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Song Y, Laskay ÜA, Vilcins IME, Barbour AG, Wysocki VH. Top-down-assisted bottom-up method for homologous protein sequencing: hemoglobin from 33 bird species. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1875-84. [PMID: 26111519 PMCID: PMC6467653 DOI: 10.1007/s13361-015-1185-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/08/2015] [Accepted: 05/08/2015] [Indexed: 05/12/2023]
Abstract
Ticks are vectors for disease transmission because they are indiscriminant in their feeding on multiple vertebrate hosts, transmitting pathogens between their hosts. Identifying the hosts on which ticks have fed is important for disease prevention and intervention. We have previously shown that hemoglobin (Hb) remnants from a host on which a tick fed can be used to reveal the host's identity. For the present research, blood was collected from 33 bird species that are common in the U.S. as hosts for ticks but that have unknown Hb sequences. A top-down-assisted bottom-up mass spectrometry approach with a customized searching database, based on variability in known bird hemoglobin sequences, has been devised to facilitate fast and complete sequencing of hemoglobin from birds with unknown sequences. These hemoglobin sequences will be added to a hemoglobin database and used for tick host identification. The general approach has the potential to sequence any set of homologous proteins completely in a rapid manner. Graphical Abstract ᅟ.
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Affiliation(s)
- Yang Song
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Ünige A Laskay
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Inger-Marie E Vilcins
- Emerging and Acute Infectious Diseases Branch, Department of State Health Services, Austin, TX, 78756, USA
| | - Alan G Barbour
- Microbiology and Molecular Genetics, Medicine, and Ecology and Evolutionary Biology, University of California, Irvine, CA, 92687, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA.
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Grispo MT, Natarajan C, Projecto-Garcia J, Moriyama H, Weber RE, Storz JF. Gene duplication and the evolution of hemoglobin isoform differentiation in birds. J Biol Chem 2012; 287:37647-58. [PMID: 22962007 PMCID: PMC3488042 DOI: 10.1074/jbc.m112.375600] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 09/06/2012] [Indexed: 11/06/2022] Open
Abstract
The majority of bird species co-express two functionally distinct hemoglobin (Hb) isoforms in definitive erythrocytes as follows: HbA (the major adult Hb isoform, with α-chain subunits encoded by the α(A)-globin gene) and HbD (the minor adult Hb isoform, with α-chain subunits encoded by the α(D)-globin gene). The α(D)-globin gene originated via tandem duplication of an embryonic α-like globin gene in the stem lineage of tetrapod vertebrates, which suggests the possibility that functional differentiation between the HbA and HbD isoforms may be attributable to a retained ancestral character state in HbD that harkens back to a primordial, embryonic function. To investigate this possibility, we conducted a combined analysis of protein biochemistry and sequence evolution to characterize the structural and functional basis of Hb isoform differentiation in birds. Functional experiments involving purified HbA and HbD isoforms from 11 different bird species revealed that HbD is characterized by a consistently higher O(2) affinity in the presence of allosteric effectors such as organic phosphates and Cl(-) ions. In the case of both HbA and HbD, analyses of oxygenation properties under the two-state Monod-Wyman-Changeux allosteric model revealed that the pH dependence of Hb-O(2) affinity stems primarily from changes in the O(2) association constant of deoxy (T-state)-Hb. Ancestral sequence reconstructions revealed that the amino acid substitutions that distinguish the adult-expressed Hb isoforms are not attributable to the retention of an ancestral (pre-duplication) character state in the α(D)-globin gene that is shared with the embryonic α-like globin gene.
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MESH Headings
- Algorithms
- Amino Acid Sequence
- Animals
- Binding Sites/genetics
- Binding, Competitive
- Birds/blood
- Birds/classification
- Birds/genetics
- Cloning, Molecular
- Evolution, Molecular
- Gene Duplication
- Genetic Variation
- Hemoglobin A/chemistry
- Hemoglobin A/genetics
- Hemoglobin A/metabolism
- Hemoglobins/chemistry
- Hemoglobins/genetics
- Hemoglobins/metabolism
- Hemoglobins, Abnormal/chemistry
- Hemoglobins, Abnormal/genetics
- Hemoglobins, Abnormal/metabolism
- Kinetics
- Models, Molecular
- Molecular Sequence Data
- Oxygen/chemistry
- Oxygen/metabolism
- Protein Binding
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Protein Structure, Tertiary
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
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Affiliation(s)
- Michael T. Grispo
- From the School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588 and
| | | | - Joana Projecto-Garcia
- From the School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588 and
| | - Hideaki Moriyama
- From the School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588 and
| | - Roy E. Weber
- Zoophysiology, Institute for Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jay F. Storz
- From the School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588 and
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Reischl E, Dafre AL, Franco JL, Wilhelm Filho D. Distribution, adaptation and physiological meaning of thiols from vertebrate hemoglobins. Comp Biochem Physiol C Toxicol Pharmacol 2007; 146:22-53. [PMID: 17368111 DOI: 10.1016/j.cbpc.2006.07.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 06/16/2006] [Accepted: 07/20/2006] [Indexed: 12/19/2022]
Abstract
In the present review, the sequences of hemoglobins (Hb) of 267 adult vertebrate species belonging to eight major vertebrate taxa are examined for the presence and location of cysteinyl residues in an attempt at correlation with their ecophysiology. Essentially, all vertebrates have surface cysteinyl residues in Hb molecules whereby their thiol groups may become highly reactive. Thiol-rich Hbs may display eight or more thiols per tetramer. In vertebrates so far examined, the cysteinyl residues occur in 44 different sequence positions in alpha chains and 41 positions in beta chains. Most of them are conservatively located and occur in only a few positions in Teleostei, Aves and Mammalia, whereas they are dispersed in Amphibia. The internal cysteinyl residue alpha104 is ubiquitous in vertebrates. Residue beta93 is highly conserved in reptiles, birds and mammals. The number of cysteine residues per tetramer with solvent access varies in vertebrates, mammalians and bony fish having the lowest number of external residues, whereas nearly all external cysteine residues in Aves and Lepidosauria are of the surface crevice type. In cartilaginous fish, amphibians, Crocodylidae and fresh water turtles, a substantial portion of the solvent accessible thiols are of the totally external type. Recent evidence shows that some Hb thiol groups are highly reactive and undergo extensive and reversible S-thiolation, and that they may be implicated in interorgan redox equilibrium processes. Participation of thiol groups in nitric oxide ((*)NO) metabolism has also been proved. The evidence argues for a new physiologically relevant role for Hb via involvement in free radical and antioxidant metabolism.
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Affiliation(s)
- Evaldo Reischl
- Departamento de Biofísica and Curso de Pós-Graduação em Ciências Biológicas: Fisiologia, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil.
| | - Alcir Luiz Dafre
- Departamento de Ciências Fisiológicas, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, 8804-900 Florianópolis, SC, Brazil.
| | - Jeferson Luis Franco
- Departamento de Ciências Fisiológicas, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, 8804-900 Florianópolis, SC, Brazil
| | - Danilo Wilhelm Filho
- Departamento de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil.
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Hoffmann FG, Storz JF. The alphaD-globin gene originated via duplication of an embryonic alpha-like globin gene in the ancestor of tetrapod vertebrates. Mol Biol Evol 2007; 24:1982-90. [PMID: 17586601 DOI: 10.1093/molbev/msm127] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Gene duplication is thought to play an important role in the co-option of existing protein functions to new physiological pathways. The globin superfamily of genes provides an excellent example of the kind of physiological versatility that can be attained through the functional and regulatory divergence of duplicated genes that encode different subunit polypeptides of the tetrameric hemoglobin protein. In contrast to prevailing views about the evolutionary history of the alpha-globin gene family, here we present phylogenetic evidence that the alpha(A)- and alpha(D)-globin genes are not the product of a single, tandem duplication of an ancestral globin gene with adult function in the common ancestor of extant birds, reptiles, and mammals. Instead, our analysis reveals that the alpha(D)-globin gene of amniote vertebrates arose via duplication of an embryonic alpha-like globin gene that predated the radiation of tetrapods. The important evolutionary implication is that the distinct biochemical properties of alpha(D)-hemoglobin (HbD) are not exclusively derived characters that can be attributed to a post-duplication process of neofunctionalization. Rather, many of the distinct biochemical properties of HbD are retained ancestral characters that reflect the fact that the alpha(D)-globin gene arose via duplication of a gene that had a larval/embryonic function. These insights into the evolutionary origin of HbD illustrate how adaptive modifications of physiological pathways may result from the retention and opportunistic co-option of ancestral protein functions.
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Sumin MN, Salimov DF, Yushkov BG. Study of red blood cells of the house sparrow Paster domesticus L. in hypobaric hypoxia. J EVOL BIOCHEM PHYS+ 2007. [DOI: 10.1134/s002209300702010x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Eguchi Y, Eguchi T. Amino acid sequence of Kalinowaski's Tinamou (Nothoprocta kalinowskii) hemoglobin and the rate of evolution of bird alphaD-globin. JOURNAL OF PROTEIN CHEMISTRY 2001; 20:543-9. [PMID: 11838542 DOI: 10.1023/a:1013317112913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two hemoglobin components are recognized in erythrocytes of the adult Tinamou. We determined the amino acid sequences of Tinamou alphaD-, alphaA-, and beta-globins from intact globin chains and several chemically cleaved fragments. A remarkable feature of Tinamou hemoglobin was a deletion in the alphaD-globin chain. This has not been reported in the literature, except in pigeon embryonic alphaD-globin. The amino acid sequences of Tinamou globin were highly similar to those of Ostrich and Rhea hemoglobin. Comparison between Tinamou, Ostrich, and Rhea that suggested the evolution speed of globin, alphaD = alphaA > beta, was related with the early appearance birds. The important residues in Tinamou hemoglobin as the heme contact and oxygen binding regions were highly conserved in other species.
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Affiliation(s)
- Y Eguchi
- Research Laboratory Center, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan.
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Vossbrinck CR, Debrunner-Vossbrinck BA, Crang RFE, Kuras M. Insect hemoglobin production: A unique system utilizing ribosome clusters and iron/polyphosphate bodies. Naturwissenschaften 1994. [DOI: 10.1007/bf01131578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Prinzinger R, Misovic A. Vogelblut — eine allometrische Übersicht der Bestandteile. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf01640285] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Eguchi Y, Nakashima Y, Takei H. Amino-acid sequence of the alpha D- and beta-polypeptide chains of the Japanese quail hemoglobin. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1993; 374:111-6. [PMID: 8471178 DOI: 10.1515/bchm3.1993.374.1-6.111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Two hemoglobin components are recognized in the erythrocytes of the adult Japanese quail: a major (Q-II) and a minor (Q-I) component. We have determined the amino-acid sequence of the alpha D-globin of the minor component and the beta-globin which is common to both components by conventional protein sequence analysis. The sequences of both the alpha D- and the beta-globins showed close homology with those of their counterpart constituents in other avian hemoglobins. Proline at position 119 in the alpha D-globin which is known to be critical for the altitude respiration by the alpha 1 beta 1 interface is conserved in the Japanese quail hemoglobin.
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Affiliation(s)
- Y Eguchi
- Department of Biochemistry, University of the Ryukyus Faculty of Medicine
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Giardina B, Corda M, Pellegrini MG, Sanna MT, Brix O, Clementi ME, Condo SG. Flight and heat dissipation in birds. A possible molecular mechanism. FEBS Lett 1990; 270:173-6. [PMID: 2226779 DOI: 10.1016/0014-5793(90)81260-u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Birds during normal sustained flight must be able to dissipate more than 8 times as much heat as during rest in order not to be overheated. The experiments reported in this note on the hemoglobin systems from two different birds indicate the existence of a molecular mechanism by which hemoglobin is used simultaneously for oxygen transport and heat dissipation.
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Affiliation(s)
- B Giardina
- Department of Experimental Medicine and Biochemical Sciences, II University of Rome, Italy
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Rücknagel KP, Wiesner H, Braunitzer G. Carnivora: the primary structure of the beach marten (Martes foina, Mustelidae) hemoglobin. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1990; 371:503-9. [PMID: 2390216 DOI: 10.1515/bchm3.1990.371.1.503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The primary structures of alpha- and beta-chains from the hemoglobin of the Beach Marten (Martes foina, Carnivora) are presented. The globin chains were separated on CM-cellulose in 8M urea buffer. The amino-acid sequences were established by automatic liquid- and gas-phase Edman degradation of the intact chains and the tryptic peptides from oxidized chains. Comparison of the sequences with human hemoglobin shows 21 exchanges in the alpha- and 12 in the beta-chains. The differences concerning heme and interchain contact sites as well as the substitution alpha 77 (EF6)Pro----Ala are discussed. The latter is observed for the first time in a mammalian hemoglobin. The sequences are compared with those of other Carnivora. The beta-chains of Martes foina and Pteronura brasiliensis (Giant Otter) are found to be identical, but their alpha-chains differ in 7 positions. The surprising small numbers of exchanges between the hemoglobin from Beach marten and that from Lesser and Greater Panda are discussed.
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Affiliation(s)
- K P Rücknagel
- Max-Planck-Institut für Biochemie, Abteilung Proteinchemie, Martinsried bei München
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