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Article

Bioinformatic Characterization and Molecular Evolution of the Lucina pectinata Hemoglobins

by
Ingrid M. Montes-Rodríguez
1,
Carmen L. Cadilla
2,*,
Juan López-Garriga
3 and
Ricardo González-Méndez
4,*
1
Cancer Biology Division, PROMIC, Comprehensive Cancer Center of the University of Puerto Rico, San Juan, PR 00936-3027, USA
2
Department of Biochemistry, School of Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936-5067, USA
3
Department of Chemistry, Faculty of Arts and Sciences, University of Puerto Rico—Mayagüez Campus, Mayagüez, PR 00681-9000, USA
4
Department of Radiological Sciences, School of Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936-5067, USA
*
Authors to whom correspondence should be addressed.
Genes 2022, 13(11), 2041; https://doi.org/10.3390/genes13112041
Submission received: 12 September 2022 / Revised: 24 October 2022 / Accepted: 26 October 2022 / Published: 5 November 2022
(This article belongs to the Special Issue Genetic Evolution of Marine Shellfish)
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Abstract

:
(1) Introduction: Lucina pectinata is a clam found in sulfide-rich mud environments that has three hemoglobins believed to be responsible for the transport of hydrogen sulfide (HbILp) and oxygen (HbIILp and HbIIILp) to chemoautotrophic endosymbionts. The physiological roles and evolution of these globins in sulfide-rich environments are not well understood. (2) Methods: We performed bioinformatic and phylogenetic analyses with 32 homologous mollusk globin sequences. Phylogenetics suggests a first gene duplication resulting in sulfide binding and oxygen binding genes. A more recent gene duplication gave rise to the two oxygen-binding hemoglobins. Multidimensional scaling analysis of the sequence space shows evolutionary drift of HbIILp and HbIIILp, while HbILp was closer to the Calyptogena hemoglobins. Further corroboration is seen by conservation in the coding region of hemoglobins from L. pectinata compared to those from Calyptogena. (3) Conclusions: Presence of glutamine in position E7 in organisms living in sulfide-rich environments can be considered an adaptation to prevent loss of protein function. In HbILp a substitution of phenylalanine in position B10 is accountable for its unique reactivity towards H2S. It appears that HbILp has been changing over time, apparently not subject to functional constraints of binding oxygen, and acquired a unique function for a specialized environment.

Graphical Abstract

1. Introduction

Invertebrate hemoglobins (Hbs) display higher variability in terms of amino acid chain constitution, quaternary structures, and functional properties when compared to their vertebrate counterpart [1]. Some are monomeric, while others can form large polymers. In invertebrates, Hbs can be expressed differentially in different anatomical sites, and show differences in their ligand kinetics [1]. Since invertebrates can be found in a wide range of habitats, the variation encountered in their Hbs is indicative of how these molecules must adapt to fulfill their function regardless of the environmental challenges in the surrounding areas where they live [2].
The globin fold is a well characterized protein structure, first described for sperm whale myoglobin (Mb) and horse oxyhemoglobin, composed of up to eight α helices, labeled A to H, and residues within each helix segment are numbered from the amino end [3,4,5]. Perutz [6] established structural similarities between various globins and sperm whale myoglobin that allows the use of the same notation for equivalent structural residues in all hemoglobins, regardless of additions or deletions in their primary structure. Bashford, Chothia, & Lesk [7] postulated that at least 32 internal conserved regions, possessing mostly hydrophobic residues, define the overall globin fold structure. Lesk & Chothia [8] demonstrated that the differences in amino acid sequences between these molecules lead to the formation of a well conserved globin structure by a series of low-energy mutations producing limited structural changes and by the functional advantage of any modulation of the ligand affinity caused by these changes.
In sulfide-rich habitats, Hbs are essential for the sustainability of the chemoautotrophic based symbiosis found in many invertebrates [9,10]. The hosts supply the symbionts with inorganic substrates, such as sulfide, while the symbionts are believed to provide the host with autotrophically fixed carbon [11]. A remarkable aspect of the Hbs of these organisms is their ability to retain their function in presence of hydrogen sulfide (H2S) without the covalent modification of the heme pyrrole rings that leads to formation of sulfhemoglobin, as has been seen in most mammalian myoglobins (Mbs) and Hbs [12]. However, the biochemical characteristics of the Hbs from these species differ substantially.
Chemosymbiosis with sulfide-oxidizing bacteria is found in members of the Lucinidae family, which have an extensive variety of species and are found across the globe [13]. The clam Lucina pectinata is found in the southwest coast of Puerto Rico and throughout the Caribbean Sea. As it lives in sulphide-rich muds, it has developed a symbiotic relation with intracellular bacteria for which the clam provides both hydrogen sulfide (H2S) and oxygen (O2). Three different Hbs have been identified in L. pectinata: hemoglobin I (HbILp), a sulfide-reactive hemoglobin, and hemoglobin II (HbIILp) and hemoglobin III (HbIIILp), which are oxygen-reactive hemoglobins [14].
The sulfide binding HbILp is a monomeric globular protein, composed of 143 amino acid residues [15]. HbILp has a conventional globin fold lacking the D helix. This is similar to plant and truncated hemoglobins [16]. “HbILp is characterized by an unusual distribution of phenylalanines at the heme distal positions B10, CD1 and E11” [17]. HbIILp and HbIIILp (150 and 153 amino acid respectively) have a tyrosine residue at position B10 [18] (Figure 1 below). Structural alignment of HbILp protein structure (PDB 1FLP) and Sperm Whale Myoglobin (SWM) (PDB 1A6M) showing their amino acid distribution in the heme pocket. For SWM there is a leucine at position B10, a histidine at position E7 and a valine in position E11. (see Supplementary Figure S1).
Amino acid sequences of HbIILp and HbIIILp have a 65% of identity and they both have lower sequence identity with HbILp (32% of identity with HbIILp and 33% of identity with HbIIILp). In these three hemoglobins the heme distal E7 position has a glutamine residue instead of the typical distal histidine (Figure 1 shows the comparison of the heme pockets of HbILp and the sperm whale myoglobin). These three Hbs have been extensively studied in order to understand their chemistry, the factors that affect their specificity, and they have been used as models to understand distal ligand binding control [19,20,21,22,23]. How the environment influences the evolution of function in these hemoglobins has yet to be elucidated. We compared the L. pectinata Hbs to other homologous globin sequences from mollusks to identify conserved features and evolutionary relationships. We also compared the coding sequences of L. pectinata Hbs between them and with those available for Calyptogena spp. in order to obtain a better understanding of globin gene structure and sequence conservation in mollusks.

2. Materials and Methods

2.1. Bioinformatic Analyses

The sequences of L. pectinata’s Hbs (mRNA: HbILp-AF187049; HbIILp-AY243364; HbIIILp-EU040120; protein: HbILp -AAG01380; HbIILp-AAO89499; HbIIILp-ABS87592) were retrieved from the National Center for Biotechnology Information (NCBI) GenBank and GenPept databases [24]. Retrieval of sequences homologous to the three protein sequences of the L. pectinata hemoglobins was performed with the Basic Local Alignment Search Tool (BLAST) [25,26,27] using blastp with default parameters and selecting to search only in the mollusks (taxonomic id 6447). Thirty-two unique protein sequences were retrieved from the three BLAST homology searches with an expectation value threshold smaller than 0.0001 for significance and/or sequence similarity of approximately 25% or greater. The accession numbers of these sequences together with the BLAST search result summaries are shown in Supplementary Table S1.
Multiple sequence alignment (MSA) was performed with globin sequences homologous to HbILp, HbIILp and HbIIILp. The MSA includes globins from the deep-sea clam species of Calyptogena, marine gastropods from Aplysia spp., ark clams, also known as blood clams (Anadara spp., Barbatia spp., Scapharca spp. and Tegillarca spp.), the Atlantic surf clam Spisula solidissima and the Antarctic bivalve Yoldia eightsi. The Physeter catodon (Sperm Whale) myoglobin amino acid sequence (Accession number NP_001277651) and the helical segments of its globin three-dimensional structure (Accession number 1EBC_A) were included in the MSA as reference, to aid identification of amino acid residues based on the myoglobin fold [7,8] and the standard globin fold nomenclature [6].
Multiple sequence alignment (MSA) of these 32 homologous sequences was performed using the PSI-COFFEE alignment program. This algorithm is used to align distantly related proteins using the consistency function and profile information with homology extension [28]. Given the low sequence similarity, around the so-called ‘twilight zone’ for detection of homology, this is the method of choice for aligning these sequences. These results were visualized using GeneDoc [29].
The structural alignment of the protein structures of HbILp (PDB:1FLP) and HbIILp (PDB:2OLP), and HbILp (PDB:1FLP) and Sperm Whale Myoglobin (SWM) (PDB:1A6M), showing the spatial orientation and distribution of amino acids in the heme pocket was performed using the MultiSeq bioinformatics analysis environment [30] using the Structural Alignment of Multiple Proteins algorithm [31] and the RMSD function in the VMD software [32]. These comparisons help illustrate the overall structural conservation of the hemoglobin fold and the heme O2/H2S binding pockets.

2.2. Phylogenetic Analysis

Phylogenetic analysis of these globin sequences was performed as follows. The MSA of the 32 amino acid sequences was trimmed using trimAl with the automated heuristic setting ‘automated 1’ [33]. The trimmed MSA was then converted to the PHYLYP format. Using the PHYLIP suite of programs [34], an unrooted Maximum Likelihood phylogenetic tree with 1000 bootstrap replicates (SEQBOOT) was constructed using the protein maximum likelihood routine (ProML) in its parallel implementation (MPI-ProML) [35] using 16 processors in the BioU computer cluster at the Pittsburgh Supercomputing Center. A consensus phylogenetic tree was generated with the CONSENSE routine using the extended majority rule and visualized with FigTree [36]. A rooted species phylogenetic tree was built using the Taxonomy resource at NCBI [37,38] and was verified using the Tree-of-Life resource [39]. The gene tree and the species tree were then reconciled using the program NOTUNG [40,41] and a root was placed on the globin gene tree using the rooting procedure in NOTUNG [40,41,42,43]. Visualization of the reconciled phylogenetic trees was done with NOTUNG routines that are based on the ATV routine in FORESTER [44].

2.3. Metric Multidimensional Scaling Analysis

The trimmed MSA was used as input for metric multidimensional scaling (MMDS) analysis and exploration of the sequence space. The MMDS analysis was performed with the R package bios2mds [45], using a JTT similarity matrix to construct the distance matrix required for the analysis. A clustering analysis was performed as part of the MMDS using the routines in the package and optimized based on a Silhouette analysis. These were performed as described in [45,46].

2.4. Coding Region Alignments

Multiple Sequence Alignments (MSA) of the coding sequences of the three L. pectinata hemoglobin sequences were constructed using M-COFFEE [47]. Motif analysis was done using the Maximum Entropy Motif Elicitation program (MEME) in the zero-or-one-per-sequence mode, requesting 6 motifs [48]. All the alignment results were visualized using the program GeneDoc [29].
Retrieval of sequences homologous to the mRNA sequences of the L. pectinata Hbs was performed with BLAST [25,26,27] using blastn with default parameters and optimized for somewhat dissimilar sequences. The only sequences that showed homology with a significant expectation value were the L. pectinata hemoglobin sequences for HbIILp and HbIIILp, and that homology was with each other. HbILp did not retrieve any nucleotide sequence. The sequences of coding regions of Calyptogena spp. Hbs (C. nautilei HbIV-AB186050.1; C. nautilei HbIII-AB186049.1; C. soyoae HbI-AB186047.1; C. soyoae HbII-AB186048.1; C. tsubasa HbI-AB186401.1; C. tsubasa HbII-AB186402.1; C. kaikoi HbI-AB186045.1; C. kaikoi HbII-AB186046.1) were also retrieved from the NCBI GenBank. MSA, MEME analysis and visualization was performed as indicated in the previous paragraph.

3. Results

3.1. Multiple Sequence Alignment

The MSA shows a high quality alignment confirmed by the conservation of the invariant proximal histidine at position F8 (His-F8), the highly conserved phenylalanine at position CD1 (Phe-CD1), and the phenylalanine at position B14 (Phe-B14) (Figure 2). A tryptophan at position H8 replaces the methionine found in sperm whale myoglobin. This is an amino acid replacement found in invertebrate Hbs [7,49]. The conservation of key positions in hemoglobins can be explained by the previous work of Ptitsyn and Ting [50] with the analysis of sequences from twelve globin subfamilies. In this analysis, Ptitsyn and co-workers showed that there are two common conserved clusters of amino acids between these globins. The first cluster includes residues in direct contact with the heme (CD1, F8, E11, FG5, F4, and G5), and heme neighboring residues (C2, B14, B10, E4, CD4, H19 and B13). The second cluster incudes hydrophobic residues distant from the heme center that may play an important role in the first steps of the protein folding process (A8, A12, G12, G16, H8 and H12) [50]. Additionally, the work of Liong et al. [51] with sperm whale myoglobin showed the relevance of residues at positions F4, FG3, FG5, and G5, in retaining the porphyrin prosthetic group. They demonstrated that the residues in positions Leu-F4, His-FG3, Ile-FG5, and Leu-G5 create a hydrophobic environment around the porphyrin preventing hydration of the heme. In our analysis, positions A12, B6, B13, B14, E4, FG5 and H8 show a high level of conservation (100% or >80% conservation level) presenting either the same residue or residues with the same physicochemical properties. The positions A8, B10, C2, CD4, E11, F4, G5, G12, G16, H12 and H19 have lower conservation (>50% conservation level), or no conservation among the sequences.

3.2. Phylogenetic Analyses

Figure 3 shows the results of our phylogenetic analyses. A maximum likelihood (ML) gene tree constructed with 32 mollusk globin sequences is shown in Figure 3A. The un-rooted ML gene tree shows three major clades: One clade corresponds to the Heterodonta subclass grouping the globins of L. pectinata with the Calyptogena spp. and S. solidissima. Another clade corresponds to those clams belonging to the Pteriomophia subclass grouping the globins of Barbatia spp., Tegillarca spp., Anadara spp., and Scapharca spp. A third clade clusters the members of the subclass Opisthobranchia, the myoglobins of the gastropods Aplysia spp.; Y. eightsi, a clam that belongs to the subclass Protobranchia is shown in black and does not cluster with any group. The rooted-species-reconciled gene tree is shown in Figure 3B. The species tree (Figure 3C), even though it is polytomic, has a well-defined root between the Gastropoda (Aplysia spp.) and the Bivalvia (all other groups in our analysis).
The ML phylogenetic tree divides these globin sequences in three main clusters: Bivalves belonging to the Heterodonta subclass; Bivalves belonging to the Pteriomophia subclass; and the Gastropods belonging to the Opisthobranchia subclass. We can group the globin sequences according to the clade that they belong to, and examine the amino acid conservation within each group (Figure 4).
We will discuss the similarities of those organisms that live in environments similar to that of L. pectinata, where the levels of hydrogen sulfide are high. The members of the Calyptogena spp., as well as L. pectinata, rely on the symbiosis with chemoautotrophic sulfur-oxidizing bacteria for their nutrition [52,53,54,55,56] and live in reduced environments where low to moderate concentrations of hydrogen sulfide are found, i.e., cold seeps and hydrothermal vents [57]. There are a few positions with conserved residues in this group that are different from the other groups: the distal heme positions Gln-E7, Phe-E11, position Phe-B9, and the B10 position, occupied mainly by a tyrosine, with the exception of HbILp from L. pectinata that has phenylalanine. The topological positions B10, E7 and E11 are shown in the structural alignments of HbILp vs. HbIILp (Figure 1) and HbILp vs. SWM (Supplementary Figure S1).
Table 1 shows amino acids in positions B9, B10, E7 and E11 for this subgroup. The nerve Hb of S. solidissima, which is grouped in the Heterodonta clade with the Hbs from L. pectinata and Calyptogena spp., has His-E7 and inhabits sandy continental shelf habitats. Hence, this organism was not included when we looked for similarities between organisms living in sulfide-rich environments.

3.3. Metric Multi-Dimensional Scaling Analysis

The Metric Multi-Dimensional Scaling analysis (MMDS) was performed with the trimmed alignment of the 32 mollusk globin sequences creating a multi-dimensional sequence space, with a 3D projection of major principal components shown in Figure 5.
This type of analysis is a powerful method used to visualize distance between sequences and complements phylogeny providing evolutionary information [46]. This sequence space is defined by the principal components (PCs). In Figure 5 we show the 3-D projection of the first three PCs. It is highly informative about the evolution and drift of these proteins. In this analysis we observed, as expected, that these globins are also clustered according to their subfamilies. However, the 3D sequence space clearly shows how HbIILp and HbIIILp are close to each other and separated from the other members of the Heterodonta subfamily. On the other hand, HbILp is closer to other members of the Heterodonta subfamily despite its unique hydrogen sulfide reactivity. This data shows that HbIILp and HbIIILp have drifted evolutionarily in the sequence space. The 2D projections for pairs of these three PC are also shown in Supplementary Figure S2 as B, C and D. In this analysis we observed, as expected, that these globins are also clustered according to their subfamilies. The 2D sequence space of PC1 and PC2, Figure S2B, resembles the unrooted phylogenetic tree previously shown. However, the 3D sequence space clearly shows how HbIILp and HbIIILp are close to each other and separated from the other members of the Heterodonta subfamily. This can also be seen in the other two 2D sequence space shown in Figure S2C,D. These results revealed that even though HbIILp and HbIIILp are O2 transporting Hbs like the ones found in the Calyptogena spp., they are evolving independently as an outgroup while the HbILp sequence conserves a higher degree of evolutionary similarity to the Calyptogena spp. Hemoglobins.

3.4. Coding Region Bioinformatic Analyses

The level of conservation between the three coding region sequences of HbILp, HbIILp and HbIIILp of L. pectinata is presented in the multiple sequence alignment in Figure 6A.
The three Hbs from L. pectinata have intron insertions at the conserved positions B12.2 and G7.0 [58], indicated by the arrows in Figure 6A that mark these intron-insertion positions, respectively (B12.2 is the intron inserted after the second base of the codon of amino acid 12 on the B-helix and G7.0 is the intron inserted between the codons of amino acids 6 and 7 on the G-helix). For the three coding regions we observed high conservation surrounding the regions of intron insertion at the B12.2 position (after nucleotides 95, 98 and 101 in the coding region of HbILp, HbIILp and HbIIILp, respectively), while there is more variability in the region of the third intron insertion at position G7.0 (after nucleotides 324, 327 and 330 in the coding regions of HbILp, HbIILp and HbIIILp, respectively). Overall, the region before the second and third intron insertion is more conserved between the three Hb, while the region after the intron insertion at G7.0 is more conserved between HbIILp and HbIIILp, but not for HbILp. This variability is corroborated at the protein level where motif analysis using MEME showed three major motifs (see Figure 6B), two of them are in the three Hbs (blue and red motifs), while the last motif (colored in gray) is not detected in HbILp.
Motif analysis of the hemoglobin coding regions from L. pectinata and the genus Calyptogena showed that two out of six motifs, colored in brown and light-gray, are shared between all of the members of the Heterodonta clade (see Figure 7).
However, for the HbILp coding region we find a weak signal for the motifs shared with the Calyptogena spp. sequences, indicated in yellow, pink and blue, with p-values of 7.99 × 10−5, 6.39 × 10−5, and 3.01 × 10−5 respectively. The HbIILp coding region also shows a weak signal for a motif with a p-value of 1.23 × 10−5, indicated in blue.

4. Discussion

Bioinformatic analyses between L. pectinata hemoglobins and globin sequences from other mollusks living in sulfide-rich environments revealed sequence conservation in the B10, E7, and E11 residues that give these proteins a unique distal site structure allowing them to carry their normal function in such extreme environments. The mollusk globin sequences used for this analysis differ in terms of subunit structure and ligand specificities. For example, HbICk and HbIICk from C. kaikoi can assume homodimeric or homotetrameric conformation in a concentration dependent manner. Since the amino acid sequence of HbICk and HbIICk are identical to MbICk and MbIICk, respectively, found in this clam’s muscle tissue, it has been suggested that they may serve as oxygen storage molecules [59]. C. nautilei hemoglobins HbIIICn and HbIVCn are monomeric hemoglobins while hemoglobins HbICt and HbIICt from C. tsubasa form dimers [60]. In the case of C. soyoae, it has two homodimeric hemoglobins, HbICs and HbIICs, and for HbIICs the autoxidation rate under physiological temperature is three times slower than the one observed for human hemoglobin, which, in combination with its relatively high O2 affinity, is indicative that it can transport O2 under physiological conditions [53,54]. On the other hand, globins from blood clams tend to form dimers and tetramers that bind oxygen cooperatively [57,61,62]. Bao et al. [63] described a new role for the Hbs from the blood clam T. granosa, since they are involved in the immune defense after the clams were exposed to bacterial infection. Dewilde and collaborators [64] concluded that the nerve hemoglobin (nHb) from the surf clam S. solidissima has a myoglobin-like function since it has a moderate O2 affinity and phylogenetic analysis with mollusks Hb and vertebrate nHb placed this globin with mollusks [65]. Finally, the Antartic clam Y. eightsi possesses a hemoglobin with O2 affinity similar to that of mammalian Hb, at the clam’s physiological temperature. This affinity decreases significantly at 25 °C, suggestive of this clam’s adaptation to a low temperature environment [66].
We looked for similarities between the globins from members of the Calyptogena spp. and L. pectinata since both organisms live in environments that have high concentration of H2S. For the set of mollusk globin sequences in this study, they show clade-specific conservation or structurally conservative substitutions. The positions with residues conserved in this group are the Gln-E7, Phe-E11, and the Tyr-B10 (with the exception of HbI from L. pectinata that has Phe-B10) and position Phe-B9. The globins from members of the Heterodonta subclass and Y. eightsi have a phenylalanine at E11, while the rest of the globin sequences possess an aliphatic residue (Val, Ile, or Leu). Several studies have demonstrated the importance of the residue occupying the E11 position since it is part of an overall kinetic barrier for the ligand in the heme pocket [67,68]. The residue at position E7 is considered to be essential for the stabilization of the bound ligand through hydrogen bonding, serves as a gate for ligand entry, and plays a crucial role in the prevention of the autoxidation of the heme [66,69,70,71]. The stabilization of ligands by hydrogen bonding with glutamine in the E7 position has been described for the three L. pectinata Hbs [17,21,72] Previous work where the HbILp heme pocket was mutated to mimic the human myoglobin distal site demonstrated that His-E7, in the presence of H2S and H2O2 or O2, is essential for the formation of sulfhemoglobin, where sulfide is covalently bound in the pyrrole of the porphyrin ring resulting in a non-functional hemoglobin [73]. Interestingly, polymeric-hemoglobin from symbiont-containing tubeworms living in deep-sea hydrothermal vents contain histidine at the E7 position [56] and are capable of binding simultaneously and reversibly O2 (in their heme pockets) and H2S by the formation of zinc-sulfide complexes with Zn ions that are bound to specific residues (B7, B12, B16, CD10, G9, G13 and G16) across the globin chain [74,75]. This zinc-binding function has not been described in the Lucinidae spp. or Calyptogena spp. hemoglobins.
We previously mentioned some studies that described the role of several positions across the globin structure and observed that some positions showed less conservation across the mollusk globin sequences in our analysis. Some of these positions correspond to residues located at the immediate distal heme pocket vicinity. Studies have shown that the variability in ligand affinity and autoxidation of these globins are mostly determined by the physicochemical properties of the residues occupying positions at the distal heme pocket. In their review, Springer et al. [66] discussed myoglobin ligand binding recognition in studies where site-directed mutagenesis of distal residues was combined with their structural and physicochemical characterization. Based on that review, it becomes clear that a combination of steric hindrance and polarity of the distal pocket governs hemoglobin ligand recognition, affinity and autoxidation. The positions B10, E11 and E7 of the distal heme environment play a predominant role in the control of ligand binding kinetics [76]. One of the most relevant similarities between these globins is the invariant presence of a glutamine residue in the E7 position. As mentioned before, the existence of a histidine residue in this particular position will promote the formation of sulfhemoglobin in the presence of H2S and O2 or H2O2, resulting in a nonfunctional protein. This single amino acid substitution may be considered an evolutionary adaptation of these organisms in order to increase their fitness in these sulphide-rich environments.
Like HbIILp and HbIIILp from L. pectinata, the hemoglobins from Calyptogena spp. included in this study bind and transport O2 in the presence of H2S and their identical distal site residues distribution may imply a similar binding mechanism. The main difference in the distal cavity between the sulfide reactive hemoglobin from L. pectinata, HbILp, and the oxygen reactive hemoglobins is a single substitution of a phenylalanine in the B10 position instead of a tyrosine, which has been demonstrated to be accountable of HbILp’s unique reactivity towards H2S [77]. HbIILp and HbIIILp have high O2 affinities and they remain oxygenated in the presence of H2S [78,79] and their O2 dissociation rates are three times slower than dissociation from HbILp and very slow compared when compared with other Hbs [14]. In presence of H2S, HbILp forms a ferric hemoglobin sulfide [14]. Studies with other hemoglobins that also have Gln-E7 and Tyr-B10 in their heme pockets, revealed that Tyr-B10 directly interacts with the bound O2, forming a hydrogen bond network between Gln-E7, B10 Tyr, and O2, that accounts for the low O2 dissociation rate of these hemoglobins [80,81,82]. Several studies have shown how Phe-B9 affects the orientation of the aromatic residues in the positions B10 and E11 due to electrostatic aromatic interactions [17,83]. Therefore, comparing the hemoglobin sequences from L. pectinata to sperm whale myoglobin allows presenting that a single amino acid in the heme proteins: Gln-E7 leads to transport of hydrogen sulphide in L. pectinata hemoglobin I, while His-E7 leads to the modification of the heme group to generate sulfmyoglobin. Thus, a single amino acid substitution can lead to differences in these heme proteins’ function. Studies with the sperm whale myoglobin triple mutant (LeuB10Phe, HisE7Gln, and ValE11Phe), mimicking the HbILp distal environment, showed a change in orientation, not only in Phe-B10 but also for Phe-E11, which assume a more perpendicular position to the heme plane, since the B9 position is a isoleucine residue, resulting in destabilization of the bound ligand [84].
The phylogenetic analysis shows a consistent and robust gene tree. Based on these analyses, we suggest that a first gene duplication at an early evolutionary stage resulted in the ancestor of the HbILp gene and an ancestor of the HbIILp/HbIIILp gene. A more recent gene duplication of the oxygen-binding gene occurred to give rise to genes for two oxygen-binding proteins, HbIILp, and HbIIILp. This hypothesis is supported with the fact that HbILp not only showed lower sequence similarity to both HbIILp and HbIIILp but also has different ligand kinetics. Furthermore, this corroborates the similarities at the sequence level and kinetic mechanisms between HbIILp and HbIIILp. In addition, HbILp appears to have been changing over time, apparently not subject to the constraint of binding oxygen, acquiring a unique function for a specialized environment.
Metric Multi-Dimensional Scaling analysis of mollusk hemoglobins showed evolutionary drift of HbIILp and HbIIILp, while HbILp was closer to the Calyptogena spp. hemoglobins in sequence space. The MMDS shows that HbIILp and HbIIILp have drifted evolutionarily in the sequence space. These results revealed that even though HbIILp and HbIIILp are O2 transporting Hbs like the ones found in the Calyptogena spp., they are evolving independently as a separate subgroup while the HbILp sequence maintains a higher degree of similarity to the Calyptogena spp. hemoglobins.
The coding region analysis of hemoglobins from L. pectinata with those from Calyptogena spp., suggest that HbILp from L. pectinata has features that are shared with the Calyptogena spp. hemoglobins. These similarities are supported by previous work by Suzuki and collaborators, who proposed that the L. pectinata and Calyptogena spp. hemoglobin chains evolved from a common ancestor [59]. The conservation of intron locations interrupting the coding region of their cognate genes is further evidence of the conservation of globin gene structure in invertebrate hemoglobins.

5. Conclusions

Bioinformatic analyses between L. pectinata hemoglobins and globin sequences from other mollusks living in sulfide-rich environments revealed what appears to be clade-specific sequence conservation in residues that give these proteins a unique distal heme pocket site structure that allows for normal function in such extreme environments. One of the most relevant similarities between these globins is the invariant presence of a glutamine residue in the E7 position. This single amino acid substitution may be considered an evolutionary adaptation of these organisms in order to increase their fitness in these sulphide-rich environments. Phylogenetics suggests that in L. pectinata a first gene duplication resulting in sulfide binding and oxygen binding genes. A more recent gene duplication gave rise to the two oxygen-binding hemoglobins. Metric Multi-Dimensional Scaling analysis of mollusk hemoglobins showed evolutionary drift of HbIILp and HbIIILp, while HbILp was closer to the Calyptogena spp. hemoglobins in sequence space. This is further corroborated by the conservation seen in the coding region of hemoglobins from L. pectinata with those from Calyptogena spp.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes13112041/s1: (a) Table S1: List of organism and globins used for MSA and abbreviations used for analysis, including BLAST results. Includes the abbreviations used, the description of the sequence, the percent similarity and E-value of the BLAST searches carried out using the L. pectinata hemoglobins, and the accession numbers of all sequences used for this work; (b) Figure S1: (A) Structural alignment of HbILp protein structure (PDB 1FLP) and HbIILp (PDB 2OLP) showing their amino acid distribution in the heme pocket. Alignment was done using the STAMP algorithm as implemented in MultiSeq in VMD. The only difference between the two heme pockets is the amino acid in position B10, a phenylalanine for HbILp and a tyrosine for HbIILp. Both hemoglobins have a phenylalanine at positions CD1 and E11, a glutamine at position E7 and a histidine at position F8. HbIILp and HbIIILp have the same heme pocket amino acid distribution. (B) Structural alignment of HbILp protein structure (PDB 1FLP) and Sperm Whale Myoglobin (SWM) (PDB 1A6M) showing their amino acid distribution in the heme pocket. Amino acid residues of heme pocket of SWM are colored in blue. For SWM there is a leucine at position B10, a histidine at position E7 and a valine in position E11. Figure S2: (A) 3D representation of the mollusk globins sequence space. A typical multiple sequence alignment of 32 homologous mollusk globins was analyzed by MMDS, with distances based on the JTT distance matrix. The 3D space is defined by the first three components of the MDS analysis. HbILp is colored in gold, HbIILp is colored in pink and HbIIILp is colored purple. The rest of the sequences are color coded according to mollusk sub-families they belong to: colored in red are Heterodonta subclass, in green are the Pteriomophia subclass, in blue are the Opisthobranchia subclass, and in black the Bivalve, Y. eightsi, member of the Protobranchia subclass. (B) The 2D sequence space of mollusk globin formed by PC1 and PC2. (C) The 2D sequence space of mollusk globin formed by PC3 and PC2. (D) The 2D sequence space of mollusk globin formed by PC1 and PC3. We show the 3-D projection of the first three PC. It is highly informative about the evolution and drift of these proteins. The 2D projections for pairs of these three PC are also shown in Supplementary Figure S2 as B, C and D. In this analysis we observed, as expected, that these globins are also clustered according to their subfamilies. The 2D sequence space of PC1 and PC2, Supplementary Figure S2B, resembles the unrooted phylogenetic tree previously shown. However, the 3D sequence space clearly shows how HbIILp and HbIIILp are close to each other and separated from the other members of the Heterodonta subfamily. This can also be seen in the other two 2D sequence space shown in Supplementary Figure S2C,D. This data shows that HbIILp and HbIIILp have drifted evolutionarily in the sequence space.

Author Contributions

I.M.M.-R. carried out parts of the bioinformatic and structural analysis and drafted and edited the manuscript. R.G.-M. contributed to the design of the study and contributed to the bioinformatic experimental design, analysis, and interpretation, performed the phylogenetic analyses, the structural alignment, the MMDS analysis, and helped to draft and edit the manuscript. C.L.C. helped with the interpretation of bioinformatic analysis and helped to draft and edit the manuscript. J.L.-G. contributed to the design of the study, helped with the structural interpretation, and helped to draft and edit the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

NIH grants U54MD007600 and P20GM103475, NSF grant MCB-0843608, UPRM RISE 2BEST NIH-R25GM088023, and UPRM-SLOAN grants provided partial support for this project. This research was also supported in part by the National Institutes of Health through resources provided by the National Resource for Biomedical Supercomputing (P41 RR06009), which is part of the Pittsburgh Supercomputing Center (PSC). This work, and in part RGM and IMMR, were supported by National Institutes of Health Minority Access to Research Careers (MARC) grant T36-GM095335 to the PSC. Specifically, this work used the computational resource BioU, which was made available by National Institutes of Health grant T36-GM008789 to the PSC.

Institutional Review Board Statement

Not Applicable. This work relies on a reanalysis of protein, nucleic acid sequences, and structures using publicly available data from international repositories.

Informed Consent Statement

Not Applicable. We did not use human data for this work.

Data Availability Statement

Not applicable.

Acknowledgments

This work was done in partial fulfillment of the doctoral dissertation requirements of I.M.M.-R.

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

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Figure 1. Structural alignment of HbILp protein structure (PDB 1FLP) and HbIILp (PDB 2OLP) showing their amino acid distribution in the heme pocket. Alignment was done using the STAMP algorithm as implemented in MultiSeq in VMD. The only difference between the two heme pockets is the amino acid in position B10, a phenylalanine for HbILp and a tyrosine for HbIILp. Both hemoglobins have a phenylalanine at positions CD1 and E11, a glutamine at position E7 and a histidine at position F8. HbIILp and HbIIILp have the same heme pocket amino acid distribution. The RMSD for the backbones (residues 2–147) is 6.54 angstrom.
Figure 1. Structural alignment of HbILp protein structure (PDB 1FLP) and HbIILp (PDB 2OLP) showing their amino acid distribution in the heme pocket. Alignment was done using the STAMP algorithm as implemented in MultiSeq in VMD. The only difference between the two heme pockets is the amino acid in position B10, a phenylalanine for HbILp and a tyrosine for HbIILp. Both hemoglobins have a phenylalanine at positions CD1 and E11, a glutamine at position E7 and a histidine at position F8. HbIILp and HbIIILp have the same heme pocket amino acid distribution. The RMSD for the backbones (residues 2–147) is 6.54 angstrom.
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Figure 2. GeneDoc visualization of Multiple Sequence Alignment of 32 mollusk protein sequences using PSI-COFFEE. The conservation is shown in three levels based on similarity groups: Black for 100% conservation, Gray for 75% of conservation and light blue for 50% conservation. The abbreviations are the following: L.p (L. pectinata), C.n. (C. nautilei), C.k. (C. kaikoi), C.t. (C. tsubasa), C.s. (C. soyoae), B.l. (Barbatia lima), S.s. (Spisula solidissima), Y.e. (Y. eightsi), A.l. (Aplysia limacine), A.k. (Aplysia kurodai), A.j. (Aplysia juliana), S.k. (Scapharca kagoshimensis), S.i. (Scapharca inaequivalvis), T.g. (Tegillarca granosa), B.v. (Barbatia virescens), A.t. (Anadara trapezia), S.b. (Scapharca broughtonii), and P.c. (P. catodon). On top of the alignment the secondary structure of P. catodon myoglobin is indicated, according to its crystallographic structure (accession number 1EBC_A). The organism identifiers are shaded based on the clade division of phylogenetic analysis: red indicates the Bivalves belonging to the Heterodonta subclass; in ‘olive’, we indicate the Bivalves belonging to the Pteriomophia subclass; blue was used for the Gastropods belonging to the Opisthobranchia subclass; and in black the Bivalve, Y. eightsi, a member of the Protobranchia subclass.
Figure 2. GeneDoc visualization of Multiple Sequence Alignment of 32 mollusk protein sequences using PSI-COFFEE. The conservation is shown in three levels based on similarity groups: Black for 100% conservation, Gray for 75% of conservation and light blue for 50% conservation. The abbreviations are the following: L.p (L. pectinata), C.n. (C. nautilei), C.k. (C. kaikoi), C.t. (C. tsubasa), C.s. (C. soyoae), B.l. (Barbatia lima), S.s. (Spisula solidissima), Y.e. (Y. eightsi), A.l. (Aplysia limacine), A.k. (Aplysia kurodai), A.j. (Aplysia juliana), S.k. (Scapharca kagoshimensis), S.i. (Scapharca inaequivalvis), T.g. (Tegillarca granosa), B.v. (Barbatia virescens), A.t. (Anadara trapezia), S.b. (Scapharca broughtonii), and P.c. (P. catodon). On top of the alignment the secondary structure of P. catodon myoglobin is indicated, according to its crystallographic structure (accession number 1EBC_A). The organism identifiers are shaded based on the clade division of phylogenetic analysis: red indicates the Bivalves belonging to the Heterodonta subclass; in ‘olive’, we indicate the Bivalves belonging to the Pteriomophia subclass; blue was used for the Gastropods belonging to the Opisthobranchia subclass; and in black the Bivalve, Y. eightsi, a member of the Protobranchia subclass.
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Figure 3. (A) Maximum-likelihood tree of based on 32 mollusk globin sequences with 1000 bootstraps (bootstrap values are shown in the reconciled tree). (B) Gene Tree. A rooted-species-reconciled phylogenetic gene tree was constructed using PHYLIP, followed by reconciling the gene tree with the species tree and rooting using NOTUNG, as described in Materials and Methods. Numbers represent the bootstrap values from the Maximum Likelihood phylogenetic analysis. (C) Species tree. A rooted species phylogenetic tree was built using the Taxonomy resource at NCBI and verified using the Tree-of-Life resource at http://tolweb.org (accessed on 12 November 2018).
Figure 3. (A) Maximum-likelihood tree of based on 32 mollusk globin sequences with 1000 bootstraps (bootstrap values are shown in the reconciled tree). (B) Gene Tree. A rooted-species-reconciled phylogenetic gene tree was constructed using PHYLIP, followed by reconciling the gene tree with the species tree and rooting using NOTUNG, as described in Materials and Methods. Numbers represent the bootstrap values from the Maximum Likelihood phylogenetic analysis. (C) Species tree. A rooted species phylogenetic tree was built using the Taxonomy resource at NCBI and verified using the Tree-of-Life resource at http://tolweb.org (accessed on 12 November 2018).
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Figure 4. Visualization of Multiple Sequence Alignment showing amino acid residues that are conserved between each clade. (A) Bivalves belonging to the Heterodonta subclass. (B) Bivalves belonging to Pteriomophia subclass. (C) Gastropods belonging to Opisthobranchia subclass. For abbreviations see legend of Figure 2. Above each of the alignments, we indicate the secondary structure of P. catodon Myoglobin according to its crystallographic structure (accession number 1EBC_A). The alignments were visualized using GeneDoc.
Figure 4. Visualization of Multiple Sequence Alignment showing amino acid residues that are conserved between each clade. (A) Bivalves belonging to the Heterodonta subclass. (B) Bivalves belonging to Pteriomophia subclass. (C) Gastropods belonging to Opisthobranchia subclass. For abbreviations see legend of Figure 2. Above each of the alignments, we indicate the secondary structure of P. catodon Myoglobin according to its crystallographic structure (accession number 1EBC_A). The alignments were visualized using GeneDoc.
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Figure 5. 3D representation of the mollusk globins sequence space. A trimmed multiple sequence alignment of 32 homologous mollusk globins was analyzed by MMDS, with distances based on the JTT distance matrix. The 3D space is defined by the first three components of the MDS analysis. HbILp is colored ‘salmon’, HbIILp is colored in magenta and HbIIILp is colored purple. The rest of the sequences are color coded according to mollusk sub-families they belong to: colored in red are Heterodonta subclass, in tan are the Pteriomophia subclass, in blue are the Opisthobranchia subclass, and in black the Bivalve, Y. eightsi, member of the Protobranchia subclass.
Figure 5. 3D representation of the mollusk globins sequence space. A trimmed multiple sequence alignment of 32 homologous mollusk globins was analyzed by MMDS, with distances based on the JTT distance matrix. The 3D space is defined by the first three components of the MDS analysis. HbILp is colored ‘salmon’, HbIILp is colored in magenta and HbIIILp is colored purple. The rest of the sequences are color coded according to mollusk sub-families they belong to: colored in red are Heterodonta subclass, in tan are the Pteriomophia subclass, in blue are the Opisthobranchia subclass, and in black the Bivalve, Y. eightsi, member of the Protobranchia subclass.
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Figure 6. (A) Multiple sequence alignment and conservation levels of the coding regions of hemoglobins from L. pectinata. Conservation levels between the three coding region sequences of HbILp, HbIILp and HbIIILp of L. pectinata were visualized using GeneDoc. Nucleotides shaded in black represent 100% of conservation, in gray, 66% conservation, and nucleotides having less than 66% conservation were not shaded. Red arrows indicate position of intron insertions. (B) Multiple sequence alignment of L. pectinata hemoglobins. MSAs were carried out using M-COFFEE and visualized in GeneDoc. Motif analysis was performed using MEME and identified motifs are represented in different colors.
Figure 6. (A) Multiple sequence alignment and conservation levels of the coding regions of hemoglobins from L. pectinata. Conservation levels between the three coding region sequences of HbILp, HbIILp and HbIIILp of L. pectinata were visualized using GeneDoc. Nucleotides shaded in black represent 100% of conservation, in gray, 66% conservation, and nucleotides having less than 66% conservation were not shaded. Red arrows indicate position of intron insertions. (B) Multiple sequence alignment of L. pectinata hemoglobins. MSAs were carried out using M-COFFEE and visualized in GeneDoc. Motif analysis was performed using MEME and identified motifs are represented in different colors.
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Figure 7. Multiple sequence alignment of coding regions of hemoglobins from Lucina pectinata and Calyptogena. Multiple sequence alignments were carried out using M-COFFEE, motif analysis was done using MEME and aligned sequences visualized in GeneDoc. The abbreviations are as follows: L.p. (L. pectinata), C.n. (C. nautilei), C.k. (C. kaikoi), C.t. (C. tsubasa), C.s. (C. soyoae). Detected motifs are represented in different colors.
Figure 7. Multiple sequence alignment of coding regions of hemoglobins from Lucina pectinata and Calyptogena. Multiple sequence alignments were carried out using M-COFFEE, motif analysis was done using MEME and aligned sequences visualized in GeneDoc. The abbreviations are as follows: L.p. (L. pectinata), C.n. (C. nautilei), C.k. (C. kaikoi), C.t. (C. tsubasa), C.s. (C. soyoae). Detected motifs are represented in different colors.
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Table
Table 1. Amino acids in positions conserved in organism living in sulfide-rich environments.
Table 1. Amino acids in positions conserved in organism living in sulfide-rich environments.
OrganismGlobinAbbreviationAmino Acids in Positions:
B9B10E7E11
L. pectinataHemoglobin IHbILpPhePheGlnPhe
L. pectinataHemoglobin IIHbIILpPheTyrGlnPhe
L. pectinataHemoglobin IIIHbIIILpPheTyrGlnPhe
C. nautileiHemoglobin IVHbIVCnPheTyrGlnPhe
C. nautileiHemoglobin IIIHbIIICnPheTyrGlnPhe
C. kaikoiHemoglobin IIHbIICkPheTyrGlnPhe
C. tsubasaHemoglobin IIHbIICtPheTyrGlnPhe
C. soyoaeHemoglobin IIHbIICsPheTyrGlnPhe
C. kaikoiHemoglobin IHbICkPheTyrGlnPhe
C. soyoaeHemoglobin IHbICsPheTyrGlnPhe
C. tsubasaHemoglobin IHbICtPheTyrGlnPhe
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Montes-Rodríguez, I.M.; Cadilla, C.L.; López-Garriga, J.; González-Méndez, R. Bioinformatic Characterization and Molecular Evolution of the Lucina pectinata Hemoglobins. Genes 2022, 13, 2041. https://doi.org/10.3390/genes13112041

AMA Style

Montes-Rodríguez IM, Cadilla CL, López-Garriga J, González-Méndez R. Bioinformatic Characterization and Molecular Evolution of the Lucina pectinata Hemoglobins. Genes. 2022; 13(11):2041. https://doi.org/10.3390/genes13112041

Chicago/Turabian Style

Montes-Rodríguez, Ingrid M., Carmen L. Cadilla, Juan López-Garriga, and Ricardo González-Méndez. 2022. "Bioinformatic Characterization and Molecular Evolution of the Lucina pectinata Hemoglobins" Genes 13, no. 11: 2041. https://doi.org/10.3390/genes13112041

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