RESUMO
Whole-genome phylogenetic analysis, the most suitable strategy for subtyping bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2, is not feasible for many laboratories. Consequently, BVDV isolates/strains have been frequently subtyped based on analysis of single genomic regions, mainly the 5' untranslated region (UTR). This approach, however, may lead to inaccurate and/or poorly statistically supported viral classification. Herein, we describe novel primer sets whose amplicons may be easily sequenced and used for BVDV subtyping. Initially, genomic regions previously described as the most suitable targets for BVDV subtyping were analyzed for design of high-coverage primers. The putative amplicons were analyzed in silico for their suitability to reproduce the phylogenetic classification of 118 BVDV-1 and 88 BVDV-2 complete/near-complete genomes (CNCGs) (GenBank). This analysis was also performed considering the region amplifiable by primers HCV90-368, 324-326 and BP189-389 (5'UTR), which have been used for BVDV diagnosis and/or classification. After confirming the agreement between the analyses of our primers' amplicon versus the CNCGs, we optimized the RT-PCRs and evaluated their performance for amplification of BVDV isolates/strains (n = 35 for BVDV-1; n = 33 for BVDV-2). Among the potential targets for BVDV subtyping, we designed high-coverage primers for NS3-NS4A (BVDV-1) (526 bp amplicon) and NS5B (BVDV-2) (728 bp). The classification based on these regions fully reproduced the subtyping of all CNCGs. On the other hand, subtyping based on the putative amplicons from primers HCV90-368, 324-326 and BP189-389 showed disagreements in relation the CNCG analysis. The NS3-NS4A and NS5B primers also allowed the amplification of all BVDV isolates/strains tested. Finally, we suggest the use of these primers in future phylogenetic and epidemiological studies of BVDVs.
Assuntos
Doença das Mucosas por Vírus da Diarreia Viral Bovina , Vírus da Diarreia Viral Bovina Tipo 1 , Vírus da Diarreia Viral Bovina Tipo 2 , Vírus da Diarreia Viral Bovina , Animais , Bovinos , Vírus da Diarreia Viral Bovina Tipo 1/genética , Vírus da Diarreia Viral Bovina Tipo 2/genética , Filogenia , Genômica , Regiões 5' não Traduzidas/genética , Vírus da Diarreia Viral Bovina/genéticaRESUMO
The spread of Zika virus (ZIKV) from the African continent to the Americas promoted its molecular evolution, as reflected by mutations in its RNA genome. Most of the ZIKV genome sequences in the GenBank database have incomplete 5' and 3' UTR sequences, reflecting the deficiency of whole-genome sequencing technologies to resolve the sequences of the genome ends. We modified a protocol for rapid amplification of cDNA ends (RACE) to determine the complete sequences of the 5' and 3' UTRs of a previously reported ZIKV isolate (GenBank no. MH544701.1). This strategy is useful for determining 5' and 3' UTR sequences of ZIKV isolates and will be useful for comparative genomics applications.
Assuntos
Infecção por Zika virus , Zika virus , Humanos , Zika virus/genética , Regiões 3' não Traduzidas/genética , RNA Viral/genética , Evolução Molecular , Regiões 5' não Traduzidas/genética , Genoma Viral/genéticaRESUMO
Bovine pestiviruses are members of the species Pestivirus A (bovine viral diarrhea virus 1, BVDV-1), Pestivirus B (BVDV-2) or Pestivirus H (HoBiPeV). To date, BVDV-2 isolates/strains have been classified into three subtypes (a-c) by phylogenetic analysis, and an additional subtype (d) has been proposed based on 5' untranslated region (UTR) secondary structures. In a previous study, we identified some BVDV-2 sequences in the GenBank database that could not be classified as subtype a, b or c by phylogenetic analysis of their genomes, UTRs or individual genes. Here, we performed a detailed study of these sequences and assessed whether they might represent a distinct BVDV-2 subtype. Initially, we collected 85 BVDV-2 complete/near-complete genomes (CNCGs) from GenBank and performed a "proof of equivalence" between phylogenetic analyses based on CNCGs and open reading frames (ORFs), which showed that ORFs may be reliably used as a reference target for BVDV-2 phylogeny, allowing us to increase our dataset to 139 sequences. Among these, we found seven sequences that could not be classified as BVDV-2a-c. The same was observed in the phylogenetic analysis of CNCGs and viral genes. In addition, the seven non-BVDV-2a-c sequences formed a distinct cluster in all phylogenetic trees, which we propose to term BVDV-2e. BVDV-2e also showed 44 amino acid changes compared to BVDV-2a-c, 20 of which are in well-defined positions. Importantly, an additional phylogenetic analysis including BVDV-2d and a pairwise comparison of BVDV-2e and BVDV-2d sequences also supported the difference between these subtypes. Finally, we propose the recognition of BVDV-2e as a distinct BVDV-2 subtype and encourage its inclusion in future phylogenetic analyses to understand its distribution and evolution.
Assuntos
Doença das Mucosas por Vírus da Diarreia Viral Bovina , Vírus da Diarreia Viral Bovina Tipo 1 , Vírus da Diarreia Viral Bovina Tipo 2 , Vírus da Diarreia Viral Bovina , Pestivirus , Animais , Bovinos , Vírus da Diarreia Viral Bovina Tipo 2/genética , Filogenia , Vírus da Diarreia Viral Bovina Tipo 1/genética , Vírus da Diarreia Viral Bovina/genética , Pestivirus/genética , Regiões 5' não Traduzidas/genéticaRESUMO
Since the beginning of the SARS-CoV-2 spread in Brazil, few studies have been published analysing the variability of viral genome. Herein, we described the dynamic of SARS-CoV-2 strains circulating in Brazil from May to September 2020, to better understand viral changes that may affect the ongoing pandemic. Our data demonstrate that some of the mutations identified are currently observed in variants of interest and variants of concern, and emphasize the importance of studying previous periods in order to comprehend the emergence of new variants. From 720 SARS-CoV-2 genome sequences, we found few sites under positive selection pressure, such as the D614G (98.5â%) in the spike, that has replaced the old variant; the V1167F in the spike (41â%), identified in the P.2 variant that emerged from Brazil during the period of analysis; and I292T (39â%) in the N protein. There were a few alterations in the UTRs, which was expected, however, our data suggest that the emergence of new variants was not influenced by mutations in UTR regions, since it maintained its conformational structure in most analysed sequences. In phylogenetic analysis, the spread of SARS-CoV-2 from the large urban centres to the countryside during these months could be explained by the flexibilization of social isolation measures and also could be associated with possible new waves of infection. These results allow a better understanding of SARS-CoV-2 strains that have circulated in Brazil, and thus, with relevant infomation, provide the potential viral changes that may have affected and/or contributed to the current and future scenario of the COVID-19 pandemic.
Assuntos
COVID-19/virologia , Genoma Viral , Mutação , SARS-CoV-2/genética , Regiões 5' não Traduzidas/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Substituição de Aminoácidos , Brasil/epidemiologia , COVID-19/epidemiologia , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Conformação de Ácido Nucleico , RNA Viral/química , RNA Viral/genética , Seleção Genética , Adulto JovemRESUMO
Cervical cancer is the fourth most common cause of cancer in women worldwide in terms of both incidence and mortality. Persistent infection with high-risk types of human papillomavirus (HPV), namely 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68, constitute a necessary cause for the development of cervical cancer. Viral oncoproteins E6 and E7 play central roles in the carcinogenic process by virtue of their interactions with cell master proteins such as p53, retinoblastoma (Rb), mammalian target of rapamycin (mTOR), and c-MYC. For the synthesis of E6 and E7, HPVs use a bicistronic messenger RNA (mRNA) that has been studied in cultured cells. Here, we report that in cervical tumors, HPV-18, -39, and -45 transcribe E6/E7 mRNAs with extremely short 5' untranslated regions (UTRs) or even lacking a 5' UTR (i.e., zero to three nucleotides long) to express E6. We show that the translation of HPV-18 E6 cistron is regulated by the motif ACCaugGCGCG(C/A)UUU surrounding the AUG start codon, which we term Translation Initiation of Leaderless mRNAs (TILM). This motif is conserved in all HPV types of the phylogenetically coherent group forming genus alpha, species 7, which infect mucosal epithelia. We further show that the translation of HPV-18 E6 largely relies on the cap structure and eIF4E and eIF4AI, two key translation initiation factors linking translation and cancer but does not involve scanning. Our results support the notion that E6 forms the center of the positive oncogenic feedback loop node involving eIF4E, the mTOR cascade, and p53.
Assuntos
Proteínas de Ligação a DNA/genética , Fator de Iniciação 4A em Eucariotos/genética , Fator de Iniciação 4E em Eucariotos/genética , Papillomavirus Humano 18/genética , Proteínas Oncogênicas Virais/genética , RNA Mensageiro/genética , Regiões 5' não Traduzidas/genética , Linhagem Celular Tumoral , Códon de Iniciação/genética , Proteínas de Ligação a DNA/biossíntese , Feminino , Regulação Viral da Expressão Gênica/genética , Células HEK293 , Células HaCaT , Células HeLa , Papillomavirus Humano 18/metabolismo , Humanos , Proteínas Oncogênicas Virais/biossíntese , Iniciação Traducional da Cadeia Peptídica/genética , RNA Viral/genética , Serina-Treonina Quinases TOR/genética , Proteína Supressora de Tumor p53/genética , Neoplasias do Colo do Útero/tratamento farmacológico , Neoplasias do Colo do Útero/patologia , Neoplasias do Colo do Útero/virologiaRESUMO
Bovine viral diarrhea virus (BVDV) is a major pathogen in cattle herds. Considering the epidemiological importance of pestiviruses and the process of wild boar invasion in Brazil, this study aimed to investigate the presence of BVDV in free-living boars. Forty-nine free-living wild boars were collected by exotic wildlife controller agents in 2017 and 2018. The presence of BVDV antibodies was evaluated in 42 serum samples using the virus neutralization test, and the detection of BVDV RNA was performed from the 5'UTR genomic region by RT-PCR assay in 49 lung tissue samples followed by sequencing of amplicons. BVDV neutralizing antibodies in serum were not identified in any of the evaluated samples. However, 3/49 (6.12%) lung samples were positive for BVDV RNA and classified one as BVDV-1a and two as 1d subgenotype. This report identified BVDV RNA in free-living wild boars and these results should be considered in BVDV control programs, especially in extensive beef cattle rearing systems.
Assuntos
Animais Selvagens/virologia , Vírus da Diarreia Viral Bovina Tipo 1/isolamento & purificação , Sus scrofa/virologia , Regiões 5' não Traduzidas/genética , Animais , Anticorpos Antivirais/sangue , Brasil , Vírus da Diarreia Viral Bovina Tipo 1/classificação , Vírus da Diarreia Viral Bovina Tipo 1/genética , Vírus da Diarreia Viral Bovina Tipo 1/imunologia , Genótipo , Pulmão/virologia , Infecções por Pestivirus/veterinária , Infecções por Pestivirus/virologia , Filogenia , RNA Viral/genética , Suínos , Doenças dos Suínos/virologiaRESUMO
Leprosy is a prevalent disease in Brazil, which ranks as the country with the second highest number of cases in the world. The disease manifests in a spectrum of forms, and genetic differences in the host can help to elucidate the immunopathogenesis. For a better understanding of MICA association with leprosy, we performed a case-control and a family-based study in two endemic populations in Brazil. MICA and HLA-B alleles were evaluated in 409 leprosy patients and in 419 healthy contacts by PCR-SSOP-Luminex-based technology. In the familial study, analysis of 46 families was completed by direct sequencing of all exons and 3'/5'untranslated regions, using the Ilumina MiSeq platform. All data were collected between 2006 and 2009. Statistical analysis was performed using the Chi-square or Fisher's exact test together with a multivariate analysis. Family-based association was assessed by transmission disequilibrium test (TDT) software FBAT 2.0.4. We found associations between the haplotype MICA*002-HLA-B*35 with leprosy in both the per se and the multibacillary (MB) forms when compared to healthy contacts. The MICA allele *008 was associated with the clinical forms of paucibacillary (PB). Additionally, MICA*029 was associated with the clinical forms of MB. The association of MICA*029 allele (MICA-A4 variant) with the susceptibility to the MB form suggests this variant for the transmembrane domain of the MICA molecule may be a risk factor for leprosy. Two MICA and nine HLA-B variants were found associated with leprosy per se in the Colônia do Prata population. Linkage disequilibrium analysis revealed perfect linkage disequilibrium (LD) between HLA-B markers rs2596498 and rs2507992, and high LD (R2 = .92) between these and the marker rs2442718. This familial study demonstrates that MICA association signals are not independent from those observed for HLA-B. Our findings contribute the knowledge pool of the immunogenetics of Hansen's disease and reveals a new association of the MICA*029 allele.
Assuntos
Antígenos HLA-B/genética , Antígenos de Histocompatibilidade Classe I/genética , Hanseníase/imunologia , Regiões 3' não Traduzidas/genética , Regiões 5' não Traduzidas/genética , Adolescente , Adulto , Alelos , Brasil/epidemiologia , Estudos de Casos e Controles , Criança , Doenças Endêmicas , Etnicidade/genética , Éxons/genética , Saúde da Família , Feminino , Frequência do Gene , Predisposição Genética para Doença , Genótipo , Haplótipos/genética , Humanos , Hanseníase/epidemiologia , Hanseníase/genética , Desequilíbrio de Ligação , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único , Domínios Proteicos , Adulto JovemRESUMO
Survivin (BIRC5) is an anti-apoptotic protein that is important in cancer. Mechanisms responsible for controlling Survivin levels in cells include transcriptional regulation and modulation of protein stability via post-translational modifications; however to date, translational control has been poorly studied. Here, we focused particularly on the primary control elements present in the Survivin 5' untranslated region (5'UTR). Bioinformatic analysis of ribosome occupancy on the Survivin 5'UTR revealed the presence of elongating ribosomes upstream of the canonical initiator AUG, suggesting an alternative upstream initiator AUG (uAUG) might exist. This uAUG was found out-of-frame at position -71 and appeared as a conserved element in mammals. RACE analysis revealed different transcriptional start sites for BIRC5, which indicated that translational control by this uAUG is restricted to longer 5'UTR variants. We studied the activity of the uAUG in different cell types by cloning the Survivin 5'UTR DNA sequence (wild-type and mutated variants) upstream of renilla luciferase (RLuc) into a pcDNA3 plasmid. Changes in RLuc activity were determined by luminescence assays and Western blotting. Results showed that when this uAUG was mutated to AUU or AGG in the cloned Survivin 5'UTR, RLuc activity was significantly increased. Similar results were obtained when uAUG was positioned inframe with the RLuc initiator AUG. Immunodetection of Renilla (35 kDa) by Western blotting revealed the presence of a second band (37 kDa approximately) in cells transfected with the Inframe reporter constructs, indicating that the uAUG was functional in our experimental conditions. In conclusion, our experimental data demonstrate the presence of an alternative and inhibitory initiator uAUG in the Survivin 5' UTR. This inhibitory uAUG may help understanding how Survivin expression is downregulated under physiological or pathological conditions.
Assuntos
Regiões 5' não Traduzidas/genética , Códon de Iniciação/genética , Survivina/genética , Animais , Sequência de Bases , Linhagem Celular Tumoral , Sequência Conservada/genética , Células HEK293 , Humanos , Luciferases/metabolismo , Mamíferos/genética , Fases de Leitura Aberta/genética , Biossíntese de Proteínas/genéticaRESUMO
Bovine pestiviruses, e.g., bovine viral diarrhea virus types 1 (BVDV-1 or Pestivirus A), BVDV-2 (Pestivirus B), and HoBi-like pestiviruses (HoBiPeV or Pestivirus H), have been shown to circulate in Brazilian cattle in varied proportions. In this study, we identified genetically pestiviruses circulating in beef cattle in Rio Grande do Sul, the southern most Brazilian state. Screening of serum of 15.584 beef calves destined to be export by an antigen capture ELISA and, subsequently, by reverse-transcription polymerase chain reaction (RT-PCR), revealed 135 containing pestivirus RNA. Genetic typing of these viruses based on nucleotide sequencing and phylogenetic analysis of the 5' untranslated region (5' UTR) of the viral genome allowed for the identification of 90 different viruses, being 38 BVDV-1 (42.2%), 31 BVDV-2 (34.4%), and 21 HoBiPeV (23.4%). Among BVDV-1, only subtypes BVDV-1a (n = 28, 31.1%) and BVDV-1b (n = 10, 11.1%) were identified. All 31 BVDV-2 isolates belonged to BVDV-2b subtype and the 21 HoBiPeV viruses clustered to subgroup 3a. Thus, this study provides an approximate genetic profile of pestiviruses circulating in beef cattle in a traditional Brazilian beef cattle-raising state.
Assuntos
Doenças dos Bovinos/epidemiologia , Vírus da Diarreia Viral Bovina Tipo 1/genética , Vírus da Diarreia Viral Bovina Tipo 1/isolamento & purificação , Vírus da Diarreia Viral Bovina Tipo 2/genética , Vírus da Diarreia Viral Bovina Tipo 2/isolamento & purificação , Regiões 5' não Traduzidas/genética , Animais , Sequência de Bases , Brasil/epidemiologia , Bovinos , Doenças dos Bovinos/virologia , Genoma Viral/genética , Tipagem Molecular , Filogenia , RNA Viral/genética , Carne Vermelha/virologiaRESUMO
Heme may represent a major iron-source for bacteria. In the symbiotic nitrogen-fixing bacterium Ensifer meliloti 1021, iron acquisition from heme depends on the outer-membrane heme-receptor ShmR. Expression of shmR gene is repressed by iron in a RirA dependent manner while under iron-limitation its expression requires the small protein HmuP. In this work, we identified highly conserved nucleotide motifs present upstream the shmR gene. These motifs are widely distributed among Alpha and Beta Proteobacteria, and correlate with the presence of HmuP coding sequences in bacterial genomes. According to data presented in this work, we named these new motifs as HmuP-responsive elements (HPREs). In the analyzed genomes, the HPREs were always present upstream of genes encoding putative heme-receptors. Moreover, in those Alpha and Beta Proteobacteria where transcriptional start sites for shmR homologs are known, HPREs were located in the 5'UTR region. In this work we show that in E. meliloti 1021, HPREs are involved in HmuP-dependent shmR expression. Moreover, we show that changes in sequence composition of the HPREs correlate with changes in a predicted RNA secondary structure element and affect shmR gene expression.
Assuntos
Regiões 5' não Traduzidas/genética , Proteínas da Membrana Bacteriana Externa/genética , Proteínas de Bactérias/genética , Sequência Conservada/genética , Motivos de Nucleotídeos/genética , Receptores de Superfície Celular/genética , Sinorhizobium meliloti/genética , Reação em Cadeia da Polimerase em Tempo Real , Sinorhizobium meliloti/crescimento & desenvolvimentoRESUMO
The helicase eIF4A is part of the cellular eIF4F translation initiation complex. The main functions of eIF4A are to remove secondary complex structures within the 5'-untranslated region and to displace proteins attached to mRNA. As intracellular parasites, viruses regulate the processes involved in protein synthesis, and different mechanisms related to controlling translation factors, such as eIF4A, have been found. The inhibitors of this factor are currently known; these substances could be used in the near future as part of antiviral pharmacological therapies in instances of replication cycles in which eIF4A is required. In this review, the particularities of how some viruses make use of this initiation factor to synthesize their proteins are discussed.
Assuntos
Fator de Iniciação 4A em Eucariotos/genética , Biossíntese de Proteínas , Viroses/genética , Regiões 5' não Traduzidas/genética , Humanos , Ligação Proteica/genética , RNA Mensageiro/genética , Viroses/virologiaRESUMO
BACKGROUND: Bovine Viral Diarrhea Virus causes significant economic losses in cattle. BVDV has high genomic diversity, with two species, BVDV-1 and BVDV-2, and at least twenty-one subgenotypes for BVDV-1 and four subgenotypes for BVDV-2. Vaccines are important tools to reduce the economic losses caused by this virus. However, vaccine strains must correspond to the antigenic profile of the viruses present in the region where the vaccine is applied. A restricted phylogenetic study with 14 viruses isolated from cattle between 1993 and 2001 showed that the genetic profile of BVDV in Chile consisted of viruses of both species and sub-genotypes 1a, 1b, 1c (currently 1j) and 2a. To determine more accurately the genetic profile of BVDV in Chile, in this study a larger number of viruses obtained from bovines between 2003 and 2007 were typed. RESULTS: The study was performed using partial sequences from the 5' noncoding region (5'UTR) and E2 coding region of the viral genome of thirty-five Chilean viruses isolated from geographic regions that have 84.6% of the Chilean cattle. All tested viruses belonged to species BVDV-1. Eighteen viruses belonged to BVDV-1j subgenotype (51.4%), twelve belonged to BVDV-1b (34.3%) and five belonged to BVDV-1a (14.3%). The Chilean BVDV-1j viruses showed low genetic diversity, both among themselves and with the BVDV-1j present in other regions of the world. This could be explained by a relatively recent introduction of this viral subgenotype in cattle, which agrees with its low geographical distribution worldwide. Otherwise, Chilean BVDV-1b viruses grouped into a single cluster, different even than the viruses present in Argentina and Brazil, countries geographically close to Chile, a process of local evolution that could generate antigenic differences between the Chilean viruses and the viruses used as vaccine strains. CONCLUSIONS: The high presence of viruses of the BVDV-1j subgenotype, which show major antigenic differences with BVDV-1a and BVDV-1b subgenotypes used in the commercial vaccines, suggest that BVDV-1j viruses could be an emergent subgenotype of BVDV in cattle in South America and suggest evaluating an update of the vaccines used in Chile.
Assuntos
Doença das Mucosas por Vírus da Diarreia Viral Bovina/virologia , Vírus da Diarreia Viral Bovina/genética , Regiões 5' não Traduzidas/genética , Animais , Doença das Mucosas por Vírus da Diarreia Viral Bovina/epidemiologia , Bovinos/virologia , Chile/epidemiologia , Vírus da Diarreia Viral Bovina Tipo 1/genética , Vírus da Diarreia Viral Bovina Tipo 2/genética , Variação Genética/genética , Genótipo , Filogenia , Reação em Cadeia da Polimerase Via Transcriptase Reversa/veterinária , Análise de Sequência de DNA/veterináriaRESUMO
Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL). The HTLV-1 basic leucine zipper protein (HBZ) is expressed in all cases of ATL and is directly associated with virus pathogenicity. The two isoforms of the HBZ protein are synthesized from antisense messenger RNAs (mRNAs) that are either spliced (sHBZ) or unspliced (usHBZ) versions of the HBZ transcript. The sHBZ and usHBZ mRNAs have entirely different 5'untranslated regions (5'UTR) and are differentially expressed in cells, with the sHBZ protein being more abundant. Here, we show that differential expression of the HBZ isoforms is regulated at the translational level. Translation initiation of the usHBZ mRNA relies on a cap-dependent mechanism, while the sHBZ mRNA uses internal initiation. Based on the structural data for the sHBZ 5'UTR generated by SHAPE in combination with 5' and 3' deletion mutants, the minimal region harboring IRES activity was mapped to the 5'end of the sHBZ mRNA. In addition, the sHBZ IRES recruited the 40S ribosomal subunit upstream of the initiation codon, and IRES activity was found to be dependent on the ribosomal protein eS25 and eIF5A.
Assuntos
Fatores de Transcrição de Zíper de Leucina Básica/genética , Vírus Linfotrópico T Tipo 1 Humano/genética , Iniciação Traducional da Cadeia Peptídica , RNA Mensageiro/genética , RNA Viral/genética , Proteínas dos Retroviridae/genética , Regiões 5' não Traduzidas/genética , Animais , Fatores de Transcrição de Zíper de Leucina Básica/metabolismo , Células COS , Chlorocebus aethiops , Regulação Viral da Expressão Gênica , Células HEK293 , Células HeLa , Vírus Linfotrópico T Tipo 1 Humano/metabolismo , Humanos , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Splicing de RNA , RNA Mensageiro/metabolismo , RNA Viral/metabolismo , Proteínas dos Retroviridae/metabolismoRESUMO
The HLA-G 5'URR extending 1.4 kb from the ATG presents a unique set of regulatory elements among HLA genes. Several variable sites have been described that coincide with or are close to these elements, thus HLA-G 5'URR polymorphism might influence the HLA-G expression level. We cloned the ten most frequent HLA-G 5'URR haplotypes to evaluate their activity on a luciferase reporter gene in HLA-G+ cell lines (JEG-3/choriocarcinoma and FON+/melanoma). We also investigated associations between the plasma HLA-G (sHLA-G) levels and the HLA-G 5'URR variability in 157 healthy individuals. Cell lines were transfected with pGL3-Basic vector constructions containing HLA-G 5'URR sequences. The G010101a (in JEG-3) and G010101b (in FON+) haplotypes exhibited higher promoter activity, whereas the G010101d (in JEG-3) and G010102a (in FON+) haplotypes exhibited lower promoter activity. In the presence of HLA-G inducers (interferon-ß and progesterone) or repressors (cyclopamine) HLA-G promoter activity was modulated, but certain haplotypes exhibited differential responses. No strict association was observed between plasma sHLA-G levels and the 5'URR haplotypes or genotypes; however, the G010101b haplotype was underrepresented among HLA-G-negative plasmas. Therefore, the HLA-G 5'URR polymorphism may have an impact on the modulation of HLA-G gene expression, but alone provides a limited predictive value for sHLA-G levels in vivo.
Assuntos
Regiões 5' não Traduzidas/genética , Microambiente Celular , Antígenos HLA-G/genética , Haplótipos , Polimorfismo de Nucleotídeo Único , Sequências Reguladoras de Ácido Nucleico , Fatores de Transcrição/metabolismo , Adulto , Coriocarcinoma/genética , Coriocarcinoma/patologia , Feminino , Genótipo , Antígenos HLA-G/metabolismo , Humanos , Masculino , Melanoma/genética , Melanoma/patologia , Células Tumorais CultivadasRESUMO
The HCV 5'UTR, Core/E1, and NS5B regions of samples from fifty patients infected with the hepatitis C virus (HCV) were analyzed. Seventeen patients were identified with genotype (GT) 1b, eleven with GT-1a, nine with GT-2b and four with GT-3a. Two rare subtypes were detected: GT-2j in two patients and GT-2r in one patient. Three patients had mixed infections: one with GT-2k + 2j and two with GT-1b + 2b. This work identifies HCV GTs, 2j, 2k, and 2r for the first time in Mexico.
Assuntos
Variação Genética , Genótipo , Hepacivirus/classificação , Hepacivirus/genética , Hepatite C/virologia , Regiões 5' não Traduzidas/genética , Adulto , Cidades , Feminino , Técnicas de Genotipagem , Hepacivirus/isolamento & purificação , Humanos , Masculino , México , Pessoa de Meia-Idade , Análise de Sequência de DNA , Proteínas do Core Viral/genética , Proteínas do Envelope Viral/genética , Proteínas não Estruturais Virais/genéticaRESUMO
Novel allele, HLA-B*51:220 generated by a gene conversion event was identified in a Brazilian individual.
Assuntos
Alelos , Antígenos HLA-B/genética , Regiões 5' não Traduzidas/genética , Sequência de Bases , Brasil , Éxons/genética , Humanos , Íntrons/genéticaRESUMO
We analyzed the compositional changes and the stable base pairs in the predicted secondary structure of the 5' UTR calmodulin mRNA in T. cruzi. The three copies of calmodulin in T. cruzi genome display variable position of the trans splicing sites and give rise to several mRNA that differs slightly on 5' UTR composition in the epimastigote stage. We show that the pattern of high probability base pairs in the minimum free energy predicted secondary structures of the calmodulin 5' UTR remains unchanged despite the nucleotide composition variation. However, the 39 nt spliced leader (mini-exon, the 5' exon sequence transferred to trypanosome mRNAs by the mechanism of trans splicing) shows a variable pattern of high and low probability base pairing as consequence of the altered composition of the 5' UTR.
Assuntos
Regiões 5' não Traduzidas/genética , Calmodulina/genética , RNA Líder para Processamento/genética , Trans-Splicing/genética , Trypanosoma cruzi/genética , Animais , Pareamento de Bases , Bovinos , Reação em Cadeia da Polimerase Via Transcriptase ReversaRESUMO
To identify putative cis-elements involved in gene expression regulation in Leishmania, we previously conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L. major, L. infantum, and L. braziliensis. Here, the CICS databank was explored to search for sequences that were present in the untranslated regions (UTRs) of groups of genes showing similar expression profiles during in vitro differentiation. Using a selectable marker as a reporter gene, flanked by either an intact 3' UTR or a UTR lacking the conserved element, the regulatory role of a CICS was confirmed. We observed that the pattern of modulation of the mRNA levels was altered in the absence of the CICS. We also identified putative CICS RNA-binding proteins. This study suggests that the publicly available CICS database is a useful tool for identifying regulatory cis-elements for Leishmania genes and suggests the existence of post-transcriptional regulons in Leishmania.
Assuntos
Regulação da Expressão Gênica/genética , Leishmaniose Cutânea/genética , Proteínas de Ligação a RNA/genética , Sequências Reguladoras de Ácido Nucleico/genética , Regiões 3' não Traduzidas/genética , Regiões 5' não Traduzidas/genética , Simulação por Computador , Sequência Conservada/genética , Genoma , Humanos , Leishmania braziliensis/genética , Leishmania infantum/genética , Leishmania major/genética , Leishmaniose Cutânea/parasitologiaRESUMO
AtHB1 is an Arabidopsis (Arabidopsis thaliana) homeodomain-leucine zipper transcription factor that participates in hypocotyl elongation under short-day conditions. Here, we show that its expression is posttranscriptionally regulated by an upstream open reading frame (uORF) located in its 5' untranslated region. This uORF encodes a highly conserved peptide (CPuORF) that is present in varied monocot and dicot species. The Arabidopsis uORF and its maize (Zea mays) homolog repressed the translation of the main open reading frame in cis, independent of the sequence of the latter. Published ribosome footprinting results and the analysis of a frame-shifted uORF, in which the repression capability was lost, indicated that the uORF causes ribosome stalling. The regulation exerted by the CPuORF was tissue specific and did not act in the absence of light. Moreover, a photosynthetic signal is needed for the CPuORF action, since plants with uncoupled chloroplasts did not show uORF-dependent repression. Plants transformed with the native AtHB1 promoter driving AtHB1 expression did not show differential phenotypes, whereas those transformed with a construct in which the uORF was mutated exhibited serrated leaves, compact rosettes, and, most significantly, short nondehiscent anthers and siliques containing fewer or no seeds. Thus, we propose that the uncontrolled expression of AtHB1 is deleterious for the plant and, hence, finely repressed by a translational mechanism.
Assuntos
Proteínas de Arabidopsis/metabolismo , Fases de Leitura Aberta/genética , Especificidade de Órgãos/genética , Fatores de Transcrição/metabolismo , Regiões 5' não Traduzidas/genética , Sequência de Aminoácidos , Arabidopsis/genética , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Códon/genética , Sequência Conservada/genética , Regulação da Expressão Gênica de Plantas/efeitos da radiação , Homozigoto , Mutação/genética , Especificidade de Órgãos/efeitos da radiação , Fenótipo , Biossíntese de Proteínas , Ribossomos/metabolismo , Fatores de Transcrição/química , Fatores de Transcrição/genética , Zea mays/genéticaRESUMO
Mammarenaviruses are enveloped viruses with a bisegmented negative-stranded RNA genome that encodes the nucleocapsid protein (NP), the envelope glycoprotein precursor (GPC), the RNA polymerase (L), and a RING matrix protein (Z). Viral proteins are synthesized from subgenomic mRNAs bearing a capped 5' untranslated region (UTR) and lacking 3' poly(A) tail. We analyzed the translation strategy of Tacaribe virus (TCRV), a prototype of the New World mammarenaviruses. A virus-like transcript that carries a reporter gene in place of the NP open reading frame and transcripts bearing modified 5' and/or 3' UTR were evaluated in a cell-based translation assay. We found that the presence of the cap structure at the 5' end dramatically increases translation efficiency and that the viral 5' UTR comprises stimulatory signals while the 3' UTR,specifically the presence of a terminal C+G-rich sequence and/or a stem-loop structure, down-modulates translation. Additionally, translation was profoundly reduced in eukaryotic initiation factor (eIF) 4G-inactivated cells, whereas depletion of intracellular levels of eIF4E had less impact on virus-like mRNA translation than on a cell-like transcript. Translation efficiency was independent of NP expression or TCRV infection. Our results indicate that TCRV mRNAs are translated using a cap-dependent mechanism, whose efficiency relies on the interplay between stimulatory signals in the 5' UTR and a negative modulatory element in the 3' UTR. The low dependence on eIF4E suggests that viral mRNAs may engage yet-unknown noncanonical host factors for a cap-dependent initiation mechanism.IMPORTANCE Several members of the Arenaviridae family cause serious hemorrhagic fevers in humans. In the present report, we describe the mechanism by which Tacaribe virus, a prototypic nonpathogenic New World mammarenavirus, regulates viral mRNA translation. Our results highlight the impact of untranslated sequences and key host translation factors on this process. We propose a model that explains how viral mRNAs outcompete cellular mRNAs for the translation machinery. A better understanding of the mechanism of translation regulation of this virus can provide the bases for the rational design of new antiviral tools directed to pathogenic arenaviruses.