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Lecomte JTJ, Johnson EA. The globins of cyanobacteria and green algae: An update. Adv Microb Physiol 2024; 85:97-144. [PMID: 39059824 DOI: 10.1016/bs.ampbs.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
The globin superfamily of proteins is ancient and diverse. Regular assessments based on the increasing number of available genome sequences have elaborated on a complex evolutionary history. In this review, we present a summary of a decade of advances in characterising the globins of cyanobacteria and green algae. The focus is on haem-containing globins with an emphasis on recent experimental developments, which reinforce links to nitrogen metabolism and nitrosative stress response in addition to dioxygen management. Mention is made of globins that do not bind haem to provide an encompassing view of the superfamily and perspective on the field. It is reiterated that an effort toward phenotypical and in-vivo characterisation is needed to elucidate the many roles that these versatile proteins fulfil in oxygenic photosynthetic microbes. It is also proposed that globins from oxygenic organisms are promising proteins for applications in the biotechnology arena.
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Affiliation(s)
- Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States.
| | - Eric A Johnson
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
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2
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Reeder BJ. Insights into the function of cytoglobin. Biochem Soc Trans 2023; 51:1907-1919. [PMID: 37721133 PMCID: PMC10657185 DOI: 10.1042/bst20230081] [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: 07/31/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
Since its discovery in 2001, the function of cytoglobin has remained elusive. Through extensive in vitro and in vivo research, a range of potential physiological and pathological mechanisms has emerged for this multifunctional member of the hemoglobin family. Currently, over 200 research publications have examined different aspects of cytoglobin structure, redox chemistry and potential roles in cell signalling pathways. This research is wide ranging, but common themes have emerged throughout the research. This review examines the current structural, biochemical and in vivo knowledge of cytoglobin published over the past two decades. Radical scavenging, nitric oxide homeostasis, lipid binding and oxidation and the role of an intramolecular disulfide bond on the redox chemistry are examined, together with aspects and roles for Cygb in cancer progression and liver fibrosis.
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Affiliation(s)
- Brandon J Reeder
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, U.K
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3
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GLB-3: A resilient, cysteine-rich, membrane-tethered globin expressed in the reproductive and nervous system of Caenorhabditis elegans. J Inorg Biochem 2023; 238:112063. [PMID: 36370505 DOI: 10.1016/j.jinorgbio.2022.112063] [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: 09/14/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/05/2022]
Abstract
The popular genetic model organism Caenorhabditis elegans (C. elegans) encodes 34 globins, whereby the few that are well-characterized show divergent properties besides the typical oxygen carrier function. Here, we present a biophysical characterization and expression analysis of C. elegans globin-3 (GLB-3). GLB-3 is predicted to exist in two isoforms and is expressed in the reproductive and nervous system. Knockout of this globin causes a 99% reduction in fertility and reduced motility. Spectroscopic analysis reveals that GLB-3 exists as a bis-histidyl-ligated low-spin form in both the ferrous and ferric heme form. A function in binding of diatomic gases is excluded on the basis of the slow CO-binding kinetics. Unlike other globins, GLB-3 is also not capable of reacting with H2O2, H2S, and nitrite. Intriguingly, not only does GLB-3 contain a high number of cysteine residues, it is also highly stable under harsh conditions (pH = 2 and high concentrations of H2O2). The resilience diminishes when the N- and C-terminal extensions are removed. Redox potentiometric measurements reveal a slightly positive redox potential (+8 ± 19 mV vs. SHE), suggesting that the heme iron may be able to oxidize cysteines. Electron paramagnetic resonance shows that formation of an intramolecular disulphide bridge, involving Cys70, affects the heme-pocket region. The results suggest an involvement of the globin in (cysteine) redox chemistry.
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4
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Farhana R, Lei R, Pham K, Derrien V, Cedeño J, Rodriquez V, Bernad S, Lima FF, Miksovska J. Globin X: A highly stable intrinsically hexacoordinate globin. J Inorg Biochem 2022; 236:111976. [PMID: 36058051 DOI: 10.1016/j.jinorgbio.2022.111976] [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: 06/29/2022] [Revised: 08/10/2022] [Accepted: 08/18/2022] [Indexed: 12/15/2022]
Abstract
Several novel members of the vertebrate globin family were recently discovered with unique structural features that are not found in traditional penta-coordinate globins. Here we combine structural tools to better understand and recognize molecular determinants that contribute to the stability of hexacoordinate globin X (GbX) from Danio rerio (zebrafish). pH-induced unfolding data indicates increased stability of GbX with pHmid of 1.9 ± 0.1 for met GbXWT, 2.4 ± 0.1 for met GbXC65A, and 3.4 ± 0.1 for GbXH90V. These results are in good agreement with GbX unfolding experiments using GuHCl, where a ΔGunf 13.8 ± 2.5 kcal mol-1 and 16.3 ± 2.6 kcal mol-1 are observed for metGbXWT, and metGbXC65A constructs, respectively, and diminished stability is measured for GbXH90V, ΔGunf = 9.5 ± 3.6 kcal mol-1. The metGbXWT and metGbXC65A also exhibit high thermal stability (melting points of 118 °C and 107 °C, respectively). Native ion mobility - mass spectrometry (IM-MS) experiments showed a narrow charge state distribution (9-12+) characteristics of a native, structured protein; a single mobility band was observed for the native states. Collision induced unfolding IM-MS experiments showed a two-state transition, in good agreement with the solution studies. GbXWT retains the heme over a wide range of charge states, suggesting strong interactions between the prosthetic group and the apoprotein. The above results indicate that in addition to the disulfide bond and the heme iron hexa-coordination, other structural determinants enhance stability of this protein.
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Affiliation(s)
- Rifat Farhana
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Ruipeng Lei
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Khoa Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Valerie Derrien
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Jonathan Cedeño
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Veronica Rodriquez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Sophie Bernad
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Francisco Fernandez Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America; Biomedical Science Institute, Florida International University, Miami, FL, United States of America
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America; Biomedical Science Institute, Florida International University, Miami, FL, United States of America.
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Hoffmann FG, Storz JF, Kuraku S, Vandewege MW, Opazo JC. Whole-Genome Duplications and the Diversification of the Globin-X Genes of Vertebrates. Genome Biol Evol 2021; 13:evab205. [PMID: 34480557 PMCID: PMC8525914 DOI: 10.1093/gbe/evab205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 12/28/2022] Open
Abstract
Globin-X (GbX) is an enigmatic member of the vertebrate globin gene family with a wide phyletic distribution that spans protostomes and deuterostomes. Unlike canonical globins such as hemoglobins and myoglobins, functional data suggest that GbX does not have a primary respiratory function. Instead, evidence suggests that the monomeric, membrane-bound GbX may play a role in cellular signaling or protection against the oxidation of membrane lipids. Recently released genomes from key vertebrates provide an excellent opportunity to address questions about the early stages of the evolution of GbX in vertebrates. We integrate bioinformatics, synteny, and phylogenetic analyses to characterize the diversity of GbX genes in nonteleost ray-finned fishes, resolve relationships between the GbX genes of cartilaginous fish and bony vertebrates, and demonstrate that the GbX genes of cyclostomes and gnathostomes derive from independent duplications. Our study highlights the role that whole-genome duplications (WGDs) have played in expanding the repertoire of genes in vertebrate genomes. Our results indicate that GbX paralogs have a remarkably high rate of retention following WGDs relative to other globin genes and provide an evolutionary framework for interpreting results of experiments that examine functional properties of GbX and patterns of tissue-specific expression. By identifying GbX paralogs that are products of different WGDs, our results can guide the design of experimental work to explore whether gene duplicates that originate via WGDs have evolved novel functional properties or expression profiles relative to singleton or tandemly duplicated copies of GbX.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Juan C Opazo
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile
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6
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Razin SV, Ioudinkova ES, Kantidze OL, Iarovaia OV. Co-Regulated Genes and Gene Clusters. Genes (Basel) 2021; 12:907. [PMID: 34208174 PMCID: PMC8230824 DOI: 10.3390/genes12060907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/27/2022] Open
Abstract
There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.
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Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Elena S. Ioudinkova
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Omar L. Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Olga V. Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
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7
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Hammerschmid D, Germani F, Drusin SI, Fagnen C, Schuster CD, Hoogewijs D, Marti MA, Venien-Bryan C, Moens L, Van Doorslaer S, Sobott F, Dewilde S. Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens. Comput Struct Biotechnol J 2021; 19:1874-1888. [PMID: 33995893 PMCID: PMC8076648 DOI: 10.1016/j.csbj.2021.03.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Globin-coupled sensors (GCS) usually consist of three domains: a sensor/globin, a linker, and a transmitter domain. The globin domain (GD), activated by ligand binding and/or redox change, induces an intramolecular signal transduction resulting in a response of the transmitter domain. Depending on the nature of the transmitter domain, GCSs can have different activities and functions, including adenylate and di-guanylate cyclase, histidine kinase activity, aerotaxis and/or oxygen sensing function. The gram-negative delta-proteobacterium Geobacter sulfurreducens expresses a protein with a GD covalently linked to a four transmembrane domain, classified, by sequence similarity, as GCS (GsGCS). While its GD is fully characterized, not so its transmembrane domain, which is rarely found in the globin superfamily. In the present work, GsGCS was characterized spectroscopically and by native ion mobility-mass spectrometry in combination with cryo-electron microscopy. Although lacking high resolution, the oligomeric state and the electron density map were valuable for further rational modeling of the full-length GsGCS structure. This model demonstrates that GsGCS forms a transmembrane domain-driven tetramer with minimal contact between the GDs and with the heme groups oriented outward. This organization makes an intramolecular signal transduction less likely. Our results, including the auto-oxidation rate and redox potential, suggest a potential role for GsGCS as redox sensor or in a membrane-bound e-/H+ transfer. As such, GsGCS might act as a player in connecting energy production to the oxidation of organic compounds and metal reduction. Database searches indicate that GDs linked to a four or seven helices transmembrane domain occur more frequently than expected.
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Key Words
- AfGcHK, Anaeromyxobacter sp. Fw109-5 GcHK
- AsFRMF, Ascaris suum FRMF-amide receptor
- AvGReg, Azotobacter vinilandii Greg
- BpGReg, Bordetella pertussis Greg
- BsHemAT, Bacillus subtilis HemAT
- CCS, collision cross section
- CIU, collision-induced unfolding
- CMC, critical micelle concentration
- CV, cyclic voltammetry
- CeGLB26, Caenorhabditis elegans globin 26
- CeGLB33, Caenorhabditis elegans globin 33
- CeGLB6, Caenorhabditis elegans globin 6
- DDM, n-dodecyl-β-d-maltoside
- DPV, differential pulse voltammetry
- EcDosC, Escherichia coli Dos with DGC activity
- FMRF, H-Phe-Met-Arg-Phe-NH2 neuropeptide
- GCS, globin-coupled sensor
- GD, globin domain
- GGDEF, Gly-Gly-Asp-Glu-Phe motive
- Gb, globin
- Geobacter sulfurreducens
- GintHb, hemoglobin from Gasterophilus intestinalis
- Globin-coupled sensor
- GsGCS, Geobacter sulfurreducens GCS
- GsGCS162, GD of GsGCS
- IM-MS, ion mobility-mass spectrometry
- LmHemAC, Leishmania major HemAC
- MaPgb, Methanosarcina acetivorans protoglobin
- MtTrHbO, Mycobacterium tuberculosis truncated hemoglobin O
- NH4OAc, ammonium acetate
- OG, n-octyl-β-d-glucopyranoside
- PDE, phosphodiesterase
- PcMb, Physether catodon myoglobin
- PccGCS, Pectobacterium carotivorum GCS
- PsiE, phosphate-starvation-inducible E
- RR, resonance Raman
- SCE, saturated calomel electrode
- SHE, standard hydrogen electrode
- SaktrHb, Streptomyces avermitilis truncated hemoglobin-antibiotic monooxygenase
- SwMb, myoglobin from sperm whale
- TD, Transmitter domain
- TmD, Transmembrane domain
- Transmembrane domain
- Transmembrane-coupled globins
- mNgb, mouse neuroglobin
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Affiliation(s)
- Dietmar Hammerschmid
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Francesca Germani
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Salvador I. Drusin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Charline Fagnen
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Claudio D. Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - David Hoogewijs
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, Switzerland
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Catherine Venien-Bryan
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Luc Moens
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sabine Van Doorslaer
- Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Sylvia Dewilde
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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Song S, Starunov V, Bailly X, Ruta C, Kerner P, Cornelissen AJM, Balavoine G. Globins in the marine annelid Platynereis dumerilii shed new light on hemoglobin evolution in bilaterians. BMC Evol Biol 2020; 20:165. [PMID: 33371890 PMCID: PMC7771090 DOI: 10.1186/s12862-020-01714-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/28/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND How vascular systems and their respiratory pigments evolved is still debated. While many animals present a vascular system, hemoglobin exists as a blood pigment only in a few groups (vertebrates, annelids, a few arthropod and mollusk species). Hemoglobins are formed of globin sub-units, belonging to multigene families, in various multimeric assemblages. It was so far unclear whether hemoglobin families from different bilaterian groups had a common origin. RESULTS To unravel globin evolution in bilaterians, we studied the marine annelid Platynereis dumerilii, a species with a slow evolving genome. Platynereis exhibits a closed vascular system filled with extracellular hemoglobin. Platynereis genome and transcriptomes reveal a family of 19 globins, nine of which are predicted to be extracellular. Extracellular globins are produced by specialized cells lining the vessels of the segmental appendages of the worm, serving as gills, and thus likely participate in the assembly of a previously characterized annelid-specific giant hemoglobin. Extracellular globin mRNAs are absent in smaller juveniles, accumulate considerably in growing and more active worms and peak in swarming adults, as the need for O2 culminates. Next, we conducted a metazoan-wide phylogenetic analysis of globins using data from complete genomes. We establish that five globin genes (stem globins) were present in the last common ancestor of bilaterians. Based on these results, we propose a new nomenclature of globins, with five clades. All five ancestral stem-globin clades are retained in some spiralians, while some clades disappeared early in deuterostome and ecdysozoan evolution. All known bilaterian blood globin families are grouped in a single clade (clade I) together with intracellular globins of bilaterians devoid of red blood. CONCLUSIONS We uncover a complex "pre-blood" evolution of globins, with an early gene radiation in ancestral bilaterians. Circulating hemoglobins in various bilaterian groups evolved convergently, presumably in correlation with animal size and activity. However, all hemoglobins derive from a clade I globin, or cytoglobin, probably involved in intracellular O2 transit and regulation. The annelid Platynereis is remarkable in having a large family of extracellular blood globins, while retaining all clades of ancestral bilaterian globins.
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Affiliation(s)
- Solène Song
- Institut Jacques Monod, Université de Paris / CNRS, UMR7592, Paris, France
- Laboratoire Matière et Systèmes Complexes, Université de Paris / CNRS, UMR7057, Paris, France
| | - Viktor Starunov
- Laboratory of Evolutionary Morphology, Zoological Institute, Russian Academy of Sciences, Universitetskaja nab. 1, 199034, Saint Petersburg, Russia
| | - Xavier Bailly
- Laboratoire des Modèles Marins Multicellulaires, Station Biologique de Roscoff, Sorbonne Université / CNRS, FR2424, Roscoff, France
| | - Christine Ruta
- Laboratory of Integrative Biology of Marine Organisms, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Pierre Kerner
- Institut Jacques Monod, Université de Paris / CNRS, UMR7592, Paris, France
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Giordano D, Corti P, Coppola D, Altomonte G, Xue J, Russo R, di Prisco G, Verde C. Regulation of globin expression in Antarctic fish under thermal and hypoxic stress. Mar Genomics 2020; 57:100831. [PMID: 33250437 DOI: 10.1016/j.margen.2020.100831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 01/27/2023]
Abstract
In the freezing waters of the Southern Ocean, Antarctic teleost fish, the Notothenioidei, have developed unique adaptations to cope with cold, including, at the extreme, the loss of hemoglobin in icefish. As a consequence, icefish are thought to be the most vulnerable of the Antarctic fish species to ongoing ocean warming. Some icefish also fail to express myoglobin but all appear to retain neuroglobin, cytoglobin-1, cytoglobin-2, and globin-X. Despite the lack of the inducible heat shock response, Antarctic notothenioid fish are endowed with physiological plasticity to partially compensate for environmental changes, as shown by numerous physiological and genomic/transcriptomic studies over the last decade. However, the regulatory mechanisms that determine temperature/oxygen-induced changes in gene expression remain largely unexplored in these species. Proteins such as globins are susceptible to environmental changes in oxygen levels and temperature, thus playing important roles in mediating Antarctic fish adaptations. In this study, we sequenced the full-length transcripts of myoglobin, neuroglobin, cytoglobin-1, cytoglobin-2, and globin-X from the Antarctic red-blooded notothenioid Trematomus bernacchii and the white-blooded icefish Chionodraco hamatus and evaluated transcripts levels after exposure to high temperature and low oxygen levels. Basal levels of globins are similar in the two species and both stressors affect the expression of Antarctic fish globins in brain, retina and gills. Temperature up-regulates globin expression more effectively in white-blooded than in red-blooded fish while hypoxia strongly up-regulates globins in red-blooded fish, particularly in the gills. These results suggest globins function as regulators of temperature and hypoxia tolerance. This study provides the first insights into globin transcriptional changes in Antarctic fish.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Napoli 80121, Italy.
| | - Paola Corti
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Daniela Coppola
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Napoli 80121, Italy
| | - Giovanna Altomonte
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Jianmin Xue
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Roberta Russo
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Napoli 80121, Italy
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10
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The rise and fall of globins in the amphibia. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 37:100759. [PMID: 33202310 DOI: 10.1016/j.cbd.2020.100759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 12/28/2022]
Abstract
The globin gene repertoire of gnathostome vertebrates is dictated by differential retention and loss of nine paralogous genes: androglobin, neuroglobin, globin X, cytoglobin, globin Y, myoglobin, globin E, and the α- and β-globins. We report the globin gene repertoire of three orders of modern amphibians: Anura, Caudata, and Gymnophiona. Combining phylogenetic and conserved synteny analysis, we show that myoglobin and globin E were lost only in the Batrachia clade, but retained in Gymnophiona. The major amphibian groups also retained different paralogous copies of globin X. None of the amphibian presented αD-globin gene. Nevertheless, two clades of β-globins are present in all amphibians, indicating that the amphibian ancestor possessed two paralogous proto β-globins. We also show that orthologs of the gene coding for the monomeric hemoglobin found in the heart of Rana catesbeiana are present in Neobatrachia and Pelobatoidea species we analyzed. We suggest that these genes might perform myoglobin- and globin E-related functions. We conclude that the repertoire of globin genes in amphibians is dictated by both retention and loss of the paralogous genes cited above and the rise of a new globin gene through co-option of an α-globin, possibly facilitated by a prior event of transposition.
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11
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Lessons from the post-genomic era: Globin diversity beyond oxygen binding and transport. Redox Biol 2020; 37:101687. [PMID: 32863222 PMCID: PMC7475203 DOI: 10.1016/j.redox.2020.101687] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Vertebrate hemoglobin (Hb) and myoglobin (Mb) were among the first proteins whose structures and sequences were determined over 50 years ago. In the subsequent pregenomic period, numerous related proteins came to light in plants, invertebrates and bacteria, that shared the myoglobin fold, a signature sequence motif characteristic of a 3-on-3 α-helical sandwich. Concomitantly, eukaryote and bacterial globins with a truncated 2-on-2 α-helical fold were discovered. Genomic information over the last 20 years has dramatically expanded the list of known globins, demonstrating their existence in a limited number of archaeal genomes, a majority of bacterial genomes and an overwhelming majority of eukaryote genomes. In vertebrates, 6 additional globin types were identified, namely neuroglobin (Ngb), cytoglobin (Cygb), globin E (GbE), globin X (GbX), globin Y (GbY) and androglobin (Adgb). Furthermore, functions beyond the familiar oxygen transport and storage have been discovered within the vertebrate globin family, including NO metabolism, peroxidase activity, scavenging of free radicals, and signaling functions. The extension of the knowledge on globin functions suggests that the original roles of bacterial globins must have been enzymatic, involved in defense against NO toxicity, and perhaps also as sensors of O2, regulating taxis away or towards high O2 concentrations. In this review, we aimed to discuss the evolution and remarkable functional diversity of vertebrate globins with particular focus on the variety of non-canonical expression sites of mammalian globins and their according impressive variability of atypical functions.
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12
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Prothmann A, Hoffmann FG, Opazo JC, Herbener P, Storz JF, Burmester T, Hankeln T. The Globin Gene Family in Arthropods: Evolution and Functional Diversity. Front Genet 2020; 11:858. [PMID: 32922435 PMCID: PMC7457136 DOI: 10.3389/fgene.2020.00858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/14/2020] [Indexed: 01/23/2023] Open
Abstract
Globins are small heme-proteins that reversibly bind oxygen. Their most prominent roles in vertebrates are the transport and storage of O2 for oxidative energy metabolism, but recent research has suggested alternative, non-respiratory globin functions. In the species-rich and ecologically highly diverse taxon of arthropods, the copper-containing hemocyanin is considered the main respiratory protein. However, recent studies have suggested the presence of globin genes and their proteins in arthropod taxa, including model species like Drosophila. To systematically assess the taxonomic distribution, evolution and diversity of globins in arthropods, we systematically searched transcriptome and genome sequence data and found a conserved, widespread occurrence of three globin classes in arthropods: hemoglobin-like (HbL), globin X (GbX), and globin X-like (GbXL) protein lineages. These globin types were previously identified in protostome and deuterostome animals including vertebrates, suggesting their early ancestry in Metazoa. The HbL genes show multiple, lineage-specific gene duplications in all major arthropod clades. Some HbL genes (e.g., Glob2 and 3 of Drosophila) display particularly fast substitution rates, possibly indicating the evolution of novel functions, e.g., in spermatogenesis. In contrast, arthropod GbX and GbXL globin genes show high evolutionary stability: GbXL is represented by a single-copy gene in all arthropod groups except Brachycera, and representatives of the GbX clade are present in all examined taxa except holometabolan insects. GbX and GbXL both show a brain-specific expression. Most arthropod GbX and GbXL proteins, but also some HbL variants, include sequence motifs indicative of potential N-terminal acylation (i.e., N-myristoylation, 3C-palmitoylation). All arthropods except for the brachyceran Diptera harbor at least one such potentially acylated globin copy, confirming the hypothesis of an essential, conserved globin function associated with the cell membrane. In contrast to other animals, the fourth ancient globin lineage, represented by neuroglobin, appears to be absent in arthropods, and the putative arthropod orthologs of the fifth metazoan globin lineage, androglobin, lack a recognizable globin domain. Thus, the remarkable evolutionary stability of some globin variants is contrasted by occasional dynamic gene multiplication or even loss of otherwise strongly conserved globin lineages in arthropod phylogeny.
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Affiliation(s)
- Andreas Prothmann
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, University of Mainz, Mainz, Germany
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS, United States.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS, United States
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Valdivia, Chile
| | - Peter Herbener
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, University of Mainz, Mainz, Germany
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, University of Mainz, Mainz, Germany
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13
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Daane JM, Giordano D, Coppola D, di Prisco G, Detrich HW, Verde C. Adaptations to environmental change: Globin superfamily evolution in Antarctic fishes. Mar Genomics 2019; 49:100724. [PMID: 31735579 DOI: 10.1016/j.margen.2019.100724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 02/08/2023]
Abstract
The ancient origins and functional versatility of globins make them ideal subjects for studying physiological adaptation to environmental change. Our goals in this review are to describe the evolution of the vertebrate globin gene superfamily and to explore the structure/function relationships of hemoglobin, myoglobin, neuroglobin and cytoglobin in teleost fishes. We focus on the globins of Antarctic notothenioids, emphasizing their adaptive features as inferred from comparisons with human proteins. We dedicate this review to Guido di Prisco, our co-author, colleague, friend, and husband of C.V. Ever thoughtful, creative, and enthusiastic, Guido spearheaded study of the structure, function, and evolution of the hemoglobins of polar fishes - this review is testimony to his wide-ranging contributions. Throughout his career, Guido inspired younger scientists to embrace polar biological research, and he challenged researchers of all ages to explore evolutionary adaptation in the context of global climate change. Beyond his scientific contributions, we will miss his warmth, his culture, and his great intellect. Guido has left an outstanding legacy, one that will continue to inspire us and our research.
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Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Daniela Coppola
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
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14
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Nikinmaa M, Berenbrink M, Brauner CJ. Regulation of erythrocyte function: Multiple evolutionary solutions for respiratory gas transport and its regulation in fish. Acta Physiol (Oxf) 2019; 227:e13299. [PMID: 31102432 DOI: 10.1111/apha.13299] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/03/2019] [Accepted: 05/13/2019] [Indexed: 01/01/2023]
Abstract
Gas transport concepts in vertebrates have naturally been formulated based on human blood. However, the first vertebrates were aquatic, and fish and tetrapods diverged hundreds of millions years ago. Water-breathing vertebrates live in an environment with low and variable O2 levels, making environmental O2 an important evolutionary selection pressure in fishes, and various features of their gas transport differ from humans. Erythrocyte function in fish is of current interest, because current environmental changes affect gas transport, and because especially zebrafish is used as a model in biomedical studies, making it important to understand the differences in gas transport between fish and mammals to be able to carry out meaningful studies. Of the close to thirty thousand fish species, teleosts are the most species-numerous group. However, two additional radiations are discussed: agnathans and elasmobranchs. The gas transport by elasmobranchs may be closest to the ancestors of tetrapods. The major difference in their haemoglobin (Hb) function to humans is their high urea tolerance. Agnathans differ from other vertebrates by having Hbs, where cooperativity is achieved by monomer-oligomer equilibria. Their erythrocytes also lack the anion exchange pathway with profound effects on CO2 transport. Teleosts are characterized by highly pH sensitive Hbs, which can fail to become fully O2 -saturated at low pH. An adrenergically stimulated Na+ /H+ exchanger has evolved in their erythrocyte membrane, and plasma-accessible carbonic anhydrase can be differentially distributed among their tissues. Together, and differing from other vertebrates, these features can maximize O2 unloading in muscle while ensuring O2 loading in gills.
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Affiliation(s)
| | - Michael Berenbrink
- Institute of Integrative Biology, Department of Evolution, Ecology and Behaviour University of Liverpool Liverpool UK
| | - Colin J. Brauner
- Department of Zoology University of British Columbia Vancouver British Columbia Canada
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15
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Amdahl MB, Petersen EE, Bocian K, Kaliszuk SJ, DeMartino AW, Tiwari S, Sparacino-Watkins CE, Corti P, Rose JJ, Gladwin MT, Fago A, Tejero J. The Zebrafish Cytochrome b5/Cytochrome b5 Reductase/NADH System Efficiently Reduces Cytoglobins 1 and 2: Conserved Activity of Cytochrome b5/Cytochrome b5 Reductases during Vertebrate Evolution. Biochemistry 2019; 58:3212-3223. [PMID: 31257865 DOI: 10.1021/acs.biochem.9b00406] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cytoglobin is a heme protein evolutionarily related to hemoglobin and myoglobin. Cytoglobin is expressed ubiquitously in mammalian tissues; however, its physiological functions are yet unclear. Phylogenetic analyses indicate that the cytoglobin gene is highly conserved in vertebrate clades, from fish to reptiles, amphibians, birds, and mammals. Most proposed roles for cytoglobin require the maintenance of a pool of reduced cytoglobin (FeII). We have shown previously that the human cytochrome b5/cytochrome b5 reductase system, considered a quintessential hemoglobin/myoglobin reductant, can reduce human and zebrafish cytoglobins ≤250-fold faster than human hemoglobin or myoglobin. It was unclear whether this reduction of zebrafish cytoglobins by mammalian proteins indicates a conserved pathway through vertebrate evolution. Here, we report the reduction of zebrafish cytoglobins 1 and 2 by the zebrafish cytochrome b5 reductase and the two zebrafish cytochrome b5 isoforms. In addition, the reducing system also supports reduction of Globin X, a conserved globin in fish and amphibians. Indeed, the zebrafish reducing system can maintain a fully reduced pool for both cytoglobins, and both cytochrome b5 isoforms can support this process. We determined the P50 for oxygen to be 0.5 Torr for cytoglobin 1 and 4.4 Torr for cytoglobin 2 at 25 °C. Thus, even at low oxygen tensions, the reduced cytoglobins may exist in a predominant oxygen-bound form. Under these conditions, the cytochrome b5/cytochrome b5 reductase system can support a conserved role for cytoglobins through evolution, providing electrons for redox signaling reactions such as nitric oxide dioxygenation, nitrite reduction, and phospholipid oxidation.
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Affiliation(s)
- Matthew B Amdahl
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Bioengineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Elin E Petersen
- Department of Bioscience , Aarhus University , DK-8000 Aarhus C, Denmark
| | - Kaitlin Bocian
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Stefan J Kaliszuk
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Anthony W DeMartino
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Sagarika Tiwari
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Courtney E Sparacino-Watkins
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Paola Corti
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Jason J Rose
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Bioengineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Division of Pulmonary, Allergy and Critical Care Medicine , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Mark T Gladwin
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Bioengineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Division of Pulmonary, Allergy and Critical Care Medicine , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Angela Fago
- Department of Bioscience , Aarhus University , DK-8000 Aarhus C, Denmark
| | - Jesús Tejero
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Bioengineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Division of Pulmonary, Allergy and Critical Care Medicine , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Pharmacology and Chemical Biology , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
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16
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Mannino MH, Patel RS, Eccardt AM, Perez Magnelli RA, Robinson CLC, Janowiak BE, Warren DE, Fisher JS. Myoglobin as a versatile peroxidase: Implications for a more important role for vertebrate striated muscle in antioxidant defense. Comp Biochem Physiol B Biochem Mol Biol 2019; 234:9-17. [PMID: 31051268 DOI: 10.1016/j.cbpb.2019.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/29/2019] [Accepted: 04/23/2019] [Indexed: 12/17/2022]
Abstract
Myoglobins (Mb) are ubiquitous proteins found in striated muscle of nearly all vertebrate taxa. Although their function is most commonly associated with facilitating oxygen storage and diffusion, Mb has also been implicated in cellular antioxidant defense. The oxidized (Fe3+) form of Mb (metMB) can react with hydrogen peroxide (H2O2) to produce ferrylMb. FerrylMb can be reduced back to metMb for another round of reaction with H2O2. In the present study, we have shown that horse skeletal muscle Mb displays peroxidase activity using 2,2'-azino-di-(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) and 3,3',5,5'-tetramethylbenzidine (TMB) as reducing substrates, as well as the biologically-relevant substrates NADH/NADPH, ascorbate, caffeic acid, and resveratrol. We have also shown that ferrylMb can be reduced by both ethanol and acetaldehyde, which are known to accumulate in some vertebrate tissues under anaerobic conditions, such as anoxic goldfish and crucian carp, implying a potential mechanism for ethanol detoxification in striated muscle. We found that metMb peroxidase activity is pH-dependent, increasing as pH decreases from 7.4 to 6.1, which is biologically relevant to anaerobic vertebrate muscle when incurring intracellular lactic acidosis. Finally, we found that metMb reacts with hypochlorite in a heme-dependent fashion, indicating that Mb could play a role in hypochlorite detoxification. Taken together, these data suggest that Mb peroxidase activity might be an important antioxidant mechanism in vertebrate cardiac and skeletal muscle under a variety of physiological conditions, such as those that might occur in contracting skeletal muscle or during hypoxia.
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17
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Lüdemann J, Verissimo KM, Dreger K, Fago A, Schneider I, Burmester T. Globin E is a myoglobin-related, respiratory protein highly expressed in lungfish oocytes. Sci Rep 2019; 9:280. [PMID: 30670817 PMCID: PMC6343008 DOI: 10.1038/s41598-018-36592-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/23/2018] [Indexed: 11/23/2022] Open
Abstract
Globins are a classical model system for the studies of protein evolution and function. Recent studies have shown that – besides the well-known haemoglobin and myoglobin – additional globin-types occur in vertebrates that serve different functions. Globin E (GbE) was originally identified as an eye-specific protein of birds that is distantly related to myoglobin. GbE is also present in turtles and the coelacanth but appeared to have been lost in other vertebrates. Here, we show that GbE additionally occurs in lungfish, the closest living relatives of the tetrapods. Each lungfish species harbours multiple (≥5) GbE gene copies. Surprisingly, GbE is exclusively and highly expressed in oocytes, with mRNA levels that exceed that of myoglobin in the heart. Thus, GbE is the first known oocyte-specific globin in vertebrates. No GbE transcripts were found in the ovary or egg transcriptomes of other vertebrates, suggesting a lungfish-specific function. Spectroscopic analysis and kinetic studies of recombinant GbE1 of the South American lungfish Lepidosiren paradoxa revealed a typical pentacoordinate globin with myoglobin-like O2-binding kinetics, indicating similar functions. Our findings suggest that the multiple copies of GbE evolved to enhance O2-supply in the developing embryo of lungfish, analogous to the embryonic and fetal haemoglobins of other vertebrates. In evolution, GbE must have changed its expression site from oocytes to eyes, or vice versa.
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Affiliation(s)
- Julia Lüdemann
- Institute of Zoology, University of Hamburg, D-20146, Hamburg, Germany
| | | | - Kimberley Dreger
- Institute of Zoology, University of Hamburg, D-20146, Hamburg, Germany
| | - Angela Fago
- Department of Bioscience, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
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18
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Smith HL, Pavasovic A, Surm JM, Phillips MJ, Prentis PJ. Evidence for a Large Expansion and Subfunctionalization of Globin Genes in Sea Anemones. Genome Biol Evol 2018; 10:1892-1901. [PMID: 29947797 PMCID: PMC6077788 DOI: 10.1093/gbe/evy128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2018] [Indexed: 02/07/2023] Open
Abstract
The globin gene superfamily has been well-characterized in vertebrates, however, there has been limited research in early-diverging lineages, such as phylum Cnidaria. This study aimed to identify globin genes in multiple cnidarian lineages, and use bioinformatic approaches to characterize the evolution, structure, and expression of these genes. Phylogenetic analyses and in silico protein predictions showed that all cnidarians have undergone an expansion of globin genes, which likely have a hexacoordinate protein structure. Our protein modeling has also revealed the possibility of a single pentacoordinate globin lineage in anthozoan species. Some cnidarian globin genes displayed tissue and development specific expression with very few orthologous genes similarly expressed across species. Our phylogenetic analyses also revealed that eumetazoan globin genes form a polyphyletic relationship with vertebrate globin genes. Overall, our analyses suggest that a Ngb-like and GbX-like gene were most likely present in the globin gene repertoire for the last common ancestor of eumetazoans. The identification of a large-scale expansion and subfunctionalization of globin genes in actiniarians provides an excellent starting point to further our understanding of the evolution and function of the globin gene superfamily in early-diverging lineages.
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Affiliation(s)
- Hayden L Smith
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Ana Pavasovic
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Joachim M Surm
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Peter J Prentis
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, Australia
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19
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Hoffmann FG, Vandewege MW, Storz JF, Opazo JC. Gene Turnover and Diversification of the α- and β-Globin Gene Families in Sauropsid Vertebrates. Genome Biol Evol 2018; 10:344-358. [PMID: 29340581 PMCID: PMC5786229 DOI: 10.1093/gbe/evy001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2018] [Indexed: 11/24/2022] Open
Abstract
The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here, we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster, which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globin genes that diversified independently in each lineage. These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | | | - Jay F Storz
- School of Biological Sciences, University of Nebraska
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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20
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Jiang H, Zhang X, Chen X, Aramsangtienchai P, Tong Z, Lin H. Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies. Chem Rev 2018; 118:919-988. [PMID: 29292991 DOI: 10.1021/acs.chemrev.6b00750] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein lipidation, including cysteine prenylation, N-terminal glycine myristoylation, cysteine palmitoylation, and serine and lysine fatty acylation, occurs in many proteins in eukaryotic cells and regulates numerous biological pathways, such as membrane trafficking, protein secretion, signal transduction, and apoptosis. We provide a comprehensive review of protein lipidation, including descriptions of proteins known to be modified and the functions of the modifications, the enzymes that control them, and the tools and technologies developed to study them. We also highlight key questions about protein lipidation that remain to be answered, the challenges associated with answering such questions, and possible solutions to overcome these challenges.
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Affiliation(s)
- Hong Jiang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiaoyu Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiao Chen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Pornpun Aramsangtienchai
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Zhen Tong
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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21
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Hanai S, Tsujino H, Yamashita T, Torii R, Sawai H, Shiro Y, Oohora K, Hayashi T, Uno T. Roles of N- and C-terminal domains in the ligand-binding properties of cytoglobin. J Inorg Biochem 2017; 179:1-9. [PMID: 29149638 DOI: 10.1016/j.jinorgbio.2017.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/04/2017] [Accepted: 11/04/2017] [Indexed: 01/12/2023]
Abstract
Cytoglobin (Cygb) is a member of the hexacoordinated globin protein family and is expressed ubiquitously in rat and human tissues. Although Cygb is reportedly upregulated under hypoxic conditions both in vivo and in vitro, suggesting a physiological function to protect cells under hypoxic/ischemic conditions by scavenging reactive oxygen species or by signal transduction, the mechanisms associated with this function have not been fully elucidated. Recent studies comparing Cygbs among several species suggest that mammalian Cygbs show a distinctly longer C-terminal domain potentially involved in unique physiological functions. In this study, we prepared human Cygb mutants (ΔC, ΔN, and ΔNC) with either one or both terminal domains truncated and investigated the enzymatic functions and structural features by spectroscopic methods. Evaluation of the superoxide-scavenging activity between Cygb variants showed that the ΔC and ΔNC mutants exhibited slightly higher activity involving superoxide scavenging as compared with wild-type Cygb. Subsequent experiments involving ligand titration, flash photolysis, and resonance Raman spectroscopic studies suggested that the truncation of the C- and N-terminal domains resulted in less effective to dissociation constants and binding rates for carbon monoxide, respectively. Furthermore, structural stability was assessed by guanidine hydrochloride and revealed that the C-terminal domain might play a vital role in improving structure, whereas the N-terminal domain did not exert a similar effect. These findings indicated that long terminal domains could be important not only in regulating enzymatic activity but also for structural stability, and that the domains might be relevant to other hypothesized physiological functions for Cygb.
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Affiliation(s)
- Shumpei Hanai
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Hirofumi Tsujino
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Taku Yamashita
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Hyogo, Japan.
| | - Ryo Torii
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | | | - Koji Oohora
- Department of Applied Chemistry, Osaka University, Osaka, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Osaka University, Osaka, Japan
| | - Tadayuki Uno
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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22
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Sun S, Xuan F, Fu H, Zhu J, Ge X, Wu X. Molecular cloning, mRNA expression and characterization of membrane-bound hemoglobin in oriental river prawn Macrobrachium nipponense. Comp Biochem Physiol A Mol Integr Physiol 2017; 207:36-42. [DOI: 10.1016/j.cbpa.2017.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 11/15/2022]
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23
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Globin X is a six-coordinate globin that reduces nitrite to nitric oxide in fish red blood cells. Proc Natl Acad Sci U S A 2016; 113:8538-43. [PMID: 27407144 DOI: 10.1073/pnas.1522670113] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The discovery of novel globins in diverse organisms has stimulated intense interest in their evolved function, beyond oxygen binding. Globin X (GbX) is a protein found in fish, amphibians, and reptiles that diverged from a common ancestor of mammalian hemoglobins and myoglobins. Like mammalian neuroglobin, GbX was first designated as a neuronal globin in fish and exhibits six-coordinate heme geometry, suggesting a role in intracellular electron transfer reactions rather than oxygen binding. Here, we report that GbX to our knowledge is the first six-coordinate globin and the first globin protein apart from hemoglobin, found in vertebrate RBCs. GbX is present in fish erythrocytes and exhibits a nitrite reduction rate up to 200-fold faster than human hemoglobin and up to 50-fold higher than neuroglobin or cytoglobin. Deoxygenated GbX reduces nitrite to form nitric oxide (NO) and potently inhibits platelet activation in vitro, to a greater extent than hemoglobin. Fish RBCs also reduce nitrite to NO and inhibit platelet activation to a greater extent than human RBCs, whereas GbX knockdown inhibits this nitrite-dependent NO signaling. The description of a novel, six-coordinate globin in RBCs with dominant electron transfer and nitrite reduction functionality provides new insights into the evolved signaling properties of ancestral heme-globins.
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Tejero J, Kapralov AA, Baumgartner MP, Sparacino-Watkins CE, Anthonymutu TS, Vlasova II, Camacho CJ, Gladwin MT, Bayir H, Kagan VE. Peroxidase activation of cytoglobin by anionic phospholipids: Mechanisms and consequences. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1861:391-401. [PMID: 26928591 PMCID: PMC4821708 DOI: 10.1016/j.bbalip.2016.02.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/02/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
Cytoglobin (Cygb) is a hexa-coordinated hemoprotein with yet to be defined physiological functions. The iron coordination and spin state of the Cygb heme group are sensitive to oxidation of two cysteine residues (Cys38/Cys83) and/or the binding of free fatty acids. However, the roles of redox vs lipid regulators of Cygb's structural rearrangements in the context of the protein peroxidase competence are not known. Searching for physiologically relevant lipid regulators of Cygb, here we report that anionic phospholipids, particularly phosphatidylinositolphosphates, affect structural organization of the protein and modulate its iron state and peroxidase activity both conjointly and/or independently of cysteine oxidation. Thus, different anionic lipids can operate in cysteine-dependent and cysteine-independent ways as inducers of the peroxidase activity. We establish that Cygb's peroxidase activity can be utilized for the catalysis of peroxidation of anionic phospholipids (including phosphatidylinositolphosphates) yielding mono-oxygenated molecular species. Combined with the computational simulations we propose a bipartite lipid binding model that rationalizes the modes of interactions with phospholipids, the effects on structural re-arrangements and the peroxidase activity of the hemoprotein.
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Affiliation(s)
- Jesús Tejero
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA; Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - Alexandr A Kapralov
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA; Center for Free Radical and Antioxidant Health and Center for Medical Countermeasures against Radiation, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Matthew P Baumgartner
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Courtney E Sparacino-Watkins
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA; Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Tamil S Anthonymutu
- Center for Free Radical and Antioxidant Health and Center for Medical Countermeasures against Radiation, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Critical Care Medicine, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Irina I Vlasova
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA; Center for Free Radical and Antioxidant Health and Center for Medical Countermeasures against Radiation, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Mark T Gladwin
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA; Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Hülya Bayir
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA; Center for Free Radical and Antioxidant Health and Center for Medical Countermeasures against Radiation, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Critical Care Medicine, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15219, USA.
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA; Center for Free Radical and Antioxidant Health and Center for Medical Countermeasures against Radiation, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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Abstract
In recent years, moderate levels of reactive oxygen species (ROS) have become recognized as signaling cues that participate at all levels of cellular organization. Globins, with their redox-active heme iron and ubiquitous presence, seem ideally suited to participate in ROS metabolism. Here we comment on our recent findings that show the participation of a globin, GLB-12, in a redox signaling pathway in Caenorhabditis elegans. We found that GLB-12 produces superoxide, a type of ROS, after which this is converted to what appears to be a hydrogen peroxide gradient over the plasma membrane by the activity of intracellular and extracellular superoxide dismutases. In the first part, we discuss in more detail the different regulatory mechanisms that increase the effectiveness of this redox signal. In the second part, we comment on how specific structural and biochemical properties allow this globin to perform redox reactions. Interestingly, these properties are also observed in 2 other C. elegans globins that appear to be involved in redox biology. We therefore hypothesize that globins involved in redox signaling display similar structural and biochemical characteristics and propose that a subgroup of globins can be added to the group of proteins that play a vital role in redox signaling.
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Affiliation(s)
- Sasha De Henau
- Biomedical Genetics, University Medical Center Utrecht , Utrecht, The Netherlands
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26
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Membrane-bound globin X protects the cell from reactive oxygen species. Biochem Biophys Res Commun 2016; 469:275-80. [DOI: 10.1016/j.bbrc.2015.11.105] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/23/2015] [Indexed: 12/21/2022]
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Corti P, Ieraci M, Tejero J. Characterization of zebrafish neuroglobin and cytoglobins 1 and 2: Zebrafish cytoglobins provide insights into the transition from six-coordinate to five-coordinate globins. Nitric Oxide 2015; 53:22-34. [PMID: 26721561 DOI: 10.1016/j.niox.2015.12.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/11/2015] [Accepted: 12/19/2015] [Indexed: 12/30/2022]
Abstract
Neuroglobin (Ngb) and cytoglobin (Cygb) are two six-coordinate heme proteins of unknown physiological function. Although studies on the mammalian proteins have elucidated aspects of Ngb and Cygb biophysics and indicated potential functions, the properties of non-mammalian Ngbs and Cygbs are largely uncharacterized. We have expressed the recombinant zebrafish proteins Ngb, Cygb1, and Cygb2 in Escherichia coli and characterized their nitrite reduction rates, spectral properties, autoxidation rate constants, redox potentials and lipid binding properties. The three zebrafish proteins can catalyze the reduction of nitrite to nitric oxide with a broad range of reaction rate constants. (Ngb, 0.68 ± 0.04 M(-1) s(-1); Cygb1, 28.6 ± 3.1 M(-1) s(-1); Cygb2, 0.94 ± 0.18 M(-1) s(-1)). We observe that zebrafish Ngb and Cygb2 have comparable spectral features to those of human Ngb and Cygb, consistent with a six-coordinate heme, whereas unexpectedly Cygb1 has a five-coordinate heme, a slower autoxidation and in general has properties more akin to oxygen transport proteins. In agreement with a possible oxygen carrier and nitrite reductase role, we detect mRNA transcript for Cygb1 but not Cygb2 or Ngb in zebrafish blood. Unlike human Cygb, neither of the zebrafish globins binds oleic acid with high affinity. This finding suggests that lipid binding may be a trait acquired later during evolution and not an ancestral property of cytoglobins. Altogether, our results uncover unexpected properties of zebrafish globins and reveal the pivotal role of cytoglobins in the transition of heme globins from six-coordinate to five-coordinate oxygen carriers and nitrite reductases.
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Affiliation(s)
- Paola Corti
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Matthew Ieraci
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jesús Tejero
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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Christensen AB, Herman JL, Elphick MR, Kober KM, Janies D, Linchangco G, Semmens DC, Bailly X, Vinogradov SN, Hoogewijs D. Phylogeny of Echinoderm Hemoglobins. PLoS One 2015; 10:e0129668. [PMID: 26247465 PMCID: PMC4527676 DOI: 10.1371/journal.pone.0129668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/12/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Recent genomic information has revealed that neuroglobin and cytoglobin are the two principal lineages of vertebrate hemoglobins, with the latter encompassing the familiar myoglobin and α-globin/β-globin tetramer hemoglobin, and several minor groups. In contrast, very little is known about hemoglobins in echinoderms, a phylum of exclusively marine organisms closely related to vertebrates, beyond the presence of coelomic hemoglobins in sea cucumbers and brittle stars. We identified about 50 hemoglobins in sea urchin, starfish and sea cucumber genomes and transcriptomes, and used Bayesian inference to carry out a molecular phylogenetic analysis of their relationship to vertebrate sequences, specifically, to assess the hypothesis that the neuroglobin and cytoglobin lineages are also present in echinoderms. RESULTS The genome of the sea urchin Strongylocentrotus purpuratus encodes several hemoglobins, including a unique chimeric 14-domain globin, 2 androglobin isoforms and a unique single androglobin domain protein. Other strongylocentrotid genomes appear to have similar repertoires of globin genes. We carried out molecular phylogenetic analyses of 52 hemoglobins identified in sea urchin, brittle star and sea cucumber genomes and transcriptomes, using different multiple sequence alignment methods coupled with Bayesian and maximum likelihood approaches. The results demonstrate that there are two major globin lineages in echinoderms, which are related to the vertebrate neuroglobin and cytoglobin lineages. Furthermore, the brittle star and sea cucumber coelomic hemoglobins appear to have evolved independently from the cytoglobin lineage, similar to the evolution of erythroid oxygen binding globins in cyclostomes and vertebrates. CONCLUSION The presence of echinoderm globins related to the vertebrate neuroglobin and cytoglobin lineages suggests that the split between neuroglobins and cytoglobins occurred in the deuterostome ancestor shared by echinoderms and vertebrates.
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Affiliation(s)
- Ana B. Christensen
- Biology Department, Lamar University, Beaumont, Texas, United States of America
| | - Joseph L. Herman
- Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
- Division of Mathematical Biology, National Institute of Medical Research, London, NW7 1AA, United Kingdom
| | - Maurice R. Elphick
- School of Biological & Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Kord M. Kober
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Daniel Janies
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States of America
| | - Gregorio Linchangco
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States of America
| | - Dean C. Semmens
- School of Biological & Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Xavier Bailly
- Marine Plants and Biomolecules, Station Biologique de Roscoff, 2968 Roscoff, France
| | - Serge N. Vinogradov
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, United States of America
| | - David Hoogewijs
- Institute of Physiology, University of Duisburg-Essen, Essen, Germany
- * E-mail:
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29
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Burmester T. Evolution of Respiratory Proteins across the Pancrustacea. Integr Comp Biol 2015; 55:792-801. [PMID: 26130703 DOI: 10.1093/icb/icv079] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Respiratory proteins enhance the capacity of the blood for oxygen transport and support intracellular storage and delivery of oxygen. Hemocyanin and hemoglobin are the respiratory proteins that occur in the Pancrustacea. The copper-containing hemocyanins evolved from phenoloxidases in the stem lineage of arthropods. For a long time, hemocyanins had only been known from the malacostracan crustaceans but recent studies identified hemocyanin also in Remipedia, Ostracoda, and Branchiura. Hemoglobins are common in the Branchiopoda but have also been sporadically found in other crustacean classes (Malacostraca, Copepoda, Thecostraca). Respiratory proteins had long been considered unnecessary in the hexapods because of the tracheal system. Only chironomids, some backswimmers, and the horse botfly, which all live under hypoxic conditions, were known exceptions and possess hemoglobins. However, recent data suggest that hemocyanins occur in most ametabolous and hemimetabolous insects. Phylogenetic analysis showed the hemocyanins of insects and Remipedia to be similar, suggesting a close relationship of these taxa. Hemocyanin has been lost in dragonflies, mayflies, and Eumetabola (Hemiptera + Holometabola). In cockroaches and grasshoppers, hemocyanin expression is restricted to the developing embryo while in adults oxygen is supplied solely by the tracheal system. This pattern suggests that hemocyanin was the oxygen-transport protein in the hemolymph of the last common ancestor of the pancrustaceans. The loss was probably associated with miniaturization, a period of restricted availability of oxygen, a change in life-style, or morphological changes. Once lost, hemocyanin was not regained. Some pancrustaceans also possess cellular globin genes with uncertain functions, which are expressed at low levels. When a respiratory protein was again required, hemoglobins evolved several times independently from cellular globins.
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Affiliation(s)
- Thorsten Burmester
- Institute of Zoology, Biocenter Grindel, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
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30
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Schwarze K, Singh A, Burmester T. The Full Globin Repertoire of Turtles Provides Insights into Vertebrate Globin Evolution and Functions. Genome Biol Evol 2015; 7:1896-913. [PMID: 26078264 PMCID: PMC4524481 DOI: 10.1093/gbe/evv114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Globins are small heme proteins that play an important role in oxygen supply, but may also have other functions. Globins offer a unique opportunity to study the functional evolution of genes and proteins. We have characterized the globin repertoire of two different turtle species: the Chinese softshell turtle (Pelodiscus sinensis) and the western painted turtle (Chrysemys picta bellii). In the genomes of both species, we have identified eight distinct globin types: hemoglobin (Hb), myoglobin, neuroglobin, cytoglobin, globin E, globin X, globin Y, and androglobin. Therefore, along with the coelacanth, turtles are so far the only known vertebrates with a full globin repertoire. This fact allows for the first time a comparative analysis of the expression of all eight globins in a single species. Phylogenetic analysis showed an early divergence of neuroglobin and globin X before the radiation of vertebrates. Among the other globins, cytoglobin diverged first, and there is a close relationship between myoglobin and globin E; the position of globin Y is not resolved. The globin E gene was selectively lost in the green anole, and the genes coding for globin X and globin Y were deleted in chicken. Quantitative real-time reverse transcription polymerase chain reaction experiments revealed that myoglobin, neuroglobin, and globin E are highly expressed with tissue-specific patterns, which are in line with their roles in the oxidative metabolism of the striated muscles, the brain, and the retina, respectively. Histochemical analyses showed high levels of globin E in the pigment epithelium of the eye. Globin E probably has a myoglobin-like role in transporting O2 across the pigment epithelium to supply in the metabolically highly active retina.
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Affiliation(s)
- Kim Schwarze
- Institute of Zoology, Department of Biology, University of Hamburg, Germany
| | - Abhilasha Singh
- Institute of Zoology, Department of Biology, University of Hamburg, Germany
| | - Thorsten Burmester
- Institute of Zoology, Department of Biology, University of Hamburg, Germany
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31
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Rhéault JF, Gagné È, Guertin M, Lamoureux G, Auger M, Lagüe P. Molecular Model of Hemoglobin N from Mycobacterium tuberculosis Bound to Lipid Bilayers: A Combined Spectroscopic and Computational Study. Biochemistry 2015; 54:2073-84. [DOI: 10.1021/bi5010624] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jean-François Rhéault
- Department
of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Québec, Canada
| | | | - Michel Guertin
- Department
of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Québec, Canada
| | - Guillaume Lamoureux
- Centre for Research
in Molecular Modeling (CERMM), Concordia University, Montréal, Québec, Canada
| | | | - Patrick Lagüe
- Department
of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Québec, Canada
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32
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Opazo JC, Lee AP, Hoffmann FG, Toloza-Villalobos J, Burmester T, Venkatesh B, Storz JF. Ancient Duplications and Expression Divergence in the Globin Gene Superfamily of Vertebrates: Insights from the Elephant Shark Genome and Transcriptome. Mol Biol Evol 2015; 32:1684-94. [PMID: 25743544 DOI: 10.1093/molbev/msv054] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Comparative analyses of vertebrate genomes continue to uncover a surprising diversity of genes in the globin gene superfamily, some of which have very restricted phyletic distributions despite their antiquity. Genomic analysis of the globin gene repertoire of cartilaginous fish (Chondrichthyes) should be especially informative about the duplicative origins and ancestral functions of vertebrate globins, as divergence between Chondrichthyes and bony vertebrates represents the most basal split within the jawed vertebrates. Here, we report a comparative genomic analysis of the vertebrate globin gene family that includes the complete globin gene repertoire of the elephant shark (Callorhinchus milii). Using genomic sequence data from representatives of all major vertebrate classes, integrated analyses of conserved synteny and phylogenetic relationships revealed that the last common ancestor of vertebrates possessed a repertoire of at least seven globin genes: single copies of androglobin and neuroglobin, four paralogous copies of globin X, and the single-copy progenitor of the entire set of vertebrate-specific globins. Combined with expression data, the genomic inventory of elephant shark globins yielded four especially surprising findings: 1) there is no trace of the neuroglobin gene (a highly conserved gene that is present in all other jawed vertebrates that have been examined to date), 2) myoglobin is highly expressed in heart, but not in skeletal muscle (reflecting a possible ancestral condition in vertebrates with single-circuit circulatory systems), 3) elephant shark possesses two highly divergent globin X paralogs, one of which is preferentially expressed in gonads, and 4) elephant shark possesses two structurally distinct α-globin paralogs, one of which is preferentially expressed in the brain. Expression profiles of elephant shark globin genes reveal distinct specializations of function relative to orthologs in bony vertebrates and suggest hypotheses about ancestral functions of vertebrate globins.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Alison P Lee
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology, and Research Biopolis, Singapore
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | - Jessica Toloza-Villalobos
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology, and Research Biopolis, Singapore Departments of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln
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Götting M, Nikinmaa M. More than hemoglobin - the unexpected diversity of globins in vertebrate red blood cells. Physiol Rep 2015; 3:3/2/e12284. [PMID: 25649247 PMCID: PMC4393193 DOI: 10.14814/phy2.12284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In many multicellular organisms, oxygen is transported by respiratory proteins, which are globins in vertebrates, between respiratory organs and tissues. In jawed vertebrates, eight globins are known which are expressed in a highly tissue-specific manner. Until now, hemoglobin (Hb) had been agreed to be the only globin expressed in vertebrate erythrocytes. Here, we investigate for the first time the mRNA expression of globin genes in nucleated and anucleated erythrocytes of model vertebrate species by quantitative real-time reverse transcription PCR (qRT-PCR). Surprisingly, we found transcripts of the whole gnathostome globin superfamily in RBCs. The mRNA expression levels varied among species, with Hb being by far the dominant globin. Only in stickleback, a globin previously thought to be neuron-specific, neuroglobin, had higher mRNA expression. We furthermore show that in birds transcripts of globin E, which was earlier reported to be transcribed only in the eye, are also present in RBCs. Even in anucleated RBCs of mammals, we found transcripts of myoglobin, neuroglobin, and cytoglobin. Our findings add new aspects to the current knowledge on the expression of globins in vertebrate tissues. However, whether or not the mRNA expression of these globin genes has any functional significance in RBCs has to be investigated in future studies.
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Affiliation(s)
- Miriam Götting
- Zoological Institute and Zoological Museum, Biocenter Grindel, University of Hamburg, Hamburg, Germany
| | - Mikko Nikinmaa
- Department of Biology, Laboratory of Animal Physiology, University of Turku, Turku, Finland
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Jusman SW, Iswanti FC, Suyatna FD, Ferdinal F, Wanandi SI, Sadikin M. Cytoglobin expression in oxidative stressed liver during systemic chronic normobaric hypoxia and relation with HIF-1α. MEDICAL JOURNAL OF INDONESIA 2014. [DOI: 10.13181/mji.v23i3.1025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Background: Liver is sensitive against hypoxia and hypoxia will stabilize HIF-1α. At the same time, hypoxia will produce reactive oxygen species (ROS) which can be scavenged by Cygb. The purpose of our study is to know, if normobaric hypoxia can induce Cygb expression and its association with HIF-1α stabilization.Methods: This is an experimental study using 28 male Sprague-Dawley rats, 150-200 g weight. Rats are divided into 7 groups: control group and treatment groups that are kept in hypoxic chamber (10% O2: 90% N2) for 6 hours, 1, 2, 3, 7 and 14 days. All rats are euthanized after treatment and liver tissue are isolated, homogenized and analyzed for oxidative stress parameter, expression of Cygb and HIF-1α.Results: Expression of Cygb mRNA and protein was increased on the day-1 after treatment and reach the maximum expression on the day-2 of hypoxia treatment. But, the expression was decreased after the day-3 and slightly increased at the day-14 of hypoxia. The correlation between expression of Cygb and oxidative stress parameter was strongly correlated. Cygb mRNA, as well as protein, showed the same kinetic as the HIF-1, all increased about day-1 and day-2.Conclusion: Systemic chronic hypoxia and/or oxidative stress up-regulated HIF-1α mRNA which is correlated with the Cygb mRNA and protein expression. Cygb mRNA as well as Cygb protein showed the same kinetic as the HIF-1, all increased about day-1 and day-2 suggesting that Cygb could be under the regulation of HIF-1, but could be controlled also by other factor than HIF-1.
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35
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Schwarze K, Campbell KL, Hankeln T, Storz JF, Hoffmann FG, Burmester T. The globin gene repertoire of lampreys: convergent evolution of hemoglobin and myoglobin in jawed and jawless vertebrates. Mol Biol Evol 2014; 31:2708-21. [PMID: 25061084 DOI: 10.1093/molbev/msu216] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Agnathans (jawless vertebrates) occupy a key phylogenetic position for illuminating the evolution of vertebrate anatomy and physiology. Evaluation of the agnathan globin gene repertoire can thus aid efforts to reconstruct the origin and evolution of the globin genes of vertebrates, a superfamily that includes the well-known model proteins hemoglobin and myoglobin. Here, we report a comprehensive analysis of the genome of the sea lamprey (Petromyzon marinus) which revealed 23 intact globin genes and two hemoglobin pseudogenes. Analyses of the genome of the Arctic lamprey (Lethenteron camtschaticum) identified 18 full length and five partial globin gene sequences. The majority of the globin genes in both lamprey species correspond to the known agnathan hemoglobins. Both genomes harbor two copies of globin X, an ancient globin gene that has a broad phylogenetic distribution in the animal kingdom. Surprisingly, we found no evidence for an ortholog of neuroglobin in the lamprey genomes. Expression and phylogenetic analyses identified an ortholog of cytoglobin in the lampreys; in fact, our results indicate that cytoglobin is the only orthologous vertebrate-specific globin that has been retained in both gnathostomes and agnathans. Notably, we also found two globins that are highly expressed in the heart of P. marinus, thus representing functional myoglobins. Both genes have orthologs in L. camtschaticum. Phylogenetic analyses indicate that these heart-expressed globins are not orthologous to the myoglobins of jawed vertebrates (Gnathostomata), but originated independently within the agnathans. The agnathan myoglobin and hemoglobin proteins form a monophyletic group to the exclusion of functionally analogous myoglobins and hemoglobins of gnathostomes, indicating that specialized respiratory proteins for O2 transport in the blood and O2 storage in the striated muscles evolved independently in both lineages. This dual convergence of O2-transport and O2-storage proteins in agnathans and gnathostomes involved the convergent co-option of different precursor proteins in the ancestral globin repertoire of vertebrates.
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Affiliation(s)
- Kim Schwarze
- Institute of Zoology and Zoological Museum, University of Hamburg, Hamburg, Germany
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Thomas Hankeln
- Institute of Molecular Genetics, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | - Thorsten Burmester
- Institute of Zoology and Zoological Museum, University of Hamburg, Hamburg, Germany
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Burmester T, Hankeln T. Function and evolution of vertebrate globins. Acta Physiol (Oxf) 2014; 211:501-14. [PMID: 24811692 DOI: 10.1111/apha.12312] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/17/2014] [Accepted: 04/30/2014] [Indexed: 02/06/2023]
Abstract
Globins are haem-proteins that bind O2 and thus play an important role in the animal's respiration and oxidative energy production. However, globins may also have other functions such as the decomposition or production of NO, the detoxification of reactive oxygen species or intracellular signalling. In addition to the well-investigated haemoglobins and myoglobins, genome sequence analyses have led to the identification of six further globin types in vertebrates: androglobin, cytoglobin, globin E, globin X, globin Y and neuroglobin. Here, we review the present state of knowledge on the functions, the taxonomic distribution and evolution of vertebrate globins, drawing conclusions about the functional changes underlying present-day globin diversity.
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Affiliation(s)
- T. Burmester
- Institute of Zoology and Zoological Museum; University of Hamburg; Hamburg Germany
| | - T. Hankeln
- Institute of Molecular Genetics; Johannes Gutenberg-University Mainz; Mainz Germany
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Dröge J, Buczek D, Suzuki Y, Makałowski W. Amoebozoa possess lineage-specific globin gene repertoires gained by individual horizontal gene transfers. Int J Biol Sci 2014; 10:689-701. [PMID: 25013378 PMCID: PMC4081604 DOI: 10.7150/ijbs.8327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/24/2014] [Indexed: 12/13/2022] Open
Abstract
The Amoebozoa represent a clade of unicellular amoeboid organisms that display a wide variety of lifestyles, including free-living and parasitic species. For example, the social amoeba Dictyostelium discoideum has the ability to aggregate into a multicellular fruiting body upon starvation, while the pathogenic amoeba Entamoeba histolytica is a parasite of humans. Globins are small heme proteins that are present in almost all extant organisms. Although several genomes of amoebozoan species have been sequenced, little is known about the phyletic distribution of globin genes within this phylum. Only two flavohemoglobins (FHbs) of D. discoideum have been reported and characterized previously while the genomes of Entamoeba species are apparently devoid of globin genes. We investigated eleven amoebozoan species for the presence of globin genes by genomic and phylogenetic in silico analyses. Additional FHb genes were identified in the genomes of four social amoebas and the true slime mold Physarum polycephalum. Moreover, a single-domain globin (SDFgb) of Hartmannella vermiformis, as well as two truncated hemoglobins (trHbs) of Acanthamoeba castellanii were identified. Phylogenetic evidence suggests that these globin genes were independently acquired via horizontal gene transfer from some ancestral bacteria. Furthermore, the phylogenetic tree of amoebozoan FHbs indicates that they do not share a common ancestry and that a transfer of FHbs from bacteria to amoeba occurred multiple times.
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Affiliation(s)
- Jasmin Dröge
- 1. Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Str. 14, 48149 Muenster, Germany
| | - Dorota Buczek
- 1. Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Str. 14, 48149 Muenster, Germany ; 2. Institute of Molecular Biology and Biotechnology, A. Mickiewicz University, Poznan, Poland
| | - Yutaka Suzuki
- 3. Department of Medical Genomic Sciences, University of Tokyo, Tokyo, Japan
| | - Wojciech Makałowski
- 1. Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Str. 14, 48149 Muenster, Germany ; 3. Department of Medical Genomic Sciences, University of Tokyo, Tokyo, Japan
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Tiedke J, Thiel R, Burmester T. Molecular response of estuarine fish to hypoxia: a comparative study with ruffe and flounder from field and laboratory. PLoS One 2014; 9:e90778. [PMID: 24595439 PMCID: PMC3940940 DOI: 10.1371/journal.pone.0090778] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 02/05/2014] [Indexed: 11/18/2022] Open
Abstract
On a global scale, the frequencies and magnitudes of hypoxic events in coastal and estuarine waters have increased dramatically over the past 20 years. Fish populations are suitable indicators for the assessment of the quality of aquatic ecosystems, as they are omnipresent and often comprise a variety of different lifestyles and adaption strategies. We have investigated on the molecular level the impact of hypoxia on two fish species typical of European estuaries. We monitored the expression of eleven putatively hypoxia-responsive genes by means of quantitative real-time RT-PCR in brains, gills and hearts of the ruffe (Gymnocephalus cernua) and the flounder (Platichthys flesus). We first investigated the effect of naturally occurring hypoxia in the Elbe estuary. In a second approach, expression changes in the response to hypoxia were monitored under controlled laboratory conditions. The genes that showed the strongest effect were two respiratory proteins, myoglobin and neuroglobin, as well as the apoptosis enzyme caspase 3. As previously observed in other fish, myoglobin, which was considered to be muscle-specific, was found in brain and gills as well. Comparison of field and laboratory studies showed that--with the exception of the heart of flounder--that mRNA levels of the selected genes were about the same, suggesting that laboratory conditions reflect natural conditions. Likewise, trends of gene expression changes under hypoxia were the same, although hypoxia response was more pronounced in the Elbe estuary. In general, the flounder displayed a stronger response to hypoxia than the ruffe, suggesting that the flounder is more susceptible to hypoxia. The most pronounced differences were found among tissues within a species, demonstrating that hypoxia response is largely tissue-specific. In summary, our data suggest that laboratory experiments essentially mimic field data, but additional environmental factors enhance hypoxia response in nature.
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Affiliation(s)
- Jessica Tiedke
- Institute of Zoology and Zoological Museum, University of Hamburg, Hamburg, Germany
| | - Ralf Thiel
- Institute of Zoology and Zoological Museum, University of Hamburg, Hamburg, Germany
| | - Thorsten Burmester
- Institute of Zoology and Zoological Museum, University of Hamburg, Hamburg, Germany
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39
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Schwarze K, Burmester T. Conservation of globin genes in the "living fossil" Latimeria chalumnae and reconstruction of the evolution of the vertebrate globin family. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1801-12. [PMID: 23360762 DOI: 10.1016/j.bbapap.2013.01.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
Abstract
The (hemo-)globins are among the best-investigated proteins in biomedical sciences. These small heme-proteins play an important role in oxygen supply, but may also have other functions. In addition to well known hemoglobin and myoglobin, six other vertebrate globin types have been identified in recent years: neuroglobin, cytoglobin, globin E, globin X, globin Y, and androglobin. Analyses of the genome of the "living fossil" Latimeria chalumnae show that the coelacanth is the only known vertebrate that includes all eight globin types. Thus, Latimeria can also be considered as a "globin fossil". Analyses of gene synteny and phylogenetic reconstructions allow us to trace the evolution and the functional changes of the vertebrate globin family. Neuroglobin and globin X diverged from the other globin types before the separation of Protostomia and Deuterostomia. The cytoglobins, which are unlikely to be involved in O2 supply, form the earliest globin branch within the jawed vertebrates (Gnathostomata), but do not group with the agnathan hemoglobins, as it has been proposed before. There is strong evidence from phylogenetic reconstructions and gene synteny that the eye-specific globin E and muscle-specific myoglobin constitute a common clade, suggesting a similar role in intracellular O2 supply. Latimeria possesses two α- and two β-hemoglobin chains, of which one α-chain emerged prior to the divergence of Actinopterygii and Sarcopterygii, but has been retained only in the coelacanth. Notably, the embryonic hemoglobin α-chains of Gnathostomata derive from a common ancestor, while the embryonic β-chains - with the exception of a more complex pattern in the coelacanth and amphibians - display a clade-specific evolution. Globin Y is associated with the hemoglobin gene cluster, but its phylogenetic position is not resolved. Our data show an early divergence of distinct globin types in the vertebrate evolution before the emergence of tetrapods. The subsequent loss of globins in certain taxa may be associated with changes in the oxygen-dependent metabolism. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Kim Schwarze
- Institute of Zoology and Zoological Museum, University of Hamburg, Hamburg, Germany
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40
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Lechauve C, Jager M, Laguerre L, Kiger L, Correc G, Leroux C, Vinogradov S, Czjzek M, Marden MC, Bailly X. Neuroglobins, pivotal proteins associated with emerging neural systems and precursors of metazoan globin diversity. J Biol Chem 2013; 288:6957-67. [PMID: 23288852 DOI: 10.1074/jbc.m112.407601] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neuroglobins, previously thought to be restricted to vertebrate neurons, were detected in the brain of a photosymbiotic acoel, Symsagittifera roscoffensis, and in neurosensory cells of the jellyfish Clytia hemisphaerica. For the neuroglobin of S. roscoffensis, a member of a lineage that originated either at the base of the bilateria or of the deuterostome clade, we report the ligand binding properties, crystal structure at 2.3 Å, and brain immunocytochemical pattern. We also describe in situ hybridizations of two neuroglobins specifically expressed in differentiating nematocytes (neurosensory cells) and in statocytes (ciliated mechanosensory cells) of C. hemisphaerica, a member of the early branching animal phylum cnidaria. In silico searches using these neuroglobins as queries revealed the presence of previously unidentified neuroglobin-like sequences in most metazoan lineages. Because neural systems are almost ubiquitous in metazoa, the constitutive expression of neuroglobin-like proteins strongly supports the notion of an intimate association of neuroglobins with the evolution of animal neural systems and hints at the preservation of a vitally important function. Neuroglobins were probably recruited in the first protoneurons in early metazoans from globin precursors. Neuroglobins were identified in choanoflagellates, sponges, and placozoans and were conserved during nervous system evolution. Because the origin of neuroglobins predates the other metazoan globins, it is likely that neuroglobin gene duplication followed by co-option and subfunctionalization led to the emergence of globin families in protostomes and deuterostomes (i.e. convergent evolution).
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Affiliation(s)
- Christophe Lechauve
- INSERM, UMR S 968, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR)_7210, Institut de la Vision Université Pierre et Marie Curie (UPMC)/Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, 17 rue Moreau, 75012 Paris, France
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41
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Gardner PR. Hemoglobin: a nitric-oxide dioxygenase. SCIENTIFICA 2012; 2012:683729. [PMID: 24278729 PMCID: PMC3820574 DOI: 10.6064/2012/683729] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/04/2012] [Indexed: 05/09/2023]
Abstract
Members of the hemoglobin superfamily efficiently catalyze nitric-oxide dioxygenation, and when paired with native electron donors, function as NO dioxygenases (NODs). Indeed, the NOD function has emerged as a more common and ancient function than the well-known role in O2 transport-storage. Novel hemoglobins possessing a NOD function continue to be discovered in diverse life forms. Unique hemoglobin structures evolved, in part, for catalysis with different electron donors. The mechanism of NOD catalysis by representative single domain hemoglobins and multidomain flavohemoglobin occurs through a multistep mechanism involving O2 migration to the heme pocket, O2 binding-reduction, NO migration, radical-radical coupling, O-atom rearrangement, nitrate release, and heme iron re-reduction. Unraveling the physiological functions of multiple NODs with varying expression in organisms and the complexity of NO as both a poison and signaling molecule remain grand challenges for the NO field. NOD knockout organisms and cells expressing recombinant NODs are helping to advance our understanding of NO actions in microbial infection, plant senescence, cancer, mitochondrial function, iron metabolism, and tissue O2 homeostasis. NOD inhibitors are being pursued for therapeutic applications as antibiotics and antitumor agents. Transgenic NOD-expressing plants, fish, algae, and microbes are being developed for agriculture, aquaculture, and industry.
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Affiliation(s)
- Paul R. Gardner
- Miami Valley Biotech, 1001 E. 2nd Street, Suite 2445, Dayton, OH 45402, USA
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42
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An N-myristoylated globin with a redox-sensing function that regulates the defecation cycle in Caenorhabditis elegans. PLoS One 2012; 7:e48768. [PMID: 23251335 PMCID: PMC3520999 DOI: 10.1371/journal.pone.0048768] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 10/04/2012] [Indexed: 01/17/2023] Open
Abstract
Globins occur in all kingdoms of life where they fulfill a wide variety of functions. In the past they used to be primarily characterized as oxygen transport/storage proteins, but since the discovery of new members of the globin family like neuroglobin and cytoglobin, more diverse and complex functions have been assigned to this heterogeneous family. Here we propose a function for a membrane-bound globin of C. elegans, GLB-26. This globin was predicted to be myristoylated at its N-terminus, a post-translational modification only recently described in the globin family. In vivo, this globin is found in the membrane of the head mesodermal cell and in the tail stomato-intestinal and anal depressor muscle cells. Since GLB-26 is almost directly oxidized when exposed to oxygen, we postulate a possible function as electron transfer protein. Phenotypical studies show that GLB-26 takes part in regulating the length of the defecation cycle in C. elegans under oxidative stress conditions.
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43
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Dröge J, Pande A, Englander EW, Makałowski W. Comparative genomics of neuroglobin reveals its early origins. PLoS One 2012; 7:e47972. [PMID: 23133533 PMCID: PMC3485006 DOI: 10.1371/journal.pone.0047972] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 09/24/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neuroglobin (Ngb) is a hexacoordinated globin expressed mainly in the central and peripheral nervous system of vertebrates. Although several hypotheses have been put forward regarding the role of neuroglobin, its definite function remains uncertain. Ngb appears to have a neuro-protective role enhancing cell viability under hypoxia and other types of oxidative stress. Ngb is phylogenetically ancient and has a substitution rate nearly four times lower than that of other vertebrate globins, e.g. hemoglobin. Despite its high sequence conservation among vertebrates Ngb seems to be elusive in invertebrates. PRINCIPAL FINDINGS We determined candidate orthologs in invertebrates and identified a globin of the placozoan Trichoplax adhaerens that is most likely orthologous to vertebrate Ngb and confirmed the orthologous relationship of the polymeric globin of the sea urchin Strongylocentrotus purpuratus to Ngb. The putative orthologous globin genes are located next to genes orthologous to vertebrate POMT2 similarly to localization of vertebrate Ngb. The shared syntenic position of the globins from Trichoplax, the sea urchin and of vertebrate Ngb strongly suggests that they are orthologous. A search for conserved transcription factor binding sites (TFBSs) in the promoter regions of the Ngb genes of different vertebrates via phylogenetic footprinting revealed several TFBSs, which may contribute to the specific expression of Ngb, whereas a comparative analysis with myoglobin revealed several common TFBSs, suggestive of regulatory mechanisms common to globin genes. SIGNIFICANCE Identification of the placozoan and echinoderm genes orthologous to vertebrate neuroglobin strongly supports the hypothesis of the early evolutionary origin of this globin, as it shows that neuroglobin was already present in the placozoan-bilaterian last common ancestor. Computational determination of the transcription factor binding sites repertoire provides on the one hand a set of transcriptional factors that are responsible for the specific expression of the Ngb genes and on the other hand a set of factors potentially controlling expression of a couple of different globin genes.
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Affiliation(s)
- Jasmin Dröge
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany
| | - Amit Pande
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany
| | - Ella W. Englander
- Department of Surgery, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Wojciech Makałowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany
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44
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Storz JF, Opazo JC, Hoffmann FG. Gene duplication, genome duplication, and the functional diversification of vertebrate globins. Mol Phylogenet Evol 2012; 66:469-78. [PMID: 22846683 DOI: 10.1016/j.ympev.2012.07.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Revised: 06/21/2012] [Accepted: 07/16/2012] [Indexed: 11/28/2022]
Abstract
The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto α- and β-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (α(2)β(2)). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of α- and β-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA.
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45
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Hoffmann FG, Opazo JC, Hoogewijs D, Hankeln T, Ebner B, Vinogradov SN, Bailly X, Storz JF. Evolution of the globin gene family in deuterostomes: lineage-specific patterns of diversification and attrition. Mol Biol Evol 2012; 29:1735-45. [PMID: 22319164 PMCID: PMC3375472 DOI: 10.1093/molbev/mss018] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In the Metazoa, globin proteins display an underlying unity in tertiary structure that belies an extraordinary diversity in primary structures, biochemical properties, and physiological functions. Phylogenetic reconstructions can reveal which of these functions represent novel, lineage-specific innovations, and which represent ancestral functions that are shared with homologous globin proteins in other eukaryotes and even prokaryotes. To date, our understanding of globin diversity in deuterostomes has been hindered by a dearth of genomic sequence data from the Ambulacraria (echinoderms + hemichordates), the sister group of chordates, and the phylum Xenacoelomorpha, which includes xenoturbellids, acoelomorphs, and nemertodermatids. Here, we report the results of a phylogenetic and comparative genomic analysis of the globin gene repertoire of deuterostomes. We first characterized the globin genes of the acorn worm, Saccoglossus kowalevskii, a representative of the phylum Hemichordata. We then integrated genomic sequence data from the acorn worm into a comprehensive analysis of conserved synteny and phylogenetic relationships among globin genes from representatives of the eight lineages that comprise the superphylum Deuterostomia. The primary aims were 1) to unravel the evolutionary history of the globin gene superfamily in deuterostomes and 2) to use the estimated phylogeny to gain insights into the functional evolution of deuterostome globins. Results of our analyses indicate that the deuterostome common ancestor possessed a repertoire of at least four distinct globin paralogs and that different subsets of these ancestral genes have been retained in each of the descendant organismal lineages. In each major deuterostome group, a different subset of ancestral precursor genes underwent lineage-specific expansions of functional diversity through repeated rounds of gene duplication and divergence. By integrating results of the phylogenetic analysis with available functional data, we discovered that circulating oxygen-transport hemoglobins evolved independently in several deuterostome lineages and that intracellular nerve globins evolved independently in chordates and acoelomorph worms.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry and Molecular Biology, Mississippi State University, USA.
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46
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Blank M, Burmester T. Widespread occurrence of N-terminal acylation in animal globins and possible origin of respiratory globins from a membrane-bound ancestor. Mol Biol Evol 2012; 29:3553-61. [PMID: 22718912 DOI: 10.1093/molbev/mss164] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Proteins of the (hemo-)globin superfamily have been identified in many different animals but also occur in plants, fungi, and bacteria. Globins are renowned for their ability to store and to transport oxygen, but additional globin functions such as sensing, signaling, and detoxification have been proposed. Recently, we found that the zebrafish globin X protein is myristoylated and palmitoylated at its N-terminus. The addition of fatty acids results in an association with the cellular membranes, suggesting a previously unrecognized globin function. In this study, we show that N-terminal acylation likely occurs in globin proteins from a broad range of phyla. An N-terminal myristoylation site was identified in 90 nonredundant globins from Chlorophyta, Heterokontophyta, Cnidaria, Mollusca, Arthropoda, Nematoda, Echinodermata, Hemichordata, and Chordata (including Cephalochordata), of which 66 proteins carry an additional palmitoylation site. Bayesian phylogenetic analyses identified five major globin families, which may mirror the ancient globin diversity of the Metazoa. Globin X-like proteins form two related clades, which diverged before the radiation of the Eumetazoa. Vertebrate hemoglobin (Hb), myoglobin, cytoglobin, globin E, and globin Y form a strongly supported common clade, which is the sister group of a clade consisting of invertebrate Hbs and relatives. The N-terminally acylated globins do not form a single monophyletic group but are distributed to four distinct clades. This pattern may be either explained by multiple introduction of an N-terminal acylation site into distinct globin lineages or by the origin of animal respiratory globins from a membrane-bound ancestor. Similarly, respiratory globins were not monophyletic. This suggests that respiratory globins might have emerged independently several times and that the early metazoan globins might have been associated with a membrane and carried out a function that was related to lipid protection or signaling.
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Affiliation(s)
- Miriam Blank
- Institute of Zoology and Zoological Museum, Department of Biology, University of Hamburg, Hamburg, Germany
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47
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McRonald FE, Risk JM, Hodges NJ. Protection from intracellular oxidative stress by cytoglobin in normal and cancerous oesophageal cells. PLoS One 2012; 7:e30587. [PMID: 22359545 PMCID: PMC3281032 DOI: 10.1371/journal.pone.0030587] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 12/22/2011] [Indexed: 01/09/2023] Open
Abstract
Cytoglobin is an intracellular globin of unknown function that is expressed mostly in cells of a myofibroblast lineage. Possible functions of cytoglobin include buffering of intracellular oxygen and detoxification of reactive oxygen species. Previous work in our laboratory has demonstrated that cytoglobin affords protection from oxidant-induced DNA damage when over expressed in vitro, but the importance of this in more physiologically relevant models of disease is unknown. Cytoglobin is a candidate for the tylosis with oesophageal cancer gene, and its expression is strongly down-regulated in non-cancerous oesophageal biopsies from patients with TOC compared with normal biopsies. Therefore, oesophageal cells provide an ideal experimental model to test our hypothesis that downregulation of cytoglobin expression sensitises cells to the damaging effects of reactive oxygen species, particularly oxidative DNA damage, and that this could potentially contribute to the TOC phenotype. In the current study, we tested this hypothesis by manipulating cytoglobin expression in both normal and oesophageal cancer cell lines, which have normal physiological and no expression of cytoglobin respectively. Our results show that, in agreement with previous findings, over expression of cytoglobin in cancer cell lines afforded protection from chemically-induced oxidative stress but this was only observed at non-physiological concentrations of cytoglobin. In addition, down regulation of cytoglobin in normal oesophageal cells had no effect on their sensitivity to oxidative stress as assessed by a number of end points. We therefore conclude that normal physiological concentrations of cytoglobin do not offer cytoprotection from reactive oxygen species, at least in the current experimental model.
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Affiliation(s)
- Fiona E. McRonald
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, United Kingdom
- School of Dentistry, The University of Liverpool, Liverpool, United Kingdom
| | - Janet M. Risk
- School of Dentistry, The University of Liverpool, Liverpool, United Kingdom
| | - Nikolas J. Hodges
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, United Kingdom
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