22.二酸化窒素の呼吸器に及ぼす影響に関する形態学的研究(第614回千葉医学会例会・第14回肺癌研究施設例会)

<p>The first two columns are the protein IDs of the JGI <i>P</i>. <i>ostreatus</i> genome database.</p

Transposable elements versus the fungal genome: impact on whole-genome architecture and transcriptional profiles

Incluye 10 ficheros de datosTransposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.This work was supported by Spanish National Research Plan (Projects AGL2011-30495 and AGL2014-55971-R) and FEDER funds; Public University of Navarre; U.S. Department of Energy Joint Genome Institute; and Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Análisis genómico y transcriptómico de genes capturados por helitrones en "Pleurotus ostreatus"

El creciente número de organismos eucariotas secuenciados permite estudiar la aparición de elementos de transposición en gran cantidad de genomas. Dentro de los transposones de clase II se encuentran los transposones de círculo rodante (también conocidos como helitrones), que han sido descritos recientemente en plantas, animales y hongos utilizando herramientas bioinformáticas. Los helitrones se caracterizan fundamentalmente por codificar una proteína con un origen de replicación REP y un dominio helicasa PIF1 y por la capacidad de capturar genes enteros o fragmentos de genes, incrementando su número y dispersándolos por el genoma del huésped. En el genoma de P. ostreatus se han descrito dos familias de helitrones denominadas HELPO1 y HELPO2, que contienen elementos potencialmente autónomos que codifican helicasas RepHel, además de genes capturados de función desconocida. En este trabajo hemos analizado el efecto de la dosis génica (número de copias) y el perfil transcriptómico de estos helitrones portadores de genes utilizando PCR en tiempo real. Como resultados presentamos un protocolo basado en la PCR a tiempo real para cuantificar el número de copias de estos elementos en otras cepas monocarióticas de P. ostreatus de las que no se dispone de secuencia genómica y que existe expresión de algunos genes capturados cuya función aún no se conoceThe increasing number of sequenced eukaryotic organisms allows to study the occurrence of transposable elements (TE) in large amount of genomes. Within the class II transposons are rolling-circle transposons (also known as helitrons), which have recently been described in plants, animals and fungi using bioinformatic tools. Helitrons are mainly characterized by encoding a protein with a replication initiator Rep and a PIF1 helicase domain as well as by the ability to capture whole genes or fragments of genes, increasing the number and spreading by the host genome. Two families of helitrons have been described in the P. ostreatus genome, called HELPO1 and HELPO2, which contain putative autonomous elements encoding RepHel helicases besides captured genes of unknown function. In this work we have analyzed the effect of the gene dosage (copy number) and the transcriptomic profile of these helitron captured genes using real-time PCR. The results showed that it is possible to use this experimental method of analysis by qPCR in other monokaryotic strains of P. ostreatus, whose genomic sequences are not available and that there is expression of some captured genes whose function is not yet knownGraduado o Graduada en Ingeniería Agroalimentaria y del Medio Rural por la Universidad Pública de NavarraNekazaritzako Elikagaien eta Landa Ingurunearen Ingeniaritzan graduatua Nafarroako Unibertsitate Publikoa

Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales.

BackgroundConiophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size.ResultsIn this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation. Using similarity clustering and protein structure prediction we identified a new family of 10&nbsp;putative lytic polysaccharide monooxygenase genes. This family is conserved in basidiomycota and lacks of previous functional annotation. Further analyses showed that C. olivacea has a low repetitive genome, with 2.91% of repeats and a restrained content of transposable elements (TEs). The annotation of TEs in four related Boletales yielded important differences in repeat content, ranging from 3.94 to 41.17% of the genome size. The distribution of insertion ages of LTR-retrotransposons showed that differential expansions of these repetitive elements have shaped the genome architecture of Boletales over the last 60 million years.ConclusionsConiophora olivacea has a small, compact genome that shows macrosynteny with Coniophora puteana. The functional annotation revealed the enzymatic signature of a canonical brown-rot. The annotation and comparative genomics of transposable elements uncovered their particular contraction in the Coniophora genera, highlighting their role in the differential genome expansions found in Boletales species

Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

Background: Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. [br/] Results: In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation. Using similarity clustering and protein structure prediction we identified a new family of 10 putative lytic polysaccharide monooxygenase genes. This family is conserved in basidiomycota and lacks of previous functional annotation. Further analyses showed that C. olivacea has a low repetitive genome, with 2.91% of repeats and a restrained content of transposable elements (TEs). The annotation of TEs in four related Boletales yielded important differences in repeat content, ranging from 3.94 to 41.17% of the genome size. The distribution of insertion ages of LTR-retrotransposons showed that differential expansions of these repetitive elements have shaped the genome architecture of Boletales over the last 60 million years. [br/] Conclusions: Coniophora olivacea has a small, compact genome that shows macrosynteny with Coniophora puteana. The functional annotation revealed the enzymatic signature of a canonical brown-rot. The annotation and comparative genomics of transposable elements uncovered their particular contraction in the Coniophora genera, highlighting their role in the differential genome expansions found in Boletales species

Angiotensin-(1-9) regulates cardiac hypertrophy in vivo and in vitro

Background: Angiotensin-(1-9) is present in human and rat plasma and its circulating levels increased early after myocardial infarction or in animals treated with angiotensin-converting enzyme inhibitor. However, the cardiovascular effects of this peptide are unknown. Objective: To determine whether angiotensin-(1-9) is a novel anti-cardiac hypertrophy factor in vitro and in vivo and whether this peptide is involved in the pharmacological effects of cardiovascular drugs acting on the renin-angiotensin system. Methods and results The administration of angiotensin(1-9) to myocardial infarcted rats by osmotic minipumps (450 ng/kg per min, n=6) vs. vehicle (n=8) for 2 weeks decreased plasma angiotensin II levels, inhibited angiotensin- converting enzyme activity and also prevented cardiac myocyte hypertrophy. However, cardiac myocyte hypertrophy attenuation triggered by angiotensin-(1-9) was not modified with the simultaneous administration of the angiotensin-(1-7) receptor antagonist A779 (100 ng/kg per min, n=6). In experiments in vitro with cultured cardiac myocytes incubated with norepinephrine (10 mu mol/l) or with insulin-like growth factor-1 (10 nmol/l), angiotensin(1-9) also prevented hypertrophy. In other experimental setting, myocardial infarcted rats (n=37) were randomized to receive either vehicle (n=12), enalapril (10 mg/kg per day, n=12) or angiotensin II receptor blocker candesartan (10 mg/kg per day, n=13) for 8 weeks. Both drugs prevented left ventricle hypertrophy and increased plasma angiotensin-(1-9) levels by several folds. Angiotensin-(1-9) levels correlated negatively with different left ventricular hypertrophy markers even after adjustment for blood pressure reduction. Conclusion Angiotensin-(1-9) is an effective and a novel anti-cardiac hypertrophy agent not acting via the Mas receptor

Additional file 3: Figure S1. of Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

Snapshot of synteny dot plot between C. olivacea and C. puteana. (TIFF 582 kb