving the 3D structure of SVCV RNP and screened antiviral drugs based on the structure. It is found that suramin could competitively bind to the RNA binding groove and has good antiviral effects both in vivo and in vitro. Our study provides a template for rational drug discovery efforts to treat and prevent SVCV infections.
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Affiliation(s)
- Zhao-Xi Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Bing Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Tian Yang
- School of Physics, Peking University, Beijing, China
| | - Daqi Yu
- School of Physics, Peking University, Beijing, China
| | - Chu Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Liming Zheng
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jin Xie
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bin Liu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Mengxi Liu
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Hailin Peng
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Luhua Lai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Physics, Peking University, Beijing, China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yong-An Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
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Mao Y, Huang W, Jia R, Bian Y, Pan MH, Ye X. Correlation between Protein Features and the Properties of pH-Driven-Assembled Nanoparticles: Control of Particle Size. J Agric Food Chem 2023; 71:5686-5699. [PMID: 37012896 DOI: 10.1021/acs.jafc.3c00147] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
This study sought to understand how the features of proteins impact the properties of nanoparticles assembled using the pH-shifting approach and the mechanism behind. Four legume protein isolates from faba bean, mung bean, soy, and pea were fractionated into natural aqueous-soluble (Sup) and aqueous-insoluble (Sed) fractions, which were proved to serve as shell and core, respectively, for the pH-driven-assembled nanoparticles. Using zein instead of Sed fractions as the core improved size uniformity, and particle size can be precisely controlled by adjusting core/shell ratios. Using the proteomic technique and silico characterization, the features of identified proteins indicated that hydrophobicity rather than molecular weight, surface charge, etc., mainly determined particle size. With molecular docking, structural analysis, and dissociation tests, the assembly of zein/Sup-based nanoparticles was dominantly driven by hydrophobic interactions. This study provides constructive information on the correlation between protein features and the properties of pH-driven-assembled nanoparticles, achieving a precise control of particle size.
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Affiliation(s)
- Yuhong Mao
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Technology, Fuzhou University, Fuzhou 350116, P.R. China
| | - Wenting Huang
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Technology, Fuzhou University, Fuzhou 350116, P.R. China
| | - Rongju Jia
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Technology, Fuzhou University, Fuzhou 350116, P.R. China
| | - Yangyang Bian
- The College of Life Science, Northwest University, Xi'an 710069, P.R. China
| | - Min-Hsiung Pan
- Institute of Food Sciences and Technology, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Xiuyun Ye
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Technology, Fuzhou University, Fuzhou 350116, P.R. China
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Bernardini A, Mukherjee P, Scheer E, Kamenova I, Antonova S, Sanchez PKM, Yayli G, Morlet B, Timmers HM, Tora L. Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID. bioRxiv 2023:2023.04.05.535704. [PMID: 37066372 PMCID: PMC10104070 DOI: 10.1101/2023.04.05.535704] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1 - the largest protein in the complex - as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Pooja Mukherjee
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Ivanka Kamenova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Simona Antonova
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - H.T. Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
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Wang HL, Liu D, Jia JH, Liu JL, Ruan ZY, Deng W, Yang S, Wu SG, Tong ML. High-stability spherical lanthanide nanoclusters for magnetic resonance imaging. Natl Sci Rev 2023; 10:nwad036. [PMID: 37200676 PMCID: PMC10187785 DOI: 10.1093/nsr/nwad036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 10/17/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2023] Open
Abstract
High-nuclear lanthanide clusters have shown great potential for the administration of high-dose mononuclear gadolinium chelates in magnetic resonance imaging (MRI). The development of high-nuclear lanthanide clusters with excellent solubility and high stability in water or solution has been challenging and is very important for expanding the performance of MRI. We used N-methylbenzimidazole-2-methanol (HL) and LnCl3·6H2O to synthesize two spherical lanthanide clusters, Ln32 (Ln = Ho, Ho32; and Ln = Gd, Gd32), which are highly stable in solution. The 24 ligands L- are all distributed on the periphery of Ln32 and tightly wrap the cluster core, ensuring that the cluster is stable. Notably, Ho32 can remain highly stable when bombarded with different ion source energies in HRESI-MS or immersed in an aqueous solution of different pH values for 24 h. The possible formation mechanism of Ho32 was proposed to be Ho(III), (L)- and H2O → Ho3(L)3/Ho3(L)4 → Ho4(L)4/Ho4(L)5 → Ho6(L)6/Ho6(L)7 → Ho16(L)19 → Ho28(L)15 → Ho32(L)24/Ho32(L)21/Ho32(L)23. To the best of our knowledge, this is the first study of the assembly mechanism of spherical high-nuclear lanthanide clusters. Spherical cluster Gd32, a form of highly aggregated Gd(III), exhibits a high longitudinal relaxation rate (1 T, r1 = 265.87 mM-1·s-1). More notably, compared with the clinically used commercial material Gd-DTPA, Gd32 has a clearer and higher-contrast T1-weighted MRI effect in mice bearing 4T1 tumors. This is the first time that high-nuclear lanthanide clusters with high water stability have been utilized for MRI. High-nuclear Gd clusters containing highly aggregated Gd(III) at the molecular level have higher imaging contrast than traditional Gd chelates; thus, using large doses of traditional gadolinium contrast agents can be avoided.
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Affiliation(s)
- Hai-Ling Wang
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Donglin Liu
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Jian-Hua Jia
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun-Liang Liu
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Ze-Yu Ruan
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Deng
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Shiping Yang
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Si-Guo Wu
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Ming-Liang Tong
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
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10
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Zhao RZ, Zhang WJ, Zhao ZF, Qiu XC. Determinants and Assembly Mechanism of Bacterial Community Structure in Ningxia Section of the Yellow River. Microorganisms 2023; 11. [PMID: 36838461 DOI: 10.3390/microorganisms11020496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
The Yellow River is a valuable resource in the Ningxia Hui Autonomous Region and plays a vital role in local human activities and biodiversity. Bacteria are a crucial component of river ecosystems, but the driving factors and assembly mechanisms of bacterial community structure in this region remain unclear. Herein, we documented the bacterial community composition, determinants, co-occurrence pattern, and assembly mechanism for surface water and sediment. In comparison to sediment, the bacterioplankton community showed significant seasonal variation, as well as less diversity and abundance. The network topology parameters indicated that the sediment bacterial network was more stable than water, but the bacterioplankton network had higher connectivity. In this lotic ecosystem, CODMn, Chl a, and pH affected the structure of the bacterioplankton community, while TP was the primary factor influencing the structure of the sediment bacterial community. The combined results of the neutral community model and the phylogenetic null model indicate that Bacterial communities in both habitats were mainly affected by stochastic processes, with ecological processes dominated by ecological drift for bacterioplankton and dispersal limitation for sediment bacteria. These results provide essential insights into future research on microbial ecology, environmental monitoring, and classified management in the Ningxia section of the Yellow River.
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11
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Qin D, Li Y, Chen N, Hu A, Yu CP. Response and recovery mechanisms of river microorganisms to gradient concentrations of estrogen. Front Microbiol 2023; 14:1109311. [PMID: 36846800 PMCID: PMC9944024 DOI: 10.3389/fmicb.2023.1109311] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
As an important ecological system on the earth, rivers have been influenced by the rapid development of urbanization, industrialization, and anthropogenic activities. Increasingly more emerging contaminants, such as estrogens, are discharged into the river environment. In this study, we conducted river water microcosmic experiments using in situ water to investigate the response mechanisms of microbial community when exposed to different concentrations of target estrogen (estrone, E1). Results showed that both exposure time and concentrations shaped the diversity of microbial community when exposed to E1. Deterministic process played a vital role in influencing microbial community over the entire sampling period. The influence of E1 on microbial community could last for a longer time even after the E1 has been degraded. The microbial community structure could not be restored to the undisturbed state by E1, even if disturbed by low concentrations of E1(1 μg/L and 10 μg/L) for a short time. Our study suggests that estrogens could cause long-term disturbance to the microbial community of river water ecosystem and provides a theoretical basis for assessing the environmental risk of estrogens in rivers.
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Affiliation(s)
- Dan Qin
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China,*Correspondence: Dan Qin, ✉
| | - Yan Li
- School of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, Fujian, China
| | - Nengwang Chen
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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12
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Zhang Z, Ding M, Sun Y, Khattak RH, Chen J, Teng L, Liu Z. Different living environments drive deterministic microbial community assemblages in the gut of Alpine musk deer ( Moschus chrysogaster). Front Microbiol 2023; 13:1108405. [PMID: 36713154 PMCID: PMC9880224 DOI: 10.3389/fmicb.2022.1108405] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Substantial variation in the environment directly causes remodeling of the colonized gut microbiota, controlling community diversity, and functions in the host to tune-up their adaptive states. However, the mechanisms of microbial community assembly in response to environmental changes remain unclear, especially in endangered ruminants. In this study, we analyzed the microbial communities of 37 fecal samples collected from captive and wild Alpine musk deer (Moschus chrysogaster) to characterize the complexity and assembly processes using 16S rRNA gene sequencing. We found significantly different diversities and compositions of gut microbiota among both groups associated with different living environments. Heterogeneous selection was the predominant factor regulating the gut microbiota community under similar climatic conditions, indicating that microbial community assembly was largely driven by deterministic mechanisms. The species co-occurrence network showed complex and tight connections with a higher positive correlation in the wild environment. Moreover, the captive group exhibited significant differences in chemoheterotrophy and fermentation compared with the wild group, but the opposite was observed in animal parasites or symbionts, which might be closely related to diet, energy supply, and healthcare of animals. This study provides a framework basis and new insights into understanding gut microbiota in different environments.
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Affiliation(s)
- Zhirong Zhang
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China
| | - Mengqi Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Yujiao Sun
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China,College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Romaan Hayat Khattak
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China
| | - Junda Chen
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China
| | - Liwei Teng
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China,Key Laboratory of Conservation Biology, National Forestry and Grassland Administration, Harbin, China,*Correspondence: Liwei Teng ✉
| | - Zhensheng Liu
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China,Key Laboratory of Conservation Biology, National Forestry and Grassland Administration, Harbin, China,Zhensheng Liu ✉
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13
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Liu SJ, Xie ZX, Wu PF, Zheng RW, Liu Y, Lin L, Liu HP, Wang DZ. Composition and assembly of the bacterial community in the overlying waters of the coral reef of China's Xisha Islands. Front Microbiol 2022; 13:1059262. [PMID: 36590395 PMCID: PMC9797850 DOI: 10.3389/fmicb.2022.1059262] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Coral reef ecosystems are one of the most diverse and productive habitats on Earth. Microbes in the reef-overlying waters are key players in maintaining this ecosystem through regulating biogeochemical and ecological processes. However, the composition structure and assembly mechanism of microbial community in the reef-overlying waters remain largely unknown. In the present study, the bacterial communities from the overlying waters of atolls and fringing reefs as well as the surface waters of the adjacent open ocean of the Xisha Islands in the South China Sea were investigated using 16S rRNA high-throughput sequencing combined with a size-fractionation strategy. The results showed that environments of all sampling stations were similar, characterized by an almost complete lack of inorganic nutrients such as nitrogen and phosphorus. Proteobacteria, Cyanobacteria and Bacteroidetes were the dominant phyla, and Synechococcus was most abundant at the genus level in both large fraction (LF; 1.6-200 μm) and small fraction (SF; 0.2-1.6 μm) communities. Only a slight difference in community composition between LF and SF samples was observed. The bacterial communities among the three habitat types showed noticeable differences, and the bacterial composition among the atoll reefs was more varied than that among the fringing reefs. The similarity of bacterial communities significantly declined with the increasing geographic distance, and stochastic processes were more important than deterministic processes in bacterial community assembly. This study sheds lights on the bacterial biodiversity of coral reefs and the importance of stochastic process in structuring bacterial communities.
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Affiliation(s)
- Si-Jia Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ru-Wen Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuan Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, China
| | - Hai-Peng Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, China,*Correspondence: Da-Zhi Wang,
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14
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Huang Z, Hou D, Zhou R, Zeng S, Xing C, Wei D, Deng X, Yu L, Wang H, Deng Z, Weng S, Ning D, Xiao C, Yan Q, Zhou J, He Z, He J. Environmental Water and Sediment Microbial Communities Shape Intestine Microbiota for Host Health: The Central Dogma in an Anthropogenic Aquaculture Ecosystem. Front Microbiol 2021; 12:772149. [PMID: 34795658 PMCID: PMC8593368 DOI: 10.3389/fmicb.2021.772149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/07/2021] [Accepted: 10/08/2021] [Indexed: 12/22/2022] Open
Abstract
From increasing evidence has emerged a tight link among the environment, intestine microbiota, and host health status; moreover, the microbial interaction in different habitats is crucial for ecosystems. However, how the environmental microbial community assembly governs the intestinal microbiota and microbial communities of multiple habitats contribute to the metacommunity remain elusive. Here, we designed two delicate experiments from temporal and spatial scales in a shrimp culture pond ecosystem (SCPE). Of the SCPE metacommunity, the microbial diversity was mainly contributed to by the diversity of–βIntraHabitats and βInterHabitats, and water and sediment communities had a large contribution to the shrimp intestine community as shown by SourceTracker and Sloan neutral community model analyses. Also, phylogenetic bin-based null model results show that microbial assembly of three habitats in the SCPE appeared to be largely driven by stochastic processes. These results enrich our understanding of the environment–intestinal microbiota–host health closely linked relationship, making it possible to be the central dogma for an anthropogenic aquaculture ecosystem. Our findings enhance the mechanistic understanding of microbial assembly in the SCPE for further analyzing metacommunities, which has important implications for microbial ecology and animal health.
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Affiliation(s)
- Zhijian Huang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Renjun Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chengguang Xing
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongdong Wei
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xisha Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lingfei Yu
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Wang
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhixuan Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, School of Civil Engineering and Environmental Sciences, The University of Oklahoma, Norman, OK, United States
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Jizhong Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, School of Civil Engineering and Environmental Sciences, The University of Oklahoma, Norman, OK, United States
| | - Zhili He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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15
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Li J, Hu A, Bai S, Yang X, Sun Q, Liao X, Yu CP. Characterization and Performance of Lactate-Feeding Consortia for Reductive Dechlorination of Trichloroethene. Microorganisms 2021; 9:microorganisms9040751. [PMID: 33918519 PMCID: PMC8065584 DOI: 10.3390/microorganisms9040751] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/05/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding the underlying mechanism that drives the microbial community mediated by substrates is crucial to enhance the biostimulation in trichloroethene (TCE)-contaminated sites. Here, we investigated the performance of stable TCE-dechlorinating consortia by monitoring the variations in TCE-related metabolites and explored their underlying assembly mechanisms using 16S rDNA amplicon sequencing and bioinformatics analyses. The monitoring results indicated that three stable TCE-dechlorinating consortia were successfully enriched by lactate-containing anaerobic media. The statistical analysis results demonstrated that the microbial communities of the enrichment cultures changed along with time and were distinguished by their sample sources. The deterministic and stochastic processes were simultaneously responsible for shaping the TCE-dechlorinating community assembly. The indicator patterns shifted with the exhaustion of the carbon source and the pollutants, and the tceA-carrying Dehalococcoides, as an indicator for the final stage samples, responded positively to TCE removal during the incubation period. Pseudomonas, Desulforhabdus, Desulfovibrio and Methanofollis were identified as keystone populations in the TCE-dechlorinating process by co-occurrence network analysis. The results of this study indicate that lactate can be an effective substrate for stimulated bioremediation of TCE-contaminated sites, and the reduction of the stochastic forces or enhancement of the deterministic interventions may promote more effective biostimulation.
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Affiliation(s)
- Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
| | - Shijie Bai
- Institute of Deep Sea Science and Engineering, Chinese Academic of Sciences, Sanya 572000, China;
| | - Xiaoyong Yang
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
| | - Xu Liao
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
- Water Innovation, Low Carbon and Environmental Sustainability Research Center, National Taiwan University, Taipei 10617, Taiwan
- Correspondence:
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16
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Ahn J, Jeong S, Kang SM, Jo I, Park BJ, Ha NC. Separation of Coiled-Coil Structures in Lamin A/C Is Required for the Elongation of the Filament. Cells 2020; 10:E55. [PMID: 33396475 DOI: 10.3390/cells10010055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
Intermediate filaments (IFs) commonly have structural elements of a central α-helical coiled-coil domain consisting of coil 1a, coil 1b, coil 2, and their flanking linkers. Recently, the crystal structure of a long lamin A/C fragment was determined and showed detailed features of a tetrameric unit. The structure further suggested a new binding mode between tetramers, designated eA22, where a parallel overlap of coil 1a and coil 2 is the critical interaction. This study investigated the biochemical effects of genetic mutations causing human diseases, focusing on the eA22 interaction. The mutant proteins exhibited either weakened or augmented interactions between coil 1a and coil 2. The ensuing biochemical results indicated that the interaction requires the separation of the coiled-coils in the N-terminal of coil 1a and the C-terminal of coil 2, coupled with the structural transition in the central α-helical rod domain. This study provides insight into the role of coil 1a as a molecular regulator in the elongation of IF proteins.
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17
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Du X, Deng Y, Li S, Escalas A, Feng K, He Q, Wang Z, Wu Y, Wang D, Peng X, Wang S. Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process. Mol Ecol 2020; 30:1072-1085. [PMID: 33320382 DOI: 10.1111/mec.15777] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 11/04/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022]
Abstract
Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0-20 cm, Middle: 20-40 cm, and Substratum: 40-100 cm) in a typical grassland by examining both distance-decay (DDRs) and species-area relationships (SARs), taxonomically and phylogenetically, as well as community assembly processes. Each layer exhibited significant biogeographic patterns in both DDR and SAR (p < .05), with taxonomic turnover rates higher than phylogenetic ones. Specifically, the spatial turnover rates, β and z values, respectively, ranged from 0.016 ± 0.005 to 0.023 ± 0.005 and 0.065 ± 0.002 to 0.077 ± 0.004 across soil strata, and both increased with depth. Moreover, the prokaryotic community in grassland soils assembled mainly according to deterministic rather than stochastic mechanisms. By using normalized stochasticity ratio (NST) based on null model, the relative importance of deterministic ratios increased from 48.0 to 63.3% from Upper to Substratum, meanwhile a phylogenetic based method revealed average βNTI also increased with depth, from -5.29 to 19.5. Using variation partitioning and distance approaches, both geographic distance and soil properties were found to strongly affect biodiversity structure, the proportions increasing with depth, but spatial distance was always the main underlying factor. These indicated increasingly deterministic proportions in accelerating turnover rates for spatial assembly of prokaryotic biodiversity. Our study provided new insights on biogeography in different strata, revealing importance of assembly patterns and mechanisms of prokaryote communities in below-surface soils.
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Affiliation(s)
- Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China
| | - Shuzhen Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Arthur Escalas
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier Cedex 5, France
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhujun Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yueni Wu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
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Xu D, Kong H, Yang EJ, Li X, Jiao N, Warren A, Wang Y, Lee Y, Jung J, Kang SH. Contrasting Community Composition of Active Microbial Eukaryotes in Melt Ponds and Sea Water of the Arctic Ocean Revealed by High Throughput Sequencing. Front Microbiol 2020; 11:1170. [PMID: 32582106 PMCID: PMC7291953 DOI: 10.3389/fmicb.2020.01170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 09/29/2019] [Accepted: 05/07/2020] [Indexed: 01/03/2023] Open
Abstract
Melt ponds (MPs), form as the result of thawing of snow and sea ice in the summer, have lower albedo than the sea ice and are thus partly responsible for the polar amplification of global warming. Knowing the community composition of MP organisms is key to understanding their roles in the biogeochemical cycles of nutrients and elements. However, the community composition of MP microbial eukaryotes has rarely been studied. In the present study, we assessed the microbial eukaryote biodiversity, community composition, and assembly processes in MPs and surface sea water (SW) using high throughput sequencing of 18S rRNA of size-fractionated samples. Alpha diversity estimates were lower in the MPs than SW across all size fractions. The community composition of MPs was significantly different from that of SW. The MP communities were dominated by members from Chrysophyceae, the ciliate classes Litostomatea and Spirotrichea, and the cercozoan groups Filosa-Thecofilosea. One open MP community was similar to SW communities, which was probably due to the advanced stage of development of the MP enabling the exchange of species between it and adjacent SW. High portions of shared species between MPs and SW may indicate the vigorous exchange of species between these two major types of environments in the Arctic Ocean. SW microbial eukaryote communities are mainly controlled by dispersal limitation whereas those of MP are mainly controlled by ecological drift.
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Affiliation(s)
- Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Hejun Kong
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Xinran Li
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Sung-Ho Kang
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
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Kong J, Wang Y, Warren A, Huang B, Sun P. Diversity Distribution and Assembly Mechanisms of Planktonic and Benthic Microeukaryote Communities in Intertidal Zones of Southeast Fujian, China. Front Microbiol 2019; 10:2640. [PMID: 31803165 PMCID: PMC6872677 DOI: 10.3389/fmicb.2019.02640] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 07/15/2019] [Accepted: 10/30/2019] [Indexed: 01/07/2023] Open
Abstract
The intertidal zone occupies the shore between the high and low tide marks and is subjected both to natural forces and anthropogenic activities. Compared with the coastal ecosystem, studies comparing diversity and community structure of intertidal planktonic and benthic microeukaryotes are limited. Therefore, the ecological processes mediating their assemblies remain poorly understood. Environmental rRNA from two size fractions (nano- and micro-sized) of plankton and from seasonally collected (spring and summer) benthos, together with water and sediment chemistry and concentrations of heavy metals, were used to explore diversity and community structure of microeukaryotes in intertidal zones of southeast Fujian Province, China. Benthic microeukaryotes harbored significantly higher alpha-diversity than those of the plankton, whereas no distinct patterns of organism size/seasonal distribution were observed for either community. Community compositions differed significantly between planktonic and benthic microeukaryotes, with the former presenting size-fractionated discrepancies and the latter showing seasonal variation. Community turnover between planktonic and benthic microeukaryotes was mainly driven by stramenopiles and alveolates. Distance-decay patterns were found in both communities, with the rate of community turnover being higher for planktonic than benthic microeukaryotes. Among the environmental factors measured, the concentration of Cd and the water content of sediment were closely associated with benthic community variations, whereas none of the factors measured was identified as being responsible for planktonic community variation. Phylogenetic null model analysis indicated that dispersal limitation was the most crucial ecological process mediating community assembly for both planktonic and benthic microeukaryotes in intertidal zones, with heterogeneous selection making a higher contribution to community variation of benthic than planktonic microeukaryotes. Stochastic processes, mainly dispersal limitation, were found to prevail in both communities. This study thus provides new insights into the diversity distribution and assembly mechanism of microeukaryotes in intertidal zones.
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Affiliation(s)
- Jie Kong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Bangqin Huang
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
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Li AZ, Han XB, Zhang MX, Zhou Y, Chen M, Yao Q, Zhu HH. Culture-Dependent and -Independent Analyses Reveal the Diversity, Structure, and Assembly Mechanism of Benthic Bacterial Community in the Ross Sea, Antarctica. Front Microbiol 2019; 10:2523. [PMID: 31787942 PMCID: PMC6856632 DOI: 10.3389/fmicb.2019.02523] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 06/26/2019] [Accepted: 10/21/2019] [Indexed: 11/22/2022] Open
Abstract
The benthic bacterial community in Antarctic continental shelf ecosystems are not well-documented. We collected 13 surface sediments from the Ross Sea, a biological hotspot in high-latitude maritime Antarctica undergoing rapid climate change and possible microflora shift, and aimed to study the diversity, structure and assembly mechanism of benthic bacterial community using both culture-dependent and -independent approaches. High-throughput sequencing of 16S rRNA gene amplicons revealed 370 OTUs distributed in 21 phyla and 284 genera. The bacterial community was dominated by Bacteroidetes, Gamma- and Alphaproteobacteria, and constituted by a compact, conserved and positively-correlated group of anaerobes and other competitive aerobic chemoheterotrophs. Null-model test based on βNTI and RCBray indicated that stochastic processes, including dispersal limitation and undominated fractions, were the main forces driving community assembly. On the other hand, environmental factors, mainly temperature, organic matter and chlorophyll, were significantly correlated with bacterial richness, diversity and community structure. Moreover, metabolic and physiological features of the prokaryotic taxa were mapped to evaluate the adaptive mechanisms and functional composition of the benthic bacterial community. Our study is helpful to understand the structural and functional aspects, as well as the ecological and biogeochemical role of the benthic bacterial community in the Ross Sea.
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Affiliation(s)
- An-Zhang Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xi-Bin Han
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Ming-Xia Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yang Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Grass Science, Guangdong Engineering Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Sun P, Huang L, Xu D, Warren A, Huang B, Wang Y, Wang L, Xiao W, Kong J. Integrated Space-Time Dataset Reveals High Diversity and Distinct Community Structure of Ciliates in Mesopelagic Waters of the Northern South China Sea. Front Microbiol 2019; 10:2178. [PMID: 31616397 PMCID: PMC6768975 DOI: 10.3389/fmicb.2019.02178] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 06/17/2019] [Accepted: 09/05/2019] [Indexed: 12/20/2022] Open
Abstract
Little is known about diversity distribution and community structure of ciliates in mesopelagic waters, especially how they are related to spatial and temporal changes. Here, an integrative approach, combining high-throughput cDNA sequencing and quantitative protargol stain, was used to analyze ciliate communities collected temporally along a transect from coastal to oceanic regions at depths ranging from the surface to 1000 m. The mesopelagic zone exhibited comparable alpha diversity to surface water which was consistent over temporal variation, with high diversity occurring at the interface with the euphotic zone. Comparison with the northeastern and the western Pacific Ocean revealed consistency of this vertical distribution of ciliates across oceanic basins. Mesopelagic ciliates harbored distinct community structure without significant seasonal differences, with the vertical variations driven largely by members of the classes Spirotrichea and Oligohymenophorea. Operational taxonomic units (OTUs) affiliated with Scuticociliatia, Astomatida and Apostomatida, members of which are known to be bacterivorous and/or commensal/parasitic species, were more abundant in mesopelagic waters than above, implying they are an important component of food webs in the mesopelagic zone. A combination of depth, geographic distance and environment shaped the ciliate communities, with depth being the most influential factor. Phylogenetic null modeling analysis further indicated that 57.1 and 33.3% of mesopelagic community variation was governed by dispersal limitation and heterogeneous selection, respectively, probably due to the marked biochemical and physical gradients down the water column. This suggests that ciliate community structure in the mesopelagic zone is mainly controlled by stochastic processes. Collectively, this study reports mesopelagic ciliates exhibited high diversity and distinct community structure across spatiotemporal scales and informs the processes mediating ciliate assembly in the mesopelagic zone. These should be fully considered in future studies to build a more comprehensive understanding of mesopelagic microbial assemblages.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Liying Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Bangqin Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lei Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Wupeng Xiao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jie Kong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Tian LJ, Min Y, Li WW, Chen JJ, Zhou NQ, Zhu TT, Li DB, Ma JY, An PF, Zheng LR, Huang H, Liu YZ, Yu HQ. Substrate Metabolism-Driven Assembly of High-Quality CdS xSe 1- x Quantum Dots in Escherichia coli: Molecular Mechanisms and Bioimaging Application. ACS Nano 2019; 13:5841-5851. [PMID: 30969107 DOI: 10.1021/acsnano.9b01581] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Biosynthesis offers opportunities for cost-effective and sustainable production of semiconductor quantum dots (QDs), but is currently restricted by poor controllability on the synthesis process, resulting from limited knowledge on the assembly mechanisms and the lack of effective control strategies. In this work, we provide molecular-level insights into the formation mechanism of biogenic QDs (Bio-QDs) and its connection with the cellular substrate metabolism in Escherichia coli. Strengthening the substrate metabolism for producing more reducing power was found to stimulate the production of several reduced thiol-containing proteins (including glutaredoxin and thioredoxin) that play key roles in Bio-QDs assembly. This effectively diverted the transformation route of the selenium (Se) and cadmium (Cd) metabolic from Cd3(PO4)2 formation to CdS xSe1- x QDs assembly, yielding fine-sized (2.0 ± 0.4 nm), high-quality Bio-QDs with quantum yield (5.2%) and fluorescence lifetime (99.19 ns) far exceeding the existing counterparts. The underlying mechanisms of Bio-QDs crystallization and development were elucidated by density functional theory calculations and molecular dynamics simulation. The resulting Bio-QDs were successfully used for bioimaging of cancer cells and tumor tissue of mice without extra modification. Our work provides fundamental knowledge on the Bio-QDs assembly mechanisms and proposes an effective, facile regulation strategy, which may inspire advances in controlled synthesis and practical applications of Bio-QDs as well as other bionanomaterials.
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Affiliation(s)
- Li-Jiao Tian
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Yuan Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Jie-Jie Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Nan-Qing Zhou
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Ting-Ting Zhu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Dao-Bo Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Jing-Yuan Ma
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201204 , China
| | - Peng-Fei An
- Beijing Synchrotron Radiation Laboratory, Institute of High Energy Physics , Chinese Academy of Science , Beijing 100049 , China
| | - Li-Rong Zheng
- Beijing Synchrotron Radiation Laboratory, Institute of High Energy Physics , Chinese Academy of Science , Beijing 100049 , China
| | - Hai Huang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Yang-Zhong Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
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Yao Z, Du S, Liang C, Zhao Y, Dini-Andreote F, Wang K, Zhang D. Bacterial Community Assembly in a Typical Estuarine Marsh with Multiple Environmental Gradients. Appl Environ Microbiol 2019; 85:e02602-18. [PMID: 30635381 DOI: 10.1128/AEM.02602-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/16/2018] [Indexed: 01/26/2023] Open
Abstract
Bacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly is poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high marsh, using 16S rRNA gene amplicon sequencing. Bacterial community compositions differed significantly between sediment transects. Physicochemical properties, particularly sediment nutrient levels (i.e., total nitrogen [TN] and available phosphorus [AP]), as well as sediment physical structure and pH (P < 0.05), were strongly associated with the overall community variations. In addition, the topological properties of bacterial cooccurrence networks varied with distance to the water-land junction. Both node- and network-level topological features revealed that the bacterial network of sediments farthest from the junction was less intense in complexity and interactions than other sediments. Phylogenetic null modeling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, data from this study provide a detailed outline of the distribution pattern of the sediment bacterial community across an estuarine marsh and inform the mechanisms and processes mediating bacterial community assembly in marsh soils.IMPORTANCE Salt marshes represent highly dynamic ecosystems where the atmosphere, continents, and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating bacterial assembly are poorly understood for salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of bacterial communities in an estuarine marsh located in south Hangzhou Bay were investigated. The results revealed an intricate interplay between stochastic and deterministic processes mediating the assembly of bacterial communities in the studied gradient system. Collectively, our findings illustrate the main drivers of community assembly, taking into consideration changes in sediment abiotic variables and potential biotic interactions. Thus, we offer new insights into estuarine bacterial communities and illustrate the interplay of ecological processes shaping the assembly of bacterial communities in estuarine marsh ecosystems.
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Zhang H, Wang K, Shen L, Chen H, Hou F, Zhou X, Zhang D, Zhu X. Microbial Community Dynamics and Assembly Follow Trajectories of an Early-Spring Diatom Bloom in a Semienclosed Bay. Appl Environ Microbiol 2018; 84:e01000-18. [PMID: 30006403 DOI: 10.1128/AEM.01000-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/09/2018] [Indexed: 11/20/2022] Open
Abstract
Harmful algal blooms (HABs) are serious ecological disasters in coastal areas, significantly influencing biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been widely investigated, but the assembly mechanisms of microbial communities during HABs are poorly understood. Here, using 16S rRNA gene amplicon sequencing, we analyzed the microbial communities during an early-spring diatom bloom, in order to investigate the dynamics of microbial assembly processes. Rhodobacteraceae, Flavobacteriaceae, and Microbacteriaceae were the main bacterial families during the bloom. The 30 most abundant operational taxonomic units (OTUs) segregated into 4 clusters according to specific bloom stages, exhibiting clear successional patterns during the bloom process. The succession of microbial communities correlated with changes in the dynamics of algal species. Based on the β-nearest taxon distance, we constructed a simulation model, which demonstrated that the assembly of microbial communities shifted from strong heterogenous selection in the early stage of the bloom to stochasticity in the middle stage and then to strong homogeneous selection in the late and after-bloom stages. These successions were driven mainly by chlorophyll a contents, which were affected mainly by Skeletonema costatum Moreover, functional prediction of microbial communities showed that microbial metabolic functions were significantly related to nitrogen metabolism. In summary, our results clearly suggested a dominant role of determinacy in microbial community assembly in HABs and will facilitate deeper understanding of the ecological processes shaping microbial communities during the algal bloom process.IMPORTANCE Harmful algal blooms (HABs) significantly influence biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been studied intensively, but the assembly mechanisms of microbial communities during HABs are poorly understood, with limited investigation of the balance of deterministic and stochastic processes in shaping microbial communities in HABs. In this study, the dynamics and assembly of microbial communities in an early-spring diatom bloom process were investigated. Our data both confirm previously observed general microbial successional patterns and show new detailed mechanisms for microbial assembly in HABs. These results will facilitate deeper understanding of the ecological processes shaping microbial communities in HABs. In addition, predictions of metabolic potential in this study will facilitate understanding of the influence of HABs on nitrogen metabolism in marine environments.
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Abstract
The assembly mechanism for aggregation of amyloid fibril is important and fundamental for any quantitative and physical descriptions because it needs to have a deep understanding of both molecular and statistical physics. A theoretical model with three states including coil, helix and sheet is presented to describe the amyloid formation. The corresponding general mathematical expression of N molecule systems are derived, including the partition function and thermodynamic quantities. We study the equilibrium properties of the system in the solution and find that three molecules have the extreme value of free energy. The denaturant effect on molecular assemble is also discussed. Furthermore, we apply the kinetic theories to take account of the nucleation and growth of the amyloid in the solution. It has been shown that our theoretical results can be compared with experimental results.
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Affiliation(s)
- Lingyun Zhang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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26
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Liu B, Dong S, Li G, Wang W, Liu X, Wang Y, Yang C, Rao Z, Guo Y. Structural Insight into Nucleoprotein Conformation Change Chaperoned by VP35 Peptide in Marburg Virus. J Virol 2017; 91:e00825-17. [PMID: 28566377 DOI: 10.1128/JVI.00825-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 12/14/2022] Open
Abstract
Marburg virus (MARV) encodes a nucleoprotein (NP) to encapsidate its genome by oligomerization and form a ribonucleoprotein complex (RNP). According to previous investigation on nonsegmented negative-sense RNA viruses (nsNSV), the newly synthesized NPs must be prevented from indiscriminately binding to noncognate RNAs. During the viral RNA synthesis process, the RNPs undergo a transition from an RNA-bound form to a template-free form, to open access for the interaction between the viral polymerase and the RNA template. In filoviruses, this transition is regulated by VP35 peptide and other viral components. To further understand the dynamic process of filovirus RNP formation, we report here the structure of MARV NPcore, both in the apo form and in the VP35 peptide-chaperoned form. These structures reveal a typical bilobed structure, with a positive-charged RNA binding groove between two lobes. In the apo form, the MARV NP exists in an interesting hexameric state formed by the hydrophobic interaction within the long helix of the NPcore C-terminal region, which shows high structural flexibility among filoviruses and may imply critical function during RNP formation. Moreover, the VP35 peptide-chaperoned NPcore remains in a monomeric state and completely loses its affinity for single-stranded RNA (ssRNA). The structural comparison reveals that the RNA binding groove undergoes a transition from closed state to open state, chaperoned by VP35 peptide, thus preventing the interaction for viral RNA. Our investigation provides considerable structural insight into the filovirus RNP working mechanism and may support the development of antiviral therapies targeting the RNP formation of filovirus.IMPORTANCE Marburg virus is one of the most dangerous viruses, with high morbidity and mortality. A recent outbreak in Angola in 2005 caused the deaths of 272 persons. NP is one of the most essential proteins, as it encapsidates and protects the whole virus genome simultaneously with self-assembly oligomerization. Here we report the structures of MARV NPcore in two different forms. In the MARV NP apo form, we identify an interesting hexamer formed by hydrophobic interaction within a long helix, which is highly conserved and flexible among filoviruses and may indicate its critical function during the virus RNP formation. Moreover, the structural comparison with the NP-VP35 peptide complex reveals a structural transition chaperoned by VP35, in which the RNA binding groove undergoes a transition from closed state to open state. Finally, we discussed the high conservation and critical role of the VP35 binding pocket and its potential use for therapeutic development.
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Lindh MV, Sjöstedt J, Casini M, Andersson A, Legrand C, Pinhassi J. Local Environmental Conditions Shape Generalist But Not Specialist Components of Microbial Metacommunities in the Baltic Sea. Front Microbiol 2016; 7:2078. [PMID: 28066392 PMCID: PMC5180196 DOI: 10.3389/fmicb.2016.02078] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 09/13/2016] [Accepted: 12/08/2016] [Indexed: 01/06/2023] Open
Abstract
Marine microbes exhibit biogeographical patterns linked with fluxes of matter and energy. Yet, knowledge of the mechanisms shaping bacterioplankton community assembly across temporal scales remains poor. We examined bacterioplankton 16S rRNA gene fragments obtained from Baltic Sea transects to determine phylogenetic relatedness and assembly processes coupled with niche breadth. Communities were phylogenetically more related over time than expected by chance, albeit with considerable temporal variation. Hence, habitat filtering, i.e., local environmental conditions, rather than competition structured bacterioplankton communities in summer but not in spring or autumn. Species sorting (SS) was the dominant assembly process, but temporal and taxonomical variation in mechanisms was observed. For May communities, Cyanobacteria, Actinobacteria, Alpha- and Betaproteobacteria exhibited SS while Bacteroidetes and Verrucomicrobia were assembled by SS and mass effect. Concomitantly, Gammaproteobacteria were assembled by the neutral model and patch dynamics. Temporal variation in habitat filtering and dispersal highlights the impact of seasonally driven reorganization of microbial communities. Typically abundant Baltic Sea populations such as the NS3a marine group (Bacteroidetes) and the SAR86 and SAR11 clade had the highest niche breadth. The verrucomicrobial Spartobacteria population also exhibited high niche breadth. Surprisingly, variation in bacterioplankton community composition was regulated by environmental factors for generalist taxa but not specialists. Our results suggest that generalists such as NS3a, SAR86, and SAR11 are reorganized to a greater extent by changes in the environment compared to specialists and contribute more strongly to determining overall biogeographical patterns of marine bacterial communities.
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Affiliation(s)
- Markus V Lindh
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University Kalmar, Sweden
| | - Johanna Sjöstedt
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University Kalmar, Sweden
| | - Michele Casini
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences (SLU) Lysekil, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University Umeå, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University Kalmar, Sweden
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Deng A, Lin W, Shi N, Wu J, Sun Z, Sun Q, Bai H, Pan Y, Wen T. In vitro assembly of the bacterial actin protein MamK from ' Candidatus Magnetobacterium casensis' in the phylum Nitrospirae. Protein Cell 2016; 7:267-280. [PMID: 26960409 PMCID: PMC4818849 DOI: 10.1007/s13238-016-0253-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/07/2016] [Indexed: 10/29/2022] Open
Abstract
Magnetotactic bacteria (MTB), a group of phylogenetically diverse organisms that use their unique intracellular magnetosome organelles to swim along the Earth's magnetic field, play important roles in the biogeochemical cycles of iron and sulfur. Previous studies have revealed that the bacterial actin protein MamK plays essential roles in the linear arrangement of magnetosomes in MTB cells belonging to the Proteobacteria phylum. However, the molecular mechanisms of multiple-magnetosome-chain arrangements in MTB remain largely unknown. Here, we report that the MamK filaments from the uncultivated 'Candidatus Magnetobacterium casensis' (Mcas) within the phylum Nitrospirae polymerized in the presence of ATP alone and were stable without obvious ATP hydrolysis-mediated disassembly. MamK in Mcas can convert NTP to NDP and NDP to NMP, showing the highest preference to ATP. Unlike its Magnetospirillum counterparts, which form a single magnetosome chain, or other bacterial actins such as MreB and ParM, the polymerized MamK from Mcas is independent of metal ions and nucleotides except for ATP, and is assembled into well-ordered filamentous bundles consisted of multiple filaments. Our results suggest a dynamically stable assembly of MamK from the uncultivated Nitrospirae MTB that synthesizes multiple magnetosome chains per cell. These findings further improve the current knowledge of biomineralization and organelle biogenesis in prokaryotic systems.
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Affiliation(s)
- Aihua Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Lin
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Nana Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Wu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaopeng Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qinyun Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua Bai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongxin Pan
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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Rolfsson Ó, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG. Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol 2016; 428:431-48. [PMID: 26608810 PMCID: PMC4751978 DOI: 10.1016/j.jmb.2015.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [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: 09/09/2015] [Revised: 11/06/2015] [Accepted: 11/08/2015] [Indexed: 01/20/2023]
Abstract
Using cross-linking coupled to matrix-assisted laser desorption/ionization mass spectrometry and CLIP-Seq sequencing, we determined the peptide and oligonucleotide sequences at the interfaces between the capsid proteins and the genomic RNA of bacteriophage MS2. The results suggest that the same coat protein (CP)-RNA and maturation protein (MP)-RNA interfaces are used in every viral particle. The portions of the viral RNA in contact with CP subunits span the genome, consistent with a large number of discrete and similar contacts within each particle. Many of these sites match previous predictions of the locations of multiple, dispersed and degenerate RNA sites with cognate CP affinity termed packaging signals (PSs). Chemical RNA footprinting was used to compare the secondary structures of protein-free genomic fragments and the RNA in the virion. Some PSs are partially present in protein-free RNA but others would need to refold from their dominant solution conformations to form the contacts identified in the virion. The RNA-binding peptides within the MP map to two sections of the N-terminal half of the protein. Comparison of MP sequences from related phages suggests a similar arrangement of RNA-binding sites, although these N-terminal regions have only limited sequence conservation. In contrast, the sequences of the C-termini are highly conserved, consistent with them encompassing pilin-binding domains required for initial contact with host cells. These results provide independent and unambiguous support for the assembly of MS2 virions via a PS-mediated mechanism involving a series of induced-fit viral protein interactions with RNA.
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Affiliation(s)
- Óttar Rolfsson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefani Middleton
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA; The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Baochang Fan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Robert Vaughan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Eric Dykeman
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - James Ford
- The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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Tacnet P, Cheong ECC, Goeltz P, Ghebrehiwet B, Arlaud GJ, Liu XY, Lesieur C. Trimeric reassembly of the globular domain of human C1q. Biochim Biophys Acta 2008; 1784:518-29. [PMID: 18179779 PMCID: PMC2707929 DOI: 10.1016/j.bbapap.2007.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 11/19/2007] [Accepted: 12/03/2007] [Indexed: 11/25/2022]
Abstract
C1q is a versatile recognition protein which binds to a variety of targets and consequently triggers the classical pathway of complement. C1q is a hetero-trimer composed of three chains (A, B and C) arranged in three domains, a short N-terminal region, followed by a collagenous repeat domain that gives rise to the formation of (ABC) triple helices, each ending in a C-terminal hetero-trimeric globular domain, called gC1q, which is responsible for the recognition properties of C1q. The mechanism of the trimeric assembly of C1q and in particular the role of each domain in the process is unknown. Here, we have investigated if the gC1q domain was able to assemble into functional trimers, in vitro, in the absence of the collagenous domain, a motif known to promote obligatory trimers in other proteins. Acid-mediated gC1q protomers reassembled into functional trimers, once neutralized, indicating that it is the gC1q domain which possesses the information for trimerization. However, reassembly occurred after neutralization, only if the gC1q protomers had preserved a residual tertiary structure at the end of the acidic treatment. Thus, the collagenous domain of C1q might initialize the folding of the gC1q domain so that subsequent assembly of the entire molecule can occur.
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Affiliation(s)
- Pascale Tacnet
- Laboratoire d’Enzymologie Moléculaire, Institut de Biologie Structurale, CEA-CNRS-Université Joseph Fourier, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Eric Chung Chee Cheong
- National University of Singapore, Physics Department, 2 Science Drive 3, 117542, Singapore
| | - Pierrette Goeltz
- Laboratoire d’Enzymologie Moléculaire, Institut de Biologie Structurale, CEA-CNRS-Université Joseph Fourier, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Berhane Ghebrehiwet
- Department of Medicine, State University of New York, Stony Brook, New York, USA
| | - Gérard J. Arlaud
- Laboratoire d’Enzymologie Moléculaire, Institut de Biologie Structurale, CEA-CNRS-Université Joseph Fourier, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Xiang-Yang Liu
- National University of Singapore, Physics Department, 2 Science Drive 3, 117542, Singapore
| | - Claire Lesieur
- National University of Singapore, Physics Department, 2 Science Drive 3, 117542, Singapore
- iRTSV/BBSI, CEA-CNRS-Université Joseph Fourier, 17 rue des Martyrs, 38054 Grenoble, France
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