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Zhang W, Zhang Y, Shi X, Wang S, Bao Y. Hemoglobin wonders: a fascinating gas transporter dive into molluscs. Crit Rev Biochem Mol Biol 2023; 58:132-157. [PMID: 38189101 DOI: 10.1080/10409238.2023.2299381] [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: 08/22/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of globin domains and their respective locations. These Hbs exhibit variation in assembly, ranging from monomeric and dimeric to higher-order multimeric forms. Typically, molluscan Hbs display moderately high oxygen affinity, weak cooperativity, and varying pH sensitivity. Hb's potential role in antimicrobial pathways could augment the immune defense of bivalves, which may be a complement to their lack of adaptive immunity. The role of Hb as a respiratory protein in bivalves likely originated from the substitution of hemocyanin. Molluscan Hbs demonstrate adaptive evolution in response to environmental changes via various strategies (e.g. increasing Hb types, multimerization, and amino acid residue substitutions at key sites), enhancing or altering functional properties for habitat adaptation. Concurrently, an increase in Hb assembly diversity, coupled with a downward trend in oxygen affinity, is observed during molluscan differentiation and evolution. Hb in Protobranchia, Heteroconchia, and Pteriomorphia bivalves originated from separate ancestors, with Protobranchia inheriting a relative ancient molluscan Hb gene. In bivalves, extracellular Hbs share a common origin, while gill Hbs likely emerged from convergent evolution. In summary, research on molluscan Hbs offers valuable insights into the origins, biological variations, and adaptive evolution of animal Hbs.
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Affiliation(s)
- Weifeng Zhang
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Yang Zhang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xizhi Shi
- School of Marine Science, Ningbo University, Ningbo, China
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China and National Laboratory for Marine Science and Technology (LMBB & LMFSFPP), Qingdao, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
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Marchany-Rivera D, Estremera-Andújar RA, Nieves-Marrero C, Ruiz-Martínez CR, Bauer W, López-Garriga J. SAXS structure of homodimeric oxyHemoglobin III from bivalve Lucina pectinata. Biopolymers 2021; 112:e23427. [PMID: 33792032 DOI: 10.1002/bip.23427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 11/10/2022]
Abstract
Hemoglobin III (HbIII) is one of the two oxygen reactive hemoproteins present in the bivalve, Lucina pectinata. The clam inhabits a sulfur-rich environment and HbIII is the only hemoprotein present in the system which does not yet have a structure described elsewhere. It is known that HbIII exists as a heterodimer with hemoglobin II (HbII) to generate the stable Oxy(HbII-HbIII) complex but it remains unknown if HbIII can form a homodimeric species. Here, a new chromatographic methodology to separate OxyHbIII from the HbII-HbIII dimer has been developed, employing a fast performance liquid chromatography and ionic exchange chromatography column. The nature of OxyHbIII in solution at concentrations from 1.6 mg/mL to 20.4 mg/mL was studied using small angle X-ray scattering (SAXS). The results show that at all concentrations, the Oxy(HbIII-HbIII) dimer dominates in solution. However, as the concentration increases to nonphysiological values, 20.4 mg/mL, HbIII forms a 30% tetrameric fraction. Thus, there is a direct relationship between the Oxy(HbIII-HbIII) oligomeric form and hemoglobin concentration. We suggest it is likely that the OxyHbIII dimer contributes to active oxygen transport in tissues of L pectinata, where the Oxy(HbII-HbIII) complex is not present.
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Affiliation(s)
- Darya Marchany-Rivera
- Chemistry Department and Industrial Biotechnology Program, University of Puerto Rico, Mayagüez, Puerto Rico
| | | | | | | | - William Bauer
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, USA
| | - Juan López-Garriga
- Chemistry Department and Industrial Biotechnology Program, University of Puerto Rico, Mayagüez, Puerto Rico
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Nieves-Marrero CA, Ruiz-Martínez CR, Estremera-Andújar RA, González-Ramírez LA, López-Garriga J, Gavira JA. Two-step counterdiffusion protocol for the crystallization of haemoglobin II from Lucina pectinata in the pH range 4-9. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:264-8. [PMID: 20208156 PMCID: PMC2833032 DOI: 10.1107/s1744309109053081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 12/09/2009] [Indexed: 11/11/2022]
Abstract
Lucina pectinata haemoglobin II (HbII) transports oxygen in the presence of H(2)S to the symbiotic system in this bivalve mollusc. The composition of the haem pocket at the distal site includes TyrB10 and GlnE7, which are very common in other haem proteins. Obtaining crystals of oxyHbII at various pH values is required in order to elucidate the changes in the conformations of TyrB10 and GlnE7 and structural scenarios induced by changes in pH. Here, the growth of crystals of oxyHbII using the capillary counterdiffusion (CCD) technique at various pH values using a two-step protocol is reported. In the first step, a mini-screen was used to validate sodium formate as the best precipitating reagent for the growth of oxyHbII crystals. The second step, a pH screen typically used for optimization, was used to produce crystals in the pH range 4-9. Very well faceted prismatic ruby-red crystals were obtained at all pH values. X-ray data sets were acquired using synchrotron radiation of wavelength 0.886 A (for the crystals obtained at pH 5) and 0.908 A (for those obtained at pH 4, 8 and 9) to maximum resolutions of 3.30, 1.95, 1.85 and 2.00 A for the crystals obtained at pH 4, 5, 8 and 9, respectively. All of the crystals were isomorphous and belonged to space group P4(2)2(1)2.
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Affiliation(s)
- Carlos A. Nieves-Marrero
- Chemistry Department, PO Box 9019, University of Puerto Rico, Mayagüez Campus, Mayagüez, PR 00681, Puerto Rico
| | - Carlos R. Ruiz-Martínez
- Chemistry Department, PO Box 9019, University of Puerto Rico, Mayagüez Campus, Mayagüez, PR 00681, Puerto Rico
| | - Rafael A. Estremera-Andújar
- Chemistry Department, PO Box 9019, University of Puerto Rico, Mayagüez Campus, Mayagüez, PR 00681, Puerto Rico
| | - Luis A. González-Ramírez
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Edificio López Neyra, PTCS, Avenida del Conocimiento, s/n 18100 Armilla, Granada, Spain
| | - Juan López-Garriga
- Chemistry Department, PO Box 9019, University of Puerto Rico, Mayagüez Campus, Mayagüez, PR 00681, Puerto Rico
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Edificio López Neyra, PTCS, Avenida del Conocimiento, s/n 18100 Armilla, Granada, Spain
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Ruiz-Martínez CR, Nieves-Marrero CA, Estremera-Andújar RA, Gavira JA, González-Ramírez LA, López-Garriga J, García-Ruiz JM. Crystallization and diffraction patterns of the oxy and cyano forms of the Lucina pectinata haemoglobins complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:25-8. [PMID: 19153450 PMCID: PMC2628858 DOI: 10.1107/s1744309108038542] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 11/18/2008] [Indexed: 11/10/2022]
Abstract
The native oxygen-carrier haemoglobins complex (HbII-III) is composed of haemoglobin II (HbII) and haemoglobin III (HbIII), which are found in the ctenidia tissue of the bivalve mollusc Lucina pectinata. This protein complex was isolated and purified from its natural source and crystallized using the vapour-diffusion and capillary counter-diffusion methods. Oxy and cyano derivatives of the complex crystallized using several conditions, but the best crystals in terms of quality and size were obtained from sodium formate pH 5 using the counter-diffusion method in a single capillary. Crystals of the oxy and cyano complexes, which showed a ruby-red colour and nonsingular prismatic shapes, scattered X-rays to resolution limits of 2.15 and 2.20 A, respectively, using a 0.886 A synchrotron-radiation source. The crystals belonged to the tetragonal system, space group P4(2)2(1)2, with unit-cell parameters a = b = 74.07, c = 152.07 and a = b = 73.83, c = 152.49 A for the oxy and cyano complexes, respectively. The asymmetric unit of both crystals is composed of a single copy of the heterodimer, with Matthew coefficients (V(M)) of 3.08 and 3.06 A(3) Da(-1) for the oxy and cyano complexes, respectively, which correspond to a solvent content of approximately 60.0% by volume.
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Affiliation(s)
- Carlos R. Ruiz-Martínez
- Departamento de Química, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - Carlos A. Nieves-Marrero
- Departamento de Química, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - Rafael A. Estremera-Andújar
- Departamento de Química, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos, IACT (CSIC–UGRA), Avenida del Conocimiento s/n, P. T. Ciencias de la Salud, 18100 Armilla, Granada, Spain
| | - Luis A. González-Ramírez
- Laboratorio de Estudios Cristalográficos, IACT (CSIC–UGRA), Avenida del Conocimiento s/n, P. T. Ciencias de la Salud, 18100 Armilla, Granada, Spain
| | - Juan López-Garriga
- Departamento de Química, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - Juan M. García-Ruiz
- Laboratorio de Estudios Cristalográficos, IACT (CSIC–UGRA), Avenida del Conocimiento s/n, P. T. Ciencias de la Salud, 18100 Armilla, Granada, Spain
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Gavira JA, de Jesus W, Camara-Artigas A, López-Garriga J, García-Ruiz JM. Capillary crystallization and molecular-replacement solution of haemoglobin II from the clam Lucina pectinata. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:196-9. [PMID: 16511300 PMCID: PMC2197196 DOI: 10.1107/s1744309106002648] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 01/22/2006] [Indexed: 11/11/2022]
Abstract
Haemoglobin II is one of three haemoglobins present in the cytoplasm of the Lucina pectinata mollusc that inhabits the Caribbean coast. Using HBII purified from its natural source, crystallization screening was performed using the counter-diffusion method with capillaries of 0.2 mm inner diameter. Crystals of HbII suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to improve their quality. The crystals belong to the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 73.92, c = 152.35 A, and diffracted X-rays to a resolution of better than 2.0 A. The asymmetric unit is a homodimer with a corresponding Matthews coefficient (VM) of 3.15 A3 Da(-1) and a solvent content of 61% by volume.
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Affiliation(s)
- José A. Gavira
- Laboratorio de Estudios Cristalográficos–CSIC, P. T. Ciencias de la Salud, Granada, Spain
| | - Walleska de Jesus
- Departamento de Quimica, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayaguez, Mayaguez PR 00681, Puerto Rico
| | - Ana Camara-Artigas
- Departamento Química-Física, Bioquímica y Química Inorgánica, Universidad de Almería, Carretera Sacramento, Almería 04120, Spain
| | - Juan López-Garriga
- Departamento Química-Física, Bioquímica y Química Inorgánica, Universidad de Almería, Carretera Sacramento, Almería 04120, Spain
| | - Juan M. García-Ruiz
- Laboratorio de Estudios Cristalográficos–CSIC, P. T. Ciencias de la Salud, Granada, Spain
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Vinogradov SN, Walz DA, Pohajdak B, Moens L, Kapp OH, Suzuki T, Trotman CN. Adventitious variability? The amino acid sequences of nonvertebrate globins. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1993; 106:1-26. [PMID: 8403841 DOI: 10.1016/0305-0491(93)90002-m] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
1. The more than 140 amino acid sequences of non-vertebrate hemoglobins (Hbs) and myoglobins (Mbs) that are known at present, can be divided into several distinct groups: (1) single-chain globins, containing one heme-binding domain; (2) truncated, single-chain, one-domain globins; (3) chimeric, one-domain globins; (4) chimeric, two-domain globins; and (5) chimeric multi-domain globins. 2. The crystal structures of eight nonvertebrate Hbs and Mbs are known, all of them monomeric, one-domain globin chains. Although these molecules represent plants, prokaryotes and several metazoan groups, and although the inter-subunit interactions in the dimeric and tetrameric molecules differ from the ones observed in vertebrate Hbs, the secondary structures of all seven one-domain globins retain the characteristic vertebrate "myoglobin fold". No crystal structures of globins representing the other four groups have been determined. 3. Furthermore, a number of the one-, two- and multi-domain globin chains participate in a broad variety of quaternary structures, ranging from homo- and heterodimers to highly complex, multisubunit aggregates with M(r) > 3000 kDa (S. N. Vinogradov, Comp. Biochem. Physiol. 82B, 1-15, 1985). 4. (1) The single-chain, single-domain globins are comparable in size to the vertebrate globins and exhibit the widest distribution. (A) Intracellular Hbs include: (i) the monomeric and polymeric Hbs of the polychaete Glycera; (ii) the tetrameric Hb of the echiuran Urechis; (iii) the dimeric Hbs of echinoderms such as Paracaudina and Caudina; and (iv) the dimeric and tetrameric Hbs of molluscs, the bivalves Scapharca, Anadara, Barbatia and Calyptogena. (B) Extracellular Hbs include: (i) the multiple monomeric and dimeric Hbs of the larva of the insect Chironomus; (ii) the Hbs of nematodes such as Trichostrongylus and Caenorhabditis; (iii) the globin chains forming tetramers and dodecamers and comprising approximately 2/3 of the giant (approximately 3600 kDa), hexagonal bilayer (HBL) Hbs of annelids, e.g. the oligochaete Lumbricus and the polychaete Tylorrhynchus and of the vestimentiferan Lamellibrachia; and (iv) the globin chains comprising the ca 400 kDa Hbs of Lamellibrachia and the pogonophoran Oligobrachia. (C) Cytoplasmic Hbs include: (i) the Mbs of molluscs, the gastropods Aplysia, Bursatella, Cerithedea, Nassa and Dolabella and the chiton Liolophura; (ii) the three Hb of the symbiont-harboring bivalve Lucina; (iii) the dimeric Hb of the bacterium Vitreoscilla; and (iv) plant Hbs, including the Hbs of symbiont-containing legumes (Lgbs), the Hbs of symbiont-containing non-leguminous plants and the Hbs in the roots of symbiont-free plants.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- S N Vinogradov
- Department of Biochemistry, Wayne State University School of Medicine, Detroit, MI 48201
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Hockenhull-Johnson JD, Stern MS, Wittenberg JB, Vinogradov SN, Kapp OH, Walz DA. The amino acid sequence of hemoglobin III from the symbiont-harboring clam Lucina pectinata. JOURNAL OF PROTEIN CHEMISTRY 1993; 12:261-77. [PMID: 8397786 DOI: 10.1007/bf01028189] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The cytoplasmic hemoglobin III from the gill of the symbiont-harboring clam Lucina pectinata consists of 152 amino acid residues, has a calculated Mm of 18,068, including heme, and has N-acetyl-serine as the N-terminal residue. Based on the alignment of its sequence with other vertebrate and nonvertebrate globins, it retains the invariant residues Phe45 at position CD1 and His98 at the proximal position F8, as well as the highly conserved Trp16 and Pro39 at positions A12 and C2, respectively. The most likely candidate for the distal residue at position E7 is Gln66. Lucina hemoglobin III shares 95 identical residues with hemoglobin II (J. D. Hockenhull-Johnson et al., J. Prot. Chem. 10, 609-622, 1991), including Tyr at position B10, which has been shown to be capable of entering the distal heme cavity and placing its hydroxyl group within a 2.8 A of the water molecule occupying the distal ligand position, by modeling the hemoglobin II sequence using the crystal structure of sperm whale metmyoglobin. The amino acid sequences of the two Lucina globins are compared in detail with the known sequences of mollusc globins, including seven cytoplasmic and 11 intracellular globins. Relative to 75% homology between the two Lucina globins (counting identical and conserved residues), both sequences have percent homology scores ranging from 36-49% when compared to the two groups of mollusc globins. The highest homology appears to exist between the Lucina globins and the cytoplasmic hemoglobin of Busycon canaliculatum.
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Affiliation(s)
- J D Hockenhull-Johnson
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan 48201
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