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Hong W, Mei H, Shi X, Lin X, Wang S, Ni R, Wang Y, Song L. Viral community distribution, assembly mechanism, and associated hosts in an industrial park wastewater treatment plant. ENVIRONMENTAL RESEARCH 2024; 247:118156. [PMID: 38199475 DOI: 10.1016/j.envres.2024.118156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/02/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Viruses manipulate bacterial community composition and impact wastewater treatment efficiency. Some viruses pose threats to the environment and human populations through infection. Improving the efficiency of wastewater treatment and ensuring the health of the effluent and receptor pools requires an understanding of how viral communities assemble and interact with hosts in wastewater treatment plants (WWTPs). We used metagenomic analysis to study the distribution, assembly mechanism, and sensitive hosts for the viral communities in raw water, anaerobic tanks, and returned activated sludge units of a large-scale industrial park WWTP. Uroviricota (53.42% ± 0.14%) and Nucleocytoviricota (26.1% ± 0.19%) were dominant in all units. Viral community composition significantly differed between units, as measured by β diversity (P = 0.005). Compared to raw water, the relative viral abundance decreased by 29.8% in the anaerobic tank but increased by 9.9% in the activated sludge. Viral community assembly in raw water and anaerobic tanks was predominantly driven by deterministic processes (MST <0.5) versus stochastic processes (MST >0.5) in the activated sludge, indicating that differences in diffusion limits may fundamentally alter the assembly mechanisms of viral communities between the solid and liquid-phase environments. Acidobacteria was identified as the sensitive host contributing to viral abundance, exhibiting strong interactions and a mutual dependence (degree = 59). These results demonstrate the occurrence and prevalence of viruses in WWTPs, their different assembly mechanism, and sensitive hosts. These observations require further study of the mechanisms of viral community succession, ecological function, and roles in the successive wastewater treatment units.
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Affiliation(s)
- Wenqing Hong
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Hong Mei
- East China Engineering Science and Technology Co., Ltd, Hefei, 230024, China
| | - Xianyang Shi
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China.
| | - Xiaoxing Lin
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Shuijing Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Renjie Ni
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Yan Wang
- East China Engineering Science and Technology Co., Ltd, Hefei, 230024, China
| | - Liyan Song
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China.
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Queiroz VF, Tatara JM, Botelho BB, Rodrigues RAL, Almeida GMDF, Abrahao JS. The consequences of viral infection on protists. Commun Biol 2024; 7:306. [PMID: 38462656 PMCID: PMC10925606 DOI: 10.1038/s42003-024-06001-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/29/2024] [Indexed: 03/12/2024] Open
Abstract
Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.
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Affiliation(s)
- Victoria Fulgencio Queiroz
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Miranda Tatara
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Bruna Barbosa Botelho
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Magno de Freitas Almeida
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Jonatas Santos Abrahao
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
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Urquiza J, Cuesta-Geijo MÁ, García-Dorival I, Fernández Ó, del Puerto A, Díaz JF, Alonso C. Identification of a Potential Entry-Fusion Complex Based on Sequence Homology of African Swine Fever and Vaccinia Virus. Viruses 2024; 16:349. [PMID: 38543715 PMCID: PMC10975062 DOI: 10.3390/v16030349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 05/23/2024] Open
Abstract
African swine fever virus (ASFV) belongs to the family of Asfarviridae, part of the group of nucleocytoplasmic large DNA viruses (NCLDV). Little is known about the internalization of ASFV in the host cell and the fusion membrane events that take place at early stages of the infection. Poxviruses, also members of the NCLDV and represented by vaccinia virus (VACV), are large, enveloped, double-stranded DNA viruses. Poxviruses were considered unique in having an elaborate entry-fusion complex (EFC) composed of 11 highly conserved proteins integrated into the membrane of mature virions. Recent advances in methodological techniques have again revealed several connections between VACV EFC proteins. In this study, we explored the possibility of an analogous ASFV EFC by identifying ten candidate proteins exhibiting structural similarities with VACV EFC proteins. This could reveal key functions of these ASFV proteins, drawing attention to shared features between the two virus families, suggesting the potential existence of an ASFV entry-fusion complex.
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Affiliation(s)
- Jesús Urquiza
- Departamento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain; (M.Á.C.-G.); (I.G.-D.); (A.d.P.)
| | - Miguel Ángel Cuesta-Geijo
- Departamento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain; (M.Á.C.-G.); (I.G.-D.); (A.d.P.)
| | - Isabel García-Dorival
- Departamento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain; (M.Á.C.-G.); (I.G.-D.); (A.d.P.)
| | - Óscar Fernández
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (Ó.F.); (J.F.D.)
| | - Ana del Puerto
- Departamento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain; (M.Á.C.-G.); (I.G.-D.); (A.d.P.)
| | - José Fernando Díaz
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (Ó.F.); (J.F.D.)
| | - Covadonga Alonso
- Departamento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain; (M.Á.C.-G.); (I.G.-D.); (A.d.P.)
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Kao CF, Liu CY, Hsieh CL, Carillo KJD, Tzou DLM, Wang HC, Chang W. Structural and functional analyses of viral H2 protein of the vaccinia virus entry fusion complex. J Virol 2023; 97:e0134323. [PMID: 37975688 PMCID: PMC10734489 DOI: 10.1128/jvi.01343-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/02/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Vaccinia virus infection requires virus-cell membrane fusion to complete entry during endocytosis; however, it contains a large viral fusion protein complex of 11 viral proteins that share no structure or sequence homology to all the known viral fusion proteins, including type I, II, and III fusion proteins. It is thus very challenging to investigate how the vaccinia fusion complex works to trigger membrane fusion with host cells. In this study, we crystallized the ectodomain of vaccinia H2 protein, one component of the viral fusion complex. Furthermore, we performed a series of mutational, biochemical, and molecular analyses and identified two surface loops containing 170LGYSG174 and 125RRGTGDAW132 as the A28-binding region. We also showed that residues in the N-terminal helical region (amino acids 51-90) are also important for H2 function.
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Affiliation(s)
- Chi-Fei Kao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chang-Yi Liu
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chia-Lin Hsieh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | | | - Hao-Ching Wang
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Wen Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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Talbert PB, Henikoff S, Armache KJ. Giant variations in giant virus genome packaging. Trends Biochem Sci 2023; 48:1071-1082. [PMID: 37777391 DOI: 10.1016/j.tibs.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
Giant viruses (Nucleocytoviricota) have a largely conserved lifecycle, yet how they cram their large genomes into viral capsids is mostly unknown. The major capsid protein and the packaging ATPase (pATPase) comprise a highly conserved morphogenesis module in giant viruses, yet some giant viruses dispense with an icosahedral capsid, and others encode multiple versions of pATPases, including conjoined ATPase doublets, or encode none. Some giant viruses have acquired DNA-condensing proteins to compact their genomes, including sheath-like structures encasing folded DNA or densely packed viral nucleosomes that show a resemblance to eukaryotic nucleosomes at the telomeres. Here, we review what is known and unknown about these ATPases and condensing proteins, and place these variations in the context of viral lifecycles.
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Affiliation(s)
- Paul B Talbert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
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Kao CF, Tsai MH, Carillo KJ, Tzou DL, Chang W. Structural and functional analysis of vaccinia viral fusion complex component protein A28 through NMR and molecular dynamic simulations. PLoS Pathog 2023; 19:e1011500. [PMID: 37948471 PMCID: PMC10664964 DOI: 10.1371/journal.ppat.1011500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/22/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Host cell entry of vaccinia virus (a poxvirus) proceeds through multiple steps that involve many viral proteins to mediate cell infection. Upon binding to cells, vaccinia virus membrane fuses with host membranes via a viral entry fusion protein complex comprising 11 proteins: A16, A21, A28, F9, G3, G9, H2, J5, L1, L5 and O3. Despite vaccinia virus having two infectious forms, mature and enveloped, that have different membrane layers, both forms require an identical viral entry fusion complex for membrane fusion. Components of the poxvirus entry fusion complex that have been structurally assessed to date share no known homology with all other type I, II and III viral fusion proteins, and the large number of fusion protein components renders it a unique system to investigate poxvirus-mediated membrane fusion. Here, we determined the NMR structure of a truncated version of vaccinia A28 protein. We also expressed a soluble H2 protein and showed that A28 interacts with H2 protein at a 1:1 ratio in vitro. Furthermore, we performed extensive in vitro alanine mutagenesis to identify A28 protein residues that are critical for H2 binding, entry fusion complex formation, and virus-mediated membrane fusion. Finally, we used molecular dynamic simulations to model full-length A28-H2 subcomplex in membranes. In summary, we characterized vaccinia virus A28 protein and determined residues important in its interaction with H2 protein and membrane components. We also provide a structural model of the A28-H2 protein interaction to illustrate how it forms a 1:1 subcomplex on a modeled membrane.
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Affiliation(s)
- Chi-Fei Kao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Min-Hsin Tsai
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Der-Lii Tzou
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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