1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
Astaxanthin biosynthetic pathway: Molecular phylogenies and evolutionary behaviour of Crt genes in eubacteria. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
3
|
Hill R, Hargrove M, Arredondo-Peter R. Phytoglobin: a novel nomenclature for plant globins accepted by the globin community at the 2014 XVIII conference on Oxygen-Binding and Sensing Proteins. F1000Res 2016; 5:212. [PMID: 26998237 PMCID: PMC4792203 DOI: 10.12688/f1000research.8133.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2016] [Indexed: 11/20/2022] Open
Abstract
Hemoglobin (Hb) is a heme-containing protein found in the red blood cells of vertebrates. For many years, the only known Hb-like molecule in plants was leghemoglobin (Lb). The discovery that other Hb-like proteins existed in plants led to the term “nonsymbiotic Hbs (nsHbs)” to differentiate them from the Lbs. While this terminology was adequate in the early stages of research on the protein, the complexity of the research in this area necessitates a change in the definition of these proteins to delineate them from red blood cell Hb. At the 2014 XVIII Conference on Oxygen-Binding and Sensing Proteins, the group devoted to the study of heme-containing proteins, this issue was discussed and a consensus was reached on a proposed name change. We propose
Phytoglobin (Phytogb) as a logical, descriptive name to describe a heme-containing (Hb-like) protein found in plants. It will be readily recognized by the research community without a prolonged explanation of the origin of the term. The classification system that has been established can essentially remain unchanged substituting Phytogb in place of nsHb. Here, we present a guide to the new nomenclature, with reference to the existing terminology and a phylogenetic scheme, placing the known Phytogbs in the new nomenclature.
Collapse
Affiliation(s)
- Robert Hill
- Department of Plant Science, University of Manitoba, Winnipeg, Canada
| | - Mark Hargrove
- Molecular Biology Building, Deptartment of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, USA
| | - Raúl Arredondo-Peter
- Laboratorio de Biofísica y Biología Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Yue J, Hu X, Huang J. Origin of plant auxin biosynthesis. TRENDS IN PLANT SCIENCE 2014; 19:764-70. [PMID: 25129418 DOI: 10.1016/j.tplants.2014.07.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 06/30/2014] [Accepted: 07/17/2014] [Indexed: 05/05/2023]
Abstract
The recent finding of the tryptophan aminotransferase (TAA)/flavin monooxygenase (YUC) pathway as the principal route of auxin production in plants provides an opportunity to revisit the origin of plant auxin biosynthesis. Phylogenetic analyses of the TAA and YUC gene families provide very little evidence for the production of indole-3-acetic acid (IAA) in algae. Instead, horizontal gene transfer of YUCs from bacteria to the ancestral land plant suggests that the TAA/YUC pathway is a land plant innovation. In this Opinion article we postulate that the origin of tryptophan-dependent IAA biosynthesis in land plants might have evolved in response to interactions with microbes, particularly bacteria, allowing plants to counteract bacterial activities and control their own auxin signaling.
Collapse
Affiliation(s)
- Jipei Yue
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Xiangyang Hu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| |
Collapse
|
6
|
Leiva-Eriksson N, Pin PA, Kraft T, Dohm JC, Minoche AE, Himmelbauer H, Bülow L. Differential expression patterns of non-symbiotic hemoglobins in sugar beet (Beta vulgaris ssp. vulgaris). PLANT & CELL PHYSIOLOGY 2014; 55:834-44. [PMID: 24486763 DOI: 10.1093/pcp/pcu027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Biennial sugar beet (Beta vulgaris spp. vulgaris) is a Caryophyllidae that has adapted its growth cycle to the seasonal temperature and daylength variation of temperate regions. This is the first time a holistic study of the expression pattern of non-symbiotic hemoglobins (nsHbs) is being carried out in a member of this group and under two essential environmental conditions for flowering, namely vernalization and length of photoperiod. BvHb genes were identified by sequence homology searches against the latest draft of the sugar beet genome. Three nsHb genes (BvHb1.1, BvHb1.2 and BvHb2) and one truncated Hb gene (BvHb3) were found in the genome of sugar beet. Gene expression profiling of the nsHb genes was carried out by quantitative PCR in different organs and developmental stages, as well as during vernalization and under different photoperiods. BvHb1.1 and BvHb2 showed differential expression during vernalization as well as during long and short days. The high expression of BvHb2 indicates that it has an active role in the cell, maybe even taking over some BvHb1.2 functions, except during germination where BvHb1.2 together with BvHb1.1-both Class 1 nsHbs-are highly expressed. The unprecedented finding of a leader peptide at the N-terminus of BvHb1.1, for the first time in an nsHb from higher plants, together with its observed expression indicate that it may have a very specific role due to its suggested location in chloroplasts. Our findings open up new possibilities for research, breeding and engineering since Hbs could be more involved in plant development than previously was anticipated.
Collapse
Affiliation(s)
- Nélida Leiva-Eriksson
- Department of Pure and Applied Biochemistry, Lund University, Box 124, 221.00 Lund, Sweden
| | | | | | | | | | | | | |
Collapse
|
7
|
Igamberdiev AU, Stasolla C, Hill RD. Low Oxygen Stress, Nonsymbiotic Hemoglobins, NO, and Programmed Cell Death. LOW-OXYGEN STRESS IN PLANTS 2014. [DOI: 10.1007/978-3-7091-1254-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
8
|
Rodríguez-Alonso G, Arredondo-Peter R. Variability of non-symbiotic and truncated hemoglobin genes from the genome of cultivated monocots. Commun Integr Biol 2013; 6:e27496. [PMID: 24563718 PMCID: PMC3923788 DOI: 10.4161/cib.27496] [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: 11/28/2013] [Accepted: 12/12/2013] [Indexed: 11/19/2022] Open
Abstract
Non-symbiotic (nsHb) and truncated (tHb) hemoglobins (Hbs) have been detected in a variety of land plants. The evolution of land plant nsHbs and tHbs at the protein level is well documented; however, little is known about the evolution of genes coding for these proteins. For example, the variability of the land plant nshb and thb genes is not known. Here, we report the variability of the nshb and thb genes from the genome of the cultivated monocots Brachypodium distachyon, Hordeum vulgare (barley), Oryza glaberrima (rice), O. rufipogon (rice), O. sativa (rice) var indica, O. sativa (rice) var japonica, Panicum virgatum (switchgrass), Setaria italica (foxtail millet), Sorghum bicolor (sorghum), Triticum aestivum (wheat), and Zea mays ssp. mays (maize) using sequence comparison and computational methods. Our results revealed that in cultivated monocots variability is higher in nshbs than in thbs, and suggest that major substitution events that occurred during the evolution of the cultivated monocot hbs were A→G and T→C transitions and that these genes evolved under the effect of neutral selection.
Collapse
Affiliation(s)
- Gustavo Rodríguez-Alonso
- Laboratorio de Biofísica y Biología Molecular; Departamento de Bioquímica y Biología Molecular; Facultad de Ciencias; Universidad Autónoma del Estado de Morelos; Cuernavaca, Morelos, México
| | - 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, México
| |
Collapse
|
9
|
Matilla AJ, Rodríguez-Gacio MDC. Non-symbiotic hemoglobins in the life of seeds. PHYTOCHEMISTRY 2013; 87:7-15. [PMID: 23286879 DOI: 10.1016/j.phytochem.2012.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 11/13/2012] [Accepted: 11/21/2012] [Indexed: 06/01/2023]
Abstract
Non-symbiotic hemoglobins (nsHbs), ancestors of symbiotic-Hbs, are hexacoordinated dimeric proteins, for which the crystal structure is well described. According to the extent of hexacoordination, nsHbs are classified as belonging to class-1 (nsHbs1) or class-2 (nsHbs2). The nsHbs1 show weak hexacoordination, moderate rates of O(2)-binding, very small rates of O(2) dissociation, and a remarkably high affinity for O(2), all suggesting a function involving O(2) scavenging. In contrast, the nsHbs2 exhibit strong hexacoordination, low rates of O(2)-binding and moderately low O(2) dissociation and affinity, suggesting a sensing role for sustained low (μM) levels of O(2). The existence of spatial and specific expression of nsHbs1 suggests that nsHbs play tissue-specific rather than housekeeping functions. The permeation of O(2) into seeds is usually prevented during the desiccation phase and early imbibition, generating an internal hypoxic environment that leads to ATP limitation. During evolution, the seed has acquired mechanisms to prevent or reduce this hypoxic stress. The nsHbs1/NO cycle appear to be involved in modulating the redox state in the seed and in maintaining an active metabolism. Under O(2) deficit, NADH and NO are synthesized in the seed and nsHbs1 scavenges O(2), which is used to transform NO into NO(3)(-) with concomitant formation of Fe(3+)-nsHbs1. Expression of nsHbs1 is not detectable in dry viable seeds. However, in the seeds cross-talk occurs between nsHbs1 and NO during germination. This review considers the current status of our knowledge of seed nsHbs and considers key issues of further work to better understand their role in seed physiology.
Collapse
Affiliation(s)
- Angel J Matilla
- Department of Plant Physiology, University of Santiago de Compostela, 15782 Santiago de Compostela, A Coruña, Spain.
| | | |
Collapse
|
10
|
Mukhi N, Dhindwal S, Uppal S, Kumar P, Kaur J, Kundu S. X-ray crystallographic structural characteristics of Arabidopsis hemoglobin I and their functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1944-56. [PMID: 23485912 DOI: 10.1016/j.bbapap.2013.02.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/16/2013] [Accepted: 02/19/2013] [Indexed: 11/24/2022]
Abstract
Genome of the model dicot flowering plant, Arabidopsis thaliana, a popular tool for understanding molecular biology of plant physiology, encodes all three classes of plant hemoglobins that differ in their sequence, ligand binding and spectral properties. As such these globins are of considerable attention. Crystal structures of few members of plant class I nonsymbiotic hemoglobin have been described earlier. Here we report the crystal structure of Arabidopsis class I hemoglobin (AHb1) to 2.2Ǻ and compare its key features with the structures of similar nonsymbiotic hemoglobin from other species. Crystal structure of AHb1 is homologous to the related members with similar globin fold and heme pocket architecture. The structure is homodimeric in the asymmetric unit with both distal and proximal histidines coordinating to the heme iron atom. Residues lining the dimeric interface are also conserved in AHb1 with the exception of additional electrostatic interaction between H112 and E113 of each subunit and that involving Y119 through two water molecules. In addition, differences in heme pocket non-covalent interactions, a novel Ser residue at F7 position, Xe binding site variability, internal cavity topology differences, CD loop conformation and stability and other such properties might explain kinetic variability in AHb1. Detailed cavity analysis of AHb1 showed the presence of a novel long tunnel connecting the distal pockets of both the monomers. Presence of such tunnel, along with conformational heterogeneity observed in the two chains, might suggest cooperative ligand binding and support its role in NO scavenging. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
Collapse
Affiliation(s)
- Nitika Mukhi
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | | | | | | | | | | |
Collapse
|
11
|
Abstract
Approximately, 20 years ago, a haemoglobin gene was identified within the genome of the cyanobacterium Nostoc commune. Haemoglobins have now been confirmed in multiple species of photosynthetic microbes beyond N. commune, and the diversity of these proteins has recently come under increased scrutiny. This chapter summarizes the state of knowledge concerning the phylogeny, physiology and chemistry of globins in cyanobacteria and green algae. Sequence information is by far the best developed and the most rapidly expanding aspect of the field. Structural and ligand-binding properties have been described for just a few proteins. Physiological data are available for even fewer. Although activities such as nitric oxide dioxygenation and oxygen scavenging are strong candidates for cellular function, dedicated studies will be required to complete the story on this intriguing and ancient group of proteins.
Collapse
|
12
|
Vinogradov SN, Bailly X, Smith DR, Tinajero-Trejo M, Poole RK, Hoogewijs D. Microbial eukaryote globins. Adv Microb Physiol 2013; 63:391-446. [PMID: 24054801 DOI: 10.1016/b978-0-12-407693-8.00009-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A bioinformatics survey of about 120 protist and 240 fungal genomes and transcriptomes revealed a broad array of globins, representing five of the eight subfamilies identified in bacteria. Most conspicuous is the absence of protoglobins and globin-coupled sensors, except for a two-domain globin in Leishmanias, that comprises a nucleotidyl cyclase domain, and the virtual absence of truncated group 3 globins. In contrast to bacteria, co-occurrence of more than two globin subfamilies appears to be rare in protists. Although globins were lacking in the Apicomplexa and the Microsporidia intracellular pathogens, they occurred in the pathogenic Trypanosomatidae, Stramenopiles and certain fungi. Flavohaemoglobins (FHbs) and related single-domain globins occur across the protist groups. Fungi are unique in having FHbs co-occurring with sensor single-domain globins (SSDgbs). Obligately biotrophic fungi covered in our analysis lack globins. Furthermore, SSDgbs occur only in a heterolobosean amoeba, Naegleria and the stramenopile Hyphochytrium. Of the three subfamilies of truncated Mb-fold globins, TrHb1s appear to be the most widespread, occurring as multiple copies in chlorophyte and ciliophora genomes, many as multidomain proteins. Although the ciliates appear to have only TrHb1s, the chlorophytes have Mb-like globins and TrHb2s, both closely related to the corresponding plant globins. The presently available number of protist genomes is inadequate to provide a definitive census of their globins. Bayesian molecular analyses of single-domain 3/3 Mb-fold globins suggest a close relationship of chlorophyte and haptophyte globins, including choanoflagellate and Capsaspora globins to land plant symbiotic and non-symbiotic haemoglobins and to vertebrate neuroglobins.
Collapse
|
13
|
Vázquez-Limón C, Hoogewijs D, Vinogradov SN, Arredondo-Peter R. The evolution of land plant hemoglobins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 191-192:71-81. [PMID: 22682566 DOI: 10.1016/j.plantsci.2012.04.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 04/24/2012] [Accepted: 04/25/2012] [Indexed: 05/04/2023]
Abstract
This review discusses the evolution of land plant hemoglobins within the broader context of eukaryote hemoglobins and the three families of bacterial globins. Most eukaryote hemoglobins, including metazoan globins and the symbiotic and non-symbiotic plant hemoglobins, are homologous to the bacterial 3/3-fold flavohemoglobins. The remaining plant hemoglobins are homologous to the bacterial 2/2-fold group 2 hemoglobins. We have proposed that all eukaryote globins were acquired via horizontal gene transfer concomitant with the endosymbiotic events responsible for the origin of mitochondria and chloroplasts. Although the 3/3 hemoglobins originated in the ancestor of green algae and plants prior to the emergence of embryophytes at about 450 mya, the 2/2 hemoglobins appear to have originated via horizontal gene transfer from a bacterium ancestral to present day Chloroflexi. Unlike the 2/2 hemoglobins, the evolution of the 3/3 hemoglobins was accompanied by duplication, diversification, and functional adaptations. Duplication of the ancestral plant nshb gene into the nshb-1 and nshb-2 lineages occurred prior to the monocot-dicot divergence at ca. 140 mya. It was followed by the emergence of symbiotic hemoglobins from a non-symbiotic hemoglobin precursor and further specialization, leading to leghemoglobins in N₂-fixing legume nodules concomitant with the origin of nodulation at ca. 60 mya. The transition of non-symbiotic to symbiotic hemoglobins (including to leghemoglobins) was accompanied by the alteration of heme-Fe coordination from hexa- to penta-coordination. Additional genomic information about Charophyte algae, the sister group to land plants, is required for the further clarification of plant globin phylogeny.
Collapse
Affiliation(s)
- Consuelo Vázquez-Limón
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | | | | | | |
Collapse
|