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Liu Z, Zheng J, Li H, Fang K, Wang S, He J, Zhou D, Weng S, Chi M, Gu Z, He J, Li F, Wang M. Genome assembly of redclaw crayfish (Cherax quadricarinatus) provides insights into its immune adaptation and hypoxia tolerance. BMC Genomics 2024; 25:746. [PMID: 39080519 PMCID: PMC11290268 DOI: 10.1186/s12864-024-10673-9] [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: 04/22/2024] [Accepted: 07/29/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The introduction of non-native species is a primary driver of biodiversity loss in freshwater ecosystems. The redclaw crayfish (Cherax quadricarinatus) is a freshwater species that exhibits tolerance to hypoxic stresses, fluctuating temperatures, high ammonia concentration. These hardy physiological characteristics make C. quadricarinatus a popular aquaculture species and a potential invasive species that can negatively impact tropical and subtropical ecosystems. Investigating the genomic basis of environmental tolerances and immune adaptation in C. quadricarinatus will facilitate the development of management strategies of this potential invasive species. RESULTS We constructed a chromosome-level genome of C. quadricarinatus by integrating Nanopore and PacBio techniques. Comparative genomic analysis suggested that transposable elements and tandem repeats drove genome size evolution in decapod crustaceans. The expansion of nine immune-related gene families contributed to the disease resistance of C. quadricarinatus. Three hypoxia-related genes (KDM3A, KDM5A, HMOX2) were identified as being subjected to positive selection in C. quadricarinatus. Additionally, in vivo analysis revealed that upregulating KDM5A was crucial for hypoxic response in C. quadricarinatus. Knockdown of KDM5A impaired hypoxia tolerance in this species. CONCLUSIONS Our results provide the genomic basis for hypoxic tolerance and immune adaptation in C. quadricarinatus, facilitating the management of this potential invasive species. Additionally, in vivo analysis in C. quadricarinatus suggests that the role of KDM5A in the hypoxic response of animals is complex.
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Affiliation(s)
- Ziwei Liu
- State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519000, China
| | - Jianbo Zheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Haoyang Li
- China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Ke Fang
- State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519000, China
| | - Sheng Wang
- China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jian He
- State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Dandan Zhou
- State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519000, China
| | - Shaoping Weng
- China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Meili Chi
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Zhimin Gu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jianguo He
- State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519000, China.
- China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Fei Li
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China.
| | - Muhua Wang
- State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519000, China.
- China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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2
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Perri M, Licausi F. Thiol dioxygenases: from structures to functions. Trends Biochem Sci 2024; 49:545-556. [PMID: 38622038 DOI: 10.1016/j.tibs.2024.03.007] [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: 11/18/2023] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 04/17/2024]
Abstract
Thiol oxidation to dioxygenated sulfinic acid is catalyzed by an enzyme family characterized by a cupin fold. These proteins act on free thiol-containing molecules to generate central metabolism precursors and signaling compounds in bacteria, fungi, and animal cells. In plants and animals, they also oxidize exposed N-cysteinyl residues, directing proteins to proteolysis. Enzyme kinetics, X-ray crystallography, and spectroscopy studies prompted the formulation and testing of hypotheses about the mechanism of action and the different substrate specificity of these enzymes. Concomitantly, the physiological role of thiol dioxygenation in prokaryotes and eukaryotes has been studied through genetic and physiological approaches. Further structural characterization is necessary to enable precise and safe manipulation of thiol dioxygenases (TDOs) for therapeutic, industrial, and agricultural applications.
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Affiliation(s)
- Monica Perri
- Plant Molecular Biology Section, Department of Biology, University of Oxford, Oxford, UK
| | - Francesco Licausi
- Plant Molecular Biology Section, Department of Biology, University of Oxford, Oxford, UK.
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3
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Meybodi SM, Ejlalidiz M, Manshadi MR, Raeisi M, Zarin M, Kalhor Z, Saberiyan M, Hamblin MR. Crosstalk between hypoxia-induced pyroptosis and immune escape in cancer: From mechanisms to therapy. Crit Rev Oncol Hematol 2024; 197:104340. [PMID: 38570176 DOI: 10.1016/j.critrevonc.2024.104340] [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: 02/08/2024] [Revised: 03/12/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024] Open
Abstract
Pyroptosis can be triggered through both canonical and non-canonical inflammasome pathways, involving the cleavage of gasdermin (GSDM) protein family members, like GSDMD and GSDME. The impact of pyroptosis on tumors is nuanced, because its role in regulating cancer progression and anti-tumor immunity may vary depending on the tumor type, stage, location, and immune status. However, pyroptosis cannot be simply categorized as promoting or inhibiting tumors based solely on whether it is acute or chronic in nature. The interplay between pyroptosis and cancer is intricate, with some evidence suggesting that chronic pyroptosis may facilitate tumor growth, while the acute induction of pyroptosis could stimulate anti-cancer immune responses. Tumor hypoxia activates hypoxia inducible factor (HIF) signaling to modulate pyroptosis and immune checkpoint expression. Targeting this hypoxia-pyroptosis-immune escape axis could be a promising therapeutic strategy. This review highlights the complex crosstalk between hypoxia, pyroptosis, and immune evasion in the TME.
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Affiliation(s)
| | - Mahsa Ejlalidiz
- Medical Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadsadegh Rezaeian Manshadi
- Clinical Research Development Center, Imam Hossein Educational Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Raeisi
- Clinical Research Developmental Unit, Hajar Hospital, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Maryam Zarin
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Zahra Kalhor
- Department of Anatomical Sciences, Factulty of Medicine, Kurdistan University of Medical Scidnces, Sanandaj, Iran
| | - Mohammadreza Saberiyan
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran; Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Michael R Hamblin
- Laser Research Centre, University of Johannesburg, Doornfontein, South Africa.
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4
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Liu X, Tang J, Wang Z, Zhu C, Deng H, Sun X, Yu G, Rong F, Chen X, Liao Q, Jia S, Liu W, Zha H, Fan S, Cai X, Gui JF, Xiao W. Oxygen enhances antiviral innate immunity through maintenance of EGLN1-catalyzed proline hydroxylation of IRF3. Nat Commun 2024; 15:3533. [PMID: 38670937 PMCID: PMC11053110 DOI: 10.1038/s41467-024-47814-3] [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: 08/02/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Oxygen is essential for aerobic organisms, but little is known about its role in antiviral immunity. Here, we report that during responses to viral infection, hypoxic conditions repress antiviral-responsive genes independently of HIF signaling. EGLN1 is identified as a key mediator of the oxygen enhancement of antiviral innate immune responses. Under sufficient oxygen conditions, EGLN1 retains its prolyl hydroxylase activity to catalyze the hydroxylation of IRF3 at proline 10. This modification enhances IRF3 phosphorylation, dimerization and nuclear translocation, leading to subsequent IRF3 activation. Furthermore, mice and zebrafish with Egln1 deletion, treatment with the EGLN inhibitor FG4592, or mice carrying an Irf3 P10A mutation are more susceptible to viral infections. These findings not only reveal a direct link between oxygen and antiviral responses, but also provide insight into the mechanisms by which oxygen regulates innate immunity.
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Affiliation(s)
- Xing Liu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Jinhua Tang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, P. R. China
| | - Zixuan Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Chunchun Zhu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Hongyan Deng
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Xueyi Sun
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Guangqing Yu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Fangjing Rong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Xiaoyun Chen
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Liao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Shuke Jia
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Wen Liu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Huangyuan Zha
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Sijia Fan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Xiaolian Cai
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Jian-Fang Gui
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Wuhan Xiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China.
- Hubei Hongshan Laboratory, Wuhan, P. R. China.
- University of Chinese Academy of Sciences, Beijing, P. R. China.
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, P. R. China.
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5
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Choi SW, Graf L, Choi JW, Jo J, Boo GH, Kawai H, Choi CG, Xiao S, Knoll AH, Andersen RA, Yoon HS. Ordovician origin and subsequent diversification of the brown algae. Curr Biol 2024; 34:740-754.e4. [PMID: 38262417 DOI: 10.1016/j.cub.2023.12.069] [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: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024]
Abstract
Brown algae are the only group of heterokont protists exhibiting complex multicellularity. Since their origin, brown algae have adapted to various marine habitats, evolving diverse thallus morphologies and gamete types. However, the evolutionary processes behind these transitions remain unclear due to a lack of a robust phylogenetic framework and problems with time estimation. To address these issues, we employed plastid genome data from 138 species, including heterokont algae, red algae, and other red-derived algae. Based on a robust phylogeny and new interpretations of algal fossils, we estimated the geological times for brown algal origin and diversification. The results reveal that brown algae first evolved true multicellularity, with plasmodesmata and reproductive cell differentiation, during the late Ordovician Period (ca. 450 Ma), coinciding with a major diversification of marine fauna (the Great Ordovician Biodiversification Event) and a proliferation of multicellular green algae. Despite its early Paleozoic origin, the diversification of major orders within this brown algal clade accelerated only during the Mesozoic Era, coincident with both Pangea rifting and the diversification of other heterokont algae (e.g., diatoms), coccolithophores, and dinoflagellates, with their red algal-derived plastids. The transition from ancestral isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous Period. These are concordant with a positive character correlation between parthenogenesis and isogamy. Our new brown algal timeline, combined with a knowledge of past environmental conditions, shed new light on brown algal diversification and the intertwined evolution of multicellularity and sexual reproduction.
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Affiliation(s)
- Seok-Wan Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea; Institut de Biologie de l'École Normale Supérieure, Université Paris Sciences et Lettres, Paris 75005, France
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jihoon Jo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea; Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
| | - Ga Hun Boo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai, Nadaku, Kobe 657-8501, Japan
| | - Chang Geun Choi
- Department of Ecological Engineering, College of Environmental and Marine Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, WA 98250, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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6
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Anbalagan S. Heme-based oxygen gasoreceptors. Am J Physiol Endocrinol Metab 2024; 326:E178-E181. [PMID: 38231000 DOI: 10.1152/ajpendo.00004.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/18/2024]
Abstract
To investigate gasocrine signaling, there is a critical need to identify gasoreceptors for the essential gasotransmitters like O2. Based on existing scientific literature, I propose that heme-based O2 sensors, featuring diverse signaling domains across genera, should be explicitly designated as O2 gasoreceptors. Acknowledging that O2 gasoreceptors are likely to belong to multiple protein classes with diverse signaling domains and pathways will facilitate a comprehensive search for O2 gasoreceptors in all organisms and across every cell type. This approach will broaden the investigation beyond specialized tissues or cells, encompassing a systemic exploration.
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Affiliation(s)
- Savani Anbalagan
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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7
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Zhang Y, Pan YD, Zheng WY, Li HY, Zhu MZ, Ou Yang WJ, Qian Y, Turecki G, Mechawar N, Zhu XH. Enhancing HIF-1α-P2X2 signaling in dorsal raphe serotonergic neurons promotes psychological resilience. Redox Biol 2024; 69:103005. [PMID: 38150991 PMCID: PMC10788260 DOI: 10.1016/j.redox.2023.103005] [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: 12/11/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023] Open
Abstract
Major depressive disorder (MDD) is a devastating condition. Although progress has been made in the past seven decades, patients with MDD continue to receive an inadequate treatment, primarily due to the late onset of first-line antidepressant drugs and to their acute withdrawal symptoms. Resilience is the ability to rebound from adversity in a healthy manner and many people have psychological resilience. Revealing the mechanisms and identifying methods promoting resilience will hopefully lead to more effective prevention strategies and treatments for depression. In this study, we found that intermittent hypobaric hypoxia training (IHHT), a method for training pilots and mountaineers, enhanced psychological resilience in adult mice. IHHT produced a sustained antidepressant-like effect in mouse models of depression by inducing long-term (up to 3 months after this treatment) overexpression of hypoxia-inducible factor (HIF)-1α in the dorsal raphe nucleus (DRN) of adult mice. Moreover, DRN-infusion of cobalt chloride, which mimics hypoxia increasing HIF-1α expression, triggered a rapid and long-lasting antidepressant-like effect. Down-regulation of HIF-1α in the DRN serotonergic (DRN5-HT) neurons attenuated the effects of IHHT. HIF-1α translationally regulated the expression of P2X2, and conditionally knocking out P2rx2 (encodes P2X2 receptors) in DRN5-HT neurons, in turn, attenuated the sustained antidepressant-like effect of IHHT, but not its acute effect. In line with these results, a single sub-anesthetic dose of ketamine enhanced HIF-1α-P2X2 signaling, which is essential for its rapid and long-lasting antidepressant-like effect. Notably, we found that P2X2 protein levels were significantly lower in the DRN of patients with MDD than that of control subjects. Together, these findings elucidate the molecular mechanism underlying IHHT promoting psychological resilience and highlight enhancing HIF-1α-P2X2 signaling in DRN5-HT neurons as a potential avenue for screening novel therapeutic treatments for MDD.
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Affiliation(s)
- Yuan Zhang
- School of Psychology, Shenzhen University, Shenzhen, China; Research Center for Brain Health, Pazhou Lab, Guangzhou, China
| | - Yi-da Pan
- Research Center for Brain Health, Pazhou Lab, Guangzhou, China
| | - Wen-Ying Zheng
- School of Psychology, Shenzhen University, Shenzhen, China; Research Center for Brain Health, Pazhou Lab, Guangzhou, China
| | - Huan-Yu Li
- Research Center for Brain Health, Pazhou Lab, Guangzhou, China
| | - Min-Zhen Zhu
- Research Center for Brain Health, Pazhou Lab, Guangzhou, China
| | - Wen-Jie Ou Yang
- School of Psychology, Shenzhen University, Shenzhen, China; Research Center for Brain Health, Pazhou Lab, Guangzhou, China
| | - Yu Qian
- Research Center for Brain Health, Pazhou Lab, Guangzhou, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Gustavo Turecki
- Department of Psychiatry, McGill University, McGill Group for Suicide Studies, Douglas Mental Health University Institute, 6875 LaSalle Blvd, Verdun, (Québec), Canada
| | - Naguib Mechawar
- Department of Psychiatry, McGill University, McGill Group for Suicide Studies, Douglas Mental Health University Institute, 6875 LaSalle Blvd, Verdun, (Québec), Canada
| | - Xin-Hong Zhu
- School of Psychology, Shenzhen University, Shenzhen, China; Research Center for Brain Health, Pazhou Lab, Guangzhou, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
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8
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van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. J Proteome Res 2024; 23:185-214. [PMID: 38104260 DOI: 10.1021/acs.jproteome.3c00536] [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] [Indexed: 12/19/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource (build 2023-10) providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected post-translational modifications (PTMs), and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18,267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins, and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome: the "dark" proteome. This dark proteome is highly enriched for E3 ligases, transcription factors, and for certain (e.g., CLE, IDA, PSY) but not other (e.g., THIONIN, CAP) signaling peptides families. A machine learning model trained on RNA expression data and protein properties predicts the probability that proteins will be detected. The model aids in discovery of proteins with short half-life (e.g., SIG1,3 and ERF-VII TFs) and for developing strategies to identify the missing proteins. PeptideAtlas is linked to TAIR, tracks in JBrowse, and several other community proteomics resources.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Alyssa Kearly
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Margaret Li
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Isabell Guzchenko
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Erica Debley
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Georgia Sauermann
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Pratyush Routray
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Sagunya Malhotra
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Andrew Nelson
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, United States
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
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9
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Lavilla-Puerta M, Latter R, Bellè F, Cervelli T, Galli A, Perata P, Chini A, Flashman E, Giuntoli B. Identification of novel plant cysteine oxidase inhibitors from a yeast chemical genetic screen. J Biol Chem 2023; 299:105366. [PMID: 37863264 PMCID: PMC10692734 DOI: 10.1016/j.jbc.2023.105366] [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: 07/14/2023] [Revised: 09/28/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Hypoxic responses in plants involve Plant Cysteine Oxidases (PCOs). They catalyze the N-terminal cysteine oxidation of Ethylene Response Factors VII (ERF-VII) in an oxygen-dependent manner, leading to their degradation via the cysteine N-degron pathway (Cys-NDP) in normoxia. In hypoxia, PCO activity drops, leading to the stabilization of ERF-VIIs and subsequent hypoxic gene upregulation. Thus far, no chemicals have been described to specifically inhibit PCO enzymes. In this work, we devised an in vivo pipeline to discover Cys-NDP effector molecules. Budding yeast expressing AtPCO4 and plant-based ERF-VII reporters was deployed to screen a library of natural-like chemical scaffolds and was further combined with an Arabidopsis Cys-NDP reporter line. This strategy allowed us to identify three PCO inhibitors, two of which were shown to affect PCO activity in vitro. Application of these molecules to Arabidopsis seedlings led to an increase in ERF-VII stability, induction of anaerobic gene expression, and improvement of tolerance to anoxia. By combining a high-throughput heterologous platform and the plant model Arabidopsis, our synthetic pipeline provides a versatile system to study how the Cys-NDP is modulated. Its first application here led to the discovery of at least two hypoxia-mimicking molecules with the potential to impact plant tolerance to low oxygen stress.
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Affiliation(s)
| | - Rebecca Latter
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | | | | | - Andrea Chini
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | - Beatrice Giuntoli
- Plantlab, Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy; Biology Department, University of Pisa, Pisa, Italy.
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10
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Yang X, Lou C, Zhang Q, Liu G, Ding Y, Zhang Q, Ye C. Hypoxia-induced circRTN4IP1 promotes progression and glycolysis of hepatocellular carcinoma cells. Funct Integr Genomics 2023; 23:339. [PMID: 37982910 DOI: 10.1007/s10142-023-01256-0] [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: 07/26/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/21/2023]
Abstract
Hypoxia is one of the hallmarks of solid tumors, especially in hepatocellular carcinoma (HCC). CircRNAs are reported to be tightly connected to hypoxia and also have essential roles in cancer progression. However, many circRNAs implicated in hypoxia-mediated HCC progression are still unclear and require further exploration. In this study, a hypoxia cell model was structured by exposing cells to hypoxia conditions (1% O2) and normoxia conditions (21% O2) as a control. The effects of hypoxia and normoxia on cell viability, migration, invasion, and glycolysis were examined. The expressions of circRNARTN4IP1 under hypoxia were identified. Finally, molecular mechanisms and biological function of circRTN4IP1 were explored. We confirmed that hypoxia treatment facilitated capacities of proliferation, migration, invasion, and glycolysis in tumor cells. Hypoxia induced a significant increase expression of circRTN4IP1 in cells. Functionally, knockdown of circRTN4IP1 inhibited cell malignant progression and glycolysis under hypoxia HCC cells. Mechanistically, HIF1A targeted the promoter region of circRTN4IP1 and positively regulated the expression of circRTN4IP1. In addition, circRTN4IP1 targeted miR-532-5p/G6PC3 axis. In short, hypoxia induced activation of the HIF1A/circRTN4IP1/miR-532-5p/G6PC3 signaling axis, which promoted proliferation, migration, invasion, and glycolysis of HCC cells. This study may reveal a possible mechanism driving the progression of hypoxia HCC, so as to find potential effective candidates for targeting hypoxia microenvironment therapy.
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Affiliation(s)
- Xijing Yang
- Department of Biotherapy, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), No. 700, North Moyu Road, Jiading District, Shanghai, 201805, China
| | - Cheng Lou
- Department of Oncology, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, 201805, China
| | - Qing Zhang
- Clinical Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Guofang Liu
- Department of Biotherapy, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), No. 700, North Moyu Road, Jiading District, Shanghai, 201805, China
| | - Yongmei Ding
- Department of Biotherapy, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), No. 700, North Moyu Road, Jiading District, Shanghai, 201805, China
| | - Qian Zhang
- Department of Biotherapy, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), No. 700, North Moyu Road, Jiading District, Shanghai, 201805, China.
| | - Chun Ye
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, No. 389, Xincun Road, Putuo District, Shanghai, 200065, China.
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11
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Slingo ME. Oxygen-sensing pathways and the pulmonary circulation. J Physiol 2023. [PMID: 37843154 DOI: 10.1113/jp284591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023] Open
Abstract
The unique property of the pulmonary circulation to constrict in response to hypoxia, rather than dilate, brings advantages in both health and disease. Hypoxic pulmonary vasoconstriction (HPV) acts to optimise ventilation-perfusion matching - this is important clinically both in focal disease (such as pneumonia) and in one-lung ventilation during anaesthesia for thoracic surgery. However, during global hypoxia such as that encountered at high altitude, generalised pulmonary vasoconstriction can lead to pulmonary hypertension. There is now a growing body of evidence that links the hypoxia-inducible factor (HIF) pathway and pulmonary vascular tone - in both acute and chronic settings. Genetic and pharmacological alterations to all key components of this pathway (VHL - von Hippel-Lindau ubiquitin E3 ligase; PHD2 - prolyl hydroxylase domain protein 2; HIF1 and HIF2) have clear effects on the pulmonary circulation, particularly in hypoxia. Furthermore, knowledge of the molecular biology of the prolyl hydroxylase enzymes has led to an extensive and ongoing body of research into the importance of iron in both HPV and pulmonary hypertension. This review will explore these relationships in more detail and discuss future avenues of research.
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Affiliation(s)
- Mary E Slingo
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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12
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Tian YM, Holdship P, To TQ, Ratcliffe PJ, Keeley TP. Comparative analysis of N-terminal cysteine dioxygenation and prolyl-hydroxylation as oxygen-sensing pathways in mammalian cells. J Biol Chem 2023; 299:105156. [PMID: 37572852 PMCID: PMC10506105 DOI: 10.1016/j.jbc.2023.105156] [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: 06/03/2023] [Revised: 07/25/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023] Open
Abstract
In animals, adaptation to changes in cellular oxygen levels is coordinated largely by 2-oxoglutarate-dependent prolyl-hydroxylase domain (PHD) dioxygenase family members, which regulate the stability of their hypoxia-inducible factor (HIF) substrates to promote expression of genes that adapt cells to hypoxia. Recently, 2-aminoethanethiol dioxygenase (ADO) was identified as a novel O2-sensing enzyme in animals. Through N-terminal cysteine dioxygenation and the N-degron pathway, ADO regulates the stability of a set of non-transcription factor substrates; the regulators of G-protein signaling 4, 5. and 16 and interleukin-32. Here, we set out to compare and contrast the in cellulo characteristics of ADO and PHD enzymes in an attempt to better understand their co-evolution in animals. We find that ADO operates to regulate the stability of its substrates rapidly and with similar O2-sensitivity to the PHD/HIF pathway. ADO appeared less sensitive to iron chelating agents or transition metal exposure than the PHD enzymes, possibly due to tighter catalytic-site Fe2+ coordination. Unlike the PHD/HIF pathway, the ADO/N-degron pathway was not subject to feedback by hypoxic induction of ADO, and induction of ADO substrates was well sustained in response to prolonged hypoxia. The data also reveal strong interactions between proteolytic regulation of targets by ADO and transcriptional induction of those targets, that shape integrated cellular responses to hypoxia. Collectively, our comparative analysis provides further insight into ADO/N-degron-mediated oxygen sensing and its integration into established mechanisms of oxygen homeostasis.
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Affiliation(s)
- Ya-Min Tian
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip Holdship
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Trang Quynh To
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Peter J Ratcliffe
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; The Francis Crick Institute, London, UK.
| | - Thomas P Keeley
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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13
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Zubrycka A, Dambire C, Dalle Carbonare L, Sharma G, Boeckx T, Swarup K, Sturrock CJ, Atkinson BS, Swarup R, Corbineau F, Oldham NJ, Holdsworth MJ. ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana. Nat Commun 2023; 14:4665. [PMID: 37537157 PMCID: PMC10400637 DOI: 10.1038/s41467-023-40366-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023] Open
Abstract
Oxygen is a key signalling component of plant biology, and whilst an oxygen-sensing mechanism was previously described in Arabidopsis thaliana, key features of the associated PLANT CYSTEINE OXIDASE (PCO) N-degron pathway and Group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factor substrates remain untested or unknown. We demonstrate that ERFVIIs show non-autonomous activation of root hypoxia tolerance and are essential for root development and survival under oxygen limiting conditions in soil. We determine the combined effects of ERFVIIs in controlling gene expression and define genetic and environmental components required for proteasome-dependent oxygen-regulated stability of ERFVIIs through the PCO N-degron pathway. Using a plant extract, unexpected amino-terminal cysteine sulphonic acid oxidation level of ERFVIIs was observed, suggesting a requirement for additional enzymatic activity within the pathway. Our results provide a holistic understanding of the properties, functions and readouts of this oxygen-sensing mechanism defined through its role in modulating ERFVII stability.
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Affiliation(s)
- Agata Zubrycka
- School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
| | - Charlene Dambire
- School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
| | - Laura Dalle Carbonare
- School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
- Department of Biology, University of Oxford, OX1 3RB, Oxford, UK
| | - Gunjan Sharma
- School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
| | - Tinne Boeckx
- School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
| | - Kamal Swarup
- School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
| | - Craig J Sturrock
- School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
| | - Brian S Atkinson
- School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
| | - Ranjan Swarup
- School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
| | - Françoise Corbineau
- UMR 7622 CNRS-UPMC, Biologie du développement, Institut de Biologie Paris Seine, Sorbonne Université, Paris, France
| | - Neil J Oldham
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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14
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Miricescu A, Brazel AJ, Beegan J, Wellmer F, Graciet E. Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response. PLANT DIRECT 2023; 7:e518. [PMID: 37577136 PMCID: PMC10422865 DOI: 10.1002/pld3.518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023]
Abstract
Waterlogging leads to major crop losses globally, particularly for waterlogging-sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related quantitative trait loci have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called "core hypoxia response genes," thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study "predisposition" to waterlogging tolerance or sensitivity in barley.
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Affiliation(s)
- Alexandra Miricescu
- Department of BiologyMaynooth UniversityMaynoothIreland
- Pesticide Registration DivisionDepartment of Agriculture, Food and the Marine, Backweston CampusCelbridgeIreland
| | | | - Joseph Beegan
- Smurfit Institute of GeneticsTrinity College DublinDublinIreland
| | - Frank Wellmer
- Smurfit Institute of GeneticsTrinity College DublinDublinIreland
| | - Emmanuelle Graciet
- Department of BiologyMaynooth UniversityMaynoothIreland
- Kathleen Lonsdale Institute for Human Health ResearchMaynooth UniversityMaynoothIreland
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15
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Karakaya S, Gunnesson L, Elias E, Martos-Salvo P, Robledo M, Nilsson O, Wängberg B, Abel F, Påhlman S, Muth A, Mohlin S. Cytoplasmic HIF-2α as tissue biomarker to identify metastatic sympathetic paraganglioma. Sci Rep 2023; 13:11588. [PMID: 37463949 PMCID: PMC10354100 DOI: 10.1038/s41598-023-38606-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Pheochromocytomas (PCCs) and paragangliomas (PGLs) are rare neuroendocrine tumors. PGLs can further be divided into sympathetic (sPGLs) and head-and-neck (HN-PGLs). There are virtually no treatment options, and no cure, for metastatic PCCs and PGLs (PPGLs). Here, we composed a tissue microarray (TMA) consisting of 149 PPGLs, reflecting clinical features, presenting as a useful resource. Mutations in the pseudohypoxic marker HIF-2α correlate to an aggressive tumor phenotype. We show that HIF-2α localized to the cytoplasm in PPGLs. This subcompartmentalized protein expression differed between tumor subtypes, and strongly correlated to proliferation. Half of all sPGLs were metastatic at time of diagnosis. Cytoplasmic HIF-2α was strongly expressed in metastatic sPGLs and predicted poor outcome in this subgroup. We propose that higher cytoplasmic HIF-2α expression could serve as a useful clinical marker to differentiate paragangliomas from pheochromocytomas, and may help predict outcome in sPGL patients.
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Affiliation(s)
- Sinan Karakaya
- Division of Pediatrics, Department of Clinical Sciences, Lund University, Sölvegatan 19, BMC B11, 223 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund University Cancer Center, Lund University, Lund, Sweden
| | - Lisa Gunnesson
- Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Elias
- Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Paula Martos-Salvo
- Division of Pediatrics, Department of Clinical Sciences, Lund University, Sölvegatan 19, BMC B11, 223 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund University Cancer Center, Lund University, Lund, Sweden
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Ola Nilsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bo Wängberg
- Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Frida Abel
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Sven Påhlman
- Lund University Cancer Center, Lund University, Lund, Sweden
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Andreas Muth
- Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sofie Mohlin
- Division of Pediatrics, Department of Clinical Sciences, Lund University, Sölvegatan 19, BMC B11, 223 84, Lund, Sweden.
- Lund Stem Cell Center, Lund University, Lund, Sweden.
- Lund University Cancer Center, Lund University, Lund, Sweden.
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16
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Xu ZX, Zhu XM, Yin H, Li B, Chen XJ, Fan XL, Li NQ, Selosse MA, Gao JY, Han JJ. Symbiosis between Dendrobium catenatum protocorms and Serendipita indica involves the plant hypoxia response pathway. PLANT PHYSIOLOGY 2023; 192:2554-2568. [PMID: 36988071 PMCID: PMC10315314 DOI: 10.1093/plphys/kiad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Mycorrhizae are ubiquitous symbioses established between fungi and plant roots. Orchids, in particular, require compatible mycorrhizal fungi for seed germination and protocorm development. Unlike arbuscular mycorrhizal fungi, which have wide host ranges, orchid mycorrhizal fungi are often highly specific to their host orchids. However, the molecular mechanism of orchid mycorrhizal symbiosis is largely unknown compared to that of arbuscular mycorrhizal and rhizobial symbiosis. Here, we report that an endophytic Sebacinales fungus, Serendipita indica, promotes seed germination and the development of protocorms into plantlets in several epiphytic Epidendroideae orchid species (6 species in 2 genera), including Dendrobium catenatum, a critically endangered orchid with high medicinal value. Although plant-pathogen interaction and high meristematic activity can induce the hypoxic response in plants, it has been unclear whether interactions with beneficial fungi, especially mycorrhizal ones, also involve the hypoxic response. By studying the symbiotic relationship between D. catenatum and S. indica, we determined that hypoxia-responsive genes, such as those encoding alcohol dehydrogenase (ADH), are highly induced in symbiotic D. catenatum protocorms. In situ hybridization assay indicated that the ADH gene is predominantly expressed in the basal mycorrhizal region of symbiotic protocorms. Additionally, the ADH inhibitors puerarin and 4-methylpyrazole both decreased S. indica colonization in D. catenatum protocorms. Thus, our study reveals that S. indica is widely compatible with orchids and that ADH and its related hypoxia-responsive pathway are involved in establishing successful symbiotic relationships in germinating orchids.
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Affiliation(s)
- Zhi-Xiong Xu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Xin-Meng Zhu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Huachun Yin
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Xiao-Jie Chen
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Xu-Li Fan
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Neng-Qi Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Marc-André Selosse
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Institut de Systématique, Évolution, Biodiversité (UMR 7205-CNRS, MNHN, UPMC, EPHE), Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
- University of Gdańsk, Faculty of Biology, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
- Institut Universitaire de France (IUF), Paris, France
| | - Jiang-Yun Gao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Jia-Jia Han
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
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17
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van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Mapping the Arabidopsis thaliana proteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543322. [PMID: 37333403 PMCID: PMC10274743 DOI: 10.1101/2023.06.01.543322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected PTMs, and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for building the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome - the 'dark' proteome. This dark proteome is highly enriched for certain ( e.g. CLE, CEP, IDA, PSY) but not other ( e.g. THIONIN, CAP,) signaling peptides families, E3 ligases, TFs, and other proteins with unfavorable physicochemical properties. A machine learning model trained on RNA expression data and protein properties predicts the probability for proteins to be detected. The model aids in discovery of proteins with short-half life ( e.g. SIG1,3 and ERF-VII TFs) and completing the proteome. PeptideAtlas is linked to TAIR, JBrowse, PPDB, SUBA, UniProtKB and Plant PTM Viewer.
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18
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Langer M, Hilo A, Guan JC, Koch KE, Xiao H, Verboven P, Gündel A, Wagner S, Ortleb S, Radchuk V, Mayer S, Nicolai B, Borisjuk L, Rolletschek H. Causes and consequences of endogenous hypoxia on growth and metabolism of developing maize kernels. PLANT PHYSIOLOGY 2023; 192:1268-1288. [PMID: 36691698 PMCID: PMC10231453 DOI: 10.1093/plphys/kiad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 06/01/2023]
Abstract
Maize (Zea mays) kernels are the largest cereal grains, and their endosperm is severely oxygen deficient during grain fill. The causes, dynamics, and mechanisms of acclimation to hypoxia are minimally understood. Here, we demonstrate that hypoxia develops in the small, growing endosperm, but not the nucellus, and becomes the standard state, regardless of diverse structural and genetic perturbations in modern maize (B73, popcorn, sweet corn), mutants (sweet4c, glossy6, waxy), and non-domesticated wild relatives (teosintes and Tripsacum species). We also uncovered an interconnected void space at the chalazal pericarp, providing superior oxygen supply to the placental tissues and basal endosperm transfer layer. Modeling indicated a very high diffusion resistance inside the endosperm, which, together with internal oxygen consumption, could generate steep oxygen gradients at the endosperm surface. Manipulation of oxygen supply induced reciprocal shifts in gene expression implicated in controlling mitochondrial functions (23.6 kDa Heat-Shock Protein, Voltage-Dependent Anion Channel 2) and multiple signaling pathways (core hypoxia genes, cyclic nucleotide metabolism, ethylene synthesis). Metabolite profiling revealed oxygen-dependent shifts in mitochondrial pathways, ascorbate metabolism, starch synthesis, and auxin degradation. Long-term elevated oxygen supply enhanced the rate of kernel development. Altogether, evidence here supports a mechanistic framework for the establishment of and acclimation to hypoxia in the maize endosperm.
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Affiliation(s)
- Matthias Langer
- Molecular Genetics Department, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany
| | - Alexander Hilo
- Molecular Genetics Department, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany
| | - Jiahn-Chou Guan
- University of Florida, Horticultural Sciences Department, Fifield Hall, 2550 Hull Rd., PO Box 110690, Gainesville, Florida, 32611, USA
| | - Karen E Koch
- University of Florida, Horticultural Sciences Department, Fifield Hall, 2550 Hull Rd., PO Box 110690, Gainesville, Florida, 32611, USA
| | - Hui Xiao
- Biosystems Department, KU Leuven—University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Pieter Verboven
- Biosystems Department, KU Leuven—University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Andre Gündel
- Molecular Genetics Department, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany
| | - Steffen Wagner
- Molecular Genetics Department, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany
| | - Stefan Ortleb
- Molecular Genetics Department, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany
| | - Volodymyr Radchuk
- Molecular Genetics Department, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany
| | - Simon Mayer
- Molecular Genetics Department, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany
| | - Bart Nicolai
- Biosystems Department, KU Leuven—University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Ljudmilla Borisjuk
- Molecular Genetics Department, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany
| | - Hardy Rolletschek
- Molecular Genetics Department, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany
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19
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Nano-Electrochemical Characterization of a 3D Bioprinted Cervical Tumor Model. Cancers (Basel) 2023; 15:cancers15041327. [PMID: 36831668 PMCID: PMC9954750 DOI: 10.3390/cancers15041327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/31/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Current cancer research is limited by the availability of reliable in vivo and in vitro models that are able to reproduce the fundamental hallmarks of cancer. Animal experimentation is of paramount importance in the progress of research, but it is becoming more evident that it has several limitations due to the numerous differences between animal tissues and real, in vivo human tissues. 3D bioprinting techniques have become an attractive tool for many basic and applied research fields. Concerning cancer, this technology has enabled the development of three-dimensional in vitro tumor models that recreate the characteristics of real tissues and look extremely promising for studying cancer cell biology. As 3D bioprinting is a relatively recently developed technique, there is still a lack of characterization of the chemical cellular microenvironment of 3D bioprinted constructs. In this work, we fabricated a cervical tumor model obtained by 3D bioprinting of HeLa cells in an alginate-based matrix. Characterization of the spheroid population obtained as a function of culturing time was performed by phase-contrast and confocal fluorescence microscopies. Scanning electrochemical microscopy and platinum nanoelectrodes were employed to characterize oxygen concentrations-a fundamental characteristic of the cellular microenvironment-with a high spatial resolution within the 3D bioprinted cervical tumor model; we also demonstrated that the diffusion of a molecular model of drugs in the 3D bioprinted construct, in which the spheroids were embedded, could be measured quantitatively over time using scanning electrochemical microscopy.
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20
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Shakir D, Batie M, Rocha S. Fixed Cell Immunofluorescence for Quantification of Hypoxia-Induced Changes in Histone Methylation. Methods Mol Biol 2023; 2675:261-269. [PMID: 37258769 DOI: 10.1007/978-1-0716-3247-5_19] [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] [Indexed: 06/02/2023]
Abstract
Hypoxia and its signalling pathway play a key role in human physiology and a variety of diseases. Alterations in histone methylation coordinate transcriptional responses to hypoxia. Here, we detail a fixed cell immunofluorescence method for quantifying hypoxia-induced changes in histone methylation, exemplified by the measurement of H3K27me3.
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Affiliation(s)
- Dilem Shakir
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Michael Batie
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sonia Rocha
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
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21
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Dirr A, Gunawardana DM, Flashman E. Kinetic Measurements to Investigate the Oxygen-Sensing Properties of Plant Cysteine Oxidases. Methods Mol Biol 2023; 2648:207-230. [PMID: 37039993 DOI: 10.1007/978-1-0716-3080-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Enzymatic O2 sensors transduce the availability of O2 within the cell into a physiological, typically adaptive response. One such O2-sensing enzymatic family is the N-terminal cysteine dioxygenases in plants (plant cysteine oxidases [PCOs]). In vitro kinetic studies have determined the O2-sensing capacity of PCOs. Here we describe the rationale and experimental protocol for an assay with which the O2 sensitivity of Arabidopsis thaliana PCOs (AtPCOs) can be measured. We explain each step from the recombinant protein synthesis of AtPCOs to the steady-state kinetic assays of AtPCOs for primary substrate and O2 from which kinetic parameters can be derived. The same techniques can be applied to other N-terminal cysteine thiol dioxygenases, e.g. 2-aminoethanethiol dioxygenase (ADO), and similar principles can be applied to determine kinetic characteristics of other oxygenase enzymes towards O2.
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Affiliation(s)
- Anna Dirr
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Emily Flashman
- Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
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22
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Smith E, Keeley TP. Monitoring ADO dependent proteolysis in cells using fluorescent reporter proteins. Methods Enzymol 2023. [PMID: 37532403 DOI: 10.1016/bs.mie.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
2-Aminoethanethiol dioxygenase (ADO) is the mammalian orthologue of the plant cysteine oxidases and together these enzymes are responsible for catalysing dioxygenation of N-terminal cysteine residues of certain proteins. This modification creates an N-degron motif that permits arginylation and subsequent proteasomal degradation of such proteins via the Arg-branch of the N-degron pathway. In humans 4 proteins have been identified as substrates of ADO; regulators of G-protein signalling (RGS) 4, 5 and 16, and interleukin-32 (IL-32). Nt-cysteine dioxygenation of these proteins occurs rapidly under normoxic conditions, but ADO activity is very sensitive to O2 availability and as such the stability of substrate proteins is inversely proportional to cellular O2 levels. Much is still to understand about the biochemistry and physiology of this pathway in vitro and in vivo, and Cys N-degron targeted fluorescent proteins can provide a simple and effective tool to study this at both subcellular and high-throughput scales. This chapter describes the design, production and implementation of a fluorescent fusion protein proteolytically regulated by ADO and the N-degron pathway.
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23
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Meng J, Wang T, Li B, Li L, Zhang G. Oxygen sensing and transcriptional regulation under hypoxia exposure in the mollusk Crassostrea gigas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158557. [PMID: 36084780 DOI: 10.1016/j.scitotenv.2022.158557] [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: 06/13/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Hypoxia caused by global climate change and anthropogenic pollution has exposed marine species to increasing stress. Oxygen sensing mediated by prolyl hydroxylase (PHD) is regarded as the first line of defense under hypoxia exposure; however, the function of PHD in marine molluscan species remains unclear. In this study, we identified two PHD2 gene in the oyster Crassostrea gigas using phylogenetic tree analysis with 36 species, namely, CgPHD2A/B. Under hypoxia, the mRNA and protein expression of CgPHD2A displayed a time-dependent pattern, revealing a critical role in the response to hypoxia-induced stress. Observation of interactions between CgPHD2 and CgHIF-1α proteins under normoxia using co-immunoprecipitation and GST-pull down experiments showed that the β2β3 loop in CgPHD2A hydroxylates CgHIF-1α to promote its ubiquitination with CgVHL. With the protein recombination and site-directed mutagenesis, the hydroxylation domain and two target proline loci (P404A and 504A) in CgPHDs and CgHIF-1α were identified respectively. Moreover, the electrophoretic mobility-shift assay (EMSA) and luciferase double reporter gene assay revelaed that CgHIF-1α could regulate CgPHD2A expression through binding with the hypoxia-responsive element in the promoter region (320 bp upstream), forming a feedback loop. However, protein structure analysis indicated that six extra amino acids formed an α-helix in the β2β3 loop of CgPHD2B, inhibiting its activity. Overall, this study revealed that two CgPHD2 proteins have evolved, which encode enzymes with different activities in oyster, potentially representing a specific hypoxia-sensing mechanism in mollusks. Illustrating the functional diversity of CgPHDs could help to assess the physiological status of oyster and guide their aquaculture.
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Affiliation(s)
- Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China
| | - Ting Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China
| | - Busu Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.
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24
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Methyltransferase SMYD3 impairs hypoxia tolerance by augmenting hypoxia signaling independent of its enzymatic activity. J Biol Chem 2022; 298:102633. [PMID: 36273580 PMCID: PMC9692045 DOI: 10.1016/j.jbc.2022.102633] [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: 06/14/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Hypoxia-inducible factor (HIF)1α, a main transcriptional regulator of the cellular response to hypoxia, also plays important roles in oxygen homeostasis of aerobic organisms, which is regulated by multiple mechanisms. However, the full cellular response to hypoxia has not been elucidated. In this study, we found that expression of SMYD3, a methyltransferase, augments hypoxia signaling independent of its enzymatic activity. We demonstrated SMYD3 binds to and stabilizes HIF1α via co-immunoprecipitation and Western blot assays, leading to the enhancement of HIF1α transcriptional activity under hypoxia conditions. In addition, the stabilization of HIF1α by SMYD3 is independent of HIF1α hydroxylation by prolyl hydroxylases and the intactness of the von Hippel-Lindau ubiquitin ligase complex. Furthermore, we showed SMYD3 induces reactive oxygen species accumulation and promotes hypoxia-induced cell apoptosis. Consistent with these results, we found smyd3-null zebrafish exhibit higher hypoxia tolerance compared to their wildtype siblings. Together, these findings define a novel role of SMYD3 in affecting hypoxia signaling and demonstrate that SMYD3-mediated HIF1α stabilization augments hypoxia signaling, leading to the impairment of hypoxia tolerance.
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25
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Meinnel T, Giglione C. N-terminal modifications, the associated processing machinery, and their evolution in plastid-containing organisms. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6013-6033. [PMID: 35768189 DOI: 10.1093/jxb/erac290] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The N-terminus is a frequent site of protein modifications. Referring primarily to knowledge gained from land plants, here we review the modifications that change protein N-terminal residues and provide updated information about the associated machinery, including that in Archaeplastida. These N-terminal modifications include many proteolytic events as well as small group additions such as acylation or arginylation and oxidation. Compared with that of the mitochondrion, the plastid-dedicated N-terminal modification landscape is far more complex. In parallel, we extend this review to plastid-containing Chromalveolata including Stramenopiles, Apicomplexa, and Rhizaria. We report a well-conserved machinery, especially in the plastid. Consideration of the two most abundant proteins on Earth-Rubisco and actin-reveals the complexity of N-terminal modification processes. The progressive gene transfer from the plastid to the nuclear genome during evolution is exemplified by the N-terminus modification machinery, which appears to be one of the latest to have been transferred to the nuclear genome together with crucial major photosynthetic landmarks. This is evidenced by the greater number of plastid genes in Paulinellidae and red algae, the most recent and fossil recipients of primary endosymbiosis.
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Affiliation(s)
- Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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26
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Song B, Modjewski LD, Kapust N, Mizrahi I, Martin WF. The origin and distribution of the main oxygen sensing mechanism across metazoans. Front Physiol 2022; 13:977391. [PMID: 36324306 PMCID: PMC9618697 DOI: 10.3389/fphys.2022.977391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
Oxygen sensing mechanisms are essential for metazoans, their origin and evolution in the context of oxygen in Earth history are of interest. To trace the evolution of a main oxygen sensing mechanism among metazoans, the hypoxia induced factor, HIF, we investigated the phylogenetic distribution and phylogeny of 11 of its components across 566 eukaryote genomes. The HIF based oxygen sensing machinery in eukaryotes can be traced as far back as 800 million years (Ma) ago, likely to the last metazoan common ancestor (LMCA), and arose at a time when the atmospheric oxygen content corresponded roughly to the Pasteur point, or roughly 1% of present atmospheric level (PAL). By the time of the Cambrian explosion (541–485 Ma) as oxygen levels started to approach those of the modern atmosphere, the HIF system with its key components HIF1α, HIF1β, PHD1, PHD4, FIH and VHL was well established across metazoan lineages. HIF1α is more widely distributed and therefore may have evolved earlier than HIF2α and HIF3α, and HIF1β and is more widely distributed than HIF2β in invertebrates. PHD1, PHD4, FIH, and VHL appear in all 13 metazoan phyla. The O2 consuming enzymes of the pathway, PHDs and FIH, have a lower substrate affinity, Km, for O2 than terminal oxidases in the mitochondrial respiratory chain, in line with their function as an environmental signal to switch to anaerobic energy metabolic pathways. The ancient HIF system has been conserved and widespread during the period when metazoans evolved and diversified together with O2 during Earth history.
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Affiliation(s)
- Bing Song
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Luca David Modjewski
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be’er-Sheva, Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- *Correspondence: William F. Martin,
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27
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Bacteriolytic therapy with Clostridium ghonii for experimental solid tumors. Biochem Biophys Res Commun 2022; 634:114-121. [DOI: 10.1016/j.bbrc.2022.09.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/13/2022] [Accepted: 09/27/2022] [Indexed: 11/20/2022]
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28
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Si P, Zhu C. Biological and neurological activities of astaxanthin (Review). Mol Med Rep 2022; 26:300. [PMID: 35946443 PMCID: PMC9435021 DOI: 10.3892/mmr.2022.12816] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/30/2022] [Indexed: 11/06/2022] Open
Abstract
Astaxanthin is a lipid‑soluble carotenoid produced by various microorganisms and marine animals, including bacteria, yeast, fungi, microalgae, shrimps and lobsters. Astaxanthin has antioxidant, anti‑inflammatory and anti‑apoptotic properties. These characteristics suggest that astaxanthin has health benefits and protects against various diseases. Owing to its ability to cross the blood‑brain barrier, astaxanthin has received attention for its protective effects against neurological disorders, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, cerebral ischemia/reperfusion, subarachnoid hemorrhage, traumatic brain injury, spinal cord injury, cognitive impairment and neuropathic pain. Previous studies on the neurological effects of astaxanthin are mostly based on animal models and cellular experiments. Thus, the biological effects of astaxanthin on humans and its underlying mechanisms are still not fully understood. The present review summarizes the neuroprotective effects of astaxanthin, explores its mechanisms of action and draws attention to its potential clinical implications as a therapeutic agent.
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Affiliation(s)
- Pan Si
- Department of Neurology Intervention, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Chenkai Zhu
- Department of Pediatrics, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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29
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Meteorin links the bone marrow hypoxic state to hematopoietic stem/progenitor cell mobilization. Cell Rep 2022; 40:111361. [PMID: 36130501 DOI: 10.1016/j.celrep.2022.111361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/20/2022] [Accepted: 08/23/2022] [Indexed: 11/21/2022] Open
Abstract
Hematopoietic stem/progenitor cells (HSPCs) are supported and regulated by niche cells in the bone marrow with an important characterization of physiological hypoxia. However, how hypoxia regulates HSPCs is still unclear. Here, we find that meteorin (Metrn) from hypoxic macrophages restrains HSPC mobilization. Hypoxia-induced factor 1α and Yin Yang 1 induce the high expression of Metrn in macrophages, and macrophage-specific Metrn knockout increases HSPC mobilization through modulating HSPC proliferation and migration. Mechanistically, Metrn interacts with its receptor 5-hydroxytryptamine receptor 2b (Htr2b) to regulate the reactive oxygen species levels in HSPCs through targeting phospholipase C signaling. The reactive oxygen species levels are reduced in HSPCs of macrophage-specific Metrn knockout mice with activated phospholipase C signaling. Targeting the Metrn/Htr2b axis could therefore be a potential strategy to improve HSPC mobilization for stem cell-based therapy.
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30
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Salminen A. Mutual antagonism between aryl hydrocarbon receptor and hypoxia-inducible factor-1α (AhR/HIF-1α) signaling: Impact on the aging process. Cell Signal 2022; 99:110445. [PMID: 35988806 DOI: 10.1016/j.cellsig.2022.110445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/27/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022]
Abstract
The ambient oxygen level, many environmental toxins, and the rays of ultraviolet light (UV) provide a significant risk for the maintenance of organismal homeostasis. The aryl hydrocarbon receptors (AhR) represent a complex sensor system not only for environmental toxins and UV radiation but also for many endogenous ligands, e.g., L-tryptophan metabolites. The AhR signaling system is evolutionarily conserved and AhR homologs existed as many as 600 million years ago. The ancient atmosphere demanded the evolution of an oxygen-sensing system, i.e., hypoxia-inducible transcription factors (HIF) and their prolyl hydroxylase regulators (PHD). Given that both signaling systems have important roles in embryogenesis, it seems that they have been involved in the evolution of multicellular organisms. The evolutionary origin of the aging process is unknown although it is most likely associated with the evolution of multicellularity. Intriguingly, there is compelling evidence that while HIF-1α signaling extends the lifespan, that of AhR promotes many age-related degenerative processes, e.g., it increases oxidative stress, inhibits autophagy, promotes cellular senescence, and aggravates extracellular matrix degeneration. In contrast, HIF-1α signaling stimulates autophagy, inhibits cellular senescence, and enhances cell proliferation. Interestingly, there is a clear antagonism between the AhR and HIF-1α signaling pathways. For instance, (i) AhR and HIF-1α factors heterodimerize with the same factor, ARNT/HIF-1β, leading to their competition for DNA-binding, (ii) AhR and HIF-1α signaling exert antagonistic effects on autophagy, and (iii) co-chaperone p23 exhibits specific functions in the signaling of AhR and HIF-1α factors. One might speculate that it is the competition between the AhR and HIF-1α signaling pathways that is a driving force in the aging process.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
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31
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Jacques F, Baratchart E, Pienta KJ, Hammarlund EU. Origin and evolution of animal multicellularity in the light of phylogenomics and cancer genetics. Med Oncol 2022; 39:160. [PMID: 35972622 PMCID: PMC9381480 DOI: 10.1007/s12032-022-01740-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 11/07/2022]
Abstract
The rise of animals represents a major but enigmatic event in the evolutionary history of life. In recent years, numerous studies have aimed at understanding the genetic basis of this transition. However, genome comparisons of diverse animal and protist lineages suggest that the appearance of gene families that were previously considered animal specific indeed preceded animals. Animals' unicellular relatives, such as choanoflagellates, ichthyosporeans, and filastereans, demonstrate complex life cycles including transient multicellularity as well as genetic toolkits for temporal cell differentiation, cell-to-cell communication, apoptosis, and cell adhesion. This has warranted further exploration of the genetic basis underlying transitions in cellular organization. An alternative model for the study of transitions in cellular organization is tumors, which exploit physiological programs that characterize both unicellularity and multicellularity. Tumor cells, for example, switch adhesion on and off, up- or downregulate specific cell differentiation states, downregulate apoptosis, and allow cell migration within tissues. Here, we use insights from both the fields of phylogenomics and tumor biology to review the evolutionary history of the regulatory systems of multicellularity and discuss their overlap. We claim that while evolutionary biology has contributed to an increased understanding of cancer, broad investigations into tissue-normal and transformed-can also contribute the framework for exploring animal evolution.
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Affiliation(s)
- Florian Jacques
- Tissue Development and Evolution (TiDE), Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Etienne Baratchart
- Tissue Development and Evolution (TiDE), Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Kenneth J Pienta
- The Cancer Ecology Center, Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, USA
| | - Emma U Hammarlund
- Tissue Development and Evolution (TiDE), Department of Laboratory Medicine, Lund University, Lund, Sweden.
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden.
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32
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Taylor-Kearney LJ, Madden S, Wilson J, Myers WK, Gunawardana DM, Pires E, Holdship P, Tumber A, Rickaby REM, Flashman E. Plant Cysteine Oxidase Oxygen-Sensing Function Is Conserved in Early Land Plants and Algae. ACS BIO & MED CHEM AU 2022; 2:521-528. [PMID: 36281301 PMCID: PMC9585510 DOI: 10.1021/acsbiomedchemau.2c00032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
![]()
All aerobic organisms require O2 for survival.
When
their O2 is limited (hypoxia), a response is required to
reduce demand and/or improve supply. A hypoxic response mechanism
has been identified in flowering plants: the stability of certain
proteins with N-terminal cysteine residues is regulated in an O2-dependent manner by the Cys/Arg branch of the N-degron pathway.
These include the Group VII ethylene response factors (ERF-VIIs),
which can initiate adaptive responses to hypoxia. Oxidation of their
N-terminal cysteine residues is catalyzed by plant cysteine oxidases
(PCOs), destabilizing these proteins in normoxia; PCO inactivity in
hypoxia results in their stabilization. Biochemically, the PCOs are
sensitive to O2 availability and can therefore act as plant
O2 sensors. It is not known whether oxygen-sensing mechanisms
exist in other phyla from the plant kingdom. Known PCO targets are
only conserved in flowering plants, however PCO-like sequences appear
to be conserved in all plant species. We sought to determine whether
PCO-like enzymes from the liverwort, Marchantia polymorpha (MpPCO), and the freshwater algae, Klebsormidium nitens (KnPCO), have a similar function as PCO enzymes from Arabidopsis
thaliana. We report that MpPCO and KnPCO show O2-sensitive N-terminal cysteine dioxygenase activity toward known
AtPCO ERF-VII substrates as well as a putative endogenous substrate,
MpERF-like, which was identified by homology to the Arabidopsis ERF-VIIs transcription factors. This work confirms functional and
O2-dependent PCOs from Bryophyta and Charophyta, indicating
the potential for PCO-mediated O2-sensing pathways in these
organisms and suggesting PCO O2-sensing function could
be important throughout the plant kingdom.
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Affiliation(s)
- Leah J. Taylor-Kearney
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Samuel Madden
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Jack Wilson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - William K. Myers
- Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Dona M. Gunawardana
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Elisabete Pires
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Philip Holdship
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Rosalind E. M. Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, United Kingdom
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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Saraiva FMS, Cosentino-Gomes D, Inacio JDF, Almeida-Amaral EE, Louzada-Neto O, Rossini A, Nogueira NP, Meyer-Fernandes JR, Paes MC. Hypoxia Effects on Trypanosoma cruzi Epimastigotes Proliferation, Differentiation, and Energy Metabolism. Pathogens 2022; 11:pathogens11080897. [PMID: 36015018 PMCID: PMC9416468 DOI: 10.3390/pathogens11080897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, faces changes in redox status and nutritional availability during its life cycle. However, the influence of oxygen fluctuation upon the biology of T. cruzi is unclear. The present work investigated the response of T. cruzi epimastigotes to hypoxia. The parasites showed an adaptation to the hypoxic condition, presenting an increase in proliferation and a reduction in metacyclogenesis. Additionally, parasites cultured in hypoxia produced more reactive oxygen species (ROS) compared to parasites cultured in normoxia. The analyses of the mitochondrial physiology demonstrated that hypoxic condition induced a decrease in both oxidative phosphorylation and mitochondrial membrane potential (ΔΨm) in epimastigotes. In spite of that, ATP levels of parasites cultivated in hypoxia increased. The hypoxic condition also increased the expression of the hexokinase and NADH fumarate reductase genes and reduced NAD(P)H, suggesting that this increase in ATP levels of hypoxia-challenged parasites was a consequence of increased glycolysis and fermentation pathways. Taken together, our results suggest that decreased oxygen levels trigger a shift in the bioenergetic metabolism of T. cruzi epimastigotes, favoring ROS production and fermentation to sustain ATP production, allowing the parasite to survive and proliferate in the insect vector.
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Affiliation(s)
- Francis M. S. Saraiva
- Trypanosomatids and Vectors Interaction Laboratory, Department of Biochemistry, Roberto Alcantara Gomes Institute of Biology, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil
| | - Daniela Cosentino-Gomes
- Institute of Medical Biochemistry Leopoldo De Meis, Center for Health Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Job D. F. Inacio
- Tripanosomatide Biochemistry Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Elmo E. Almeida-Amaral
- Tripanosomatide Biochemistry Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Orlando Louzada-Neto
- Laboratory of Toxicology and Molecular Biology, Department of Biochemistry, IBRAG- UERJ, Rio de Janeiro 20511-010, Brazil
| | - Ana Rossini
- Laboratory of Toxicology and Molecular Biology, Department of Biochemistry, IBRAG- UERJ, Rio de Janeiro 20511-010, Brazil
| | - Natália P. Nogueira
- Trypanosomatids and Vectors Interaction Laboratory, Department of Biochemistry, Roberto Alcantara Gomes Institute of Biology, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil
- National Institute of Science and Technology—Molecular Entomology (INCT-EM), Brasília 70000-000, Brazil
| | - José R. Meyer-Fernandes
- Institute of Medical Biochemistry Leopoldo De Meis, Center for Health Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Marcia C. Paes
- Trypanosomatids and Vectors Interaction Laboratory, Department of Biochemistry, Roberto Alcantara Gomes Institute of Biology, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil
- National Institute of Science and Technology—Molecular Entomology (INCT-EM), Brasília 70000-000, Brazil
- Correspondence:
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HIF-1-Dependent Induction of β3 Adrenoceptor: Evidence from the Mouse Retina. Cells 2022; 11:cells11081271. [PMID: 35455951 PMCID: PMC9029465 DOI: 10.3390/cells11081271] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/01/2023] Open
Abstract
A major player in the homeostatic response to hypoxia is the hypoxia-inducible factor (HIF)-1 that transactivates a number of genes involved in neovessel proliferation in response to low oxygen tension. In the retina, hypoxia overstimulates β-adrenoceptors (β-ARs) which play a key role in the formation of pathogenic blood vessels. Among β-ARs, β3-AR expression is increased in proliferating vessels in concomitance with increased levels of HIF-1α and vascular endothelial growth factor (VEGF). Whether, similarly to VEGF, hypoxia-induced β3-AR upregulation is driven by HIF-1 is still unknown. We used the mouse model of oxygen-induced retinopathy (OIR), an acknowledged model of retinal angiogenesis, to verify the hypothesis of β3-AR transcriptional regulation by HIF-1. Investigation of β3-AR regulation over OIR progression revealed that the expression profile of β3-AR depends on oxygen tension, similar to VEGF. The additional evidence that HIF-1α stabilization decouples β3-AR expression from oxygen levels further indicates that HIF-1 regulates the expression of the β3-AR gene in the retina. Bioinformatics predicted the presence of six HIF-1 binding sites (HBS #1-6) upstream and inside the mouse β3-AR gene. Among these, HBS #1 has been identified as the most suitable HBS for HIF-1 binding. Chromatin immunoprecipitation-qPCR demonstrated an effective binding of HIF-1 to HBS #1 indicating the existence of a physical interaction between HIF-1 and the β3-AR gene. The additional finding that β3-AR gene expression is concomitantly activated indicates the possibility that HIF-1 transactivates the β3-AR gene. Our results are indicative of β3-AR involvement in HIF-1-mediated response to hypoxia.
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Yan Y, Xu Y, Yang X, Li Z, Niu K, Liu C, Zhao M, Xiao Q, Wu W. Electron Transfer Flavoprotein (ETF) α Controls Blood Vessel Development by Regulating Endothelial Mitochondrial Bioenergetics and Oxygen Consumption. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7969916. [PMID: 35313640 PMCID: PMC8933654 DOI: 10.1155/2022/7969916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/05/2022] [Indexed: 11/17/2022]
Abstract
While impairment of vascular homeostasis induced by hypercholesterolemia is the first step of cardiovascular diseases, the molecular mechanism behind such impairment is not well known. Here, we reported that high-cholesterol diet (HCD) induced defective vessel sprouting in zebrafish larvae. Electron transfer flavoprotein subunit α (ETFα) (encoded by the ETFA gene), a protein that mediates transfer of electrons from a series of mitochondrial flavoenzymes to the respiratory chain, was downregulated in HCD-fed zebrafish and in endothelial cells treated with oxidized low-density lipoprotein. Knockdown of ETFα with morpholino antisense oligonucleotides reproduced vascular sprouting defects in zebrafish larvae, while replenishing with exogeneous ETFA mRNA could successfully rescue these defects. ETFA knockdown in endothelial cells reduces cell migration, proliferation, and tube formation in vitro. Finally, knockdown of ETFA in endothelial cells also reduced fatty acid oxidation, oxygen consumption rate, and hypoxia-inducible factor-1α (HIF1α) protein levels. Taken together, we demonstrate that downregulation of ETFα is involved in hypercholesterolemia-induced defective vessel sprouting in zebrafish larvae via inhibition of endothelial proliferation and migration. The molecular mechanism behind this phenomenon is the decrease of HIF1α induced by downregulation of ETFα in endothelial cells. This work suggests that disturbance of ETFα-mediated oxygen homeostasis is one of the mechanisms behind hypercholesterolemia-induced vascular dysfunction.
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Affiliation(s)
- Yi Yan
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou 510000, China
| | - Yingyi Xu
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Xuewen Yang
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Zhonghao Li
- Department of Pathophysiology, Key Lab for Shock and Microcirculation Research of Guangdong Province, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kaiyuan Niu
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Chenxin Liu
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ming Zhao
- Department of Pathophysiology, Key Lab for Shock and Microcirculation Research of Guangdong Province, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qingzhong Xiao
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Key Laboratory of Cardiovascular Diseases at The Second Affiliated Hospital and Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Xinzao Town, Panyu District, Guangzhou, Guangdong 511436, China
| | - Wei Wu
- Department of Pathophysiology, Key Lab for Shock and Microcirculation Research of Guangdong Province, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
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Zhang H, Liu T, Li Q, Zhang X, Zhao H, Zheng Y, Qin F, Zhang Z, Sheng T, Tian Y. Large-scale sensitivity adjustment for Gd-HMME room temperature phosphorescence oxygen sensing. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120490. [PMID: 34688061 DOI: 10.1016/j.saa.2021.120490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
The oxygen sensing enhancement based on room temperature phosphorescence (RTP) of Gd-HMME adjusted by imidazole was studied. The phosphorescence intensity IP0 and the Stern-Volmer equations under different imidazole concentration were obtained, and the physical mechanism of imidazole regulating the oxygen quenching constant KSV was analyzed. It was found that the KSV value increased by ∼46 folds in the range of 12.4(1)-576.1(5) kPa-1, and the large-scale variation of KSV is conducive to the realization of high precision oxygen concentration measurement in a wide range. In addition, the standard deviation σ of continuous measurement results was given, and the limit of detection (LOD) was determined to be 6.6 ppm.
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Affiliation(s)
- Honglin Zhang
- School of Physics, Harbin Institute of Technology, Harbin 150001, China
| | - Ting Liu
- School of Physics, Harbin Institute of Technology, Harbin 150001, China
| | - Qiuhe Li
- School of Physics, Harbin Institute of Technology, Harbin 150001, China
| | - Xiyu Zhang
- School of Physics, Harbin Institute of Technology, Harbin 150001, China
| | - Hua Zhao
- School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Yangdong Zheng
- School of Physics, Harbin Institute of Technology, Harbin 150001, China
| | - Feng Qin
- School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Zhiguo Zhang
- School of Physics, Harbin Institute of Technology, Harbin 150001, China; School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin 150001, China.
| | - Tianqi Sheng
- Zhong Sheng(Shen Zhen)Medical Equipment Science and Technology Co., Ltd, Guangdong 518000, China
| | - Ye Tian
- Division of Cardiology, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China
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Taylor-Kearney LJ, Flashman E. Targeting plant cysteine oxidase activity for improved submergence tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:779-788. [PMID: 34817108 DOI: 10.1111/tpj.15605] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Plant cysteine oxidases (PCOs) are plant O2 -sensing enzymes. They catalyse the O2 -dependent step which initiates the proteasomal degradation of Group VII ethylene response transcription factors (ERF-VIIs) via the N-degron pathway. When submerged, plants experience a reduction in O2 availability; PCO activity therefore decreases and the consequent ERF-VII stabilisation leads to upregulation of hypoxia-responsive genes which enable adaptation to low O2 conditions. Resulting adaptations include entering an anaerobic quiescent state to maintain energy reserves and rapid growth to escape floodwater and allow O2 transport to submerged tissues. Stabilisation of ERF-VIIs has been linked to improved survival post-submergence in Arabidopsis, rice (Oryza sativa) and barley (Hordeum vulgare). Due to climate change and increasing flooding events, there is an interest in manipulating the PCO/ERF-VII interaction as a method of improving yields in flood-intolerant crops. An effective way of achieving this may be through PCO inhibition; however, complete ablation of PCO activity is detrimental to growth and phenotype, likely due to other PCO-mediated roles. Targeting PCOs will therefore require either temporary chemical inhibition or careful engineering of the enzyme structure to manipulate their O2 sensitivity and/or substrate specificity. Sufficient PCO structural and functional information should make this possible, given the potential to engineer site-directed mutagenesis in vivo using CRISPR-mediated base editing. Here, we discuss the knowledge still required for rational manipulation of PCOs to achieve ERF-VII stabilisation without a yield penalty. We also take inspiration from the biocatalysis field to consider how enzyme engineering could be accelerated as a wider strategy to improve plant stress tolerance and productivity.
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Affiliation(s)
| | - Emily Flashman
- Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Erythrocyte transglutaminase-2 combats hypoxia and chronic kidney disease by promoting oxygen delivery and carnitine homeostasis. Cell Metab 2022; 34:299-316.e6. [PMID: 35108516 PMCID: PMC9380699 DOI: 10.1016/j.cmet.2021.12.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 09/29/2021] [Accepted: 12/21/2021] [Indexed: 02/03/2023]
Abstract
Due to lack of nuclei and de novo protein synthesis, post-translational modification (PTM) is imperative for erythrocytes to regulate oxygen (O2) delivery and combat tissue hypoxia. Here, we report that erythrocyte transglutminase-2 (eTG2)-mediated PTM is essential to trigger O2 delivery by promoting bisphosphoglycerate mutase proteostasis and the Rapoport-Luebering glycolytic shunt for adaptation to hypoxia, in healthy humans ascending to high altitude and in two distinct murine models of hypoxia. In a pathological hypoxia model with chronic kidney disease (CKD), eTG2 is critical to combat renal hypoxia-induced reduction of Slc22a5 transcription and OCNT2 protein levels via HIF-1α-PPARα signaling to maintain carnitine homeostasis. Carnitine supplementation is an effective and safe therapeutic approach to counteract hypertension and progression of CKD by enhancing erythrocyte O2 delivery. Altogether, we reveal eTG2 as an erythrocyte protein stabilizer orchestrating O2 delivery and tissue adaptive metabolic reprogramming and identify carnitine-based therapy to mitigate hypoxia and CKD progression.
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Zhou J, Li J, Zhang KY, Liu S, Zhao Q. Phosphorescent iridium(III) complexes as lifetime-based biological sensors for photoluminescence lifetime imaging microscopy. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214334] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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40
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Abstract
Iron is an irreplaceable component of proteins and enzyme systems required for life. This need for iron is a well-characterized evolutionary mechanism for genetic selection. However, there is limited consideration of how iron bioavailability, initially determined by planetary accretion but fluctuating considerably at global scale over geological time frames, has shaped the biosphere. We describe influences of iron on planetary habitability from formation events >4 Gya and initiation of biochemistry from geochemistry through oxygenation of the atmosphere to current host–pathogen dynamics. By determining the iron and transition element distribution within the terrestrial planets, planetary core formation is a constraint on both the crustal composition and the longevity of surface water, hence a planet’s habitability. As such, stellar compositions, combined with metallic core-mass fraction, may be an observable characteristic of exoplanets that relates to their ability to support life. On Earth, the stepwise rise of atmospheric oxygen effectively removed gigatons of soluble ferrous iron from habitats, generating evolutionary pressures. Phagocytic, infectious, and symbiotic behaviors, dating from around the Great Oxygenation Event, refocused iron acquisition onto biotic sources, while eukaryotic multicellularity allows iron recycling within an organism. These developments allow life to more efficiently utilize a scarce but vital nutrient. Initiation of terrestrial life benefitted from the biochemical properties of abundant mantle/crustal iron, but the subsequent loss of iron bioavailability may have been an equally important driver of compensatory diversity. This latter concept may have relevance for the predicted future increase in iron deficiency across the food chain caused by elevated atmospheric CO2.
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Lee H, Shin W, Kim HJ, Kim J. Turn-On Fluorescence Sensing of Oxygen with Dendrimer-Encapsulated Platinum Nanoparticles as Tunable Oxidase Mimics for Spatially Resolved Measurement of Oxygen Gradient in a Human Gut-on-a-Chip. Anal Chem 2021; 93:16123-16132. [PMID: 34807579 DOI: 10.1021/acs.analchem.1c03891] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Turn-on type fluorescence sensing of O2 is considered a promising approach to developing ways to measure O2 in microenvironments with spatially distributed O2 levels. As a class of nanomaterials with a high degree of control over composition and structure, dendrimer-encapsulated nanoparticles (DENs) are promising candidates to mimic biological enzymes. Here, we report a strategy to monitor spatially distributed O2 across a three-dimensional (3D) human intestinal epithelial layer in a gut-on-a-chip in a turn-on fluorescence sensing manner. The strategy is based on the oxidase-mimetic activity of Pt DENs for catalytic oxidation of nonfluorescent Amplex Red to highly fluorescent resorufin in the presence of O2. We synthesized Pt DENs using two different types of dendrimers (i.e., amine-terminated or hydroxyl-terminated generation 6 polyamidoamine (PAMAM) dendrimers) with six different Pt2+/dendrimer ratios (i.e., 55, 200, 220, 550, 880, and 1320). After clarifying the intrinsic oxidase-mimetic activity of Pt DENs, we determined tunable oxidase-mimetic activity of Pt DENs, especially with fine-tuning the ratios of the Pt precursor ions and dendrimers. Particularly, the optimal Pt DENs having a Pt2+/dendrimer ratio of 1320 exhibited an ∼117-fold increase in the oxidase-mimetic activity for catalyzing the aerobic oxidation of Amplex Red to resorufin compared to one having a Pt2+/dendrimer ratio of 200. This study exemplified a simple yet effective approach for spatially resolved imaging of O2 using metal nanoparticle-based oxidase mimics in microphysiological environments like a human gut-on-a-chip.
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Affiliation(s)
- Hyein Lee
- Department of Chemistry, Research Institute for Basic Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Woojung Shin
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Hyun Jung Kim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Joohoon Kim
- Department of Chemistry, Research Institute for Basic Sciences, Kyung Hee University, Seoul 02447, Republic of Korea.,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea
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Abstract
Oxygen (O2) is essential for life and therefore the supply of sufficient O2 to the tissues is a major physiological challenge. In mammals, a deficit of O2 (hypoxia) triggers rapid cardiorespiratory reflexes (e.g. hyperventilation and increased heart output) that within a few seconds increase the uptake of O2 by the lungs and its distribution throughout the body. The prototypical acute O2-sensing organ is the carotid body (CB), which contains sensory glomus cells expressing O2-regulated ion channels. In response to hypoxia, glomus cells depolarize and release transmitters which activate afferent fibers terminating at the brainstem respiratory and autonomic centers. In this review, we summarize the basic properties of CB chemoreceptor cells and the essential role played by their specialized mitochondria in acute O2 sensing and signaling. We focus on recent data supporting a "mitochondria-to-membrane signaling" model of CB chemosensory transduction. The possibility that the differential expression of specific subunit isoforms and enzymes could allow mitochondria to play a generalized adaptive O2-sensing and signaling role in a wide variety of cells is also discussed.
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Affiliation(s)
- José López-Barneo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Fisiología Médica y Biofísica, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Patricia Ortega-Sáenz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Fisiología Médica y Biofísica, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
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Shokoohi-Rad S, Heidarzadeh HR. In Vivo Imaging of Plant Oxygen Levels. PLANT & CELL PHYSIOLOGY 2021; 62:1251-1258. [PMID: 33725087 PMCID: PMC8410434 DOI: 10.1093/pcp/pcab039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/01/2021] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Oxygen is essential for multicellular aerobic life due to its central role in energy metabolism. The availability of oxygen can drop below the level to sustain oxidative phosphorylation when plants are flooded, posing a severe threat to survival. However, under non-stressful conditions, the internal oxygen concentration of most plant tissue is not in equilibrium with the environment, which is attributed to cellular respiration and diffusion constrains imposed by O2 barriers and bulky tissue. This is exemplified by the observations of steep oxygen gradients in roots, fruits, tubers, anthers and meristems. To adapt to a varying availability of oxygen, plants sense O2 via the conditional proteolysis of transcriptional regulators. This mechanism acts to switch oxidative metabolism to anaerobic fermentation, but it was also shown to play a role in plant development and pathogen defense. To investigate how dynamic and spatial distribution of O2 impacts on these processes, accurate mapping of its concentration in plants is essential. Physical oxygen sensors have been employed for decades to profile internal oxygen concentrations in plants, while genetically encoded oxygen biosensors have only recently started to see use. Driven by the critical role of hypoxia in human pathology and development, several novel oxygen-sensing devices have also been characterized in cell lines and animal model organisms. This review aims to provide an overview of available oxygen biosensors and to discuss their potential application to image oxygen levels in plants.
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Affiliation(s)
- Saeed Shokoohi-Rad
- Eye Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Nishikawa K, Seno S, Yoshihara T, Narazaki A, Sugiura Y, Shimizu R, Kikuta J, Sakaguchi R, Suzuki N, Takeda N, Semba H, Yamamoto M, Okuzaki D, Motooka D, Kobayashi Y, Suematsu M, Koseki H, Matsuda H, Yamamoto M, Tobita S, Mori Y, Ishii M. Osteoclasts adapt to physioxia perturbation through DNA demethylation. EMBO Rep 2021; 22:e53035. [PMID: 34661337 PMCID: PMC8647016 DOI: 10.15252/embr.202153035] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
Oxygen plays an important role in diverse biological processes. However, since quantitation of the partial pressure of cellular oxygen in vivo is challenging, the extent of oxygen perturbation in situ and its cellular response remains underexplored. Using two‐photon phosphorescence lifetime imaging microscopy, we determine the physiological range of oxygen tension in osteoclasts of live mice. We find that oxygen tension ranges from 17.4 to 36.4 mmHg, under hypoxic and normoxic conditions, respectively. Physiological normoxia thus corresponds to 5% and hypoxia to 2% oxygen in osteoclasts. Hypoxia in this range severely limits osteoclastogenesis, independent of energy metabolism and hypoxia‐inducible factor activity. We observe that hypoxia decreases ten‐eleven translocation (TET) activity. Tet2/3 cooperatively induces Prdm1 expression via oxygen‐dependent DNA demethylation, which in turn activates NFATc1 required for osteoclastogenesis. Taken together, our results reveal that TET enzymes, acting as functional oxygen sensors, regulate osteoclastogenesis within the physiological range of oxygen tension, thus opening new avenues for research on in vivo response to oxygen perturbation.
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Affiliation(s)
- Keizo Nishikawa
- Laboratory of Cell Biology and Metabolic Biochemistry, Department of Medical Life Systems, Graduate School of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan.,Department of Immunology and Cell Biology, WPI-Immunology Frontier Research Center, Osaka University, Suita, Japan.,Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Shigeto Seno
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Toshitada Yoshihara
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Japan
| | - Ayako Narazaki
- Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University, Tokyo, Japan
| | - Reito Shimizu
- Laboratory of Cell Biology and Metabolic Biochemistry, Department of Medical Life Systems, Graduate School of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Junichi Kikuta
- Department of Immunology and Cell Biology, WPI-Immunology Frontier Research Center, Osaka University, Suita, Japan.,Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan.,Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Reiko Sakaguchi
- WPI-Research Initiative-Institute for Integrated Cell-Material Science, Kyoto University, Kyoto, Japan.,Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Norio Suzuki
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Norihiko Takeda
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Semba
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Cardiovascular Medicine/Basic Research, The Cardiovascular Institute, Tokyo, Japan
| | - Masamichi Yamamoto
- Department of Artificial Kidneys, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Daisuke Okuzaki
- Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yasuhiro Kobayashi
- Institute for Oral Science, Matsumoto Dental University, Shiojiri, Japan
| | | | - Haruhiko Koseki
- Developmental Genetics Group, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Hideo Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Seiji Tobita
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Japan
| | - Yasuo Mori
- WPI-Research Initiative-Institute for Integrated Cell-Material Science, Kyoto University, Kyoto, Japan.,Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Masaru Ishii
- Department of Immunology and Cell Biology, WPI-Immunology Frontier Research Center, Osaka University, Suita, Japan.,Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan.,Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
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Zhang J, Li C, Zhang Y. Geological evidences and mechanisms for oceanic anoxic events during the Early Paleozoic. CHINESE SCIENCE BULLETIN-CHINESE 2021. [DOI: 10.1360/tb-2021-0535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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The PhoPR two-component system responds to oxygen deficiency and regulates the pathways for energy supply in Corynebacterium glutamicum. World J Microbiol Biotechnol 2021; 37:160. [PMID: 34436681 DOI: 10.1007/s11274-021-03131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
The PhoPR two-component system, a highly conserved system in corynebacteria and mycobacteria, is involved in the cellular response to environmental stress. When analysing the transcriptomic data of Corynebacterium glutamicum strains under different dissolved oxygen (DO) levels, PhoPR was found to be the most responsive two-component system to DO changes. Here, we systematically investigated the expression of PhoPR in response to different DO levels and its impact on genes related to global regulation and energy metabolism. Using Green fluorescent protein as a reporter, we confirmed that PhoPR was significantly upregulated upon decrease of DO. Through real-time quantitative PCR and electrophoretic mobility shift assay, we found that the effector protein PhoP directly activated glxR (encoding a global regulator), pfk and gapA (encoding the glycolytic enzymes) and ctaD (encoding cytochrome c in the electron transport chain), while downregulated aceE and gltA (encoding the TCA cycle enzymes). Overexpression of phoP or phoR resulted in a decreased intracellular NAD+/NADH ratio and increased intracellular ATP level, consistent with the gene expression changes regulated by PhoP. These results reveal the PhoPR system respond to oxygen deficiency and is responsible for the regulation of pathways involved in the sustainability of the energy levels required under low oxygen conditions. Our findings in this study not only provide new insights into the adaptation pathways of C. glutamicum in response to low oxygen conditions but also identify new possible genetic targets for the construction of the new cell factories aimed toward industrial applications.
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Archacka K, Grabowska I, Mierzejewski B, Graffstein J, Górzyńska A, Krawczyk M, Różycka AM, Kalaszczyńska I, Muras G, Stremińska W, Jańczyk-Ilach K, Walczak P, Janowski M, Ciemerych MA, Brzoska E. Hypoxia preconditioned bone marrow-derived mesenchymal stromal/stem cells enhance myoblast fusion and skeletal muscle regeneration. Stem Cell Res Ther 2021; 12:448. [PMID: 34372911 PMCID: PMC8351116 DOI: 10.1186/s13287-021-02530-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/08/2021] [Indexed: 12/19/2022] Open
Abstract
Background The skeletal muscle reconstruction occurs thanks to unipotent stem cells, i.e., satellite cells. The satellite cells remain quiescent and localized between myofiber sarcolemma and basal lamina. They are activated in response to muscle injury, proliferate, differentiate into myoblasts, and recreate myofibers. The stem and progenitor cells support skeletal muscle regeneration, which could be disturbed by extensive damage, sarcopenia, cachexia, or genetic diseases like dystrophy. Many lines of evidence showed that the level of oxygen regulates the course of cell proliferation and differentiation. Methods In the present study, we analyzed hypoxia impact on human and pig bone marrow-derived mesenchymal stromal cell (MSC) and mouse myoblast proliferation, differentiation, and fusion. Moreover, the influence of the transplantation of human bone marrow-derived MSCs cultured under hypoxic conditions on skeletal muscle regeneration was studied. Results We showed that bone marrow-derived MSCs increased VEGF expression and improved myogenesis under hypoxic conditions in vitro. Transplantation of hypoxia preconditioned bone marrow-derived MSCs into injured muscles resulted in the improved cell engraftment and formation of new vessels. Conclusions We suggested that SDF-1 and VEGF secreted by hypoxia preconditioned bone marrow-derived MSCs played an essential role in cell engraftment and angiogenesis. Importantly, hypoxia preconditioned bone marrow-derived MSCs more efficiently engrafted injured muscles; however, they did not undergo myogenic differentiation. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02530-3.
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Affiliation(s)
- Karolina Archacka
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Iwona Grabowska
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Bartosz Mierzejewski
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Joanna Graffstein
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Alicja Górzyńska
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Marta Krawczyk
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Anna M Różycka
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Ilona Kalaszczyńska
- Department of Histology and Embryology, Medical University of Warsaw, 02-004, Warsaw, Poland.,Laboratory for Cell Research and Application, Medical University of Warsaw, 02-097, Warsaw, Poland
| | - Gabriela Muras
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Władysława Stremińska
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Katarzyna Jańczyk-Ilach
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Piotr Walczak
- Department of Pathophysiology, Faculty of Medical Sciences, University of Warmia and Mazury, Warszawska 30 St, 10-082, Olsztyn, Poland.,Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, the Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mirosław Janowski
- Center for Advanced Imaging Research, Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland, Baltimore, MD, 21201, USA.,NeuroRepair Department, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5 St, 02-106, Warsaw, Poland
| | - Maria A Ciemerych
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Edyta Brzoska
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland.
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48
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Gunawardana DM, Heathcote KC, Flashman E. Emerging roles for thiol dioxygenases as oxygen sensors. FEBS J 2021; 289:5426-5439. [PMID: 34346181 DOI: 10.1111/febs.16147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 08/03/2021] [Indexed: 12/22/2022]
Abstract
Cysteine dioxygenases, 3-mercaptopropionate dioxygenases and mercaptosuccinate dioxygenases are all thiol dioxygenases (TDOs) that catalyse oxidation of thiol molecules to sulphinates. They are Fe(II)-dependent dioxygenases with a cupin fold that supports a 3xHis metal-coordinating triad at the active site. They also have other, broadly common features including arginine residues involved in substrate carboxylate binding and a conserved trio of residues at the active site featuring a tyrosine important in substrate binding catalysis. Recently, N-terminal cysteinyl dioxygenase enzymes (NCOs) have been identified in plants (plant cysteine oxidases, PCOs), while human 2-aminoethanethiol dioxygenase (ADO) has been shown to act as both an NCO and a small molecule TDO. Although the cupin fold and 3xHis Fe(II)-binding triad seen in the small molecule TDOs are conserved in NCOs, other active site features and aspects of the overall protein architecture are quite different. Furthermore, the PCOs and ADO appear to act as biological O2 sensors, as shown by kinetic analyses and hypoxic regulation of the stability of their biological targets (N-terminal cysteine oxidation triggers protein degradation via the N-degron pathway). Here, we discuss the emergence of these two subclasses of TDO including structural features that could dictate their ability to bind small molecule or polypeptide substrates. These structural features may also underpin the O2 -sensing capability of the NCOs. Understanding how these enzymes interact with their substrates, including O2 , could reveal strategies to manipulate their activity, relevant to hypoxic disease states and plant adaptive responses to flooding.
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Pral LP, Fachi JL, Corrêa RO, Colonna M, Vinolo MAR. Hypoxia and HIF-1 as key regulators of gut microbiota and host interactions. Trends Immunol 2021; 42:604-621. [PMID: 34171295 DOI: 10.1016/j.it.2021.05.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
Oxygen (O2) availability is a key factor regulating microbiota composition and the homeostatic function of cells in the intestinal mucosa of vertebrates. Microbiota-derived metabolites increase O2 consumption by intestinal epithelial cells (IECs), reducing its availability in the gut and leading to hypoxia. This physiological hypoxia activates cellular hypoxic sensors that adapt the metabolism and function of IECs and mucosa-resident cells, such as type-3 innate lymphoid cells (ILC3s). In this review, we discuss recent evidence suggesting that the intricate and multidirectional interactions among the microbiota, hypoxia/hypoxic sensors, and mammalian host cells (IECs and ILC3s) determine how the intestinal barrier and host-microbiota-pathogens connections are molded. Understanding these interactions might provide new treatment possibilities for dysbiosis, as well as certain inflammatory and infectious diseases.
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Affiliation(s)
- Laís P Pral
- Laboratory of Immunoinflammation, Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - José L Fachi
- Laboratory of Immunoinflammation, Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Renan O Corrêa
- Laboratory of Immunoinflammation, Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Marco A R Vinolo
- Laboratory of Immunoinflammation, Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil; Experimental Medicine Research Cluster, Campinas, Brazil; Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, Brazil.
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50
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Carroll C, Engström N, Nilsson PF, Haxen ER, Mohlin S, Berg P, Glud RN, Hammarlund EU. Hypoxia Generated by Avian Embryo Growth Induces the HIF-α Response and Critical Vascularization. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.675800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cancer research has transformed our view on cellular mechanisms for oxygen sensing. It has been documented that these mechanisms are important for maintaining animal tissues and life in environments where oxygen (O2) concentrations fluctuate. In adult animals, oxygen sensing is governed by the Hypoxia Inducible Factors (HIFs) that are stabilized at low oxygen concentrations (hypoxia). However, the importance of hypoxia itself during development and for the onset of HIF-driven oxygen sensing remains poorly explored. Cellular responses to hypoxia associates with cell immaturity (stemness) and proper tissue and organ development. During mammalian development, the initial uterine environment is hypoxic. The oxygenation status during avian embryogenesis is more complex since O2 continuously equilibrates across the porous eggshell. Here, we investigate HIF dynamics and use microelectrodes to determine O2 concentrations within the egg and the embryo during the first four days of development. To determine the increased O2 consumption rates, we also obtain the O2 transport coefficient (DO2) of eggshell and associated inner and outer shell membranes, both directly (using microelectrodes in ovo for the first time) and indirectly (using water evaporation at 37.5°C for the first time). Our results demonstrate a distinct hypoxic phase (<5% O2) between day 1 and 2, concurring with the onset of HIF-α expression. This phase of hypoxia is demonstrably necessary for proper vascularization and survival. Our indirectly determined DO2 values are about 30% higher than those determined directly. A comparison with previously reported values indicates that this discrepancy may be real, reflecting that water vapor and O2 may be transported through the eggshell at different rates. Based on our obtained DO2 values, we demonstrate that increased O2 consumption of the growing embryo appears to generate the phase of hypoxia, which is also facilitated by the initially small gas cell and low membrane permeability. We infer that the phase of in ovo hypoxia facilitates correct avian development. These results support the view that hypoxic conditions, in which the animal clade evolved, remain functionally important during animal development. The study highlights that insights from the cancer field pertaining to the cellular capacities by which both somatic and cancer cells register and respond to fluctuations in O2 concentrations can broadly inform our exploration of animal development and success.
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