Thermal Vent Clam (Calyptogena magnifica) Hemoglobin

Discovery of deep-sea acoels from a chemosynthesis-based ecosystem

Chemosynthesis-based ecosystems such as hydrothermal vents and hydrocarbon seeps harbour various endemic species, each uniquely adapted to the extreme conditions. While some species rely on obligatory relationships with bacterial symbionts for nutrient uptake, scavengers and predators also play important roles in food web dynamics in these ecosystems. Acoels, members of the phylum Xenacoelomorpha, are simple, worm-like invertebrates found in marine environments worldwide but are scarcely understood taxa. This study presents a novel genus and species of acoel from a deep-sea hydrocarbon seep off Hatsushima, Japan, Hoftherma hatsushimaensis gen. et sp. nov. Our multi-locus phylogenetic analysis revealed that the acoels are nested within Hofsteniidae, a family previously known exclusively from shallow waters. This finding suggests that at least two independent colonization events occurred in the chemosynthesis-based environments from the phylum Xenoacoelomorpha, represented by hofsteniid acoels and Xenoturbella. Previous reports of hofsteniid species from low-oxygen and sulfide-rich environments, including intertidal habitats with decomposing leaves, in addition to H. hatsushimaensis gen. et sp. nov. from a deep-sea hydrocarbon seep, imply a common ancestral adaptation to sulfide-rich ecosystems within Hofsteniidae. Moreover, the sister relationship between solenofilomorphid acoels predominating in sulfide-rich habitats indicates common ancestral adaptation to sulfide-rich ecosystems between these two families.

Hemoglobin wonders: a fascinating gas transporter dive into molluscs

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.

Globin's structure and function in vesicomyid bivalves from the Gulf of Guinea cold seeps as an adaptation to life in reduced sediments

Vesicomyid bivalves form dense clam beds in both deep-sea cold seeps and hydrothermal vents. The species diversity within this family raises questions about niche separation and specific adaptations. To compare their abilities to withstand hypoxia, we have studied the structure and function of erythrocyte hemoglobin (Hb) and foot myoglobin (Mb) from two vesicomyid species, Christineconcha regab and Laubiericoncha chuni, collected from the Regab pockmark in the Gulf of Guinea at a depth of 3,000 m. Laubiericoncha chuni possesses three monomeric globins, G1 (15,361 Da), G2 (15,668 Da), and G3 (15,682 Da) in circulating erythrocytes (Hb), and also three globins, G1, G3, and G4 (14,786 Da) in foot muscle (Mb). Therefore, globins G2 and G4 appear to be specific for erythrocytes and muscle, respectively, but globins G1 and G3 are common. In contrast, C. regab lacks erythrocyte Hb completely and possesses only globin monomers G1' (14,941 Da), G2' (15,169 Da), and G3' (15,683 Da) in foot muscle. Thus, these two vesicomyid species, C. regab and L. chuni, show a remarkable diversity in globin expression when examined by electrospray ionization mass spectrometry. Oxygen-binding affinities reveal extremely high oxygen affinities (P50 < 1 Torr, from 5° to 15°C at pH 7.5), in particular L. chuni globins, which might be an advantage allowing L. chuni to dig deeply for sulfides and remain buried for long periods in reduced sediments.

Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters

To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach ‘types’. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and Imparidentia new clade ( = Euheterodonta excluding Anomalodesmata) were recovered across analyses, irrespective of data treatment or analytical framework. Another clade supported by our analyses but not formally recognised in the literature includes Palaeoheterodonta and Archiheterodonta, which emerged under multiple analytical conditions. The origin and diversification of each of these major clades is Cambrian or Ordovician, except for Archiheterodonta, which diverged from Palaeoheterodonta during the Cambrian, but diversified during the Mesozoic. Although the radiation of some lineages was shifted towards the Palaeozoic (Pteriomorphia, Anomalodesmata), or presented a gap between origin and diversification (Archiheterodonta, Unionida), Imparidentia showed steady diversification through the Palaeozoic and Mesozoic. Finally, a classification system with six major monophyletic lineages is proposed to comprise modern Bivalvia: Protobranchia, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia.

Cu/Zn- and Mn-superoxide dismutase (SOD) from the copepod Tigriopus japonicus: molecular cloning and expression in response to environmental pollutants

Superoxide dismutase (SOD) is an important antioxidant enzyme which catalyzes conversion of superoxide to oxygen and hydrogen peroxide in aerobic organisms. Here, we cloned and sequenced the full-length cDNA and genomic DNA of two SODs from the copepod, Tigriopus japonicus: copper/zinc SOD (TJ-Cu/Zn-SOD) and manganese SOD (TJ-Mn-SOD). To define whether TJ-Mn-SOD is a cytosolic or a mitochondrial protein, a phylogenetic analysis was performed. The genomic structure of both TJ-SOD genes was determined with the promoter region sequences. In order to investigate their potential role in response to environmental pollutants, T. japonicus were treated with heavy metal (copper, zinc, and silver; 0, 10, 25, 50, and 100 μg L(-1)) and industrial chemicals (benzo[α]pyrene, 4-nonylphenol, and tributyltin; 0, 1, 5, 10, and 20 μg L(-1)) for 96 h. Subsequently, the TJ-Cu/Zn-SOD and TJ-Mn-SOD mRNA level was measured with quantitative real-time RT-PCR along with total SOD activity. The deduced amino acid residues of TJ-Cu/Zn-SOD and TJ-Mn-SOD possessed evolutionary conserved domains that are required for metal binding and Cu/ZnSOD-conserved signature sequences. The phylogenetic analysis revealed that TJ-Mn-SOD was closely clustered to mitochondrial Mn-SOD of another copepod, Lepeophtheirus salmonis. TJ-Cu/Zn-SOD gene had four exons and three introns, while the TJ-Mn-SOD gene consisted of two exons interrupted by one intron. In the 5'-flanking region of TJ-Cu/Zn-SOD and TJ-Mn-SOD, we observed several transcription regulatory elements such as p53, XRE, MRE, and ERE-half sites. In the response to heavy metals, Cu, Zn, and Ag, both TJ-Cu/Zn-SOD and TJ-Mn-SOD transcript levels along with enzyme levels were significantly increased at high concentrations (50 μg L(-1) and 100 μg L(-1)). Particularly, in the Cu- and Ag-exposed group, the expression of TJ-Mn-SOD mRNA was regulated more sensitively than the TJ-Cu/Zn-SOD mRNA level, indicating that the chemical susceptibility would be not correlated with the form of chemicals. B[a]P treatment showed a significant increase in the expression of both TJ-SODs mRNA level and enzyme level from 5 μg L(-1) concentration, while TBT decreased its expression at high concentrations (10 μg L(-1) and 20 μg L(-1)). 4-NP increased both TJ-SODs mRNA level at 1 μg L(-1) concentration, and then inhibited its expression from 5 μg L(-1) concentration to a lower level than the control. This finding suggests that TJ-Cu/Zn-SOD and TJ-Mn-SOD would be an inducible gene upon exposure to heavy metals and B[α]P, and could be used as a potential biomarker for the risk assessment of these environmental pollutants. This is the first report to elucidate response of SOD to environmental pollutants in copepods. Therefore, this study would give a clue to better understand the mode of action of antioxidant genes and enzymes under oxidative stress in marine invertebrates.

Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts

BACKGROUND

The Vesicomyidae (Bivalvia: Mollusca) are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. Recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analyses possible.

RESULTS

To examine the genomic evolution of the vesicomyid symbionts, a comparative genomics framework, including the existing genomic data combined with heterologous microarray hybridization results, was used to analyze conserved gene content in four vesicomyid symbiont genomes. These four symbionts were chosen to include a broad phylogenetic sampling of the vesicomyid symbionts and represent distinct chemosynthetic environments: cold seeps and hydrothermal vents.

CONCLUSION

The results of this comparative genomics analysis emphasize the importance of the symbionts' chemoautotrophic metabolism within their hosts. The fact that these symbionts appear to be metabolically capable autotrophs underscores the extent to which the host depends on them for nutrition and reveals the key to invertebrate colonization of these challenging environments.

Nonvertebrate hemoglobins: functions and molecular adaptations

Hemoglobin (Hb) occurs in all the kingdoms of living organisms. Its distribution is episodic among the nonvertebrate groups in contrast to vertebrates. Nonvertebrate Hbs range from single-chain globins found in bacteria, algae, protozoa, and plants to large, multisubunit, multidomain Hbs found in nematodes, molluscs and crustaceans, and the giant annelid and vestimentiferan Hbs comprised of globin and nonglobin subunits. Chimeric hemoglobins have been found recently in bacteria and fungi. Hb occurs intracellularly in specific tissues and in circulating red blood cells (RBCs) and freely dissolved in various body fluids. In addition to transporting and storing O(2) and facilitating its diffusion, several novel Hb functions have emerged, including control of nitric oxide (NO) levels in microorganisms, use of NO to control the level of O(2) in nematodes, binding and transport of sulfide in endosymbiont-harboring species and protection against sulfide, scavenging of O(2 )in symbiotic leguminous plants, O(2 )sensing in bacteria and archaebacteria, and dehaloperoxidase activity useful in detoxification of chlorinated materials. This review focuses on the extensive variation in the functional properties of nonvertebrate Hbs, their O(2 )binding affinities, their homotropic interactions (cooperativity), and the sensitivities of these parameters to temperature and heterotropic effectors such as protons and cations. Whenever possible, it attempts to relate the ligand binding properties to the known molecular structures. The divergent and convergent evolutionary trends evident in the structures and functions of nonvertebrate Hbs appear to be adaptive in extending the inhabitable environment available to Hb-containing organisms.

Life in the extreme environment at a hydrothermal vent: haemoglobin in a deep-sea copepod

This is the first study, to my knowledge, quantifying the respiratory pigment haemoglobin discovered in a deep-sea copepod. Haemoglobin in copepods has previously been documented in only one other species from the deep water of an Italian lake. Specimens of the siphonostomatoid Scotoecetes introrsus Humes were collected during submersible dives at 2500 m depth near a hydrothermal vent at the East Pacific Rise (9 degrees N). The haemoglobin content in the copepods' haemolymph was 4.3 +/- 0.6 micrograms per individual female (n = 6) and 1.8 +/- 0.1 micrograms per individual male (n = 6). Weight-specific concentrations of haemoglobin were identical for females and males (0.25 +/- 0.04 and 0.26 +/- 0.02 microgram per microgram dry weight, respectively). These haemoglobin concentrations are higher than those found in other small crustaceans. Activity of the electron transport system indicated that the respiration rates in S. introrsus (13.7 +/- 7.7 microliters O2 per milligram dry weight per hour) were similar to those in the shallow-water copepod Acartia tonsa (9.1 +/- 1.3 microliters O2 per milligram dry weight per hour). It was concluded that the possession of highly concentrated haemoglobin allows S. introrsus to colonize a geologically young, thermally active site such as the vicinity of a hydrothermal vent, despite the prevailing oxygen depletion.

The hemoglobin gene of the deep-sea clam Calyptogena soyoae has a novel intron in A-helix

The cDNAs encoding two dimeric hemoglobins, Hbs I and II, of the deep-sea clam Calyptogena soyoae were amplified by PCR and the complete nucleotide sequences determined. The cDNA-derived amino acid sequences agreed completely with those determined chemically. Many of the molluscan intracellular globin genes have a characteristic four-exon/three-intron structure, with the precoding and two conventional introns conserved widely in animal globin genes. In this work we have determined the exon/intron organization of two hemoglobin genes of the deep-sea clam C. soyoae. Surprisingly, this gene has no precoding intron but instead contains an additional intron in the A-helix (A3.1), together with the two conventional introns (B12.2 and G6.3). This observation suggests that the precoding intron has been lost and the insertion of intron in A-helix occurred in the genes of Calyptogena. Alternatively, the sliding of intron from precoding to A-helix might have occurred.

Isolation and cDNA-derived amino acid sequences of hemoglobin and myoglobin from the deep-sea clam Calyptogena kaikoi

The heterodont clam Calyptogena kaikoi, living in the cold-seep area at a depth of 3761 m of the Nankai Trough, Japan, has abundant hemoglobins and myoglobins in erythrocytes and adductor muscle, respectively. Two types of hemoglobins (Hb I and Hb II) were isolated, and the complete amino acid sequences of Hb I (145 residues) and Hb II (137 residues) were obtained with combination of cDNA and protein sequencing. The amino acid sequences of C. kaikoi Hbs I and II differed from homologous chains of the congeneric clam Calyptogena soyoae in eight and five positions, respectively. The distal (E7) His, one of the functionally important residues in hemoglobin and myoglobin, was replaced by Gln in hemoglobins of C. kaikoi. A phylogenetic analysis of clam hemoglobins indicates that the evolutionary rate of Calyptogena hemoglobins is rather faster than those of other clams, suggesting that the mutation rate might be accelerated in the deep-sea animals around the areas of cold seeps or hydrothermal vents. On the other hand, it was found unexpectedly that two myoglobins Mbs I and II, isolated from the red adductor muscle, are identical in amino acid sequence Hbs I and II, respectively. Thus it was assumed that genes for Hbs I and II are also expressed in the muscle of C. kaikoi in substitution for myoglobin gene. This suggests that the major physiological role of globins in C. kaikoi is storage of oxygen under the low oxygen conditions, rather than circulating of oxygen.

Amino acid sequence of the dimeric hemoglobin (Hb I) from the deep-sea cold-seep clam Calyptogena soyoae and the phylogenetic relationship with other molluscan globins

The deep-sea cold-seep clam Calyptogena soyoae has two homodimeric hemoglobins (Hbs I and II) in erythrocytes. The complete amino acid sequence of Hb I has been determined. It is composed of 144 amino acid residues, has a high content of hydrophobic residues, and a calculated molecular weight of 16,350 including a heme group. The sequence of Calyptogena Hb I showed high homology (42% identity) with that of Calyptogena Hb II (Suzuki, T., Takagi T. and Ohta, S. (1989) Biochem. J. 260, 177-182), although it has a long insertion of seven residues in the C-terminal region compared with Hb II. On the other hand, it showed low homology (12-20% identity) with other molluscan globins. As well as Hb II, Calyptogena Hb I lacked the N-terminal extension of 7-9 residues characteristic of molluscan intracellular hemoglobins, and the distal (E7) histidine was replaced by glutamine. A phylogenetic tree was constructed from 13 molluscan globins belonging to the five families Aplysiidae, Galeodidae, Potamididae, Arcidae and Vesicomyidae. The globin sequences of Calyptogena (Vesicomyidae) were found to be rather distant from other globin sequences, suggesting that they might conserve a primitive form of molluscan globins.

Primary structure of a dimeric haemoglobin from the deep-sea cold-seep clam Calyptogena soyoae

The heterodont clam Calyptogena soyoae, living in the cold-seep area of the upper bathyal depth of Sagami Bay, Japan, has two homodimeric haemoglobins (Hb I and Hb II) in erythrocytes. The complete amino acid sequence of 136 residues of C. soyoae Hb II was determined. The sequence showed low homology with any other globins (at most 20% identity) and lacked the N-terminal extension of seven to nine amino acid residues characteristic of all the molluscan haemoglobins sequenced hitherto. Although the subunit assembly of molluscan haemoglobin is known to be 'back-to-front' relative to vertebrate haemoglobin, C. soyoae Hb II is unlikely to undergo such a subunit assembly because it lacks homology in the sequence involving subunit interaction. These structural features suggest that C. soyoae haemoglobin may have accomplished a unique molecular evolution. The distal (E7) histidine residue of C. soyoae Hb II is unusually replaced by glutamine. However, the oxyhaemoglobin is stable enough to act as an O2 carrier, since the autoxidation rate at near physiological temperature (3 degrees C) is about 3 times lower than that of human haemoglobin at 37 degrees C. H.p.l.c. patterns of peptides (Figs. 5-7), amino acid compositions of intact protein and peptides (Table 1) and amino acid sequences of intact protein and peptides (Tables 2 and 3) have been deposited as Supplementary Publication SUP 50150 (11 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms indicated in Biochem. J. (1989) 257, 5.