Molecular characterization of a retrotransposon in the Rhynchosciara americana genome and its association with telomere

Non-LTR retrotransposons, also known as long interspersed nuclear elements (LINEs), are transposable elements that encode a reverse transcriptase and insert into genomic locations via RNA intermediates. The sequence analysis of a cDNA library constructed from mRNA of the salivary glands of R. americana showed the presence of putative class I elements. The cDNA clone with homology to a reverse transcriptase was the starting point for the present study. Genomic phage was isolated and sequenced and the molecular structure of the element was characterized as being a non-LTR retrotransposable element. Southern blot analysis indicated that this transposable element is represented by repeat sequences in the genome of R. americana. Chromosome tips were consistently positive when this element was used as probe in in-situ hybridization. Real-time RT-PCR showed that this retrotransposon is transcribed at different periods of larval development. Most interesting, the silencing of this retrotransposon in R. americana by RNA interference resulted in reduced transcript levels and in accelerated larval development.

Oxidative stress protection of Trypanosomes requires selenophosphate synthase

Selenoproteins are characterized by the incorporation of at least one amino acid selenocysteine (Sec-U) encoded by in-frame UGA stop codons. These proteins, as well as the components of the Sec synthesis pathway, are present in members of the bacteria, archaea and eukaryote domains. Although not a ubiquitous pathway in all organisms, it was also identified in several protozoa, including the Kinetoplastida. Genetic evidence has indicated that the pathway is non-essential to the survival of Trypanosoma growing in non-stressed conditions. By analyzing the effects of RNA interference of the Trypanosoma brucei selenophosphate synthetase SPS2, we found a requirement under sub-optimal growth conditions. The present work shows that SPS2 is involved in oxidative stress protection of the parasite and its absence severely hampers the parasite survival in the presence of an oxidizing environment that results in an apoptotic-like phenotype and cell death. (C) 2011 Elsevier B.V. All rights reserved.

Human endogenous RNAs: Implications for the immunomodulation of Toll-like receptor 3

Toll-like receptors (TLRs), a family of mammalian receptors, are able to recognize nucleic acids. TLR3 recognizes double-stranded (ds)RNA, a product of the replication of certain viruses. Polyinosinic-polycytidylic acid, referred to as poly(I:C), an analog of viral dsRNA, interacts with TLR3 thereby eliciting immunoinflammatory responses characteristic of viral infection or down-regulating the expression of chemokine receptor CXCR4. It is known that dsRNA also directly activates interferon (IFN)-induced enzymes, such as the RNA-dependent protein kinase (PKR). In the present study, the mRNA expression of TLR3, CXCR4, IFN gamma and PKR was investigated in a culture of peripheral blood mononuclear cells (PBMCs) stimulated with poly(I:C) and endogenous RNA from human PBMCs. No cytotoxic effect on the cells or on the proliferation of CD3(+), CD4(+) and CD8(+) cells was observed. TLR3 expression in the PBMCs in the presence of poly(I:C) was up-regulated 9.5-fold, and TLR3 expression in the PBMCs treated with endogenous RNA was down-regulated 1.8-fold (p=0.002). The same trend was observed for IFN gamma where in the presence of poly(I:C) an 8.7-fold increase was noted and in the presence of endogenous RNA a 3.1-fold decrease was observed. In the culture activated with poly(1:C), mRNA expression of CXCR4 increased 8.0-fold and expression of PKR increased 33.0-fold. Expression of these genes decreased in the culture treated with endogenous RNA when compared to the culture without stimulus. Thus, high expression of mRNA for TLR3, IFN gamma, CXCR4 and PKR was observed in the presence of poly(I:C) and low expression was observed in the cells cultured with endogenous RNA. In conclusion, TLR3 may play major physiological roles that are not in the context of viral infection. It is possible that RNA released from cells could contain enough double-stranded structures to regulate cell activation. The involvement of endogenous RNA in endogenous gene expression and its implications in the regulation thereof, are still being studied, and will have significant implications in the future.

Estudo do genoma do vírus causador da mionecrose infecciosa em camarões e desenvolvimento de métodos para detecção de diferentes variantes

Shrimp farming is one of the activities that contribute most to the growth of global aquaculture. However, this business has undergone significant economic losses due to the onset of viral diseases such as Infectious Myonecrosis (IMN). The IMN is already widespread throughout Northeastern Brazil and affects other countries such as Indonesia, Thailand and China. The main symptom of disease is myonecrosis, which consists of necrosis of striated muscles of the abdomen and cephalothorax of shrimp. The IMN is caused by infectious myonecrosis virus (IMNV), a non-enveloped virus which has protrusions along its capsid. The viral genome consists of a single molecule of double-stranded RNA and has two Open Reading Frames (ORFs). The ORF1 encodes the major capsid protein (MCP) and a potential RNA binding protein (RBP). ORF2 encodes a probable RNA-dependent RNA polymerase (RdRp) and classifies IMNV in Totiviridae family. Thus, the objective of this research was study the IMNV complete genome and encoded proteins in order to develop a system differentiate virus isolates based on polymorphisms presence. The phylogenetic relationship among some totivirus was investigated and showed a new group to IMNV within Totiviridae family. Two new genomes were sequenced, analyzed and compared to two other genomes already deposited in GenBank. The new genomes were more similar to each other than those already described. Conserved and variable regions of the genome were identified through similarity graphs and alignments using the four IMNV sequences. This analyze allowed mapping of polymorphic sites and revealed that the most variable region of the genome is in the first half of ORF1, which coincides with the regions that possibly encode the viral protrusion, while the most stable regions of the genome were found in conserved domains of proteins that interact with RNA. Moreover, secondary structures were predicted for all proteins using various softwares and protein structural models were calculated using threading and ab initio modeling approaches. From these analyses was possible to observe that the IMNV proteins have motifs and shapes similar to proteins of other totiviruses and new possible protein functions have been proposed. The genome and proteins study was essential for development of a PCR-based detection system able to discriminate the four IMNV isolates based on the presence of polymorphic sites

A non-invasive method for silencing gene transcription in honeybees maintained under natural conditions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Caracterização genética e evolução dos vírus dengue no Estado do Rio Grande do Norte

Dengue is considered as the most important arthropod-borne viral disease throughout the world due to the high number of people at risk to be infected, mainly in tropical and subtropical regions of the planet. The etiologic agent is Dengue Virus (DENV), it is a single positive-stranded RNA virus of the family Flavivirus, genus Flaviviridae. Four serotypes are known, DENV-1, DENV-2, DENV-3 and DENV-4. One of the most important characteristic of these viruses is the genetic variability, which demands phylogenetic and evolutionary studies to understand key aspects like: epidemiology, virulence, migration patterns and antigenic characteristics. The objective of this study is the genetic characterization of dengue viruses circulating in the state of Rio Grande does Norte from January 2010 to December 2012. The complete E gene (1485 pb) of DENV1, 2 e 4 from Brazilian (Rio Grande do Norte) patients was sequenced. Phylogenetic analysis was performed using MEGA 5.2 software, Tamura-Nei model and Neighbor-Joining trees were inferred for the datasets. In Brazil, there is just one DENV-1 genotype (genotype V), one DENV-2 genotype (Asian/American) and two DENV-4 genotypes (genotypes I and II). Brazilian strains of DENV-1 are subdivided in two different lineages (BR-I and BR-II), the Brazilian strains of DENV-2 are subdivided in four lineages (BRI-IV) and genotype II of DENV-4 is subdivided in three Brazilian lineages (BRI-III). The viruses isolated in RN belong to lineage BR-II (DENV-1), BR-IV (DENV-2) and BR-III (DENV-4).The Caribbean and near Latin American countries are the main source of these viruses to Brazil. Amino acids substitutions were detected in three domains of E protein, this makes clear the necessity of studies that associate epidemiological and molecular data to better understand the effects of these mutations. This is the first study about genetic characterization and evolution of Dengue viruses in Rio Grande do Norte, Brazil

The post-transcriptional gene silencing pathway in Eucalyptus

Post-transcriptional gene silencing (PTGS) is a conserved surveillance mechanism that identifies and cleaves double-stranded RNA molecules and their cellular cognate transcripts. The RNA silencing response is actually used as a powerful technique (named RNA interference) for potent and specific inhibition of gene expression in several organisms. To identify gene products in Eucalyptus sharing similarities with enzymes involved in the PTGS pathway, we queried the expressed sequence tag database of the Brazilian Eucalyptus Genome Sequence Project Consortium (FORESTs) with the amino acid sequences of known PTGS-related proteins. Among twenty-six prospected genes, our search detected fifteen assembled sequences encoding products presenting high level of similarity (E value < 10 -40) to proteins involved in PTGS in plants and other organisms. We conclude that most of the genes known to be involved in the PTGS pathway are represented in the FORESTs database. Copyright by the Brazilian Society of Genetics.

Alpha-glucosidase promotes hemozoin formation in a blood-sucking bug: An evolutionary history

Background: Hematophagous insects digest large amounts of host hemoglobin and release heme inside their guts. In Rhodnius prolixus, hemoglobin-derived heme is detoxified by biomineralization, forming hemozoin (Hz). Recently, the involvement of the R. prolixus perimicrovillar membranes in Hz formation was demonstrated. Methodology/Principal Findings: Hz formation activity of an α-glucosidase was investigated. Hz formation was inhibited by specific α-glucosidase inhibitors. Moreover, Hz formation was sensitive to inhibition by Diethypyrocarbonate, suggesting a critical role of histidine residues in enzyme activity. Additionally, a polyclonal antibody raised against a phytophagous insect α-glucosidase was able to inhibit Hz formation. The α-glucosidase inhibitors have had no effects when used 10 h after the start of reaction, suggesting that α-glucosidase should act in the nucleation step of Hz formation. Hz formation was seen to be dependent on the substrate-binding site of enzyme, in a way that maltose, an enzyme substrate, blocks such activity. dsRNA, constructed using the sequence of α-glucosidase gene, was injected into R. prolixus females' hemocoel. Gene silencing was accomplished by reduction of both α-glucosidase and Hz formation activities. Insects were fed on plasma or hemin-enriched plasma and gene expression and activity of α-glucosidase were higher in the plasma plus hemin-fed insects. The deduced amino acid sequence of α-glucosidase shows a high similarity to the insect α-glucosidases, with critical histidine and aspartic residues conserved among the enzymes. Conclusions/Significance: Herein the Hz formation is shown to be associated to an a-glucosidase, the biochemical marker from Hemipteran perimicrovillar membranes. Usually, these enzymes catalyze the hydrolysis of glycosidic bond. The results strongly suggest that α-glucosidase is responsible for Hz nucleation in the R. prolixus midgut, indicating that the plasticity of this enzyme may play an important role in conferring fitness to hemipteran hematophagy, for instance. © 2009 Mury et al.

Caracterização estrutural e das interações entre a Proteína G do hRSV e potenciais inibidores

Pós-graduação em Microbiologia - IBILCE

Epidemiologia molecular das infecções por rotavírus G2 ao longo de 16 anos (1992 a 2008) na região amazônica, Brasil

No Brasil, estima-se que os rotavírus causem 3.352.053 episódios de diarreia, 655.853 ambulatoriais, 92.453 hospitalizações e 850 mortes envolvendo crianças menores de 5 anos de idade. Os rotavírus pertencem à família Reoviridae, gênero Rotavirus. A partícula viral é constituída por três camadas proteicas concêntricas e pelo genoma viral reunindo 11 segmentos de RNA com dupla fita. Reconhecem-se 23 genótipos G e 31 genótipos P. Dentre os genótipos G detectados até o momento, o G2 atua como um dos mais importantes, estando geralmente associado ao genótipo P[4]. Nos últimos três anos se tem observado em larga escala global a reemergência do genótipo G2, sendo um dos mais detectados nos anos que sucederam a implantação da vacina contra rotavírus, particularmente no Brasil. Este estudo teve como objetivo a caracterização molecular de amostras do tipo G2 obtidas de crianças participantes de estudos em gastroenterites virais na região amazônica, Brasil, no período de 1992 a 2008. Foram selecionadas 53 amostras positivas para rotavírus genótipo G2 que foram sequenciadas para VP7 e 38 para VP4. Inicialmente, as amostras foram genotipadas por RT-PCR e seus produtos purificados, quantificados e sequenciados. As amostras também foram testadas quanto ao perfil de migração dos segmentos de RNA. As sequências obtidas dos genes VP4 e VP7 foram alinhadas e editadas no programa Bioedit (v.6.05) e comparadas a outras sequências de RV registradas no banco de genes utilizando o programa BLAST. A árvore filogenética foi feita utilizando o programa Mega 2.1. Do total de 53 amostras sequenciadas para o gene VP7, a análise filogenética revelou a existência de duas linhagens (II e III) e três sublinhagens (IIa, IIc, IId) que circularam em períodos diferentes na população. Amostras das sub-linhagem IIa e IIc apresentaram mutação na posição no aminoácido da posição 96 (Asp/ Asn) . Essa modificação pode resultar em uma alteração conformacional dos epítopos reconhecidos por anticorpos neutralizantes. As linhagens de G2 que circularam em Belém foram idênticas àquelas de outros Estados da região amazônica envolvidos no estudo. O gene VP[4] foi sequenciado na região da VP8*, sendo 36 pertencentes do genótipo P[4] e 3 ao P[6]. No genótipo P[4] foi identificada a circulação de duas linhagens, P[4]-4 ocorrendo nos anos de 1998-2000, e P[4]-5 que circulou nos períodos de 1993-1994 e 2006-2008. Nossos resultados reforçam dados de ocorrência continental que evidenciam a reemergência do genótipo G2 com a variante gênica IIc, a qual se estabeleceu na população em associação com o genótipo P[4]-5. A grande homologia entre as cepas de G2 que circularam entre os diferentes estados envolvidos no estudo sugere que as mutações registradas ultrapassaram barreiras geográficas e temporais.

Caracterização molecular dos genótipos G e P de rotavírus tipo G9 provenientes de crianças com gastrenterite aguda na região metropolitana de Belém, Pará, no período de 1999 a 2007

O rotavírus (RV) é o principal agente viral associado às gastrenterites, ocasionando em média 39% dos casos diarreicos que culminam em hospitalizações, sendo responsável por cerca de 520.000 óbitos entre crianças menores de cinco anos de idade a cada ano. Pertencem à família Reoviridae, gênero Rotavirus, possui RNA de dupla fita (dsRNA) com 11 segmentos codificando 12 proteínas, sendo seis estruturais (VPs) e seis não estruturais (NSPs). A proteína VP4, juntamente com a VP7, compõem a camada externa do RV, designando os genótipos P e G, respectivamente. Até o momento foram descritos 23 tipos G e 31 tipos P. O genótipo G9 emergiu em escala global e é possivelmente associado a manifestação clínica mais grave, estando geralmente acompanhado do genótipo P[8]. O genótipo G9 possui 6 linhagens distintas e o P[8] 4 linhagens. Este estudo objetivou caracterizar os genes VP7 e VP4 de RV do genótipo G9, circulantes na região metropolitana de Belém, Pará, no período de 1999 a 2007. O dsRNA viral de 38 amostras selecionadas foi extraído a partir das suspensões fecais e submetido à eletroforese em gel de poliacrilamida para determinação dos eletroferotipos, seguido da reação de seqüenciamento. Na presente investigação, foi possível a análise de 32 amostras selecionadas, sendo todas genótipo G9P[8] associadas ao eletroferotipo longo. A análise filogenética do gene VP7 demonstrou que as amostras G9 agruparam na linhagem 3 com elevados índices de similaridade, apresentando 8 substituições nucleotídicas. Contudo, apenas três modificações aminoacídicas foram observadas nas posições 43 (I→V), 66 (A→V) e 73 (Q→R), sendo estes resíduos 43 e 73 exclusivos das amostras do ano de 2007. A análise do gene VP4 demonstrou que as amostras P[8] agruparam na linhagem 3, identificando-se 15 substituições nucleotídicas, as quais ocasionaram quatro modificações aminoacídicas nos resíduos 108 (V→I), 172 (R→K), 173 (I→V) e 275 (K→R). As modificações nos resíduos 172 e 275 são exclusivos das amostras dos anos de 1999 a 2002. As amostras do presente estudo apresentaram elevada similaridade ao longo do tempo estudado. As amostras de 2007 foram as mais divergentes, tanto para o gene VP4 quanto para o gene VP7. É importante se proceder ao contínuo monitoramento do genótipo G9 na região metropolitana de Belém, a fim de detectar possíveis variantes emergentes que possam representar um desafio as estratégias de imunização atuais.

Análise molecular dos genes VP4, VP7 e NSP4 de rotavírus do tipo G1 circulantes em Belém e Marituba, Pará, Brasil, de 1982 a 2008

Os rotavírus são os principais agentes virais causadores de gastrenterite aguda e responsáveis por 36% dos casos hospitalizações entre crianças menores de cinco anos, resultando em 453.000 óbitos anualmente, principalmente em países em desenvolvimento. Pertencem à família Reoviridae, gênero Rotavirus, possui RNA de dupla fita (dsRNA) com 11 segmentos codificando 12 proteínas. O genótipo G1 se apresenta geralmente com maior frequência nas investigações epidemiológicas, circulando em várias partes do mundo sob diferentes prevalências. Este estudo teve como objetivo analisar a variabilidade genética dos genes VP4, VP7 e NSP4 dos rotavírus G1 circulantes nos municípios de Belém e Marituba, Pará, Brasil, no período de 1982 a 2008. Foram selecionadas 83 amostras previamente caracterizadas como G1 e submetidas a RT-PCR. Os espécimes foram provenientes de sete estudos realizados no IEC. Foi possível a amplificação para os três genes em estudo de 63 (75,9%) espécimes. Foram detectadas as linhagens 1 (8/63, 12,7 %), 2 (29/63, 46,0%), 3 (18/63, 28,6%) e 9 (8/63, 12,7%) para o gene VP7. Co-predominaram as sublinhagens 2E e 3A concorrendo com um total de 57,1% (36/63) das amostras. Foram observadas três substituições de aminoácidos (97 [D→E], 147 [S→N] e 218 [I→V]) no gene VP7 nas regiões antigênicas (A, B e C) nas amostras das linhagens 1, 2 e 9. Todas as amostras apresentaram a especificidade P[8] para o gene VP4 e as linhagens 2 (21/63, 33,3%) e 3 (42/63, 66,7%) foram detectadas. No gene da VP4 ocorreram duas alterações (35 [I→V] e 38 [S→G]) na região antigênica em todas as amostras analisadas. Para o gene NSP4, todas as amostras pertenceram ao tipo E1. Houve mudanças de nucleotídeos nas posições 47 (C→T) e 101 (T→C), resultando em alteração aminoacídica nos resíduos 16 (S→P) e 34 (L→P) em todas as amostras analisadas e nove espécimes demonstraram alteração no sítio de toxicidade da NSP4 (aa 131). Tal análise permitiu ampliar o conhecimento da diversidade genética e da circulação de variantes de rotavírus G1, representando o primeiro estudo da epidemiologia molecular deste genótipo no Brasil e confirmar a alta heterogeneidade que este tipo apresenta.

Análise do efeito in vitro de acridonas na replicação do Vírus da Hepatite C

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Detection of isometric, dsRNA-containing viral particles in Colletotrichum gloeosporioides isolated from cashew tree

Fungi are disease-causing agents in plants and affect crops of economic importance. One control method is to induce resistance in the host by using biological control with hypovirulent phytopathogenic fungi. Here, we report the detection of a mycovirus in a strain of Colletotrichum gloeosporioides causing anthracnose of cashew tree. The strain C. gloeosporioides URM 4903 was isolated from a cashew tree (Anacardium occidentale) in Igarassu, PE, Brazil. After nucleic acid extraction and electrophoresis, the band corresponding to a possible double-stranded RNA (dsRNA) was purified by cellulose column chromatography. Nine extrachromosomal bands were obtained. Enzymatic digestion with DNAse I and Nuclease S1 had no effect on these bands, indicating their dsRNA nature. Transmission electron microscopic examination of extracts from this strain showed the presence of isometric particles (30-35 nm in diameter). These data strongly suggest the infection of this C. gloeosporioides strain by a dsRNA mycovirus. Once the hypovirulence of this strain is confirmed, the strain may be used for the biological control of cashew anthracnose.

Efficient RNAi-induced Protein Knockdown in Somatic Cells Using Diced or Chemically Produced Small Interfering RNAs (siRNA)

Background: RNA interference (RNAi) is a post-transcriptional gene silencing process in which double-stranded RNA (dsRNA) directs the degradation of a specific corresponding target mRNA. The mediators of this process are small dsRNAs of approximately 21 to 23 bp in length, called small interfering RNAs (siRNAs), which can be prepared in vitro and used to direct the degradation of specific mRNAs inside cells. Hence, siRNAs represent a powerful tool to study and control gene and cell function. Rapid progress has been made in the use of siRNA as a means to attenuate the expression of any protein for which the cDNA sequence is known. Individual siRNAs can be chemically synthesized, in vitro-transcribed, or expressed in cells from siRNA expression vectors. However, screening for the most efficient siRNAs for post-transcriptional gene silencing in cells in culture is a laborious and expensive process. In this study, the effectiveness of two siRNA production strategies for the attenuation of abundant proteins for DNA repair were compared in human cells: (a) the in vitro production of siRNA mixtures by the Dicer enzyme (Diced siRNAs); and (b) the chemical synthesis of very specific and unique siRNA sequences (Stealth RNai (TM)). Materials, Methods & Results: For in vitro-produced siRNAs, two segments of the human Ku70 (167 bp in exon 5; and 249 bp in exon 13; NM001469) and Xrcc4 (172 bp in exon 2; and 108 bp in exon 6; NM003401) genes were chosen to generate dsRNA for subsequent "Dicing" to create mixtures of siRNAs. The Diced fragments of siRNA for each gene sequence were pooled and stored at -80 degrees C. Alternatively, chemically synthesized Stealth siRNAs were designed and generated to match two very specific gene sequence regions for each target gene of interest (Ku70 and Xrcc4). HCT116 cells were plated at 30% confluence in 24- or 6-well culture plates. The next day, cells were transfected by lipofection with either Diced or Stealth siRNAs for Ku70 or Xrcc4, in duplicate, at various doses, with blank and sham transfections used as controls. Cells were harvested at 0, 24, 48, 72 and 96 h post-transfection for protein determination. The knockdown of specific targeted gene products was quantified by Western blot using GAPDH as control. Transfection of gene-specific siRNA to either Ku70 or Xrcc4 with both Diced and Stealth siRNAs resulted in a down regulation of the targeted proteins to approximately 10 to 20% of control levels 48 h after transfection, with recovery to pre-treatment levels by 96 h. Discussion: By transfecting cells with Diced or chemically synthesized Stealth siRNAs, Ku70 and Xrcc4, two highly expressed proteins in cells, were effectively attenuated, demonstrating the great potential for the use of both siRNA production strategies as tools to perform loss of function experiments in mammalian cells. In fact, down-regulation of Ku70 and Xrcc4 has been shown to reduce the activity of the non-homologous end joining DNA pathway, a very desirable approach for the use of homologous recombination technology for gene targeting or knockout studies. Stealth RNAi (TM) was developed to achieve high specificity and greater stability when compared with mixtures of enzymatically-produced (Diced) siRNA fragments. In this study, both siRNA approaches inhibited the expression of Ku70 and Xrcc4 gene products, with no detectable toxic effects to the cells in culture. However, similar knockdown effects using Diced siRNAs were only attained at concentrations 10-fold higher than with Stealth siRNAs. The application of RNAi technology will expand and continue to provide new insights into gene regulation and as potential applications for new therapies, transgenic animal production and basic research.