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Nelson DR, Mystikou A, Jaiswal A, Rad-Menendez C, Preston MJ, De Boever F, El Assal DC, Daakour S, Lomas MW, Twizere JC, Green DH, Ratcliff WC, Salehi-Ashtiani K. Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity. MOLECULAR PLANT 2024; 17:747-771. [PMID: 38614077 DOI: 10.1016/j.molp.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/31/2024] [Accepted: 03/08/2024] [Indexed: 04/15/2024]
Abstract
Macroalgae are multicellular, aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering, which are directly linked to their multicellularity phenotypes. However, their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain uncharacterized. In this study, we sequenced 110 macroalgal genomes from diverse climates and phyla, and identified key genomic features that distinguish them from their microalgal relatives. Genes for cell adhesion, extracellular matrix formation, cell polarity, transport, and cell differentiation distinguish macroalgae from microalgae across all three major phyla, constituting conserved and unique gene sets supporting multicellular processes. Adhesome genes show phylum- and climate-specific expansions that may facilitate niche adaptation. Collectively, our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.
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Affiliation(s)
- David R Nelson
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Alexandra Mystikou
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE; Biotechnology Research Center, Technology Innovation Institute, PO Box 9639, Masdar City, Abu Dhabi, UAE.
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Cecilia Rad-Menendez
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Michael J Preston
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Frederik De Boever
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Diana C El Assal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jean-Claude Twizere
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - David H Green
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
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Su L, Zhang J, Gomez H, Kellum JA, Peng Z. Mitochondria ROS and mitophagy in acute kidney injury. Autophagy 2023; 19:401-414. [PMID: 35678504 PMCID: PMC9851232 DOI: 10.1080/15548627.2022.2084862] [Citation(s) in RCA: 151] [Impact Index Per Article: 151.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 01/22/2023] Open
Abstract
Mitophagy is an essential mitochondrial quality control mechanism that eliminates damaged mitochondria and the production of reactive oxygen species (ROS). The relationship between mitochondria oxidative stress, ROS production and mitophagy are intimately interwoven, and these processes are all involved in various pathological conditions of acute kidney injury (AKI). The elimination of damaged mitochondria through mitophagy in mammals is a complicated process which involves several pathways. Furthermore, the interplay between mitophagy and different types of cell death, such as apoptosis, pyroptosis and ferroptosis in kidney injury is unclear. Here we will review recent advances in our understanding of the relationship between ROS and mitophagy, the different mitophagy pathways, the relationship between mitophagy and cell death, and the relevance of these processes in the pathogenesis of AKI.Abbreviations: AKI: acute kidney injury; AMBRA1: autophagy and beclin 1 regulator 1; ATP: adenosine triphosphate; BAK1: BCL2 antagonist/killer 1; BAX: BCL2 associated X, apoptosis regulator; BCL2: BCL2 apoptosis regulator; BECN1: beclin 1; BH3: BCL2 homology domain 3; BNIP3: BCL2 interacting protein 3; BNIP3L/NIX: BCL2 interacting protein 3 like; CASP1: caspase 1; CAT: catalase; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CI-AKI: contrast-induced acute kidney injury; CISD1: CDGSH iron sulfur domain 1; CL: cardiolipin; CNP: 2',3'-cyclic nucleotide 3'-phosphodiesterase; DNM1L/DRP1: dynamin 1 like; E3: enzyme 3; ETC: electron transport chain; FA: folic acid; FUNDC1: FUN14 domain containing 1; G3P: glycerol-3-phosphate; G6PD: glucose-6-phosphate dehydrogenase; GPX: glutathione peroxidase; GSH: glutathione; GSK3B: glycogen synthase kinase 3 beta; GSR: glutathione-disulfide reductase; HIF1A: hypoxia inducible factor 1 subunit alpha; HUWE1: HECT, UBA and WWE domain containing 1; IL1B: interleukin 1 beta; IMM: inner mitochondrial membrane; IPC: ischemic preconditioning; IRI: ischemia-reperfusion injury; LIR: LC3-interacting region; LPS: lipopolysaccharide; MA: malate-aspartate; MPT: mitochondrial permeability transition; MUL1: mitochondrial E3 ubiquitin protein ligase 1; mtROS: mitochondrial ROS; NLR: NOD-like receptor; NLRP3: NLR family pyrin domain containing 3; NOX: NADPH oxidase; OGD-R: oxygen-glucose deprivation-reperfusion; OMM: outer mitochondrial membrane; OPA1: OPA1 mitochondrial dynamin like GTPase; OXPHOS: oxidative phosphorylation; PARL: presenilin associated rhomboid like; PINK1: PTEN induced kinase 1; PLSCR3: phospholipid scramblase 3; PMP: peptidase, mitochondrial processing; PRDX: peroxiredoxin; PRKN: parkin RBR E3 ubiquitin protein ligase; RPTC: rat proximal tubular cells; ROS: reactive oxygen species; SLC7A11/xCT: solute carrier family 7 member 11; SOD: superoxide dismutase; SOR: superoxide reductase; SQSTM1/p62: sequestosome 1; TCA: tricarboxylic acid; TIMM: translocase of inner mitochondrial membrane; TOMM: translocase of outer mitochondrial membrane; TXN: thioredoxin; VDAC: voltage dependent anion channel; VCP: valosin containing protein.
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Affiliation(s)
- Lianjiu Su
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan430071, China
- Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthNeuro-Oncology, Bethesda, Maryland, USA
| | - Jiahao Zhang
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan430071, China
| | - Hernando Gomez
- Center of Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - John A Kellum
- Center of Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Zhiyong Peng
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan430071, China
- Center of Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, USA
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3
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Emodin activates BK channel in vascular smooth muscle cells and relaxes the interlobar renal artery of rat. Biomed Pharmacother 2022; 153:113452. [DOI: 10.1016/j.biopha.2022.113452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
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Jiang Y, Shen M, Chen Y, Wei Y, Tao J, Liu H. Melatonin Represses Mitophagy to Protect Mouse Granulosa Cells from Oxidative Damage. Biomolecules 2021; 11:biom11070968. [PMID: 34209255 PMCID: PMC8301909 DOI: 10.3390/biom11070968] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/15/2022] Open
Abstract
Various environmental stimuli, including oxidative stress, could lead to granulosa cell (GC) death through mitophagy. Recently, it was reported that melatonin (MEL) has a significant effect on GC survival during oxidative damage. Here, we found that MEL inhibited oxidative stress-induced mitophagy to promote GC survival. The loss of cell viability upon H2O2 exposure was significantly restored after MEL treatment. Concomitantly, MEL inhibited the activation of mitophagy during oxidative stress. Notably, blocking mitophagy repressed GC death caused by oxidative stress. However, MEL cannot further restore viability of cells treated with mitophagy inhibitor. Moreover, PTEN-induced putative kinase 1 (PINK1), a mitochondrial serine/threonine-protein kinase, was inhibited by MEL during oxidative stress. As a result, the E3 ligase Parkin failed to translocate to mitochondria, leading to impaired mitochondria clearance. Using RNAi to knock down PINK1 expression, we further verified the role of the MEL-PINK1-Parkin (MPP) pathway in maintaining GC survival by suppressing mitophagy. Our findings not only clarify the protective mechanisms of MEL against oxidative damage in GCs, but also extend the understanding about how circadian rhythms might influence follicles development in the ovary. These findings reveal a new mechanism of melatonin in defense against oxidative damage to GCs by repressing mitophagy, which may be a potential therapeutic target for anovulatory disorders.
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Affiliation(s)
- Yi Jiang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanyuan Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yinghui Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingli Tao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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