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1.
J Agric Food Chem ; 72(17): 9955-9966, 2024 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-38628059

RESUMEN

Cold-adapted proteases are capable of efficient protein hydrolysis at reduced temperatures, which offer significant potential applications in the area of low temperature food processing. In this paper, we attempted to characterize cold-adapted proteases from Antarctic krill. Antarctic krill possesses an extremely active autolytic enzyme system in their bodies, and the production of peptides and free amino acids accompanies the rapid breakdown of muscle proteins following the death. The crucial role of trypsin in this process is recognized. A cold-adapted trypsin named OUC-Pp-20 from Antarctic krill genome was cloned and expressed in Pichia pastoris. Recombinant trypsin is a monomeric protein of 26.8 ± 1.0 kDa with optimum reaction temperature at 25 °C. In addition, the catalytic specificity of OUC-Pp-20 was assessed by identifying its hydrolysis sites through LC-MS/MS. OUC-Pp-20 appeared to prefer Gln and Asn at the P1 position, which is an amino acid with an amide group in its side chain. Hydrolysis reactions on milk and shrimp meat revealed that it can effectively degrade allergenic components in milk and arginine kinase in shrimp meat. These findings update the current knowledge of cold-adapted trypsin and demonstrate the potential application of OUC-Pp-20 in low temperature food processing.


Asunto(s)
Frío , Euphausiacea , Tripsina , Animales , Euphausiacea/química , Euphausiacea/enzimología , Euphausiacea/genética , Euphausiacea/metabolismo , Hidrólisis , Tripsina/metabolismo , Tripsina/química , Tripsina/genética , Especificidad por Sustrato , Secuencia de Aminoácidos , Espectrometría de Masas en Tándem , Estabilidad de Enzimas , Regiones Antárticas
2.
BMC Genomics ; 25(1): 210, 2024 Feb 26.
Artículo en Inglés | MEDLINE | ID: mdl-38408914

RESUMEN

BACKGROUND: Due to its enormous biomass, Antarctic krill (Euphausia superba) plays a crucial role in the Antarctic Ocean ecosystem. In recent years, Antarctic krill has found extensive application in aquaculture, emerging as a sustainable source of aquafeed with ideal nutritional profiles. However, a comprehensive study focused on the detailed effects of dietary Antarctic krill on aquaculture animals, especially farmed marine fishes, is yet to be demonstrated. RESULTS: In this study, a comparative experiment was performed using juvenile P. leopardus, fed with diets supplemented with Antarctic krill (the krill group) or without Antarctic krill (the control group). Histological observation revealed that dietary Antarctic krill could reduce lipid accumulation in the liver while the intestine exhibited no obvious changes. Enzyme activity measurements demonstrated that dietary Antarctic krill had an inhibitory effect on oxidative stress in both the intestine and the liver. By comparative transcriptome analysis, a total of 1,597 and 1,161 differentially expressed genes (DEGs) were identified in the intestine and liver, respectively. Functional analysis of the DEGs showed multiple enriched terms significantly related to cholesterol metabolism, antioxidants, and immunity. Furthermore, the expression profiles of representative DEGs, such as dhcr7, apoa4, sc5d, and scarf1, were validated by qRT-PCR and fluorescence in situ hybridization. Finally, a comparative transcriptome analysis was performed to demonstrate the biased effects of dietary Antarctic krill and astaxanthin on the liver of P. leopardus. CONCLUSIONS: Our study demonstrated that dietary Antarctic krill could reduce lipid accumulation in the liver of P. leopardus, enhance antioxidant capacities in both the intestine and liver, and exhibit molecular-level improvements in lipid metabolism, immunity, and antioxidants. It will contribute to understanding the protective effects of Antarctic krill in P. leopardus and provide insights into aquaculture nutritional strategies.


Asunto(s)
Lubina , Euphausiacea , Animales , Antioxidantes , Euphausiacea/genética , Ecosistema , Hibridación Fluorescente in Situ , Perfilación de la Expresión Génica , Dieta , Lubina/genética , Lípidos , Regiones Antárticas
3.
Mol Biol Evol ; 40(11)2023 Nov 03.
Artículo en Inglés | MEDLINE | ID: mdl-37816123

RESUMEN

Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change.


Asunto(s)
Euphausiacea , Animales , Euphausiacea/genética , Filogenia , Transcriptoma , Perfilación de la Expresión Génica , Genómica , Regiones Antárticas
4.
Genes Genomics ; 45(8): 1063-1071, 2023 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-37301775

RESUMEN

BACKGROUND: The Antarctic krill, Euphausia superba (E. superba), is a key organism in the Antarctic marine ecosystem and has been widely studied. However, there is a lack of transcriptome data focusing on temperature responses. METHODS: In this study, we performed transcriptome sequencing of E. superba samples exposed to three different temperatures: -1.19 °C (low temperature, LT), - 0.37 °C (medium temperature, MT), and 3 °C (high temperature, HT). RESULTS: Illumina sequencing generated 772,109,224 clean reads from the three temperature groups. In total, 1,623, 142, and 842 genes were differentially expressed in MT versus LT, HT versus LT, and HT versus MT, respectively. Moreover, Kyoto Encyclopedia of Genes and Genomes analysis revealed that these differentially expressed genes were mainly involved in the Hippo signaling pathway, MAPK signaling pathway, and Toll-like receptor signaling pathway. Quantitative reverse-transcription PCR revealed that ESG037073 expression was significantly upregulated in the MT group compared with the LT group, and ESG037998 expression was significantly higher in the HT group than in the LT group. CONCLUSIONS: This is the first transcriptome analysis of E. superba exposed to three different temperatures. Our results provide valuable resources for further studies on the molecular mechanisms underlying temperature adaptation in E. superba.


Asunto(s)
Euphausiacea , Animales , Temperatura , Euphausiacea/genética , Euphausiacea/metabolismo , Ecosistema , Perfilación de la Expresión Génica , Transcriptoma
5.
Cell ; 186(6): 1279-1294.e19, 2023 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-36868220

RESUMEN

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.


Asunto(s)
Euphausiacea , Genoma , Animales , Relojes Circadianos/genética , Ecosistema , Euphausiacea/genética , Euphausiacea/fisiología , Genómica , Análisis de Secuencia de ADN , Elementos Transponibles de ADN , Evolución Biológica , Adaptación Fisiológica
6.
Proteomics ; 22(18): e2100404, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35778945

RESUMEN

The Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean that uses an arsenal of hydrolases for biomacromolecule decomposition to effectively digest its omnivorous diet. The present study builds on a hybrid-assembled transcriptome (13,671 ORFs) combined with comprehensive proteome profiling. The analysis of individual krill compartments allowed detection of significantly more different proteins compared to that of the entire animal (1464 vs. 294 proteins). The nearby krill sampling stations in the Bransfield Strait (Antarctic Peninsula) yielded rather uniform proteome datasets. Proteins related to energy production and lipid degradation were particularly abundant in the abdomen, agreeing with the high energy demand of muscle tissue. A total of 378 different biomacromolecule hydrolysing enzymes were detected, including 250 proteases, 99 CAZymes, 14 nucleases and 15 lipases. The large repertoire in proteases is in accord with the protein-rich diet affiliated with E. superba's omnivorous lifestyle and complex biology. The richness in chitin-degrading enzymes allows not only digestion of zooplankton diet, but also the utilisation of the discharged exoskeleton after moulting.


Asunto(s)
Euphausiacea , Animales , Regiones Antárticas , Euphausiacea/genética , Euphausiacea/metabolismo , Péptido Hidrolasas/genética , Péptido Hidrolasas/metabolismo , Proteoma/metabolismo , Transcriptoma
7.
Genes (Basel) ; 13(3)2022 03 18.
Artículo en Inglés | MEDLINE | ID: mdl-35328094

RESUMEN

Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a top-down hypothesis known as the 'krill surplus hypothesis'. However, a lack of pre-whaling population baselines has made it challenging to investigate historical changes in the abundance of the major krill predators in relation to whaling. Therefore, we used reduced representation sequencing and a coalescent-based maximum composite likelihood approach to reconstruct the recent demographic history of the Antarctic fur seal, a pinniped that was hunted to the brink of extinction by 18th and 19th century sealers. In line with the known history of this species, we found support for a demographic model that included a substantial reduction in population size around the time period of sealing. Furthermore, maximum likelihood estimates from this model suggest that the recovered, post-sealing population at South Georgia may have been around two times larger than the pre-sealing population. Our findings lend support to the krill surplus hypothesis and illustrate the potential of genomic approaches to shed light on long-standing questions in population biology.


Asunto(s)
Euphausiacea , Lobos Marinos , Animales , Regiones Antárticas , Euphausiacea/genética , Lobos Marinos/genética , Funciones de Verosimilitud , Densidad de Población
8.
Ecotoxicol Environ Saf ; 232: 113289, 2022 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-35144128

RESUMEN

Antibiotic resistance genes (ARGs) are ubiquitous in nature, especially in the current era of antibiotic abuse, and their existence is a global concern. In the present study, we discovered that Antarctic krill-related culturable bacteria are resistant to ß-lactam, tetracyclines, aminoglycosides, and sulphamethoxazole/trimethoprim based on the antibiotic efflux mechanism. In addition, the co-occurrence of ARGs with insertion sequence (IS) (tnpA, IS91) and Intl1 on the isolates and the phylogenetic analysis results of the whole-genome revealed low-frequency ARG transfer events, implying the transferability of these ARGs. These findings provide an early warning for the wide assessment of Antarctic microbiota in the spread of ARGs. Our work provides novel insights into understanding ARGs in culturable host-associated microorganisms, and their ecological risks and has important implications for future risk assessments of antibiotic resistance in extreme environments.


Asunto(s)
Antibacterianos , Euphausiacea , Animales , Bacterias/genética , Euphausiacea/genética , Genes Bacterianos , Filogenia
9.
Mol Ecol ; 30(4): 1042-1052, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33300251

RESUMEN

Antarctic krill (Euphausia superba) are amongst the most abundant animals on Earth, with a circumpolar distribution in the Southern Ocean. Genetic and genomic studies have failed to detect any population structure for the species, suggesting a single panmictic population. However, the hyper-abundance of krill slows the rate of genetic differentiation, masking potential underlying structure. Here we use high-throughput sequencing of bacterial 16S rRNA genes to show that krill bacterial epibiont communities exhibit spatial structuring, driven mainly by distance rather than environmental factors, especially for strongly krill-associated bacteria. Estimating the ecological processes driving bacterial community turnover indicated this was driven by bacterial dispersal limitation increasing with geographic distance. Furthermore, divergent epibiont communities generated from a single krill swarm split between aquarium tanks under near-identical conditions suggests physical isolation in itself can cause krill-associated bacterial communities to diverge. Our findings show that Antarctic krill-associated bacterial communities are geographically structured, in direct contrast with the lack of structure observed for krill genetic and genomic data.


Asunto(s)
Euphausiacea , Animales , Regiones Antárticas , Bacterias/genética , Euphausiacea/genética , ARN Ribosómico 16S/genética
10.
Mar Genomics ; 56: 100806, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32773253

RESUMEN

The Antarctic krill, Euphausia superba, has evolved seasonal rhythms of physiology and behaviour to survive under the extreme photoperiodic conditions in the Southern Ocean. However, the molecular mechanisms generating these rhythms remain far from understood. The aim of this study was to investigate seasonal differences in gene expression in three different latitudinal regions (South Georgia, South Orkneys/Bransfield Strait, Lazarev Sea) and to identify genes with potential regulatory roles in the seasonal life cycle of Antarctic krill. The RNA-seq data were analysed (a) for seasonal differences between summer and winter krill sampled from each region, and (b) for regional differences within each season. A large majority of genes showed an up-regulation in summer krill in all regions with respect to winter krill. However, seasonal differences in gene expression were less pronounced in Antarctic krill from South Georgia, most likely due to the milder seasonal conditions of the lower latitudes of this region, with a less extreme light regime and food availability between summer and winter. Our results suggest that in the South Orkneys/Bransfield Strait and Lazarev Sea region, Antarctic krill entered a state of metabolic depression and regressed development (winter quiescence) in winter. Moreover, seasonal gene expression signatures seem to be driven by a photoperiodic timing system that may adapt the flexible behaviour and physiology of Antarctic krill to the highly seasonal environment according to the latitudinal region. However, at the lower latitude South Georgia region, food availability might represent the main environmental cue influencing seasonal physiology.


Asunto(s)
Euphausiacea/genética , Transcriptoma , Animales , Regiones Antárticas , Islas del Atlántico , Femenino , Perfilación de la Expresión Génica , Masculino , Océanos y Mares , Estaciones del Año
11.
J Agric Food Chem ; 68(30): 7935-7945, 2020 Jul 29.
Artículo en Inglés | MEDLINE | ID: mdl-32643372

RESUMEN

A cold-active transglutaminase (TGase, EC 2.3.2.13) that catalyzes the reaction of protein glutamine + protein lysine ↔ protein with γ-glutamyl-ε-lysine cross-link + NH3 at low temperatures was reported previously. This study verified the thermal stability of the TGase from 0-80 °C. Fluorescence and CD spectra studies confirmed tertiary structural damage at 40 °C, α-helix reduction at 60 °C, and refolding during cooling to 20 °C. The TGase sequence was obtained by transcriptomics and used to build its structure. Its catalytic triad was Cys333-His403-Asp426 and its catalytic process was inferred from the model. Molecular dynamics simulation illustrated that its cold activity resulted from its flexible active site, while high thermostability was conferred by an overall rigid structure, a large amount of stable Val and Lys, and strong electrostatic interactions at the N- and C- terminals. This study fills gaps in the correlation of conformational changes with stability and activity of TGase.


Asunto(s)
Proteínas de Artrópodos/química , Euphausiacea/enzimología , Transglutaminasas/química , Secuencias de Aminoácidos , Animales , Proteínas de Artrópodos/genética , Proteínas de Artrópodos/metabolismo , Biocatálisis , Dominio Catalítico , Frío , Estabilidad de Enzimas , Euphausiacea/química , Euphausiacea/genética , Calor , Cinética , Simulación de Dinámica Molecular , Replegamiento Proteico , Electricidad Estática , Transglutaminasas/genética , Transglutaminasas/metabolismo
12.
Mar Drugs ; 18(4)2020 Mar 31.
Artículo en Inglés | MEDLINE | ID: mdl-32244466

RESUMEN

The world-famous Antarctic krill (Euphausia superba) plays a fundamental role in the Antarctic food chain. It resides in cold environments with the most abundant biomass to support the Antarctic ecology and fisheries. Here, we performed the first genome survey of the Antarctic krill, with genomic evidence for its estimated genome size of 42.1 gigabases (Gb). Such a large genome, however, is beyond our present capability to obtain a good assembly, although our sequencing data are a valuable genetic resource for subsequent polar biomedical research. We extracted 13 typical protein-coding gene sequences of the mitochondrial genome and analyzed simple sequence repeats (SSRs), which are useful for species identification and origin determination. Meanwhile, we conducted a high-throughput comparative identification of putative antimicrobial peptides (AMPs) and antihypertensive peptides (AHTPs) from whole-body transcriptomes of the Antarctic krill and its well-known counterpart, the whiteleg shrimp (Penaeus vannamei; resident in warm waters). Related data revealed that AMPs/AMP precursors and AHTPs were generally conserved, with interesting variations between the two crustacean species. In summary, as the first report of estimated genome size of the Antarctic krill, our present genome survey data provide a foundation for further biological research into this polar species. Our preliminary investigations on bioactive peptides will bring a new perspective for the in-depth development of novel marine drugs.


Asunto(s)
Euphausiacea/genética , Genoma Mitocondrial/genética , Repeticiones de Microsatélite/genética , Animales , Regiones Antárticas , Antihipertensivos/aislamiento & purificación , Péptidos Catiónicos Antimicrobianos/genética , Péptidos Catiónicos Antimicrobianos/aislamiento & purificación , Productos Biológicos/aislamiento & purificación , Perfilación de la Expresión Génica , Genómica , Secuenciación de Nucleótidos de Alto Rendimiento , Secuenciación Completa del Genoma
13.
Sci Rep ; 9(1): 13894, 2019 09 25.
Artículo en Inglés | MEDLINE | ID: mdl-31554872

RESUMEN

Antarctic krill (Euphausia superba) is a high latitude pelagic organism which plays a central role in the Southern Ocean ecosystem. E. superba shows daily and seasonal rhythms in physiology and behaviour, which are synchronized with the environmental cycles of its habitat. Recently, the main components of the krill circadian machinery have been identified and characterized. However, the exact mechanisms through which the endogenous timing system operates the control and regulation of the overt rhythms remains only partially understood. Here we investigate the involvement of the circadian clock in the temporal orchestration of gene expression by using a newly developed version of a krill microarray platform. The analysis of transcriptome data from krill exposed to both light-dark cycles (LD 18:6) and constant darkness (DD), has led to the identification of 1,564 putative clock-controlled genes. A remarkably large proportion of such genes, including several clock components (clock, period, cry2, vrille, and slimb), show oscillatory expression patterns in DD, with a periodicity shorter than 24 hours. Energy-storage pathways appear to be regulated by the endogenous clock in accordance with their ecological relevance in daily energy managing and overwintering. Our results provide the first representation of the krill circadian transcriptome under laboratory, free-running conditions.


Asunto(s)
Relojes Circadianos/genética , Ritmo Circadiano/genética , Euphausiacea/genética , Euphausiacea/fisiología , Transcriptoma/genética , Animales , Regiones Antárticas , Oscuridad , Ecosistema , Fotoperiodo
14.
Artículo en Inglés | MEDLINE | ID: mdl-30776436

RESUMEN

Thioredoxin system plays an important role in antioxidative stress, thioredoxin 2 (Trx2) being one of the most important components in the thioredoxin system. The full-length cDNA sequence of thioredoxin 2 from Euphausia superba (EsTrx2) is 1276 bp and contain a 5' untranslated region (UTR) of 94 bp, a 3' UTR of 741 bp and an open reading frame (ORF) of 441 bp, encoding a putative protein of 146 amino acids. Multiple sequence alignments have indicated that EsTrx2 possesses a conserved (-Cys-Gly-Pro-Cys-) CGPC redox-active site. EsTrx2 shares 62.3% identity with the swimming crab (Portunus trituberculatus) Trx2. The predicted three-dimensional structure of EsTrx2 consists of a thioredoxin fold. The high similarity and phylogenetic analysis have indicated that EsTrx2 is a member of the mitochondrial Trx2 sub-family. The recombinant EsTrx2 (rEsTrx2) was constructed and expressed in Escherichia coli BL21 (DE3). The rEsTrx2 protein showed high redox activity and antioxidant capacity at temperature from 4 to 37 °C. All results indicated that EsTrx2 was involved in the oxidative stress response of E. superba.


Asunto(s)
Euphausiacea/citología , Euphausiacea/genética , Regulación de la Expresión Génica , Mitocondrias/metabolismo , Tiorredoxinas/genética , Tiorredoxinas/metabolismo , Secuencia de Aminoácidos , Animales , Antioxidantes/metabolismo , Secuencia de Bases , Clonación Molecular , Modelos Moleculares , Conformación Proteica , Análisis de Secuencia , Tiorredoxinas/química
15.
J Genet ; 97(4): 995-999, 2018 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-30262712

RESUMEN

To provide massive genetic resources for the Antarctic krill (Euphausia superba), we sequenced and analysed the transcriptome by using high-throughput Illumina paired-end sequencing technology. A total of 77.1 million clean reads representing ~11.0Gb data were generated. The average length of these reads was 142 bp. De novo assembly yielded 125,211 transcripts with a N50 of 690 bp. Further analysis produced 106,250 unigenes, of which 31,683 were annotated based on protein homology searches against protein databases. Gene ontology analysis showed that ion binding, organic substance, metabolic process, and cell part were the most abundantly used terms in molecular function, biological process and cellular component categories, respectively. In addition, 3067 unigenes were mapped onto 311 signal pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, 15,224 simple sequence repeats were identified from 13,535 transcripts, and 103,593 single-nucleotide polymorphisms were found from 21.6% of total transcripts. These genetic resources obtained in this study forms a good foundation for investigating gene function, and evaluating population genetic diversity for this important Southern Ocean fisheries resource, E. superba.


Asunto(s)
Euphausiacea/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Repeticiones de Microsatélite/genética , Transcriptoma/genética , Animales , Biomarcadores , Anotación de Secuencia Molecular , Análisis de Secuencia de ADN
16.
J Sci Food Agric ; 98(8): 3049-3056, 2018 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-29194642

RESUMEN

BACKGROUND: The ability of Antarctic krill, Euphausia superba (Dana, 1852), to thrive in a cold environment comes from its capacity to synthesize cold-adapted enzymes. Its trypsin, as a main substance in the metabolic reactions, plays a key role in the adaption to low temperatures. However, the progress of research on its cold-adaption mechanism is being influenced due to the limited information on its gene and spatial structure. RESULTS: We studied the gene of E. superba trypsin with transcriptome sequencing first, and then discussed its cold-adaption mechanism with the full gene and predicted structure basing on bioinformatics. The results showed the proportion of certain residues played important roles in the cold-adaptation behavior for trypsin. Furthermore, a higher proportion of random coils and reduced steric hindrance might also be key factors promoting its cold adaption. CONCLUSION: This research aimed to reveal the cold-adaption mechanism of E. superba trypsin and provide support for basic research on molecular modification by site-directed mutagenesis of complementary DNA used to produce new and improved recombinant variants with cold adaption. Furthermore, it may broaden its commercial application on minimizing undesirable changes elevated at higher temperature in food processing and in treatment of trauma and inflammation in medicine. © 2017 Society of Chemical Industry.


Asunto(s)
Proteínas de Artrópodos/química , Proteínas de Artrópodos/genética , Euphausiacea/enzimología , Tripsina/química , Tripsina/genética , Secuencia de Aminoácidos , Animales , Proteínas de Artrópodos/metabolismo , Secuencia de Bases , Frío , Biología Computacional , Estabilidad de Enzimas , Euphausiacea/química , Euphausiacea/genética , Euphausiacea/fisiología , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Alineación de Secuencia , Mariscos/análisis , Transcriptoma , Tripsina/metabolismo
17.
Mar Genomics ; 38: 25-32, 2018 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-28601440

RESUMEN

The northern krill, Meganyctiphanes norvegica, is an important component of the pelagic food web across the North Atlantic. Widespread from the Mediterranean to the Subarctic Atlantic, populations appear to be strongly adapted to local temperatures, and seem to have very little plasticity. The goal of this study was to create and annotate a de novo transcriptome assembly to allow for comparative and physiological studies and to explore the gene expression response of M. norvegica from the Gulf of Maine to two different temperature conditions. Our Trinity assembly produced 405,497 transcripts with ~16% annotation success versus nr with a stringent cutoff (>1e-10), and substantial cross-annotation versus FlyBase and other published pelagic crustacean transcriptomes. There were 122 transcripts that were differentially expressed based on our 2-day 9 versus 12°C temperature exposure, and their annotation suggested changes in energetic metabolism and molting. These results generate a useful molecular resource for further more directed studies as well as provide initial insight into the physiological processes that may shape the temperature response of the northern krill.


Asunto(s)
Euphausiacea/genética , Transcriptoma , Animales , Océano Atlántico , Anotación de Secuencia Molecular , Agua de Mar , Temperatura
18.
Mar Genomics ; 37: 97-113, 2018 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-28964713

RESUMEN

The Northern krill Meganyctiphanes norvegica is a significant component of the zooplankton community in many regions of the North Atlantic Ocean. In the areas it inhabits, M. norvegica is of great importance ecologically, as it is both a major consumer of phytoplankton/small zooplankton and is a primary food source for higher-level consumers. One behavior of significance for both feeding and predator avoidance in Meganyctiphanes is diel vertical migration (DVM), i.e., a rising from depth at dusk and a return to depth at dawn. In this and other euphausiids, an endogenous circadian pacemaker is thought, at least in part, to control DVM. Currently, there is no information concerning the identity of the genes/proteins that comprise the M. norvegica circadian system. In fact, there is little information concerning the molecular underpinnings of circadian rhythmicity in crustaceans generally. Here, a publicly accessible transcriptome was used to identify the molecular components of a putative Meganyctiphanes circadian system. A complete set of core clock proteins was deduced from the M. norvegica transcriptome (clock, cryptochrome 2, cycle, period and timeless), as was a large suite of proteins that likely function as modulators of the core clock (e.g., doubletime), or serves as inputs to it (cryptochrome 1) or outputs from it (pigment dispersing hormone). This is the first description of a "complete" (core clock through putative output pathway signals) euphausiid clock system, and as such, provides a foundation for initiating molecular investigations of circadian signaling in M. norvegica and other krill species, including how clock systems may regulate DVM and other behaviors.


Asunto(s)
Proteínas de Artrópodos/genética , Proteínas CLOCK/genética , Relojes Circadianos/genética , Ritmo Circadiano/genética , Euphausiacea/fisiología , Transducción de Señal , Secuencia de Aminoácidos , Animales , Proteínas de Artrópodos/metabolismo , Proteínas CLOCK/metabolismo , Simulación por Computador , Euphausiacea/genética , Alineación de Secuencia , Transcriptoma
19.
PLoS One ; 12(2): e0171908, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28187156

RESUMEN

Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans). The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2 levels. The database gives access to: 1) the full list of assembled genes and transcripts; 2) their level of similarity to transcripts and proteins from other species; 3) the predicted protein domains contained within each transcript; 4) their predicted GO terms; 5) the level of expression of each transcript in the different larval stages and CO2 treatments. All references to external entities (sequences, domains, GO terms) are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web.


Asunto(s)
Bases de Datos de Ácidos Nucleicos , Euphausiacea/genética , Transcriptoma , Animales , Dióxido de Carbono/farmacología , Euphausiacea/efectos de los fármacos , Euphausiacea/crecimiento & desarrollo , Regulación del Desarrollo de la Expresión Génica , Proteoma/genética , Proteoma/metabolismo
20.
Fish Shellfish Immunol ; 63: 376-383, 2017 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-28232193

RESUMEN

Thioredoxins, with a dithiol/disulfide active site (CGPC) are major highly conserved and ubiquitous proteins that are involved in protecting organisms against various oxidative stresses. In the present study, a novel thioredoxin gene was identified in antarctic microcrustacean, Euphausia superba (designated as EsTrx1). The full-length cDNA sequences of EsTrx1 was of 621 bp, containing a 5' untranslated region (UTR) of 45 bp, a 3' UTR of 276 bp and an open reading frame (ORF) of 303 bp encoding a putative protein of 100 amino acids. The predicted molecular weight of EsTrx1 was 11.08 kDa and the theoretical isoelectric point was 4.51. Multiple sequence alignment indicated that the EsTrx1 possessed conserved CGPC redox-active site. EsTrx1 shared 68.6% similarity with the Chinese mitten crab (Eriocheir sinensis) Trx1. The predicted three-dimensional structure of EsTrx1 consisted of a central core of a four-stranded ß-sheet and four flanking α-helices. The high similarity of EsTrx1 with Trx1s from other animals together with the phylogenetic analysis indicated that EsTrx1 could be a novel member of Trx1 sub-family. In order to elucidate its biological functions, the recombinant EsTrx1 was constructed and expressed in Escherichia coli BL21 (DE3). Experiments demonstrated that the rEsTrx1 fusion protein possessed the expected redox activity in enzymatic analysis, and be more potent than GSH in antioxidant capacity. These results together indicated that EsTrx1 could be involved in the oxidative stress response of E. superba.


Asunto(s)
Proteínas de Artrópodos/genética , Euphausiacea/genética , Tiorredoxinas/genética , Secuencia de Aminoácidos , Animales , Proteínas de Artrópodos/química , Proteínas de Artrópodos/metabolismo , Secuencia de Bases , Clonación Molecular , ADN Complementario/genética , ADN Complementario/metabolismo , Escherichia coli/genética , Euphausiacea/inmunología , Euphausiacea/metabolismo , Filogenia , Estructura Terciaria de Proteína , ARN/genética , ARN/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia , Tiorredoxinas/química , Tiorredoxinas/metabolismo
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