Different Pressure Resistance of Lactate Dehydrogenases from Hagfish is Dependent on Habitat Depth and Caused by Tetrameric Structure Dissociation

Nishiguchi, Yoshikazu; Abe, Fumiyoshi; Okada, Mitsumasa

doi:10.1007/s10126-010-9299-6

Cited by 8 publications

(5 citation statements)

References 15 publications

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“…Among these characteristics, high hydrostatic pressure is regarded as the harshest for living organisms, since it can inhibit the functions of proteins through denaturing and impairing their structures [ 2 , 3 ]. This is especially for enzymes [ 4 , 5 ] and cytoskeleton proteins [ 6 ]. Besides, at low temperatures, DNA and RNA strands tend to tighten their structures, hindering the involvement of enzymes in DNA replication, transcription and translation [ 7 ] and thus disrupting the transcription and translation processes.…”

Section: Introductionmentioning

confidence: 99%

De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish

Lan

Sun

et al. 2018

BMC Genomics

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BackgroundHigh hydrostatic pressure and low temperatures make the deep sea a harsh environment for life forms. Actin organization and microtubules assembly, which are essential for intracellular transport and cell motility, can be disrupted by high hydrostatic pressure. High hydrostatic pressure can also damage DNA. Nucleic acids exposed to low temperatures can form secondary structures that hinder genetic information processing. To study how deep-sea creatures adapt to such a hostile environment, one of the most straightforward ways is to sequence and compare their genes with those of their shallow-water relatives.ResultsWe captured an individual of the fish species Aldrovandia affinis, which is a typical deep-sea inhabitant, from the Okinawa Trough at a depth of 1550 m using a remotely operated vehicle (ROV). We sequenced its transcriptome and analyzed its molecular adaptation. We obtained 27,633 protein coding sequences using an Illumina platform and compared them with those of several shallow-water fish species. Analysis of 4918 single-copy orthologs identified 138 positively selected genes in A. affinis, including genes involved in microtubule regulation. Particularly, functional domains related to cold shock as well as DNA repair are exposed to positive selection pressure in both deep-sea fish and hadal amphipod.ConclusionsOverall, we have identified a set of positively selected genes related to cytoskeleton structures, DNA repair and genetic information processing, which shed light on molecular adaptation to the deep sea. These results suggest that amino acid substitutions of these positively selected genes may contribute crucially to the adaptation of deep-sea animals. Additionally, we provide a high-quality transcriptome of a deep-sea fish for future deep-sea studies.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4720-z) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish

Lan

Sun

et al. 2018

BMC Genomics

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“…The Challenger Deep of the southern end of Mariana Trench in the Northwest Pacific is the deepest point (~11,000 m) in the ocean. Hydrostatic pressure there reaches 110 MPa, which can induce the disruption of salt bridges and promote irreversible unfolding and aggregation in proteins; thus, it is challenging for deep‐sea animals to maintain their protein structures and enzyme activities (Dahlhoff & Somero, ; Nishiguchi, Abe, & Okada, ; Ohmae, Miyashita, & Kato, ; Saad‐Nehme, Silva, & Meyer‐Fernandes, ). The temperatures there range from 1 to 2.5°C, and the nucleic acids tend to adopt unfavourable structures for genetic processes in the cells of animals lacking thermoregulation at these temperatures (Feller & Gerday, ).…”

Section: Introductionmentioning

confidence: 99%

Molecular adaptation in the world's deepest‐living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas

et al. 2017

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The Challenger Deep in the Mariana Trench is the deepest point in the oceans of our planet. Understanding how animals adapt to this harsh environment characterized by high hydrostatic pressure, food limitation, dark and cold is of great scientific interest. Of the animals dwelling in the Challenger Deep, amphipods have been captured using baited traps. In this study, we sequenced the transcriptome of the amphipod Hirondellea gigas collected at a depth of 10,929 m from the East Pond of the Challenger Deep. Assembly of these sequences resulted in 133,041 contigs and 22,046 translated proteins. Functional annotation of these contigs was made using the go and kegg databases. Comparison of these translated proteins with those of four shallow-water amphipods revealed 10,731 gene families, of which 5659 were single-copy orthologs. Base substitution analysis on these single-copy orthologs showed that 62 genes are positively selected in H. gigas, including genes related to β-alanine biosynthesis, energy metabolism and genetic information processing. For multiple-copy orthologous genes, gene family expansion analysis revealed that cold-inducible proteins (i.e., transcription factors II A and transcription elongation factor 1) as well as zinc finger domains are expanded in H. gigas. Overall, our results indicate that genetic adaptation to the hadal environment by H. gigas may be mediated by both gene family expansion and amino acid substitutions of specific proteins.

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“…In 2004, Johns and Somero [16] proposed the heat-tolerant structure of Pomacentridae LDH, and in 2008 Brindley et al [17] reported the pressuretolerant structure of Gadidae LDH-B and proposed 21 amino acid residues responsible for it. Recently, we have sequenced LDH-A genes from three hagfish species [13], examined their activities under high pressure, proposed seven amino acid residues responsible for their pressure tolerance [15,18], and found that the dissociation of tetramers caused the inactivation of Eptatretus burgeri LDH under high pressure [19]. This study aimed to determine a method for the effective expression of the LDH gene in Escherichia coli to obtain sufficient proteins to investigate the pressure-resistant structure using X-ray analysis.…”

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confidence: 99%

Expression of the Lactate Dehydrogenase Gene fromEptatretus okinoseanusinEscherichia coli

et al. 2011

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Amplified Eptatretus okinoseanus cDNA was digested with NdeI and EcoRI, cloned into pCold trigger factor (TF), and transformed with Escherichia coli strain BL 21 in which a csp A promoter was introduced to inhibit the expression of foreign peptides. Recombinant lactate dehydrogenase (LDH) was obtained in the soluble fraction after sonication of the cells. The protein was digested by HRC 3C protease, thrombin, and factor Xa. The specific activity of TF-tagged protein and tagless protein were 0.646 × 10 6 mIU/mg and 3.56 × 10 6 mIU/mg, respectively. The deletion of the TF tag enhanced the activity compared with the native protein to 13.4 × 10 6 mIU/mg, showing that this expression method is effective for the mass production of the protein to allow further study of the structure of LDH.

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Different Pressure Resistance of Lactate Dehydrogenases from Hagfish is Dependent on Habitat Depth and Caused by Tetrameric Structure Dissociation

Cited by 8 publications

References 15 publications

De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish

De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish

Molecular adaptation in the world's deepest‐living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas

Expression of the Lactate Dehydrogenase Gene fromEptatretus okinoseanusinEscherichia coli

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