Phylogeny and Polymorphism in the Long Control Region, E6, and L1 of Human Papillomavirus Types 53, 56, and 66 in Central Brazil

2011 ◽  
Vol 21 (2) ◽  
pp. 222-229 ◽  
Author(s):  
Patrícia Soares Wyant ◽  
Daniela Marreco Cerqueira ◽  
Daniella Sousa Moraes ◽  
José Paulo Gagliardi Leite ◽  
Cláudia Renata Fernandes Martins ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genetic Variability ◽  
Binding Sites ◽  
Long Control Region ◽  
Amino Acid Substitutions ◽  
Nucleotide Substitutions ◽  
Central Brazil ◽  
Hpv Types ◽  
Genomic Regions

Introduction:Several studies related that different human papillomavirus (HPV) types and intratype variants can present different oncogenic potential. In opposite to HPVs 16 and 18 variants, information about variants of other carcinogenic HPV types is still scarce. The aim of this study was to investigate the genetic variability of HPVs 53, 56, and 66 from Central Brazil isolates.Methods:The long control region (LCR), E6, and L1 genomic regions were amplified and sequenced. We evaluate for nucleotide variations in relation to the reference sequence of each HPV type and also the conservation of physicochemical properties of the deduced amino acid substitutions. In silico analysis was performed to locate binding sites for transcriptional factors within the LCR. Moreover, we performed a phylogenetic analysis with the Central Brazilian and worldwide sequences available at genomic databases.Results:Gathering LCR, E6, and L1 genomic regions, the highest genetic variability was found among HPV-53 isolates with 52 nucleotide variations, followed by HPVs 56 and 66 with 24 and 16 nucleotide substitutions, respectively. The genetic analysis revealed 11 new molecular variants of all HPV types analyzed, totalizing 31 new nucleotide and 3 new amino acid variations. Eight nonconservative amino acid substitutions were detected, which may indicate a biological and pathogenic diversity among HPV types. Furthermore, 8 nucleotide substitutions were localized at putative binding sites for transcription factors in the LCR with a potential implication on viral oncogene expression. The HPVs 53, 56, and 66 phylogenetic analysis confirmed a dichotomic division only described to HPV subtypes and different from the patterns described for HPVs 16 and 18 variants.Conclusions:The high genetic variability observed emphasizes the importance of investigating polymorphisms in types other than HPVs 16 or 18 to better understand the molecular genomic profile of viral infection by different HPV types.

scholarly journals Mechanism of Metronidazole Resistance inHelicobacter pylori: Comparison of the rdxA Gene Sequences in 30 Strains

2000 ◽  
Vol 44 (8) ◽  
pp. 2207-2210 ◽  
Author(s):  
Nadia Maggi Solcà ◽  
Marco Valerio Bernasconi ◽  
Jean-Claude Piffaretti
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Amino Acid ◽  
Resistant Strain ◽  
Point Mutations ◽  
Housekeeping Genes ◽  
Amino Acid Substitutions ◽  
Metronidazole Resistance ◽  
Nucleotide Mutation ◽  
Nucleotide Insertion

ABSTRACT The rdxA gene of 30 independently isolatedHelicobacter pylori strains was sequenced. A comparison of the rdxA sequences revealed a higher percentage of amino acid substitutions in the corresponding protein than in other housekeeping genes. Out of 122 point mutations, 41 were missense and 4 were nonsense. A resistant strain with a nucleotide insertion in therdxA sequence was also found. With the exception of the point mutations and the insertion generating a stop signal, no particular nucleotide mutation or amino acid substitution could be associated to metronidazole resistance. Moreover, phylogenetic analysis of the 30 nucleotide sequences did not demonstrate specific clusters associated with the resistance phenotype.

scholarly journals A Novel Distinct Genetic Variant of Tomato Torrado Virus with Substantially Shorter RNA1-Specific 3’untranslated Region (3’UTR)

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2454
Author(s):  
Marta Budziszewska ◽  
Przemysław Wieczorek
Keyword(s):  
Amino Acid ◽  
Genetic Variability ◽  
Untranslated Region ◽  
Genetic Variant ◽  
Sequencing Data ◽  
Sequence Analyses ◽  
Nucleotide Substitutions ◽  
Systemic Necrosis ◽  
Single Nucleotide

Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal’17 collected in 2017, derived from the ToTV-Wal’03 after long-term passages in plants. Sequence analyses of the ToTV-Wal’17 indicated twenty-eight single nucleotide substitutions in coding sequence of both RNAs, twelve of which resulted in amino acid changes in viral polyproteins. Moreover the sequencing data revealed that the 3’UTR of ToTV-Wal’17 RNA1 was 394 nts shorter in comparison to Wal’03. The performed sequence analyses revealed that 3’UTR of RNA1 of ToTV-Wal’17 is the most divergent across all previously described European isolates.

Polymorphism in the coding sequence of the horse transferrin gene

Genome ◽  
1994 ◽  
Vol 37 (1) ◽  
pp. 157-165 ◽  
Author(s):  
Margaret A. Carpenter ◽  
Tom E. Broad
Keyword(s):  
Amino Acid ◽  
Iron Transport ◽  
Nucleotide Substitution ◽  
Three Dimensional ◽  
Sequence Polymorphism ◽  
Dimensional Structure ◽  
Amino Acid Substitutions ◽  
Nucleotide Substitutions ◽  
Coding Sequence ◽  
Transferrin Gene

Transferrin, the iron transport protein of the blood, is highly polymorphic in many species, including the horse. A number of sequence polymorphisms that distinguish several of the variants of horse transferrin are reported here. Previous studies indicated that exons 12 and 15 were likely to be polymorphic. Sequencing regions of exons 12 and 15 from D and R variants revealed 10 nucleotide substitutions that encoded six amino acid replacements. The F1, F2, H2, and * variants were identical to D, and the O variant was almost identical to R, in the regions studied. The data indicated that the horse transferrin variants make up two distinct groups. The positions of differences between the D and F1 alleles were determined by analyzing single-stranded conformation polymorphisms. Sequencing then revealed three nucleotide substitutions, two of which encoded amino acid substitutions. Location of the eight polymorphic residues on the three-dimensional structure of human lactoferrin revealed that all were clustered at one end of the C-lobe.Key words: sequence polymorphism, transferrin, horse, nucleotide substitution, allele.

scholarly journals Determination of the complete genome and functional analysis of HPV6 isolate VBD19/10 from a patient with aggressive recurrent respiratory papillomatosis

2016 ◽  
Vol 144 (10) ◽  
pp. 2128-2135 ◽  
Author(s):  
R. Y. SEEDAT ◽  
C. E. COMBRINCK ◽  
P. A. BESTER ◽  
J.-Y. LEE ◽  
F. J. BURT
Keyword(s):  
Reporter Gene ◽  
Complete Genome ◽  
Promoter Sequence ◽  
Recurrent Respiratory Papillomatosis ◽  
Long Control Region ◽  
Nucleotide Substitutions ◽  
Transfected Cells ◽  
Aggressive Disease ◽  
Hpv Types

SUMMARYHuman papillomavirus (HPV) types 6 and 11 are the aetiological agent of recurrent respiratory papillomatosis (RRP). The complete genome of an HPV6 isolate with a 170 base pair (bp) duplication identified within the long control region (LCR) from a patient with aggressive recurrent respiratory papillomatosis was determined. The promoter sequence from the HPV LCR including the 170 bp duplication was placed upstream of a heterologous reporter gene and the activity of the reporter gene product determined using transfected cells. In total, mutations were observed at 157 nucleotide positions of the complete genome and included nucleotide substitutions, deletions and insertions, resulting in amino acid changes at 43 residue positions. Reporter gene activity using an HPV-derived LCR region with a 170 bp duplication was significantly higher than that using an HPV-derived LCR region with no duplication within this region. The results suggest that novel HPV variants warrant further investigation for potential biomarkers of aggressive disease.

scholarly journals Characterization of a new genotype of Betapapillomavirus HPV 17 through L1, E7, E7 and LCR sequences

2018 ◽  
Author(s):  
Ledy H Oliveira ◽  
Larissa Silva Santos ◽  
Felipe P G Neves
Keyword(s):  
Amino Acid ◽  
Evolutionary Process ◽  
Long Control Region ◽  
Nucleotide Substitutions ◽  
Specific Primers ◽  
E6 Oncoprotein ◽  
Potential Binding ◽  
New Genotype ◽  
Zinc Binding Domain

Background. Human papillomavirus (HPV) exhibits epithelial and mucosal tropism. HPV type 17 belongs to the Betapapillomavirus genus and molecular cloning experiments have identified two subtypes (17a and 17b) isolated from epidermodysplasia verruciformis (EV). HPV subtypes are characterized by dissimilarities from 2 to 10% at the nucleotide level from their referenced HPV. The aim of this study was to characterize the L1, E6, E7 and LCR sequences from an isolate from the oral mucosa of an asymptomatic woman. Methods. The whole late gene 1 (L1) was amplified using several sets of primers. The complete early genes 6 and 7 (E6, E7) and the long control region (LCR) were amplified using specific primers. Potential binding sites for transcriptional factors within the LCR were also investigated. Results. Within these sets, the DNA sequence was altered at 91 positions (68 in L1, 13 in E6, 8 in E7, and 2 in LCR sequences). L1 analysis showed high dissimilarity compared with the HPV 17 prototype, reaching 4% of nucleotide substitutions and leading to a probability third 17 subtype. The E6 oncoprotein presented the highest modification among the sequences !2 studied, with four amino acid changes in comparison with the prototype isolate. The amino acid was modified at a position 62 (S-T), a zinc-binding domain (CxxC(C)29 CxxC). Discussion. Our findings provide data on genetic variations seen in this genotype, reaching to dichotomic branching and pointing to an evolutionary process. The oral cavity has a large HPV spectrum and may be implicated in the evolution of this virus, allowing it to adapt to sites other than its original niche, may drive to produce adaptive variants of this genotype

scholarly journals CRISPR/Cas9-Mediated Multi-Allelic Gene Targeting in Sugarcane Confers Herbicide Tolerance

2021 ◽  
Vol 3 ◽  
Author(s):  
Mehmet Tufan Oz ◽  
Angelika Altpeter ◽  
Ratna Karan ◽  
Aldo Merotto ◽  
Fredy Altpeter
Keyword(s):  
Amino Acid ◽  
Gene Targeting ◽  
Crop Improvement ◽  
Herbicide Tolerance ◽  
Acetolactate Synthase ◽  
Amino Acid Substitutions ◽  
Dna Double Strand Breaks ◽  
Nucleotide Substitutions ◽  
Multiple Alleles ◽  
Homology Directed Repair

Sugarcane is the source of 80% of the sugar and 26% of the bioethanol produced globally. However, its complex, highly polyploid genome (2n = 100 – 120) impedes crop improvement. Here, we report efficient and reproducible gene targeting (GT) in sugarcane, enabling precise co-editing of multiple alleles via template-mediated and homology-directed repair (HDR) of DNA double strand breaks induced by the programmable nuclease CRISPR/Cas9. The evaluation of 146 independently transformed plants from five independent experiments revealed a targeted nucleotide replacement that resulted in both targeted amino acid substitutions W574L and S653I in the acetolactate synthase (ALS) in 11 lines in addition to single, targeted amino acid substitutions W574L or S653I in 25 or 18 lines, respectively. Co-editing of up to three ALS copies/alleles that confer herbicide tolerance was confirmed by Sanger sequencing of cloned long polymerase chain reaction (PCR) amplicons. This work will enable crop improvement by conversion of inferior alleles to superior alleles through targeted nucleotide substitutions.

scholarly journals Molecular characterization of the viral structural protein genes in the first outbreak of dengue virus type 2 in Hunan Province, inland China in 2018

2021 ◽  
Author(s):  
Jiaoqiong Guan ◽  
Zhanlong He ◽  
Meng Qin ◽  
Xialin Deng ◽  
Jun Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Protein Binding ◽  
Causative Agent ◽  
Binding Sites ◽  
Selection Pressure ◽  
Hunan Province ◽  
Genetic Characteristics ◽  
Protein Binding Sites ◽  
Dengue Outbreak

Abstract Background: An unexpected dengue outbreak occurred in Hunan Province in 2018. This was the first dengue outbreak in this area of inland China, and 172 cases were reported.Methods: To verify the causative agent of this outbreak and characterise the viral genes, the genes encoding the structural proteins C/prM/E of viruses isolated from local residents were sequenced followed by mutation and phylogenetic analysis. Recombination, selection pressure, potential secondary structure and three-dimensional structure analyses were also performed. Results: Phylogenetic analysis revealed that all epidemic strains were of the cosmopolitan DENV-2 genotype and were most closely related to the Zhejiang strain (MH010629, 2017) and then the Malaysia strain (KJ806803, 2013). Compared with the sequence of DENV-2SS, 151 base substitutions were found in the sequences of 89 isolates; these substitutions resulted in 20 non-synonymous mutations, of which 17 mutations existed in all samples (two in the capsid protein, six in the prM/M proteins, and nine in the envelope proteins). Moreover, amino acid substitutions at the 602nd (E322:Q→H) and 670th (E390: N→S) amino acids may have enhanced the virulence of the epidemic strains. One new DNA binding site and five new protein binding sites were observed. Two polynucleotide binding sites and seven protein binding sites were lost in the epidemic strains compared with DENV-2SS. Meanwhile, five changes were found in helical regions. Minor changes were observed in helical transmembrane and disordered regions. The 429th amino acid of the E protein switched from a histamine (positively charged) to an asparagine (neutral) in all 89 isolated strains. No recombination events or positive selection pressure sites were observed. To our knowledge, this study is the first to analyse the genetic characteristics of epidemic strains in the first dengue outbreak in Hunan Province in inland China.Conclusions: The causative agent is likely to come from Zhejiang Province, a neighbouring province where dengue fever broke out in 2017. This study may help clarify the intrinsic geographical relatedness of DENV-2 and contribute to further research on pathogenicity and vaccine development.

scholarly journals Molecular characterization of the viral structural gene of the first dengue virus type 2 outbreak in Hunan Province, inland China

2020 ◽  
Author(s):  
Jiaoqiong Guan ◽  
Zhanlong He ◽  
Meng Qin ◽  
Xialin Deng ◽  
Jun Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Protein Binding ◽  
Causative Agent ◽  
Binding Sites ◽  
Selection Pressure ◽  
Tertiary Structure ◽  
Hunan Province ◽  
Protein Binding Sites ◽  
Dengue Outbreak

Abstract Background: An unexpected dengue outbreak occurred in the Hunan Province in 2018. This is the first dengue outbreak in this area of inland China resulting 172 infected. Methods: To verify the causative agent of this outbreak and investigate gene characterization, the structural protein C/prM/E genes of viruses isolated from local residents were sequenced followed by mutation, phylogenetic analysis. The recombination, selection pressure, potential secondary structure and three-dimensional structure analysis were also performed. Results: Phylogenetic analysis revealed that all epidemic strains were classified as the cosmopolitan DENV-2 genotype, closest to the Zhejiang strain (MH010629, 2017) and then Malaysia strain (KJ806803, 2013). Compared with the DENV-2SS, 151 base substitutions were found in 89 sequences of isolates, resulting in 20 nonsynonymous mutations, of which 17 mutations existed among all samples (two in capsid protein, six in prM/M, and nine in envelope proteins). Moreover, amino acid substitutions at 602 th (E322:Q→H) and 670 th (E390: N→S) may result in heightened virulence of the epidemic strains. One new DNA-binding site and five new protein binding sites were observed. Two polynucleotide-binding sites and seven protein binding sites were lost compared with DENV-2SS. Meanwhile, five changes were found in helix regions. The helical transmembrane and disordered regions have minor changes. Protein tertiary structure prediction revealed the 429 th amino acid of E proteins was switch from histamine (positively charged) to asparagines (neutral) in 89 isolate strains. No recombination events or positive selection pressure sites were detected. To our knowledge, this study is the first gene analysis of epidemic strain in the first dengue outbreak in Hunan Province, inland China. Conclusions: The causative agent is likely to come from Zhejiang Province, a neighbouring Province where dengue fever broke out in 2017. This study may help understand the intrinsic geographical relatedness of DENV-2 and contributes further to research on pathogenicity and vaccine development.

scholarly journals The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh

2020 ◽  
Author(s):  
Abu Sayeed Mohmmad Mahmud ◽  
Tarannum Taznin ◽  
Md. Murshed Hasan Sarkar ◽  
Mohammad Samir Uzzaman ◽  
Eshrar Osman ◽  
...  
Keyword(s):  
Amino Acid ◽  
Mutation Rate ◽  
Local Environment ◽  
Spike Protein ◽  
Amino Acid Substitutions ◽  
List Type ◽  
Nucleotide Substitutions ◽  
Disease Manifestation ◽  
Entire Genome ◽  
Nucleotide Mutation

AbstractGenomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions, especially in target proteins, mutation events per samples, mutation rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between the 10th of May 2020 and the 27th of June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in non-synonymous 274 amino acid substitutions in 22 different proteins were detected with nucleotide mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-like protease (nsp3). Although no mutations were found in nsp7, nsp9, nsp10, and nsp11, yet orf1ab accounts for 56% of total mutations. Among the structural proteins, the highest non-synonymous amino acid substitution (at 36 positions) observed in spike proteins, in which 9 unique locations were detected relative to the global strains, including 516E>Q in the boundary of the ACE2 binding region. The most dominated variant G614 (95%) based in spike protein is circulating across the country with co-evolving other variants including L323 (94%) in RNA dependent RNA polymerase (RdRp), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2. These variants are mostly seen as linked mutations and are part of a haplotype observed in Europe. Data suggest effective containment of clade G strains (4.8%) with sub-clusters GR 82.4%, and GH clade 6.4%.HighlightsWe have sequenced 137 and analyzed 184 whole-genomes sequences of SARS-CoV-2 strains from different divisions of Bangladesh.A total of 634 mutation sites across the SARS-CoV-2 genome and 274 non-synonymous amino acid substitutions were detected.The mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year.Nine unique variants were detected based on non-anonymous amino acid substitutions in spike protein relative to the global SARS-CoV-2 strains.

scholarly journals Different Mutations in the Genome-Linked Protein VPg of Potato virus Y Confer Virulence on the pvr23 Resistance in Pepper

2006 ◽  
Vol 19 (5) ◽  
pp. 557-563 ◽  
Author(s):  
Valérie Ayme ◽  
Sylvie Souche ◽  
Carole Caranta ◽  
Mireille Jacquemond ◽  
Joël Chadœuf ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Drift ◽  
Potato Virus ◽  
High Frequency ◽  
Potato Virus Y ◽  
Relative Fitness ◽  
Amino Acid Substitutions ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Pepper Plants

Five different amino acid substitutions in the VPg of Potato virus Y were shown to be independently responsible for virulence toward pvr23 resistance gene of pepper. A consequence of these multiple mutations toward virulence involving single nucleotide substitutions is a particularly high frequency of resistance breaking (37% of inoculated plants from the first inoculation) and suggests a potentially low durability of pvr23 resistance. These five mutants were observed with significantly different frequencies, one of them being overrepresented. Genetic drift alone could not explain the observed distribution of virulent mutants. More plausible scenarios were obtained by taking into account either the relative substitution rates, the relative fitness of the mutants in pvr23 pepper plants, or both.

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