1
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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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Astegno A, Conter C, Bertoldi M, Dominici P. Structural Insights into the Heme Pocket and Oligomeric State of Non-Symbiotic Hemoglobins from Arabidopsis thaliana. Biomolecules 2020; 10:E1615. [PMID: 33260415 PMCID: PMC7761212 DOI: 10.3390/biom10121615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 11/18/2022] Open
Abstract
Non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana are hexacoordinate heme-proteins that likely have different biological roles, in view of diverse tissue localization, expression pattern, and ligand binding properties. Herein, we expand upon previous biophysical studies on these isoforms, focusing on their oligomeric states and circular dichroism (CD) characteristics. We found that AHb1 exists in solution in a concentration-dependent monomer-dimer equilibrium, while AHb2 is present only as a monomer. The quaternary structure of AHb1 affects its degree of hexacoordination with the formation of the dimer that enhances pentacoordination. Accordingly, the mutant of a conserved residue within the dimeric interface, AHb1-T45A, which is mostly monomeric in solution, has an equilibrium that is shifted toward a hexacoordinate form compared to the wild-type protein. CD studies further support differences in the globin's structure and heme moiety. The Soret CD spectra for AHb2 are opposite in sense to those for AHb1, reflecting different patterns of heme-protein side chain contacts in the two proteins. Moreover, the smaller contribution of the heme to the near-UV CD in AHb2 compared to AHb1 suggests a weaker heme-protein association in AHb2. Our data corroborate the structural diversity of AHb1 and AHb2 and confirm the leghemoglobin-like structural properties of AHb2.
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Affiliation(s)
- Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (A.A.); (C.C.)
| | - Carolina Conter
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (A.A.); (C.C.)
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie, 8, 37134 Verona, Italy;
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (A.A.); (C.C.)
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3
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Becana M, Yruela I, Sarath G, Catalán P, Hargrove MS. Plant hemoglobins: a journey from unicellular green algae to vascular plants. THE NEW PHYTOLOGIST 2020; 227:1618-1635. [PMID: 31960995 DOI: 10.1111/nph.16444] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/24/2019] [Indexed: 05/17/2023]
Abstract
Globins (Glbs) are widely distributed in archaea, bacteria and eukaryotes. They can be classified into proteins with 2/2 or 3/3 α-helical folding around the heme cavity. Both types of Glbs occur in green algae, bryophytes and vascular plants. The Glbs of angiosperms have been more intensively studied, and several protein structures have been solved. They can be hexacoordinate or pentacoordinate, depending on whether a histidine is coordinating or not at the sixth position of the iron atom. The 3/3 Glbs of class 1 and the 2/2 Glbs (also called class 3 in plants) are present in all angiosperms, whereas the 3/3 Glbs of class 2 have been only found in early angiosperms and eudicots. The three Glb classes are expected to play different roles. Class 1 Glbs are involved in hypoxia responses and modulate NO concentration, which may explain their roles in plant morphogenesis, hormone signaling, cell fate determination, nutrient deficiency, nitrogen metabolism and plant-microorganism symbioses. Symbiotic Glbs derive from class 1 or class 2 Glbs and transport O2 in nodules. The physiological roles of class 2 and class 3 Glbs are poorly defined but could involve O2 and NO transport and/or metabolism, respectively. More research is warranted on these intriguing proteins to determine their non-redundant functions.
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Affiliation(s)
- Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (CSIC), Apartado 13034, 50080, Zaragoza, Spain
| | - Inmaculada Yruela
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (CSIC), Apartado 13034, 50080, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC, Edificio I+D Campus Río Ebro, 50018, Zaragoza, Spain
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, East Campus, University of Nebraska-Lincoln, Lincoln, NE, 86583, USA
| | - Pilar Catalán
- Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC, Edificio I+D Campus Río Ebro, 50018, Zaragoza, Spain
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, 22071, Huesca, Spain
| | - Mark S Hargrove
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
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4
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Mot AC, Puscas C, Miclea P, Naumova-Letia G, Dorneanu S, Podar D, Dissmeyer N, Silaghi-Dumitrescu R. Redox control and autoxidation of class 1, 2 and 3 phytoglobins from Arabidopsis thaliana. Sci Rep 2018; 8:13714. [PMID: 30209406 PMCID: PMC6135765 DOI: 10.1038/s41598-018-31922-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/28/2018] [Indexed: 12/29/2022] Open
Abstract
Despite a recent increase in interest towards phytoglobins and their importance in plants, much is still unknown regarding their biochemical/biophysical properties and physiological roles. The present study presents data on three recombinant Arabidopsis phytoglobins in terms of their UV-vis and Raman spectroscopic characteristics, redox state control, redox potentials and autoxidation rates. The latter are strongly influenced by pH for all three hemoglobins - (with a fundamental involvement of the distal histidine), as well as by added anion concentrations - suggesting either a process dominated by nucleophilic displacement of superoxide for AtHb2 or an inhibitory effect for AtHb1 and AtHb3. Reducing agents, such as ascorbate and glutathione, are found to either enhance- (presumably via direct electron transfer or via allosteric regulation) or prevent autoxidation. HbFe3+ reduction was possible in the presence of high (presumably not physiologically relevant) concentrations of NADH, glutathione and ascorbate, with differing behaviors for the three globins. The iron coordination sphere is found to affect the autoxidation, redox state interconversion and redox potentials in these three phytoglobins.
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Affiliation(s)
- Augustin C Mot
- Research Center for Advanced Chemical Analysis, Instrumentation and Chemometrics, Babes-Bolyai University, 11 Arany Janos Street, RO-400028, Cluj-Napoca, Romania.
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, 1 Mihail Kogalniceanu Street, RO-400084, Cluj-Napoca, Romania.
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany.
| | - Cristina Puscas
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, 1 Mihail Kogalniceanu Street, RO-400084, Cluj-Napoca, Romania
| | - Patricia Miclea
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, 1 Mihail Kogalniceanu Street, RO-400084, Cluj-Napoca, Romania
| | - Galaba Naumova-Letia
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, 1 Mihail Kogalniceanu Street, RO-400084, Cluj-Napoca, Romania
| | - Sorin Dorneanu
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, 1 Mihail Kogalniceanu Street, RO-400084, Cluj-Napoca, Romania
| | - Dorina Podar
- Faculty of Biology and Geology, Babes-Bolyai University, 1 Mihail Kogalniceanu Street, RO-400084, Cluj-Napoca, Romania
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Radu Silaghi-Dumitrescu
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, 1 Mihail Kogalniceanu Street, RO-400084, Cluj-Napoca, Romania.
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5
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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6
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Mukhi N, Dhindwal S, Uppal S, Kapoor A, Arya R, Kumar P, Kaur J, Kundu S. Structural and Functional Significance of the N- and C-Terminal Appendages in Arabidopsis Truncated Hemoglobin. Biochemistry 2016; 55:1724-40. [PMID: 26913482 DOI: 10.1021/acs.biochem.5b01013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plant hemoglobins constitute three distinct groups: symbiotic, nonsymbiotic, and truncated hemoglobins. Structural investigation of symbiotic and nonsymbiotic (class I) hemoglobins revealed the presence of a vertebrate-like 3/3 globin fold in these proteins. In contrast, plant truncated hemoglobins are similar to bacterial truncated hemoglobins with a putative 2/2 α-helical globin fold. While multiple structures have been reported for plant hemoglobins of the first two categories, for plant truncated globins only one structure has been reported of late. Here, we report yet another crystal structure of the truncated hemoglobin from Arabidopsis thaliana (AHb3) with two water molecules in the heme pocket, of which one is distinctly coordinated to the heme iron, unlike the only available crystal structure of AHb3 with a hydroxyl ligand. AHb3 was monomeric in its crystallographic asymmetric unit; however, dimer was evident in the crystallographic symmetry, and the globin indeed existed as a stable dimer in solution. The tertiary structure of the protein exhibited a bacterial-like 2/2 α-helical globin fold with an additional N-terminal α-helical extension and disordered C-termini. To address the role of these extended termini in AHb3, which is yet unknown, N- and C-terminal deletion mutants were created and characterized and molecular dynamics simulations performed. The C-terminal deletion had an insignificant effect on most properties but perturbed the dimeric equilibrium of AHb3 and significantly influenced azide binding kinetics in the ferric state. These results along with the disordered nature of the C-terminus indicated its putative role in intramolecular or intermolecular interactions probably regulating protein-ligand and protein-protein interactions. While the N-terminal deletion did not change the overall globin fold, stability, or ligand binding kinetics, it seemed to have influenced coordination at the heme iron, the hydration status of the active site, and the quaternary structure of AHb3. Evidence indicated that the N-terminus is the predominant factor regulating the quaternary interaction appropriate to physiological requirements, dynamics of the side chains in the heme pocket, and tunnel organization in the protein matrix.
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Affiliation(s)
- Nitika Mukhi
- Department of Genetics, University of Delhi South Campus , New Delhi 110021, India
| | - Sonali Dhindwal
- Department of Biotechnology, Indian Institute of Technology , Roorkee, Uttarakhand 247667, India
| | - Sheetal Uppal
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Abhijeet Kapoor
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Richa Arya
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology , Roorkee, Uttarakhand 247667, India
| | - Jagreet Kaur
- Department of Genetics, University of Delhi South Campus , New Delhi 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
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7
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Pesce A, Bustamante JP, Bidon-Chanal A, Boechi L, Estrin DA, Luque FJ, Sebilo A, Guertin M, Bolognesi M, Ascenzi P, Nardini M. The N-terminal pre-A region of Mycobacterium tuberculosis 2/2HbN promotes NO-dioxygenase activity. FEBS J 2015; 283:305-22. [PMID: 26499089 DOI: 10.1111/febs.13571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 08/09/2015] [Accepted: 08/16/2015] [Indexed: 01/24/2023]
Abstract
UNLABELLED A unique defense mechanisms by which Mycobacterium tuberculosis protects itself from nitrosative stress is based on the O2 -dependent NO-dioxygenase (NOD) activity of truncated hemoglobin 2/2HbN (Mt2/2HbN). The NOD activity largely depends on the efficiency of ligand migration to the heme cavity through a two-tunnel (long and short) system; recently, it was also correlated with the presence at the Mt2/2HbN N-terminus of a short pre-A region, not conserved in most 2/2HbNs, whose deletion results in a drastic reduction of NO scavenging. In the present study, we report the crystal structure of Mt2/2HbN-ΔpreA, lacking the pre-A region, at a resolution of 1.53 Å. We show that removal of the pre-A region results in long range effects on the protein C-terminus, promoting the assembly of a stable dimer, both in the crystals and in solution. In the Mt2/2HbN-ΔpreA dimer, access of heme ligands to the short tunnel is hindered. Molecular dynamics simulations show that the long tunnel branch is the only accessible pathway for O2 -ligand migration to/from the heme, and that the gating residue Phe(62)E15 partly restricts the diameter of the tunnel. Accordingly, kinetic measurements indicate that the kon value for peroxynitrite isomerization by Mt2/2HbN-ΔpreA-Fe(III) is four-fold lower relative to the full-length protein, and that NO scavenging by Mt2/2HbN-ΔpreA-Fe(II)-O2 is reduced by 35-fold. Therefore, we speculate that Mt2/2HbN evolved to host the pre-A region as a mechanism for preventing dimerization, thus reinforcing the survival of the microorganism against the reactive nitrosative stress in macrophages. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank under accession number 5AB8.
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Affiliation(s)
| | - Juan P Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Argentina
| | - Axel Bidon-Chanal
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, University of Barcelona, Santa Coloma de Gramenet, Spain
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Argentina
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Argentina
| | - Francisco Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, University of Barcelona, Santa Coloma de Gramenet, Spain
| | - Anne Sebilo
- Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Quebec, Canada
| | - Michel Guertin
- Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Quebec, Canada
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Italy.,CNR-IBF and CIMAINA, University of Milan, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, Roma Tre University, Rome, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milan, Italy
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8
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Giordano D, Pesce A, Boechi L, Bustamante JP, Caldelli E, Howes BD, Riccio A, di Prisco G, Nardini M, Estrin D, Smulevich G, Bolognesi M, Verde C. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. FEBS J 2015; 282:2948-65. [PMID: 26040838 DOI: 10.1111/febs.13335] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/17/2015] [Accepted: 06/01/2015] [Indexed: 11/30/2022]
Abstract
Truncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two-on-two α-helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group-II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO), a cold-adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph-2/2HbO aquo-met crystal structure (at 2.21 Å resolution) shows typical features of group-II truncated hemoglobins, namely the two-on-two α-helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal-site hydrogen-bonded network that includes water molecules and several distal-site residues, including His(58)CD1. Analysis of Ph-2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph-2/2HbO can access diverse heme ligation states. Among these, detection of a low-spin heme hexa-coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme-Fe ligand. Altogether, the results show that Ph-2/2HbO maintains the general structural features of group-II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low temperature, high O2 concentration and low kinetic energy of molecules, experienced by organisms living in the Antarctic environment.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | | | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Juan Pablo Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Elena Caldelli
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Barry D Howes
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Alessia Riccio
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
| | - Dario Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Giulietta Smulevich
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Italy.,CNR-Institute of Biophysics and CIMAINA, University of Milano, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy.,Department of Biology, Roma 3 University, Italy
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9
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Peroxidase activity and involvement in the oxidative stress response of roseobacter denitrificans truncated hemoglobin. PLoS One 2015; 10:e0117768. [PMID: 25658318 PMCID: PMC4319818 DOI: 10.1371/journal.pone.0117768] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/01/2015] [Indexed: 11/19/2022] Open
Abstract
Roseobacter denitrificans is a member of the widespread marine Roseobacter genus. We report the first characterization of a truncated hemoglobin from R. denitrificans (Rd. trHb) that was purified in the heme-bound form from heterologous expression of the protein in Escherichia coli. Rd. trHb exhibits predominantly alpha-helical secondary structure and absorbs light at 412, 538 and 572 nm. The phylogenetic classification suggests that Rd. trHb falls into group II trHbs, whereas sequence alignments indicate that it shares certain important heme pocket residues with group I trHbs in addition to those of group II trHbs. The resonance Raman spectra indicate that the isolated Rd. trHb contains a ferric heme that is mostly 6-coordinate low-spin and that the heme of the ferrous form displays a mixture of 5- and 6-coordinate states. Two Fe-His stretching modes were detected, notably one at 248 cm-1, which has been reported in peroxidases and some flavohemoglobins that contain an Fe-His-Asp (or Glu) catalytic triad, but was never reported before in a trHb. We show that Rd. trHb exhibits a significant peroxidase activity with a (kcat/Km) value three orders of magnitude higher than that of bovine Hb and only one order lower than that of horseradish peroxidase. This enzymatic activity is pH-dependent with a pKa value ~6.8. Homology modeling suggests that residues known to be important for interactions with heme-bound ligands in group II trHbs from Mycobacterium tuberculosis and Bacillus subtilis are pointing toward to heme in Rd. trHb. Genomic organization and gene expression profiles imply possible functions for detoxification of reactive oxygen and nitrogen species in vivo. Altogether, Rd. trHb exhibits some distinctive features and appears equipped to help the bacterium to cope with reactive oxygen/nitrogen species and/or to operate redox biochemistry.
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10
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Abstract
Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice (
Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the
nshb genes, consisting of
hb1,
hb2,
hb3,
hb4 and
hb5, and a single copy of the
thb gene exist in
Oryza sativa var. indica and
O.
sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O
2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O
2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O
2-transport, O
2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice
nshb and
thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice
nshbs and
thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the
cis-elements and
trans-acting factors that regulate the expression of rice
hb genes, and the partial understanding of the evolution of rice Hbs.
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Affiliation(s)
- Raúl Arredondo-Peter
- Laboratorio de Biofísica y Biología Molecular, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, 62210, Mexico
| | - Jose F Moran
- Instituto de Agrobiotecnología, IdAB-CSIC-Universidad Pública de Navarra-Gobierno de Navarra, Navarre, E-31192, Spain
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, University of Nebraska-Lincoln, Lincoln, NE, 68583-0937, USA
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11
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Abstract
In the last few years, advances in algal research have identified the participation of haemoglobins in nitrogen metabolism and the management of reactive nitrogen and oxygen species. This chapter summarises the state of knowledge concerning algal haemoglobins with a focus on the most widely used model system, namely, Chlamydomonas reinhardtii. Genetic, physiologic, structural, and chemical information is compiled to provide a framework for further studies.
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Affiliation(s)
- Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.
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