RESUMEN

Recent studies have highlighted the significant role of copy number variants (CNVs) in phenotypic diversity, environmental adaptation and species divergence across eukaryotes. The presence of CNVs also has the potential to introduce genotyping biases, which can pose challenges to accurate population and quantitative genetic analyses. However, detecting CNVs in genomes, particularly in non-model organisms, presents a formidable challenge. To address this issue, we have developed a statistical framework and an accompanying r software package that leverage allelic-read depth from single nucleotide polymorphism (SNP) data for accurate CNV detection. Our framework capitalises on two key principles. First, it exploits the distribution of allelic-read depth ratios in heterozygotes for individual SNPs by comparing it against an expected distribution based on binomial sampling. Second, it identifies SNPs exhibiting an apparent excess of heterozygotes under Hardy-Weinberg equilibrium. By employing multiple statistical tests, our method not only enhances sensitivity to sampling effects but also effectively addresses reference biases, resulting in optimised SNP classification. Our framework is compatible with various NGS technologies (e.g. RADseq, Exome-capture). This versatility enables CNV calling from genomes of diverse complexities. To streamline the analysis process, we have implemented our framework in the user-friendly r package 'rCNV', which automates the entire workflow seamlessly. We trained our models using simulated data and validated their performance on four datasets derived from different sequencing technologies, including RADseq (Chinook salmon-Oncorhynchus tshawytscha), Rapture (American lobster-Homarus americanus), Exome-capture (Norway spruce-Picea abies) and WGS (Malaria mosquito-Anopheles gambiae).

Asunto(s)

Variaciones en el Número de Copia de ADN , Polimorfismo de Nucleótido Simple , Animales , Programas Informáticos , Exoma , Noruega , Algoritmos

RESUMEN

Many mutations in genes for ribosomal proteins (r-proteins) and assembly factors cause cell stress and altered cell fate, resulting in congenital diseases collectively called ribosomopathies. Even though all such mutations depress the cell's protein synthesis capacity, they generate many different phenotypes, suggesting that the diseases are not due simply to insufficient protein synthesis capacity. To learn more, we investigated how the global transcriptome in Saccharomyces cerevisiae responds to reduced protein synthesis generated in two different ways: abolishing the assembly of new ribosomes and inhibiting ribosomal function. Our results showed that the mechanism by which protein synthesis is obstructed affects the ribosomal protein transcriptome differentially: ribosomal protein mRNA abundance increases during the abolition of ribosome formation but decreases during the inhibition of ribosome function. Interestingly, the ratio between mRNAs from some, but not all, pairs of paralogous ribosomal protein genes encoding slightly different versions of a given r-protein changed differently during the two types of stress, suggesting that expression of specific ribosomal protein paralogous mRNAs may contribute to the stress response. Unexpectedly, the abundance of transcripts for ribosome assembly factors and translation factors remained relatively unaffected by the stresses. On the other hand, the state of the translation apparatus did affect cell physiology: mRNA levels for some other proteins not directly related to the translation apparatus also changed differentially, though not coordinately with the r-protein genes, in response to the stresses. IMPORTANCE Mutations in genes for ribosomal proteins or assembly factors cause a variety of diseases called ribosomopathies. These diseases are typically ascribed to a reduction in the cell's capacity for protein synthesis. Paradoxically, ribosomal mutations result in a wide variety of disease phenotypes, even though they all reduce protein synthesis. Here, we show that the transcriptome changes differently depending on how the protein synthesis capacity is reduced. Most strikingly, inhibiting ribosome formation and ribosome function had opposite effects on the abundance of mRNA for ribosomal proteins, while genes for ribosome translation and assembly factors showed no systematic responses. Thus, the process by which the protein synthesis capacity is reduced contributes decisively to global mRNA composition. This emphasis on process is a new concept in understanding ribosomopathies and other stress responses.

Asunto(s)

Proteínas Ribosómicas , Proteínas de Saccharomyces cerevisiae , Proteínas Ribosómicas/genética , Saccharomyces cerevisiae/genética , ARN Mensajero/genética , Ribosomas/genética , Proteínas de Saccharomyces cerevisiae/genética

RESUMEN

In eukaryotic cells, miRNAs regulate a plethora of cellular functionalities ranging from cellular metabolisms, and development to the regulation of biological networks and pathways, both under homeostatic and pathological states like cancer.Despite their immense importance as key regulators of cellular processes, accurate and reliable estimation of miRNAs using Next Generation Sequencing is challenging, largely due to the limited availability of robust computational tools/methods/pipelines. Here, we introduce miRPipe, an end-to-end computational framework for the identification, characterization, and expression estimation of small RNAs, including the known and novel miRNAs and previously annotated pi-RNAs from small-RNA sequencing profiles. Our workflow detects unique novel miRNAs by incorporating the sequence information of seed and non-seed regions, concomitant with clustering analysis. This approach allows reliable and reproducible detection of unique novel miRNAs and functionally same miRNAs (paralogues). We validated the performance of miRPipe with the available state-of-the-art pipelines using both synthetic datasets generated using the newly developed miRSim tool and three cancer datasets (Chronic Lymphocytic Leukemia, Lung cancer, and breast cancer). In the experiment over the synthetic dataset, miRPipe is observed to outperform the existing state-of-the-art pipelines (accuracy: 95.23% and F 1-score: 94.17%). Analysis on all the three cancer datasets shows that miRPipe is able to extract more number of known dysregulated miRNAs or piRNAs from the datasets as compared to the existing pipelines.

RESUMEN

Juvenile rainbow trout (Oncorhynchus mykiss) develop social hierarchies when competing for resources in a constrained environment. Among the physiological consequences of social status are changes in organismal energy metabolism, which generally favour anabolic pathways in dominant fish and catabolic pathways in subordinate fish. The somatotropic axis is an important regulator of metabolism and growth that could be involved in mediating metabolic changes in response to social status in juvenile rainbow trout. Here we used juvenile trout housed either in dyads or individually (sham controls) to determine whether social status changes indices of somatotropic axis function. Although pituitary growth hormone expression (gh1 and gh2) did not differ among groups, circulating growth hormone (GH) increased ∼12-fold in subordinate fish compared to sham and dominant fish. Social status caused consistent differential expression of GH receptor paralogues in liver and muscle, two principal target tissues of GH. Compared to dominant and/or sham fish, ghra paralogue expression (ghra1 and ghra2) was lower, while ghrb1 expression was higher in subordinate fish. Across tissues, ghra paralogue expression was generally positively correlated with expression of insulin growth factors (igf1, igf2), while ghrb1 expression was positively correlated with transcript abundance of hormone sensitive lipase (hsl1). Because igf and hsl expression are subject to context-dependent GH control in rainbow trout, these results suggest that increased circulating GH in conjunction with differential expression of ghr paralogues may translate into prioritization of downstream catabolic lipolytic pathways in subordinate rainbow trout. These findings support a social context-dependent role for GH signalling in mediating metabolic changes in juvenile rainbow trout.

Asunto(s)

Oncorhynchus mykiss , Animales , Hormona del Crecimiento/metabolismo , Hígado/metabolismo , Receptores de Somatotropina/genética , Receptores de Somatotropina/metabolismo , Estatus Social

RESUMEN

Intraflagellar transport (IFT) is a microtubule-based system that supports the assembly and maintenance of cilia. The dysfunction of IFT leads to ciliopathies of variable severity. Two of the IFT-B components are the paralogue proteins TTC30A and TTC30B. To investigate whether these proteins constitute redundant functions, CRISPR/Cas9 was used to generate single TTC30A or B and double-knockout hTERT-RPE1 cells. Ciliogenesis assays showed the redundancy of both proteins while the polyglutamylation of cilia was affected in single knockouts. The localization of other IFT components was not affected by the depletion of a single paralogue. A loss of both proteins led to a severe ciliogenesis defect, resulting in no cilia formation, which was rescued by TTC30A or B. The redundancy can be explained by the highly similar interaction patterns of the paralogues; both equally interact with the IFT-B machinery. Our study demonstrates that a loss of one TTC30 paralogue can mostly be compensated by the other, thus preventing severe ciliary defects. However, cells assemble shorter cilia, which are potentially limited in their function, especially because of impaired polyglutamylation. A complete loss of both proteins leads to a deficit in IFT complex B integrity followed by disrupted IFT and subsequently no cilia formation.

Asunto(s)

Cilios , Ciliopatías , Transporte Biológico , Cilios/genética , Cilios/metabolismo , Ciliopatías/genética , Ciliopatías/metabolismo , Humanos , Proteínas/metabolismo

RESUMEN

Molecular methods are increasingly used to identify species that lack conspicuous macro- or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long-read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intraindividual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogues, which can provide crucial information for species delimitation and population-level studies.

Asunto(s)

Código de Barras del ADN Taxonómico , Secuenciación de Nucleótidos de Alto Rendimiento , Código de Barras del ADN Taxonómico/métodos , ADN de Hongos/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Filogenia , ARN Ribosómico 28S , Análisis de Secuencia de ADN

RESUMEN

Synaptic vesicle glycoprotein-2 (SV2) is a family of proteins consisting of SV2A, SV2B, and SV2C. This protein family has attracted attention in recent years after SV2A was shown to be an epileptic drug target and a perhaps a biomarker of synaptic density. So far, the anatomical localization of these proteins in the rodent and human brain have been reported, but co-expression of SV2 genes on a cellular level, their expressions in the human brain, comparison to radioligand binding, any possible regulation in epilepsy are not known. We have here analyzed the expression of SV2 genes in neuronal subtypes in the temporal neocortex in selected specimens by using single nucleus-RNA sequencing, and performed quantitative PCR in populations of temporal lobe epilepsy (TLE) patients and healthy controls. [3H]-UCB-J autoradiography was performed to analyze the correlation between the mRNA transcript and binding capacity to SV2A. Our data showed that the SV2A transcript is expressed in all glutamatergic and GABAergic cortical subtypes, while SV2B expression is restricted to only the glutamatergic neurons and SV2C has very limited expression in a small subgroup of GABAergic interneurons. The level of [3H]-UCB-J binding and the concentration of SV2A mRNA is strongly correlated in each patient, and the expression is lower in the TLE patients. There is no relationship between SV2A expression and age, sex, seizure frequency, duration of epilepsy, or whether patients were recently treated with levetiracetam or not. Collectively, these findings point out a neuronal subtype-specific distribution of the expression of the three SV2 genes, and the lower levels of both radioligand binding and expression further emphasize the significance of these proteins in this disease.

Asunto(s)

Epilepsia del Lóbulo Temporal , Epilepsia , Neocórtex , Epilepsia/genética , Epilepsia del Lóbulo Temporal/genética , Humanos , Glicoproteínas de Membrana/genética , Glicoproteínas de Membrana/metabolismo , Neocórtex/metabolismo , Proteínas del Tejido Nervioso/genética , Proteínas del Tejido Nervioso/metabolismo , ARN Mensajero/genética , Vesículas Sinápticas/metabolismo

RESUMEN

MAIN CONCLUSION: A total of 278 BnWRKYs were identified and analyzed. Ectopic expression of BnWRKY149 and BnWRKY217 suggests that they function in the ABA signaling pathway. WRKY transcription factors play an important role in plant development, however, their function in Brassica napus L. abiotic stress response is still unclear. In this study, a total of 278 BnWRKY transcription factors were identified from the B. napus genome data, and they were subsequently distributed in three main groups. The protein motifs and classification of BnWRKY transcription factors were analyzed, and the locations of their corresponding encoding genes were mapped on the chromosomes of B. napus. Transcriptome analysis of rapeseed seedlings exposed to drought, salt, heat, cold and abscisic acid treatment revealed that 99 BnWRKYs responded to at least one of these stresses. The expression profiles of 12 BnWRKYs were examined with qPCR and the result coincided with RNA-seq analysis. Two genes of interest, BnWRKY149 and BnWRKY217 (homologs of AtWRKY40), were overexpressed in Arabidopsis, and the corresponding proteins were located to the nucleus. Transgene plants of BnWRKY149 and BnWRKY217 were less sensitive to ABA than Arabidopsis Col-0 plants, suggesting they might play important roles in the responses of rapeseed to abiotic stress.

Asunto(s)

Brassica napus , Brassica napus/genética , Brassica napus/metabolismo , Regulación de la Expresión Génica de las Plantas , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Estrés Fisiológico/genética , Factores de Transcripción/genética , Factores de Transcripción/metabolismo

RESUMEN

BACKGROUND: The present availability of full genome sequences of a broad range of animal species across the whole range of evolutionary history enables one to ask questions as to the distribution of genes across the chromosomes. Do newly recruited genes, as new clades emerge, distribute at random or at non-random locations? RESULTS: We extracted values for the ages of the human genes and for their current chromosome locations, from published sources. A quantitative analysis showed that the distribution of newly-added genes among and within the chromosomes appears to be increasingly non-random if one observes animals along the evolutionary series from the precursors of the tetrapoda through to the great apes, whereas the oldest genes are randomly distributed. CONCLUSIONS: Randomization will result from chromosome evolution, but less and less time is available for this process as evolution proceeds. Much of the bunching of recently-added genes arises from new gene formation as paralogues in gene families, near the location of genes that were recruited in the preceding phylostratum. As examples we cite the KRTAP, ZNF, OR and some minor gene families. We show that bunching can also result from the evolution of the chromosomes themselves when, as for the KRTAP genes, blocks of genes that had previously been on disparate chromosomes become linked together.

Asunto(s)

Evolución Molecular , Genoma , Animales , Cromosomas/genética , Humanos

RESUMEN

Interleukin-12 (IL-12) is a heterodimeric cytokine composed of a p35 subunit specific to IL-12 and a p40 subunit shared with IL-23. In this study, we unveiled the existence of two p35 paralogues in grass carp (named gcp35a and gcp35b). Notably, gcp35a and gcp35b displayed distinct inducible expression patterns, as poly I:C merely induced the gene expression of gcp35a but not gcp35b, while recombinant grass carp interferon-gamma (rgcIfn-γ) only enhanced the transcription of gcp35b but not gcp35a. Moreover, the signaling mechanisms responsible for the inducible expression of gcp35a and gcp35b mRNA were elucidated. Because of the existence of three grass carp p40 genes (gcp40a, gcp40b and gcp40c) and two p35 paralogues, six gcIl-12 isoforms were predicted by 3D modeling. Results showed that gcp40a and gcp40b but not gcp40c had the potential for forming heterodimers with both gcp35 paralogues via the disulfide bonds. Non-reducing electrophoresis experiments further disclosed that only gcp40b but not gcp40a or gcp40c could form heterodimers with gcp35 to produce secretory heterodimeric gcp35a/gcp40b (gcIl-12AB) and gcp35b/gcp40b (gcIl-12BB), which prompted us to prepare their recombinant proteins. These two recombinant proteins exhibited their extensive regulation on Ifn-γ production in various immune cells. Intriguingly, both gcIl-12 isoforms significantly enhanced the transcription of il-17a/f1 and il-22 in lymphocytes, and their regulation on il-17a/f1 expression was mediated by Stat3/Rorγt signaling, supporting the potential of gcIl-12 isoforms for inducing Th17-like responses. Additionally, stimulatory effects of gcIl-12 isoforms on il-17a/f1 and ifn-γ expression were attenuated by gcTgf-ß1 via suppressing the activation of Stat3 signaling, implying that their signaling could be manipulated. In brief, our works provide new insights into the inducible expression pattern, heterodimeric generation and functional novelty of Il-12 isoforms in teleosts.

Asunto(s)

Carpas/metabolismo , Proteínas de Peces/metabolismo , Sistema Inmunológico/metabolismo , Interleucina-12/metabolismo , Animales , Carpas/genética , Carpas/inmunología , Proteínas de Peces/genética , Proteínas de Peces/inmunología , Regulación de la Expresión Génica , Células HEK293 , Humanos , Sistema Inmunológico/citología , Sistema Inmunológico/inmunología , Interleucina-12/genética , Interleucina-12/inmunología , Isoformas de Proteínas , Transducción de Señal , Transcripción Genética

RESUMEN

Picrorhiza kurroa is a medicinal herb with diverse pharmacological applications due to the presence of iridoid glycosides, picroside-I (P-I), and picroside-II (P-II), among others. Any genetic improvement in this medicinal herb can only be undertaken if the biosynthetic pathway genes are correctly identified. Our previous studies have deciphered biosynthetic pathways for P-I and P-II, however, the occurrence of multiple copies of genes has been a stumbling block in their usage. Therefore, a methodological strategy was designed to identify and prioritize paralogues of pathway genes associated with contents of P-I and P-II. We used differential transcriptomes varying for P-I and P-II contents in different tissues of P. kurroa. All transcripts for a particular pathway gene were identified, clustered based on multiple sequence alignment to notify as a representative of the same gene (≥ 99% sequence identity) or a paralogue of the same gene. Further, individual paralogues were tested for their expression level via qRT-PCR in tissue-specific manner. In total 44 paralogues in 14 key genes have been identified out of which 19 gene paralogues showed the highest expression pattern via qRT-PCR. Overall analysis shortlisted 6 gene paralogues, PKHMGR3, PKPAL2, PKDXPS1, PK4CL2, PKG10H2 and PKIS2 that might be playing role in the biosynthesis of P-I and P-II, however, their functional analysis need to be further validated either through gene silencing or over-expression. The usefulness of this approach can be expanded to other non-model plant species for which transcriptome resources have been generated.

Asunto(s)

Glicósidos Iridoides/metabolismo , Picrorhiza , Plantas Medicinales , Vías Biosintéticas/genética , Cinamatos/metabolismo , Cinamatos/farmacología , Citoprotección/efectos de los fármacos , Citoprotección/genética , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Redes Reguladoras de Genes/fisiología , Genes de Plantas , Ensayos Analíticos de Alto Rendimiento , Glucósidos Iridoides/metabolismo , Glucósidos Iridoides/farmacología , Glicósidos Iridoides/farmacología , Hígado/efectos de los fármacos , Hígado/fisiología , Picrorhiza/química , Picrorhiza/genética , Picrorhiza/metabolismo , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Brotes de la Planta/genética , Brotes de la Planta/metabolismo , Plantas Medicinales/química , Plantas Medicinales/genética , Plantas Medicinales/metabolismo , Homología de Secuencia , Transcriptoma/fisiología

RESUMEN

Interferon regulatory factors (IRFs) as a family, are major regulators of the innate antiviral response in vertebrates principally involved in regulating the expression of interferons (IFNs) and interferon-stimulated genes (ISGs). To date, nine IRFs have been identified in mammals with a 10th member also found in several avian and fish species. Through genome mining and phylogenetic analysis, we identified and characterised 23 irf genes in 6 salmonid species. This larger repertoire of IRF in salmonids results from two additional whole-genome duplications which occurred in early teleosts and salmonids, respectively. Synteny analysis was then used to identify and confirm which paralogues belonged to each subgroup and a new nomenclature was assigned to the salmonid IRFs. Furthermore, we present a full set of Real-Time PCR primers for all rainbow trout IRFs, confirmed by sequencing to ensure paralogue specificity. RT PCR was then used to examine the response of all trout irf genes in vivo, following Vibrio anguillarum and poly I:C stimulation, indicating potential functional divergence between paralogues. Overall, this study presents a comprehensive overview of the IRF family in salmonids and highlights some novel roles for the salmonid-specific IRFs in immunity.

Asunto(s)

Evolución Molecular , Factores Reguladores del Interferón/genética , Interferones/genética , Salmonidae/genética , Animales , Genoma/genética , Familia de Multigenes/genética

RESUMEN

The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (Salvelinus alpinus) within the Quaternary period offer an ideal model to study the repeatability of evolution at the genomic level. Sympatric morphs of Arctic Charr are found across this species' circumpolar distribution. However, the specific genetic mechanisms driving this morph differentiation are largely unknown despite the cultural and economic importance of the anadromous morph. We used a newly designed 87k SNP chip to investigate the character and consistency of the genomic differences among sympatric morphs within three recently deglaciated and geographically proximate lakes in Labrador, Canada. We found genetically distinct small and large morph Arctic Charr in all three lakes consistent with resident and anadromous morphs, respectively. A degree of reproductive isolation among sympatric morphs is likely given genome-wide distributions of outlier SNPs and high genome-wide FST s. Across all lakes, outlier SNPs were largely nonoverlapping suggesting a lack of genetic parallelism driving morph differentiation. Alternatively, several genes and paralogous copies of the same gene consistently differentiated morphs across multiple lakes suggesting their importance to the manifestation of morphs. Our results confirm the utility of Arctic Charr as a model for investigating the predictability of evolution and support the importance of both genetic parallelism and nonparallelism to the incipient speciation of Arctic Charr morphs.

Asunto(s)

Lagos , Trucha , Animales , Regiones Árticas , Canadá , Terranova y Labrador , Trucha/genética

RESUMEN

This study was conducted to characterise the muscle-specific gene expression, energy metabolism level and growth rates of Atlantic salmon Salmo salar L. reared under different photoperiod regimes. The effects of two photoperiod regimes - LD 16:8 (16 h light:8 h dark) and LD 24:0 (24 h light:0 h dark) over a period of 3 months (August to October) on growth, energy metabolism enzyme activities (cytochrome c oxidase, COX; lactate dehydrogenase, LDH; and aldolase) and the gene expression levels of myogenic regulatory factors (MRFs - MyoD1 paralogues (MyoD1a, MyoD1b, MyoD1c), Myf5, MyoG), myostatin paralogues (MSTN-1a, MSTN-1b, MSTN-2a) and the fast skeletal myosin heavy chain (MyHC) in the muscles of Atlantic salmon underyearling fry (0+) were investigated. The experiment was conducted in a fish hatchery with natural variations in water temperature. The results were compared with those obtained in salmon reared under the lighting conditions of a fish hatchery (HL, hatchery lighting). The results revealed that the fry reared under constant light (LD 24:0) grew faster and were bigger at the end of the experiment. Fishes reared within the photoperiod regime LD 16:8 had a lower growth rate. COX activity was lower in fish under the LD 16:8 regime compared with the LD 24:0 group. The LDH and aldolase enzyme activities were higher in the group with constant light in comparison to control in the beginning of September. The expression level for all of the genes studied variated during the duration of the experiment, and MyHC, MyoG, MyoD1a and Myf5 expression depended on the light regime as well. The more noticeable changes in gene expression occurred in October. The MyHC and MyoG mRNA levels increased, accompanied by MyD1c gene expression, in both groups that had additional lighting (LD 16:8 and LD24:0) at the beginning of October and were higher than the HL group. In the HL group, the elevation of MyHC and MyoG mRNA was gradual during October, but there was a sharp increase in Myf5 expression at the beginning of October. MyoD1 paralogues differently expressed during the experiment. The MyoD1a mRNA level was elevated at the end of October along with MyHC and MyoG expression, but MyoD1b and MyoD1c mRNA levels decreased along with Myf5 gene expression. The expression of MSTN paralogues were elevated with increases in MyHC and MRFs transcripts. These findings show that constant light has a positive effect on the growth rate of salmon, affecting the aerobic and anaerobic capacity in their muscles. The alterations in muscle-specific gene expression between the groups with different light indicated that the mechanisms for regulating muscle growth processes in fish depend on photoperiod duration.

Asunto(s)

Proteínas de Peces/biosíntesis , Regulación Enzimológica de la Expresión Génica/fisiología , Proteínas Musculares/biosíntesis , Músculo Esquelético/enzimología , Salmo salar/metabolismo , Animales

RESUMEN

Inward rectifier K+ (Kir2) channels are critical for electrical excitability of cardiac myocytes. Here, we examine expression of Kir2 channels in the heart of three Gadiformes species, polar cod (Boreogadus saida) and navaga (Eleginus nawaga) of the Arctic Ocean and burbot (Lota lota) of the temperate lakes to find out the role of Kir2 channels in cardiac adaptation to cold. Five boreal freshwater species: brown trout (Salmo trutta fario), arctic char (Salvelinus alpinus), roach (Rutilus rutilus), perch (Perca fluviatilis) and pike (Esox lucius), and zebrafish (Danio rerio), were included for comparison. Transcript expression of genes encoding Kir2.1a, - 2.1b, - 2.2a, - 2.2b and - 2.4 was studied from atrium and ventricle of thermally acclimated or acclimatized fish by quantitative PCR. Kir2 composition in the polar cod was more diverse than in other species in that all Kir2 isoforms were relatively highly expressed. Kir2 composition of navaga and burbot differed from that of the polar cod as well as from those of other species. The relative expression of Kir2.2 transcripts, especially Kir2.2b, was higher in both atrium and ventricle of navaga and burbot (56-89% from the total Kir2 pool) than in other species (0.1-11%). Thermal acclimation induced only small changes in cardiac Kir2 transcript expression in Gadiformes species. However, Kir2.2b transcripts were upregulated in cold-acclimated navaga and burbot hearts. All in all, the cardiac Kir2 composition seems to be dependent on both phylogenetic position and thermal preference of the fish.

Asunto(s)

Organismos Acuáticos , Peces/metabolismo , Agua Dulce , Regulación de la Expresión Génica/fisiología , Canales de Potasio de Rectificación Interna/metabolismo , Animales , Clonación Molecular , Ecosistema , Peces/clasificación , Atrios Cardíacos/metabolismo , Ventrículos Cardíacos/metabolismo , Canales de Potasio de Rectificación Interna/genética , Especificidad de la Especie , Temperatura

RESUMEN

Genetic defects in SAR1B GTPase inhibit chylomicron (CM) trafficking to the Golgi and result in a huge intraenterocyte lipid accumulation with a failure to release CMs and liposoluble vitamins into the blood circulation. The central aim of this study is to test the hypothesis that SAR1B deletion (SAR1B-/- ) disturbs enterocyte lipid homeostasis (e.g., FA ß-oxidation and lipogenesis) while promoting oxidative stress and inflammation. Another issue is to compare the impact of SAR1B-/- to that of its paralogue SAR1A-/- and combined SAR1A-/- /B-/- To address these critical issues, we have generated Caco-2/15 cells with a knockout of SAR1A, SAR1B, or SAR1A/B genes. SAR1B-/- results in lipid homeostasis disruption, reflected by enhanced mitochondrial FA ß-oxidation and diminished lipogenesis in intestinal absorptive cells via the implication of PPARα and PGC1α transcription factors. Additionally, SAR1B-/- cells, which mimicked enterocytes of CM retention disease, spontaneously disclosed inflammatory and oxidative characteristics via the implication of NF-κB and NRF2. In most conditions, SAR1A-/- cells showed a similar trend, albeit less dramatic, but synergetic effects were observed with the combined defects of the two SAR1 paralogues. In conclusion, SAR1B and its paralogue are needed not only for CM trafficking but also for lipid homeostasis, prooxidant/antioxidant balance, and protection against inflammatory processes.

Asunto(s)

Homeostasis , Mucosa Intestinal/enzimología , Metabolismo de los Lípidos , Proteínas de Unión al GTP Monoméricas/metabolismo , Estrés Oxidativo , Antioxidantes/metabolismo , Células CACO-2 , Ácidos Grasos/metabolismo , Regulación Enzimológica de la Expresión Génica , Técnicas de Inactivación de Genes , Humanos , Inflamación/enzimología , Inflamación/metabolismo , Inflamación/patología , Peroxidación de Lípido , Proteínas de Unión al GTP Monoméricas/deficiencia , Proteínas de Unión al GTP Monoméricas/genética , Perilipina-2/genética , Perilipina-2/metabolismo

RESUMEN

Mammalian TNFR1 and TNFR2 bind TNFα and TNFß, and provide key communication signals to a variety of cell types during development and immune responses that are crucial for cell survival, proliferation and apoptosis. In teleost fish TNFß is absent but TNFα has been expanded by the third whole genome duplication (3R WGD) and again by a 4R WGD in some lineages, leading to the four TNFα paralogues known in salmonids. Two paralogues for each of TNFR1 and TNFR2 have been cloned in rainbow trout in this study and are present in other salmonid genomes. Whilst the TNFR2 paralogues were generated via the 4R salmonid WGD, the TNFR1 paralogues arose from a local en bloc duplication. Functional diversification of TNFR paralogues was evidenced by differential gene expression and modulation, upstream ATGs affecting translation, ATTTA motifs in the 3'-UTR regulating mRNA stability, and post-translational modification by N-glycosylation. Trout TNFR are highly expressed in immune tissues/organs, and other tissues, in a gene- and tissue-specific manner. Furthermore, their expression is differentially modulated by PAMPs and cytokines in a cell type- and stimulant-specific manner. Such findings suggest an important role of the TNF/TNFR axis in the immune response and other physiological processes in fish.

Asunto(s)

Proteínas de Peces/genética , Oncorhynchus mykiss/genética , Receptores Tipo II del Factor de Necrosis Tumoral/genética , Receptores Tipo I de Factores de Necrosis Tumoral/genética , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Línea Celular , Evolución Molecular , Duplicación de Gen , Expresión Génica/efectos de los fármacos , Perfilación de la Expresión Génica , Genoma/genética , Interferones/farmacología , Oncorhynchus mykiss/clasificación , Oncorhynchus mykiss/inmunología , Moléculas de Patrón Molecular Asociado a Patógenos/farmacología , Filogenia , Alineación de Secuencia , Distribución Tisular

RESUMEN

One of the most intriguing properties of plasma membrane intrinsic protein (PIP) aquaporins (AQPs) is their ability to modulate water transport by sensing different levels of intracellular pH through the assembly of homo- and heterotetrameric molecular species in the plasma membrane. In this work, using a phenomenological modeling approach, we demonstrate that cooperativity in PIP biological response cannot be directly attributed to a cooperative proton binding, as it is usually considered, since it could also be the consequence of a cooperative conformation transition between open and closed states of the channel. Moreover, our results show that, when mixed populations of homo- and heterotetrameric PIP channels are coexpressed in the plasma membrane of the same cell, the observed decrease in the degree of positive cooperativity would result from the simultaneous presence of molecular species with different levels of proton sensing. Indeed, the random mixing between different PIP paralogues as subunits in a single tetramer, plus the possibility of mixed populations of homo- and heterotetrameric PIP channels widen the spectrum of cooperative responses of a cell membrane. Our approach offers a deep understanding of cooperative transport of AQP channels, as members of a multiprotein family where the relevant proton binding sites of each member have not been clearly elucidated yet.

Asunto(s)

Acuaporinas/metabolismo , Protones , Proteínas de Xenopus/metabolismo , Animales , Acuaporinas/química , Membrana Celular/metabolismo , Concentración de Iones de Hidrógeno , Conformación Proteica , Agua/metabolismo , Proteínas de Xenopus/química , Xenopus laevis

RESUMEN

The hypoxia-inducible transcription factors are key regulators for the physiological response to low oxygen availability. In vertebrates, typically three Hif-α isoforms, Hif-1α, Hif-2α and Hif-3α, are expressed, each of which, together with Hif-1ß, may form a functional heterodimer under hypoxic conditions, controlling expression of hundreds of genes. A teleost-specific whole-genome duplication complicates the analysis of isoform-specific functions in fish, but recent studies suggest that the existence of paralogues of a specific isoform opens up the possibility for a subfunctionalization. In contrast to during development inside the uterus, fish eggs are freely accessible and studies analyzing Hif expression in fish embryos during development have revealed that Hif proteins are not only controlling the hypoxic response, but are also crucial for proper development and organ differentiation. Significant advances have been made in our knowledge about tissue-specific functions of Hif proteins, especially with respect to gill or gonadal tissue. The hypoxia signalling pathway is known to be tightly and mutually intertwined with the circadian clock in zebrafish and mammals. Recently, a mechanistic explanation for the hypoxia-induced dampening of the transcriptional clock was detected in zebrafish, including also metabolically induced alterations of cellular redox signalling. In turn, MAP kinase-mediated H2O2 signalling modulates the temporal expression of Hif-1α protein, similar to the redox regulation of the circadian clock itself. Once again, the zebrafish has emerged as an excellent model organism with which to explore these specific functional aspects of basic eukaryotic cell biology.

Asunto(s)

Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Relojes Circadianos/genética , Proteínas de Peces/genética , Peces/fisiología , Expresión Génica , Transcripción Genética , Animales , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Proteínas de Peces/metabolismo , Peces/genética , Subunidad alfa del Factor 1 Inducible por Hipoxia/genética , Subunidad alfa del Factor 1 Inducible por Hipoxia/metabolismo , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Pez Cebra/genética , Pez Cebra/fisiología

RESUMEN

KEY MESSAGE: The recent release of the maize genome (AGPv4) contains annotation errors of invertase genes and therefore the enzymes are bestly curated manually at the protein level in a comprehensible fashion The synthesis, transport and degradation of sucrose are determining factors for biomass allocation and yield of crop plants. Invertase (INV) is a key enzyme of carbon metabolism in both source and sink tissues. Current releases of the maize genome correctly annotates only two vacuolar invertases (ivr1 and ivr2) and four cell wall invertases (incw1, incw2 (mn1), incw3, and incw4). Our comprehensive survey identified 21 INV isogenes for which we propose a standard nomenclature grouped phylogenetically by amino acid similarity: three vacuolar (INVVR), eight cell wall (INVCW), and ten alkaline/neutral (INVAN) isogenes which form separate dendogram branches due to distinct molecular features. The acidic enzymes were curated for the presence of the DPN tripeptide which is coded by one of the smallest exons reported in plants. Particular attention was placed on the molecular role of INV in vascular tissues such as the nodes, internodes, leaf sheath, husk leaves and roots. We report the expression profile of most members of the maize INV family in nine tissues in two developmental stages, R1 and R3. INVCW7, INVVR2, INVAN8, INVAN9, INVAN10, and INVAN3 displayed the highest absolute expressions in most tissues. INVVR3, INVCW5, INVCW8, and INVAN1 showed low mRNA levels. Expressions of most INVs were repressed from stage R1 to R3, except for INVCW7 which increased significantly in all tissues after flowering. The mRNA levels of INVCW7 in the vegetative stem correlated with a higher transport rate of assimilates from leaves to the cob which led to starch accumulation and growth of the female reproductive organs.

Asunto(s)

Biología Computacional , Genoma de Planta/genética , Zea mays/enzimología , beta-Fructofuranosidasa/genética , Secuencia de Aminoácidos , Hidrolasas/genética , Hidrolasas/metabolismo , Isoenzimas , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Alineación de Secuencia , Zea mays/genética , beta-Fructofuranosidasa/metabolismo