Molecular characterization of three newly recognized rat parvoviruses

Rodent parvoviruses have been documented to interfere with both in vivo and in vitro research. In this study, three rat parvoviruses distinct from previously characterized rodent parvoviruses were identified from naturally infected rats obtained from four discrete sources. These three newly recognized parvoviruses were designated rat minute virus (RMV)-1a, -1b and -1c. In this study, the genomic nucleotide sequence and the predicted amino acid sequences of proteins for each of the three RMV-1 variants and Kilham rat virus (KRV) were determined and compared with previously characterized rodent parvoviruses. The three RMV-1 variants were shown to be closely related to each other, to be distinct from but closely related to KRV and H-1 virus, and to be significantly different from the previously identified rat parvovirus isolate, RPV-1a.

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MOLECULAR CHARACTERIZATION OF TWO NOVEL RAT MINUTE VIRUSES IN TAIWAN

Taiwan Veterinary Journal ◽

10.1142/s1682648520500109 ◽

2020 ◽

Vol 46 (02n03) ◽

pp. 101-110

Author(s):

Yi-Chun Liao ◽

Yung-Hui Chang ◽

Ming-Hseng Wang ◽

Ber-Hsiang Fang ◽

Cho-Hua Wan

Keyword(s):

Amino Acid ◽

Molecular Characterization ◽

Nucleotide Sequences ◽

Amino Acid Sequences ◽

Phylogenetic Data ◽

Laboratory Rodent ◽

Minute Virus ◽

The Common ◽

Kilham Rat Virus

Rodent parvovirus infection is one of the common viral problems in laboratory rodent colonies. In this study, two new parvoviruses were identified in naturally-infected rats from two different research colonies in Taiwan. The genomic nucleotide sequences and the predicted amino acid sequences of proteins for these two viruses were compared to the previously characterized rodent parvoviruses. The two newly identified viruses were most closely related to each other, also closely related to two variants of rat minute virus (RMV; RMV-1 and RMV-2), and distinct from but closely related to Kilham rat virus and H-1 virus. These two viruses were significantly different from variants of rat parvovirus (RPV; RPV-1 and RPV-NTU1). Phylogenetic data also supported that these two new viruses are variants of the RMV species. These two newly identified viruses were designated RMV type National Taiwan University 1 (RMV-NTU1) and RMV type National Taiwan University 2 (RMV-NTU2). RMV-NTUs are the first molecularly characterized RMV variants identified in Asia.

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Biochemical and genetic characterization of a yeast TFIID mutant that alters transcription in vivo and DNA binding in vitro

Molecular and Cellular Biology ◽

10.1128/mcb.12.5.2372-2382.1992 ◽

1992 ◽

Vol 12 (5) ◽

pp. 2372-2382

Author(s):

K M Arndt ◽

S L Ricupero ◽

D M Eisenmann ◽

F Winston

Keyword(s):

Amino Acid ◽

Dna Binding ◽

Direct Repeat ◽

Single Amino Acid ◽

Wild Type ◽

Dna Binding Specificity ◽

Selection For

A mutation in the gene that encodes Saccharomyces cerevisiae TFIID (SPT15), which was isolated in a selection for mutations that alter transcription in vivo, changes a single amino acid in a highly conserved region of the second direct repeat in TFIID. Among eight independent spt15 mutations, seven cause this same amino acid change, Leu-205 to Phe. The mutant TFIID protein (L205F) binds with greater affinity than that of wild-type TFIID to at least two nonconsensus TATA sites in vitro, showing that the mutant protein has altered DNA binding specificity. Site-directed mutations that change Leu-205 to five different amino acids cause five different phenotypes, demonstrating the importance of this amino acid in vivo. Virtually identical phenotypes were observed when the same amino acid changes were made at the analogous position, Leu-114, in the first repeat of TFIID. Analysis of these mutations and additional mutations in the most conserved regions of the repeats, in conjunction with our DNA binding results, suggests that these regions of the repeats play equivalent roles in TFIID function, possibly in TATA box recognition.

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Molecular characterization of Prunus necrotic ringspot virus isolated from rose in Brazil

Ciência Rural ◽

10.1590/0103-8478cr20141810 ◽

2015 ◽

Vol 45 (12) ◽

pp. 2197-2200 ◽

Cited By ~ 2

Author(s):

Thor Vinícius Martins Fajardo ◽

Monique Bezerra Nascimento ◽

Marcelo Eiras ◽

Osmar Nickel ◽

Gilvan Pio-Ribeiro

Keyword(s):

Amino Acid ◽

Molecular Characterization ◽

Molecular Analysis ◽

Nucleotide Sequences ◽

Amino Acid Sequences ◽

Causal Agent ◽

Ringspot Virus ◽

Prunus Necrotic Ringspot Virus ◽

First Time

ABSTRACT: There is no molecular characterization of Brazilian isolates of Prunus necrotic ringspot virus (PNRSV), except for those infecting peach. In this research, the causal agent of rose mosaic was determined and the movement (MP) and coat (CP) protein genes of a PNRSV isolate from rose were molecularly characterized for the first time in Brazil. The nucleotide and deduced amino acid sequences of MP and CP complete genes were aligned and compared with other isolates. Molecular analysis of the MP and CP nucleotide sequences of a Brazilian PNRSV isolate from rose and others from this same host showed highest identities of 96.7% and 98.6%, respectively, and Rose-Br isolate was classified in PV32 group.

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Molecular Characterization of HOXA2 and HOXA3 Binding Properties

Journal of Developmental Biology ◽

10.3390/jdb9040055 ◽

2021 ◽

Vol 9 (4) ◽

pp. 55

Author(s):

Joshua Mallen ◽

Manisha Kalsan ◽

Peyman Zarrineh ◽

Laure Bridoux ◽

Shandar Ahmad ◽

...

Keyword(s):

Transcription Factors ◽

Molecular Characterization ◽

Sequence Motif ◽

Body Parts ◽

Binding Affinities ◽

Binding Properties ◽

Functional Consequences

The highly conserved HOX homeodomain (HD) transcription factors (TFs) establish the identity of different body parts along the antero–posterior axis of bilaterian animals. Segment diversification and the morphogenesis of different structures is achieved by generating precise patterns of HOX expression along the antero–posterior axis and by the ability of different HOX TFs to instruct unique and specific transcriptional programs. However, HOX binding properties in vitro, characterised by the recognition of similar AT-rich binding sequences, do not account for the ability of different HOX to instruct segment-specific transcriptional programs. To address this problem, we previously compared HOXA2 and HOXA3 binding in vivo. Here, we explore if sequence motif enrichments observed in vivo are explained by binding affinities in vitro. Unexpectedly, we found that the highest enriched motif in HOXA2 peaks was not recognised by HOXA2 in vitro, highlighting the importance of investigating HOX binding in its physiological context. We also report the ability of HOXA2 and HOXA3 to heterodimerise, which may have functional consequences for the HOX patterning function in vivo.

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Charge influences substrate recognition and self-assembly of hydrophobic FG sequences

10.1101/090159 ◽

2016 ◽

Author(s):

Wesley G. Chen ◽

Jacob Witten ◽

Scott C. Grindy ◽

Niels Holten-Andersen ◽

Katharina Ribbeck

Keyword(s):

Amino Acid ◽

Self Assembly ◽

Amino Acid Sequences ◽

Nuclear Pore ◽

Selective Binding ◽

Charged Amino Acids ◽

Essential Components ◽

Transport Receptors

AbstractThe nuclear pore complex controls the passage of molecules via hydrophobic phenylalanine-glycine (FG) domains on nucleoporins. Such FG-domains consist of repeating units of FxFG, FG, or GLFG sequences, which can be interspersed with highly charged amino acid sequences. Despite the high density of charge exhibited in certain FG-domains, if and how charge influences FG-domain self-assembly and selective binding of nuclear transport receptors is largely unexplored. Studying how individual charged amino acids contribute to nuclear pore selectivity is challenging with modern in vivo and in vitro techniques due to the complexity of nucleoporin sequences. Here, we present a rationally designed approach to deconstruct essential components of nucleoporins down to 14 amino acid sequences. With these nucleoporin-based peptides, we systematically dissect how charge type and placement of charge influences self-assembly and selective binding of FG-containing gels. Specifically, we find that charge type determines which hydrophobic substrates FG sequences recognize while spatial localization of charge tunes hydrophobic self-assembly and receptor selectivity of FG sequences.

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In vitro and In Silico Approach For Characterization of Antimicrobial Peptide From Probiotics Against Staphylococcus Aureus and Escherichia Coli

10.21203/rs.3.rs-366314/v2 ◽

2021 ◽

Author(s):

Amrutha Bindu ◽

Lakshmi Devi

Keyword(s):

Amino Acid ◽

Antimicrobial Peptide ◽

Lactobacillus Plantarum ◽

Exchange Chromatography ◽

Amino Acid Sequences ◽

Proteinase K ◽

Kinetic Assay ◽

Wide Range

Abstract The focus of present study was to characterize antimicrobial peptide produced by probiotic cultures, Enterococcus durans DB-1aa (MCC4243), Lactobacillus plantarum Cu2-PM7 (MCC4246) and Lactobacillus fermentum Cu3-PM8 (MCC4233) against Staphylococus aureus and E. coli. The growth kinetic assay revealed 24 h of incubation to be optimum for bacteriocin production. The partially purified compound after ion-exchange chromatography was found to be thermoresistant and stable under wide range of pH. The compound was sensitive to proteinase-K, but resistant to trypsin, a-amylase and lipase. The apparent molecular weight of bacteriocin from MCC4243 and MCC4246 was found to be 3.5 KDa. Translated partial amino acid sequence of plnA gene in MCC4246 displayed 48 amino acid sequences showing 100% similarity with plantaricin A of Lactobacillus plantarum (WP_0036419). The sequence revealed 7 β sheets, 6 α sheets, 6 predicted coils and 9 predicted turns. The functions on cytoplasm show 10.82 isoelectric point and 48.6% hydrophobicity. The molecular approach of using Geneious Prime software and protein prediction data base for characterization of bacteriocin is novel and predicts “KSSAYSLQMGATAIKQVKKLFKKWGW” as peptide responsible for antimicrobial activity. The study provides information about broad spectrum bacteriocin in native probiotic culture and paves a way towards its application in functional foods as biopreservative agents.

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Molecular characterization of the grape seeds extract’s effect against chemically induced liver cancer: In vivo and in vitro analyses

Scientific Reports ◽

10.1038/s41598-018-19492-x ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 31

Author(s):

Alaaeldin Ahmed Hamza ◽

Gehan Hussein Heeba ◽

Hanan Mohamed Elwy ◽

Chandraprabha Murali ◽

Raafat El-Awady ◽

...

Keyword(s):

Liver Cancer ◽

Molecular Characterization ◽

Grape Seeds ◽

Chemically Induced

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In-silico structural, functional and immunogenic characterization of Taenia solium TS14 protein

Indian Journal of Animal Research ◽

10.18805/ijar.b-3313 ◽

2017 ◽

Author(s):

Chitra Joshi ◽

Siddharth Gautam

Keyword(s):

Amino Acid ◽

In Silico ◽

Mutational Analysis ◽

Solvent Accessibility ◽

Taenia Solium ◽

Secretory Protein ◽

Single Amino Acid

TS14, a Cysticercosis cellulosae derived protein, has been exploited for immunodiagnosis of cysticercosis in humans and pigs. However, the information on structure, function, stability and immunogenicity of TS14 derived from different isolates is primarily lacking. The present study deals with in-silico characterization of six TS14 isolates. High thermostability and an isoelectric point of 9.41 were recorded. Based on N-terminal amino acid residues, high resistance to intracellular proteases with extended in-vivo and in-vitro half-lives was predicted. TS14 is foreseen as a secretory protein with a signal peptide and an extracellular localization. Structural analysis of TS14 exhibited the dominance of helices in the secondary structure (92% coverage) with majority of residues showing high and medium solvent accessibility. High lysine content and presence of multiple nucleotide binding sites in TS14 suggests interaction with RNA/DNA and a role in their metabolism. Immunogenic profiling predicted presence of four distinct B-cell epitopes. Mutational analysis based on the single amino acid substitutions among six TS14 isolates demonstrated minor variations in structural stability; however, all the substitutions were well tolerated. Moreover, all the isolates revealed almost identical immunogenic profile with an equivocal potential to elicit the antibody-mediated immune response.

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Molecular characterization of Penicillium chrysogenum virus: reconsideration of the taxonomy of the genus Chrysovirus

Journal of General Virology ◽

10.1099/vir.0.79842-0 ◽

2004 ◽

Vol 85 (7) ◽

pp. 2111-2121 ◽

Cited By ~ 92

Author(s):

Daohong Jiang ◽

Said A. Ghabrial

Keyword(s):

Molecular Characterization ◽

Penicillium Chrysogenum ◽

Sequence Similarity ◽

Minor Component ◽

Amino Acid Sequences ◽

Nucleotide Sequencing ◽

Dsrna Segment ◽

Cdna Clones

Molecular cloning and complete nucleotide sequencing of Penicillium chrysogenum virus (PcV) dsRNAs indicated that PcV virions contained four dsRNA segments with sizes of 3562, 3200, 2976 and 2902 bp. Each dsRNA segment had unique sequences and contained a single large open reading frame (ORF). In vitro translation of transcripts derived from full-length cDNA clones of PcV dsRNAs yielded single products of sizes similar to those predicted from the deduced amino acid sequences of the individual ORFs. Sequence similarity searches revealed that dsRNA1 encodes a putative RNA-dependent RNA polymerase. In this study, it was determined that dsRNA2 encodes the major capsid protein and that p4, encoded by dsRNA4, is virion-associated as a minor component. All four dsRNAs of PcV, like the genomic segments of viruses with multipartite genomes, were found to have extended regions of highly conserved terminal sequences at both ends. In addition to the strictly conserved 5′-terminal 10 nt, a second region consisting of reiteration of the sequence CAA was found immediately upstream of the AUG initiator codon. These (CAA) n repeats are reminiscent of the translational enhancer elements of tobamoviruses. The 3′-terminal 14 nt were also strictly conserved. As PcV and related viruses with four dsRNA segments (genus Chrysovirus) have not been previously characterized at the molecular level, they were provisionally classified in the family Partitiviridae, comprising viruses with bipartite genomes. This study represents the first report on molecular characterization of a chrysovirus and the results suggest the creation of a new family of mycoviruses with multipartite dsRNA genomes to accommodate PcV and related viruses.

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