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Daakour S, Nelson DR, Fu W, Jaiswal A, Dohai B, Alzahmi AS, Koussa J, Huang X, Shen Y, Twizere JC, Salehi-Ashtiani K. Adaptive Evolution Signatures in Prochlorococcus: Open Reading Frame (ORF)eome Resources and Insights from Comparative Genomics. Microorganisms 2024; 12:1720. [PMID: 39203562 PMCID: PMC11357015 DOI: 10.3390/microorganisms12081720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/30/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 and NATL1A. Employing deep learning with robust statistical methods, we detected new protein family distributions in the strains and identified key genes differentiating the HL and LL strains. The HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while the LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). Additionally, we report the finding of variable, depth-dependent endogenous viral elements in the 40 strains. To generate biological resources to experimentally study the HL and LL adaptations, we constructed the ORFeomes of two representative strains, MED4 and NATL1A synthetically, covering 99% of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified open reading frames (ORFs). These comparative genomic analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and the systems biology exploration of Prochlorococcus ecology.
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Affiliation(s)
- Sarah Daakour
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - David R. Nelson
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Weiqi Fu
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Ashish Jaiswal
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Bushra Dohai
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Helmholtz Center Munich, Institute of Network Biology (INET), German Research Center for Environmental Health, 85764 Munich, Germany
| | - Amnah Salem Alzahmi
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Laboratory of Viral Interactomes Networks, Unit of Molecular & Computational Biology, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, 4000 Liège, Belgium
| | - Joseph Koussa
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Department of Biology, New York University, New York, NY 10012, USA
- Department of Chemical and Biological Sciences, Montgomery College, Germantown, MD 20850, USA
| | - Xiaoluo Huang
- Genome Synthesis and Editing Platform, China National GeneBank (CNGB), BGI-Research, Shenzhen 518120, China; (X.H.); (Y.S.)
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Beijing 100045, China
| | - Yue Shen
- Genome Synthesis and Editing Platform, China National GeneBank (CNGB), BGI-Research, Shenzhen 518120, China; (X.H.); (Y.S.)
| | - Jean-Claude Twizere
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Laboratory of Viral Interactomes Networks, Unit of Molecular & Computational Biology, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, 4000 Liège, Belgium
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
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Song Y, Fan S, Zhang D, Li J, Li Z, Li Z, Xiao W, Wang J. Zebrafish maoc1 Attenuates Spring Viremia of Carp Virus Propagation by Promoting Autophagy-Lysosome-Dependent Degradation of Viral Phosphoprotein. J Virol 2023; 97:e0133822. [PMID: 36744960 PMCID: PMC9972956 DOI: 10.1128/jvi.01338-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/21/2023] [Indexed: 02/07/2023] Open
Abstract
Spring viremia of carp virus (SVCV) is the causative agent of spring viremia of carp (SVC), an important infectious disease that causes high mortality in aquaculture cyprinids. How the host defends against SVCV infection and the underlying mechanisms are still elusive. In this study, we identify that a novel gene named maoc1 is induced by SVCV infection. maoc1-deficient zebrafish are more susceptible to SVCV infection, with higher virus replication and antiviral gene induction. Further assays indicate that maoc1 interacts with the P protein of SVCV to trigger P protein degradation through the autophagy-lysosomal pathway, leading to the restriction of SVCV propagation. These findings reveal a unique zebrafish defense machinery in response to SVCV infection. IMPORTANCE SVCV P protein plays an essential role in the virus replication and viral immune evasion process. Here, we identify maoc1 as a novel SVCV-inducible gene and demonstrate its antiviral capacity through attenuating SVCV replication, by directly binding to P protein and mediating its degradation via the autophagy-lysosomal pathway. Therefore, this study not only reveals an essential role of maoc1 in fighting against SVCV infection but also demonstrates an unusual host defense mechanism in response to invading viruses.
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Affiliation(s)
- Yanan Song
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, People’s Republic of China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Sijia Fan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Dawei Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Jun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Ziyi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Wuhan Xiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
- Hubei Hongshan Laboratory, Wuhan, People’s Republic of China
| | - Jing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
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Brahim Belhaouari D, Pires De Souza GA, Lamb DC, Kelly SL, Goldstone JV, Stegeman JJ, Colson P, La Scola B, Aherfi S. Metabolic arsenal of giant viruses: Host hijack or self-use? eLife 2022; 11:e78674. [PMID: 35801640 PMCID: PMC9270025 DOI: 10.7554/elife.78674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/22/2022] [Indexed: 12/11/2022] Open
Abstract
Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - David C Lamb
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
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