Evolutionary Insights into Adaptation of Hemocyanins from Deep-Sea Hydrothermal Vent Shrimps
Choi H, Yu OH, and Eyun S
Marine Pollution Bulletin 215:117872
— Figures and Tables (Colored and High resolution) —
Figure 1. Maximum likelihood phylogenetic species tree obtained based on 13 concatenated mitochondrial protein-coding genes inferred from 15 caridean species. Pandalus hypsinotus was used as the outgroup species. The bootstrap values (left) and Bayesian poster probability values (right) are labeled at each node. The names in red represent the deep-sea hydrothermal vent shrimp samples considered in this study.
Figure 2. Maximum likelihood (ML) phylogenetic gene tree based on 48 amino acid sequences of hemocyanin (Hc). Three Insecta species were used as the outgroup. The bootstrap values (left) and Bayesian posterior probability values (right) are labeled at each node. Only support values higher than 60% and 0.6 inferred from ML and Bayesian Inference, respectively, are shown on each branch. Hc obtained from deep-sea hydrothermal vent shrimps are shown in red.
Figure 3. (a) White ribbon diagram showing the three-dimensional structure of Rimicaris kairei α-type hemocyanin (Hc) (RkaHc1). The red (three) and green (six) residues represent positively selected and histidine residues within the active site, respectively. (b) Detailed interactions within the active site: three positively selected residues (red) and six histidine residues (green). Three mutations (Leucine, Serine, and Isoleucine) can be observed in close proximity to the active site. (c) Schematic representation of the domains of RkaHc1: Hemocyanin_N, Hemocyanin_M, and Hemocyanin_C. The three positively selected residues (red) detected in close proximity to the active site can be observed to be located in the Hemocyanin_M domain. (d) Multiple sequence alignment (MSA) of the Hemocyanin_M domains from 12 decapods. The four deep-sea hydrothermal vent shrimps considered in this study are indicated in blue on the left side of the MSA. Within the alignment, the green background represents six histidine residues, while the red background represents three mutation residues. The black background represents highly conserved regions. Accession numbers: Macrobrachium nipponense, AEC46861.1; Macrobrachium rosenbergii, ALN67306.1; Palaemon carinicauda, AEJ08191.1; Atyopsis moluccensis, CCF55379.1; Caridina multidentate, CCF55385.1; Homarus americanus, XP_042241812.1; Panulirus japonicus, BBO36752.1; Trinorchestia longiramus, KAF2367351.1.
Figure 4. (a) Three-dimensional structure of the α-type Hemocyanin (RkaHc1) dimer of Rimicaris kairei predicted using Cluspro 2.0 server. (a) The molecular surface of the dimer shows two RkaHc1 (yellow and white). Positively selected sites of RkaHc1 are indicated in red. (b) Ribbon diagram showing the close-up view of the interaction site. Positively selected residues (Tyr 617) are indicated in red. (c) Schematic representation of the domains of RkaHc1: Hemocyanin_N, Hemocyanin_M, and Hemocyanin_C. The three positively selected residues (red) detected within the binding site can be observed in the Hemocyanin_C domain. (d) Multiple sequence alignment (MSA) of the Hemocyanin_C domain from 12 decapods. The four deep-sea hydrothermal vent shrimps considered in this study are indicated in blue on the left side of the MSA. Mutation and highly conserved sites are indicated in red and black, respectively. Accession numbers: Macrobrachium nipponense, AEC46861.1; Macrobrachium rosenbergii, ALN67306.1; Palaemon carinicauda, AEJ08191.1; Atyopsis moluccensis, CCF55379.1; Caridina multidentate, CCF55385.1; Homarus americanus, XP_042241812.1; Panulirus japonicus, BBO36752.1; Trinorchestia longiramus, KAF2367351.
Table 1. Summary of next-generation sequencing to genome annotation for four deep-sea hydrothermal vent shrimps. Abbreviations: C, complete Benchmarking Universal Single-Copy Orthologues (BUSCOs); S, single-copy BUSCOs; D, duplicated BUSCOs; F, fragmented BUSCOs; M, missing BUSCOs.
Table 2. BLAST results for hemocyanin genes obtained from four Alvinocarididae shrimps.
Table 3. Summary of the branch model. Abbreviations: np, number of the parameter; LRT, likelihood ratio test.
Table 4. Summary of the branch-site model. Abbreviations: np, number of the parameter; LRT, likelihood ratio test; BEB, Bayes Empirical Bayes.
— Supporting Information (Colored and High resolution) —
Figure S1. Maximum likelihood (ML) tree of 12 Malacostraca species based on cytochrome c oxidase subunit 1 (COX1). Trinorchestia longiramus was used as an outgroup species. The red clade denotes a deep-sea lineage. The ML tree was utilized as an input tree file to detect positive selection analysis.
Table S1. Three types of hemocyanin (α, β, and γ) and pseudo-hemocyanin genes that were used as queries for the BLASTP search.
Table S2. Species identification using cytochrome c oxidase subunit 1 (COX1) from the mitochondrial genome of four deep-sea shrimps.
Table S3. Convergence events result from Monte-Carlo simulation.
