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

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.

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A novel distinct genetic variant of tomato torrado virus with substantially shorter RNA1-specific 3'untranslated region (3'UTR)

10.21203/rs.3.rs-502135/v1 ◽

2021 ◽

Author(s):

Marta Budziszewska ◽

Przemysław Wieczorek ◽

Aleksandra Obrępalska-Stęplowska

Keyword(s):

Amino Acid ◽

Untranslated Region ◽

Genetic Variant ◽

Sequencing Data ◽

Sequence Analyses ◽

Nucleotide Substitutions ◽

Systemic Necrosis ◽

Single Nucleotide ◽

Plant Sequence

Abstract 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 the 2017 year, derived from the ToTV-Wal'03 after long-term passages in plant. 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 pointed that 3'UTR of RNA1of ToTV-Wal'17 is the most divergent across all previously described European isolates.

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

International Journal of Gynecological Cancer ◽

10.1097/igc.0b013e318208c73d ◽

2011 ◽

Vol 21 (2) ◽

pp. 222-229 ◽

Cited By ~ 6

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.

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Genetics of adaptation of the ascomycetous fungus Podospora anserina to submerged cultivation

10.1101/488486 ◽

2018 ◽

Author(s):

Olga A. Kudryavtseva ◽

Ksenia R. Safina ◽

Olga A. Vakhrusheva ◽

Maria D. Logacheva ◽

Aleksey A. Penin ◽

...

Keyword(s):

Positive Selection ◽

Sequence Data ◽

Podospora Anserina ◽

Data Availability ◽

Submerged Cultivation ◽

Sequencing Data ◽

Russian Science ◽

Nucleotide Substitutions ◽

Ascomycetous Fungus

AbstractPodospora anserina is a model ascomycetous fungus which shows pronounced phenotypic senescence when grown on solid medium but possesses unlimited lifespan under submerged cultivation. In order to study the genetic aspects of adaptation of P. anserina to submerged cultivation, we initiated a long-term evolution experiment. In the course of the first four years of the experiment, 125 single-nucleotide substitutions and 23 short indels were fixed in eight independently evolving populations. Six proteins that affect fungal growth and development evolved in more than one population; in particular, the G-protein alpha subunit FadA evolved in seven out of eight experimental populations. Parallel evolution at the level of genes and pathways, an excess of nonsense and missense substitutions, and an elevated conservation of proteins and their sites where the changes occurred suggest that many of the observed allele replacements were adaptive and driven by positive selection.Author summaryLiving beings adapt to novel conditions that are far from their original environments in different ways. Studying mechanisms of adaptation is crucial for our understanding of evolution. The object of our interest is a multicellular fungus Podospora anserina. This fungus is known for its pronounced senescence and a definite lifespan, but it demonstrates an unlimited lifespan and no signs of senescence when grown under submerged conditions. Soon after transition to submerged cultivation, the rate of growth of P. anserina increases and its pigmentation changes. We wanted to find out whether there are any genetic changes that contribute to adaptation of P. anserina to these novel conditions and initiated a long-term evolutionary experiment on eight independent populations. Over the first four years of the experiment, 148 mutations were fixed in these populations. Many of these mutations lead to inactivation of the part of the developmental pathway in P. anserina, probably reallocating resources to vegetative proliferation in liquid medium. Our observations imply that strong positive selection drives changes in at least some of the affected protein-coding genes.Data AvailabilityGenome sequence data have been deposited at DDBJ/ENA/GenBank under accessions QHKV00000000 (founder genotype A; version QHKV01000000) and QHKU00000000 (founder genotype B; version QHKU01000000), with the respective BioSample accessions SAMN09270751 and SAMN09270757, under BioProject PRJNA473312. Sequencing data have been deposited at the SRA with accession numbers SRR7233712-SRR7233727, under the same BioProject.FundingExperimental work and sequencing were supported by the Russian Foundation for Basic Research (grants no. 16-04-01845a and 18-04-01349a). Bioinformatic analysis was supported by the Russian Science Foundation (grant no. 16-14-10173). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-19-0557 ◽

2006 ◽

Vol 19 (5) ◽

pp. 557-563 ◽

Cited By ~ 86

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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Probability of change in life: Amino acid changes in single nucleotide substitutions

Biosystems ◽

10.1016/j.biosystems.2020.104135 ◽

2020 ◽

Vol 193-194 ◽

pp. 104135 ◽

Cited By ~ 1

Author(s):

Kwok-Fong Chan ◽

Stelios Koukouravas ◽

Joshua Yi Yeo ◽

Darius Wen-Shuo Koh ◽

Samuel Ken-En Gan

Keyword(s):

Amino Acid ◽

Nucleotide Substitutions ◽

Single Nucleotide

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Tandem Substitutions in Somatic Hypermutation

Blood ◽

10.1182/blood-2021-153604 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 996-996

Author(s):

Marvyn T. Koning ◽

Julieta Haydee Sepulveda Yanez ◽

Diego Alvarez-Saravia ◽

Bas Pilzecker ◽

Pauline Van Schouwenburg ◽

...

Keyword(s):

Amino Acid ◽

Somatic Hypermutation ◽

Adaptive Immune Response ◽

Affinity Maturation ◽

Reference Sequence ◽

Nucleotide Substitutions ◽

Sequence Context ◽

Single Nucleotide ◽

Adaptive Immune ◽

Amino Acid Codon

Abstract Upon antigen recognition, activation-induced cytosine deaminase initiates affinity maturation of the B-cell receptor by somatic hypermutation (SHM) through error-prone DNA repair pathways. SHM typically creates single nucleotide substitutions, but tandem substitutions may also occur. While tandem substitutions have been described in mice and other species, the incidence of this phenomenon and its underlying mechanism in humans is currently unknown. We investigated incidence and sequence context of tandem substitutions by massive parallel sequencing of V(D)J repertoires in healthy human donors generated by unbiased ARTISAN PCR. Selection of unique, clonally unrelated, antigen-experienced sequences carrying up to 5% mutations yielded 13.532 VDJ, 7.952 VJ-kappa and 7.598 VJ-lambda. Comparison to the closest germline allele allowed for identification of a total of 122.878 single nucleotide substitutions (SNS), 10.735 tandem dinucleotide substitutions (TDNS) and 2.615 longer contiguous substitutions. After correcting for expected clusters of adjacent SNS, tandem substitutions comprised 5,7% of all AID-induced mutations. The mutation of more than one nucleotide in a single event, was shown to overcome amino acid codon redundancy and may therefore enhance the adaptive immune response. Clustering of such mutations around AID hotspots and their overall distribution indicates that tandem substitutions are an integral part of the SHM spectrum. In the majority of tandem substitutions, the mutated sequence may be identified in the directly adjacent reference sequence context. Tandem substitutions in humans therefore represent single nucleotide juxtalocations. Such juxtalocations appear to be favored in polydipyramidine stretches. These observations could be confirmed in patients with MSH2/6 deficiency, but were absent in a VDJ library from an UNG-deficient patient, indicating a strict dependence on abasic sites as an instigating mechanism. Together, these findings delineate a model where tandem substitutions are predominantly generated by translesion synthesis across an apyramidinic site that is typically created by UNG. During replication, apyrimidinic sites transiently adapt an extruded configuration, causing skipping of the extruded base. Consequent strand decontraction leads to the juxtalocation, after which exonucleases repair the apyramidinic site and any directly adjacent mismatched base pairs. The mismatch repair pathway appears to account for the remainder of tandem substitutions. Our study shows that a significant portion of mutations acquired during SHM are caused by tandem substitutions, and that this mechanism may enhance affinity maturation and expedite the adaptive immune response by overcoming amino acid codon degeneracies or mutating two adjacent amino acid residues simultaneously. Figure legend. Corrected incidence of tandem dinucleotide substitutions in healthy donors. (A) Dinucleotide substitutions from unique IGHV, IGKV and IGLV sequences and corrected after in silico predictions of dinucleotide substitutions that did not occur in tandem. Burgundy cells represent sequence inversions, light and dark purple cells represent juxtalocations of the 5' and 3' base in the pair (as seen from the non-transcribed strand), respectively. For unshaded cells, juxtalocation could not be assessed due to one or more nucleotides in the reference sequence matching the mutated sequence. (B) Relative contribution of sequence inversions and juxtalocations. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

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Tandem Substitutions in Somatic Hypermutation

Frontiers in Immunology ◽

10.3389/fimmu.2021.807015 ◽

2022 ◽

Vol 12 ◽

Author(s):

Julieta H. Sepúlveda-Yáñez ◽

Diego Alvarez Saravia ◽

Bas Pilzecker ◽

Pauline A. van Schouwenburg ◽

Mirjam van den Burg ◽

...

Keyword(s):

Amino Acid ◽

Somatic Hypermutation ◽

Cytosine Deaminase ◽

Adaptive Immune Response ◽

Cell Receptor ◽

Affinity Maturation ◽

Induced Mutations ◽

Nucleotide Substitutions ◽

Healthy Human ◽

Single Nucleotide

Upon antigen recognition, activation-induced cytosine deaminase initiates affinity maturation of the B-cell receptor by somatic hypermutation (SHM) through error-prone DNA repair pathways. SHM typically creates single nucleotide substitutions, but tandem substitutions may also occur. We investigated incidence and sequence context of tandem substitutions by massive parallel sequencing of V(D)J repertoires in healthy human donors. Mutation patterns were congruent with SHM-derived single nucleotide mutations, delineating initiation of the tandem substitution by AID. Tandem substitutions comprised 5,7% of AID-induced mutations. The majority of tandem substitutions represents single nucleotide juxtalocations of directly adjacent sequences. These observations were confirmed in an independent cohort of healthy donors. We propose a model where tandem substitutions are predominantly generated by translesion synthesis across an apyramidinic site that is typically created by UNG. During replication, apyrimidinic sites transiently adapt an extruded configuration, causing skipping of the extruded base. Consequent strand decontraction leads to the juxtalocation, after which exonucleases repair the apyramidinic site and any directly adjacent mismatched base pairs. The mismatch repair pathway appears to account for the remainder of tandem substitutions. Tandem substitutions may enhance affinity maturation and expedite the adaptive immune response by overcoming amino acid codon degeneracies or mutating two adjacent amino acid residues simultaneously.

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ADRes: a computational pipeline for detecting molecular markers of Anti-malarial Drug Resistance, from Sanger sequencing data

10.1101/066183 ◽

2016 ◽

Author(s):

Setor Amuzu ◽

Anita Ghansah

Keyword(s):

Drug Resistance ◽

Molecular Markers ◽

Amino Acid ◽

Sanger Sequencing ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Single Nucleotide ◽

Artemisinin Derivatives ◽

Base Calling ◽

Sulphadoxine Pyrimethamine

AbstractBackgroundMalaria control efforts are stifled by the emergence and dispersal of parasite strains resistant to available anti-malarials. Amino acid changes in specific positions of proteins encoded by Plasmodium falciparum genes pfcrt, dhps, dhfr, and pfmdr1 are used as molecular markers of resistance to antimalarials such as chloroquine, sulphadoxine-pyrimethamine, as well as artemisinin derivatives. However, a challenge to the detection of single nucleotide polymorphisms (SNPs) in codons responsible for these amino acid changes, in several samples, is the scarcity of automated computational pipelines for molecular biologists to; rapidly analyze ABI (Applied Biosystems) Sanger sequencing data spanning the codons of interest in order to characterize these codons and detect these molecular markers of drug resistance. The pipeline described here is an attempt to address this need.MethodThis pipeline is a combination of existing tools, notably SAMtools and Burrows Wheeler Aligner (BWA), as well as custom Python and BASH scripts. It is designed to run on the UNIX shell, a command line interpreter. To characterize the codons associated with anti-malarial drug resistance (ADR) in a particular gene using this pipeline, the following options are required; a path to reference coding sequence of the gene in FASTA format, gene symbol (pfcrt, pfmdr1, dhps or dhfr), and a path to the directory of ABI sequencing trace files for the samples. With these inputs, the pipeline performs base calling and trimming, sequence alignment, and alignment parsing.ResultsThe output of the pipeline is a CSV (Comma-separated values) file of sample names, codons and their corresponding encoded amino acids. The data generated can be readily analyzed using widely available statistical or spreadsheet software, to determine the frequency of molecular markers of resistance to anti-malarials such as chloroquine, sulphadoxine-pyrimethamine and artemisinin derivatives.ConclusionsADRes is a quick and effective pipeline for detecting common molecular markers of anti-malarial drug resistance, and could be a useful tool for surveillance. The code, description, and instructions for using this pipeline are publicly available at http://setfelix.github.io/ADRes.

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Divergent pattern of genomic variation in Plasmodium falciparum and P. vivax

F1000Research ◽

10.12688/f1000research.10255.1 ◽

2016 ◽

Vol 5 ◽

pp. 2763 ◽

Cited By ~ 1

Author(s):

Preeti Goel ◽

Gajinder Pal Singh

Keyword(s):

Plasmodium Falciparum ◽

Amino Acid ◽

Large Scale ◽

Genomic Variation ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Single Nucleotide ◽

Evolutionary Response ◽

Substitution Bias ◽

Synonymous Sites

The two main species causing malaria in humans, Plasmodium falciparum and P. vivax, differ significantly from each other in their evolutionary response to common drugs, but the reasons for this are not clear. Here we utilized the recently available large-scale genome sequencing data from these parasites and compared the pattern of single nucleotide polymorphisms, which may be related to these differences. We found that there was a five-fold higher preference for AT nucleotides compared to GC nucleotides at synonymous single nucleotide polymorphism sites in P. vivax. The preference for AT nucleotides was also present at non-synonymous sites, which lead to amino acid changes favouring those with codons of higher AT content. The substitution bias was also present at low and moderately conserved amino acid positions, but not at highly conserved positions. No marked bias was found at synonymous and non-synonymous sites in P. falciparum. The difference in the substitution bias between P. falciparum and P. vivax found in the present study may possibly contribute to their divergent evolutionary response to similar drug pressures.

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The effect of a single nucleotide polymorphism on human α2-antiplasmin activity

Blood ◽

10.1182/blood-2007-01-065185 ◽

2007 ◽

Vol 109 (12) ◽

pp. 5286-5292 ◽

Cited By ~ 20

Author(s):

Victoria J. Christiansen ◽

Kenneth W. Jackson ◽

Kyung N. Lee ◽

Patrick A. McKee

Keyword(s):

Single Nucleotide Polymorphism ◽

Amino Acid ◽

Amino Terminus ◽

Healthy Population ◽

Plasma Samples ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genotype Frequencies ◽

Polymorphic Forms

Abstract The primary inhibitor of plasmin, α2-antiplasmin (α2AP), is secreted by the liver into plasma with Met as the amino-terminus. During circulation, Met-α2AP is cleaved by antiplasmin-cleaving enzyme (APCE), yielding Asn-α2AP, which is crosslinked into fibrin approximately 13 times faster than Met-α2AP. The Met-α2AP gene codes for either Arg or Trp as the sixth amino acid, with both polymorphic forms found in human plasma samples. We determined the Arg6Trp genotype frequency in a healthy population and its effects on Met-α2AP cleavage and fibrinolysis. Genotype frequencies were RR 62.5%, RW 34.0%, and WW 3.5%. The polymorphism related to the percentage of Met-α2AP in plasma was WW (56.4%), RW (40.6%), and RR (23.6%). WW plasma tended to have shorter lysis times than RR and RW plasmas. APCE cleaved purified Met-α2AP(Arg6) approximately 8-fold faster than Met-α2AP(Trp6), which is reflected in Asn-α2AP/Met-α2AP ratios with time in RR, RW, and WW plasmas. Removal of APCE from plasma abrogated cleavage of Met-α2AP. We conclude that the Arg6Trp polymorphism is functionally significant, as it clearly affects conversion of Met-α2AP to Asn-α2AP, and thereby, the rate of α2AP incorporation into fibrin. Therefore, the Arg6Trp polymorphism may play a significant role in governing the long-term deposition/removal of intravascular fibrin.

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