Expression characteristics of sulfur dioxygenase and its function adaption to sulfide in echiuran worm Urechis unicinctus

Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data

BACKGROUND

Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes.

RESULTS

In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log₂(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct =  - 0.5405 log₂(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data.

CONCLUSION

Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.

Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in Urechis unicinctus (Annelida, Echiura)

The intertidal zone is a transitional area of the land-sea continuum, in which physical and chemical properties vary during the tidal cycle and highly toxic sulfides are rich in sediments due to the dynamic regimes. As a typical species thriving in this habitat, Urechis unicinctus presents strong sulfide tolerance and is expected to be a model species for sulfide stress research. Heat shock proteins (HSPs) consist of a large group of highly conserved molecular chaperones, which play important roles in stress responses. In this study, we systematically analyzed the composition and expression of HSPs in U. unicinctus. A total of eighty-six HSP genes from seven families were identified, in which two families, including sHSP and HSP70, showed moderate expansion, and this variation may be related to the benthic habitat of the intertidal zone. Furthermore, expression analysis revealed that almost all the HSP genes in U. unicinctus were significantly induced under sulfide stress, suggesting that they may be involved in sulfide stress response. Weighted gene co-expression network analysis (WGCNA) showed that 12 HSPs, including 5 sHSP and 4 HSP70 family genes, were highly correlated with the sulfide stress response which was distributed in steelblue and green modules. Our data indicate that HSPs, especially sHSP and HSP70 families, may play significant roles in response to sulfide stress in U. unicinctus. This systematic analysis provides valuable information for further understanding of the function of the HSP gene family for sulfide adaptation in U. unicinctus and contributes a better understanding of the species adaptation strategies of marine benthos in the intertidal zone.

The critical roles of mitochondrial alternative chains in juvenile ark shells (Anadara broughtonii) exposed to acute hypoxia with or without sulfide

Reduced oxygen levels and increased sulfide concentrations have become a concern for marine animals. This study examines respiratory and energetic adaption to acute (0-96 h) hypoxia (0.5 mg/L dissolved oxygen) with or without sulfide (0.2 mM, 1 mM, 3 mM) in the hypoxia-resistant and sulfide-tolerant ark shell, Anadara broughtonii. The different states of aerobic respiration, energy-balance, and activity of the mitochondrial sulfide oxidation chain (MSOC) under these conditions were evaluated. The results indicated that the anaerobic pathway was activated by hypoxia at 24 h without sulfide, but was activated in the presence of sulfide at only 2 h. Exposure to sulfide resulted in significant accumulation of ATP, probably due to the activated MSOC and lowered metabolism via suppression of Na⁺-K⁺ ATPase activity and protein synthesis. During hypoxia, both enzyme activity and mRNA levels of alternative oxidase (AOX) increased while the key enzymes in MSOC, sulfide: quinone oxidoreductase (SQR) and sulfur dioxygenase (SDO), were not altered. With additional sulfide, the enzyme activity and mRNA levels of AOX, SQR, SDO significantly increased. Classical aerobic respiration was significantly inhibited, and induction of alternative respiration was detected. The corresponding alternative electron transport chain (AETC) accepted the electrons originating from both the tricarboxylic acid cycle and MSOC during the challenge, indicating that the capacity of aerobic respiration and sulfide-oxidation under a reduction state might greatly depend on AETC. The synergistically induced alternative chains (AETC and MSOC) and anaerobic pathway suggested energy-balance between respiration and sulfide-oxidation, which might contribute to the endurance of ark shells to acute sulfide exposure.

Two-sided effects of prolonged hypoxia and sulfide exposure on juvenile ark shells (Anadara broughtonii)

Oxygen deficit and sulfide have been restrictive factors in mariculture zones. However, the adaptive mechanism in aquatic lives is still unclear. The commercial ark shells Anadara broughtonii were selected to test the tolerance and adaptive responses to prolonged and intermittent hypoxia with or without exogenous sulfide (mild, moderate, high) by evaluating their behavior, mortality, oxidative level, antioxidant responses, and the MAPK-mediated apoptosis in gills. The results indicated that the clams were tolerant to hypoxia and sulfide exposure but vulnerable during reoxygenation from the challenges. Even so, sulfide had remarkable effect on attenuating the accumulation of reactive oxygen species (ROS) and lipid peroxides caused by reoxygenation from prolonged hypoxia. The increase of glutathione level was probably as an early and primary protective response to prevent the expected reperfusion injury from reoxygenation. The challenges suppressed the oxidative level with a dose-dependent effect of sulfide, with an exception when exposed to mild sulfide. Synchronously, biphasic effects of exogenous sulfide on apoptotic cascade, which was induced by mild sulfide while it was inhibited by higher sulfide, were also detected in gills. The induced or inhibited apoptosis by hypoxia and sulfide kept to a typical ROS-MAPK-CASPASE cascade, desiderating further investigation.

Defense responses of sulfur dioxygenase to sulfide stress in the razor clam Sinonovacula constricta

BACKGROUND

Sulfide is a well-known toxicant widely distributed in the culture environment. As a representative burrowing benthic bivalve, the razor clam Sinonovacula constricta is highly sulfide tolerant. Mitochondrial sulfide oxidation is an important way for sulfide detoxification, where sulfur dioxygenase (SDO) is the second key enzyme.

OBJECTIVE

To investigate the mechanism of sulfide tolerance in S. constricta, the molecular characterization of its SDO (designated as ScSDO) was studied.

METHODS

The cDNA sequence of ScSDO was cloned by RACE technique. The response of ScSDO in gills and livers of S. constricta was investigated during sulfide exposure (50, 150, and 300 μM sulfide) for 0, 3, 6, 12, 24, 48, 72, and 96 h by qRT-PCR. Moreover, the temporal expression of ScSDO protein in S. constricta gills after exposure to 150 μM sulfide was detected by Western blot. The subcellular location of ScSDO was identified by TargetP 1.1 prediction and Western Blot analysis.

RESULTS

The full-length cDNA of ScSDO was 2914 bp, encoding a protein of 304 amino acids. The deduced ScSDO protein was highly conserved, containing the signature HXHXDH motif of the metallo-β-lactamase superfamily and two metal-binding sites, of which metal-binding site I is known to be the catalytically active center. Subcellular localization confirmed that ScSDO was located only in the mitochondria. Responding to the sulfide exposure, distinct time-dependent increases in ScSDO expression were detected at both mRNA and protein levels. Moreover, the gills exhibited a higher ScSDO expression level than the livers.

CONCLUSIONS

All of our results suggest that ScSDO plays an important role in mitochondrial sulfide oxidation during sulfide stress, making S. constricta highly sulfide tolerant. In addition, as a respiratory tissue, the gills play a more critical role in sulfide detoxification.

Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis

Protein sequence similarity networks (SSNs) constitute a convenient approach to analyze large polypeptide sequence datasets, and have been successfully applied to study a number of protein families over the past decade. SSN analysis is herein combined with traditional cladistic and phenetic phylogenetic analysis (respectively based on multiple sequence alignments and all-against-all three-dimensional protein structure comparisons) in order to assist the ancestral reconstruction and integrative revision of the superfamily of metallo-β-lactamases (MBLs). It is shown that only 198 out of 15,292 representative nodes contain at least one experimentally obtained protein structure in the Protein Data Bank or a manually annotated SwissProt entry, that is to say, only 1.3 % of the superfamily has been functionally and/or structurally characterized. Besides, neighborhood connectivity coloring, which measures local network interconnectivity, is introduced for detection of protein families within SSN clusters. This approach provides a clear picture of how many families remain unexplored in the superfamily, while most MBL research is heavily biased towards a few families. Further research is suggested in order to determine the SSN topological properties, which will be instrumental for the improvement of automated sequence annotation methods.

The response of sulfur dioxygenase to sulfide in the body wall of Urechis unincinctus

Background

In some sedimentary environments, such as coastal intertidal and subtidal mudflats, sulfide levels can reach millimolar concentrations (2–5 mM) and can be toxic to marine species. Interestingly, some organisms have evolved biochemical strategies to overcome and tolerate high sulfide conditions, such as the echiuran worm, Urechis unicinctus. Mitochondrial sulfide oxidation is important for detoxification, in which sulfur dioxygenase (SDO) plays an indispensable role. Meanwhile, the body wall of the surface of the worm is in direct contact with sulfide. In our study, we chose the body wall to explore the SDO response to sulfide.

Methods

Two sulfide treatment groups (50 µM and 150 µM) and a control group (natural seawater) were used. The worms, U. unicinctus, were collected from the intertidal flat of Yantai, China, and temporarily reared in aerated seawater for three days without feeding. Finally, sixty worms with similar length and mass were evenly assigned to the three groups. The worms were sampled at 0, 6, 24, 48 and 72 h after initiation of sulfide exposure. The body walls were excised, frozen in liquid nitrogen and stored at −80 °C for RNA and protein extraction. Real-time quantitative RT-PCR, enzyme-linked immunosorbent assay and specific activity detection were used to explore the SDO response to sulfide in the body wall.

Results

The body wall of U. unicinctus consists of a rugal epidermis, connective tissue, outer circular muscle and middle longitudinal muscle. SDO protein is mainly located in the epidermis. When exposed to 50 µM sulfide, SDO mRNA and protein contents almost remained stable, but SDO activity increased significantly after 6 h (P < 0.05). However, in the 150 µM sulfide treatment group, SDO mRNA and protein contents and activity all increased with sulfide exposure time; significant increases all began to occur at 48 h (P < 0.05).

Discussion

All the results indicated that SDO activity can be enhanced by sulfide in two regulation mechanisms: allosteric regulation, for low concentrations, and transcription regulation, which is activated with an increase in sulfide concentration.

Taxonomic distribution, structure/function relationship and metabolic context of the two families of sulfide dehydrogenases: SQR and FCSD

Hydrogen sulfide (H₂S) is a versatile molecule with different functions in living organisms: it can work as a metabolite of sulfur and energetic metabolism or as a signaling molecule in higher Eukaryotes. H₂S is also highly toxic since it is able to inhibit heme cooper oxygen reductases, preventing oxidative phosphorylation. Due to the fact that it can both inhibit and feed the respiratory chain, the immediate role of H₂S on energy metabolism crucially relies on its bioavailability, meaning that studying the central players involved in the H₂S homeostasis is key for understanding sulfide metabolism. Two different enzymes with sulfide oxidation activity (sulfide dehydrogenases) are known: flavocytochrome c sulfide dehydrogenase (FCSD), a sulfide:cytochrome c oxidoreductase; and sulfide:quinone oxidoreductase (SQR). In this work we performed a thorough bioinformatic study of SQRs and FCSDs and integrated all published data. We systematized several properties of these proteins: (i) nature of flavin binding, (ii) capping loops and (iii) presence of key amino acid residues. We also propose an update to the SQR classification system and discuss the role of these proteins in sulfur metabolism.

Genetic diversity and population structure of penis fish (Urechis unicinctus) based on mitochondrial and nuclear gene markers

Urechis unicinctus is distributed only in Bohai Gulf of China and Korean and Japanese coast. The wild populations of this species have sharply declined in China and Japan. We collected 105 samples from six localities of Bohai Gulf and Korea coast, and investigated genetic diversity and population structure with mitochondrial COI, 16S-rRNA and nuclear 28S-rRNA gene fragments. Genetic diversity of U. unicinctus based on COI sequences was still high (Hd: 0.9595, π: 0.0101), however, 28S-rRNA gene sequences showed low level of genetic diversity (Hd: 0.4084, π: 0.0007). Based on COI sequences, F_ST values between populations ranged from -0.00204 to 0.05210, and 99.12% genetic diversity was contributed by different individuals within population. Both phylogenetic trees and median-joining network did not show clear geographic cluster, haplotypes from different populations were mixed. Our results indicated low level of genetic divergence among different localities of U. unicinctus, and this species should be treated as a whole population among China, Japan and Korea coast during species conservation.