scholarly journals Quasispecies of TT Virus (TTV) with Sequence Divergence in Hypervariable Regions of the Capsid Protein in Chronic TTV Infection

1999 ◽  
Vol 73 (11) ◽  
pp. 9604-9608 ◽  
Author(s):  
Tsutomu Nishizawa ◽  
Hiroaki Okamoto ◽  
Fumio Tsuda ◽  
Tatsuya Aikawa ◽  
Yoshiki Sugai ◽  
...  
Keyword(s):  
Amino Acids ◽  
Capsid Protein ◽  
Immune Surveillance ◽  
Sequence Divergence ◽  
Open Reading Frame ◽  
Amino Acid Substitutions ◽  
Reading Frame ◽  
Tt Virus ◽  
Hypervariable Regions ◽  
Open Reading Frame 1

ABSTRACT Three hypervariable regions were identified in a central portion of open reading frame 1 of TT virus DNA, which codes for a putative capsid protein of 770 amino acids. TT virus circulates as quasispecies, with many amino acid substitutions in hypervariable regions, to evade immune surveillance of the hosts and to establish a persistent infection.

scholarly journals Two Nonoverlapping Domains on the Norwalk Virus Open Reading Frame 3 (ORF3) Protein Are Involved in the Formation of the Phosphorylated 35K Protein and in ORF3-Capsid Protein Interactions

2003 ◽  
Vol 77 (6) ◽  
pp. 3569-3577 ◽  
Author(s):  
Pamela J. Glass ◽  
Carl Q. Zeng ◽  
Mary K. Estes
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Capsid Protein ◽  
Full Length ◽  
Open Reading Frame ◽  
Norwalk Virus ◽  
Two Dimensional Gel Electrophoresis ◽  
Reading Frame ◽  
Orf3 Protein ◽  
Orf2 Protein

ABSTRACT Expression of the Norwalk virus open reading frame 3 (ORF3) in Spodoptera frugiperda (Sf9) cells yields two major forms, the predicted 23,000-molecular-weight (23K) form and a larger 35K form. The 23K form is able to interact with the ORF2 capsid protein and be incorporated into virus-like particles. In this paper, we provide mass spectrometry evidence that both the 23K and 35K forms are composed only of the ORF3 protein. Two-dimensional gel electrophoresis and phosphatase treatment showed that the 35K form results solely from phosphorylation and that the 35K band is composed of several different phosphorylated forms with distinct isoelectric points. Furthermore, we analyzed deletion and point mutants of the ORF3 protein. Mutants that lacked the C-terminal 33 amino acids (ORF31-179, ORF31-152, and ORF31-107) no longer produced the 35K form. An N-terminal truncation mutant (ORF351-212) and a site-directed mutant (ORF3T201V) were capable of producing the larger form, which was converted to the smaller form by treatment with protein phosphatase. These data suggest that the region between amino acids 180 and 212 is phosphorylated, and mass spectrometry showed that amino acids Arg196 to Arg211 are not phosphorylated; thus, phosphorylation of the serine-threonine-rich region from Thr181 to Ser193 must be involved in the generation of the 35K form. Studies of the interaction between the ORF2 protein and full-length and mutated ORF3 proteins showed that the full-length ORF3 protein (ORF3FL), ORF31-179, ORF31-152, and ORF351-212 interacted with the ORF2 protein, while an ORF31-107 protein did not. These results indicate that the region of the ORF3 protein between amino acids 108 and 152 is responsible for interaction with the ORF2 protein.

scholarly journals Sequence and structure of mtr, an amino acid transport gene of Neurospora crassa

Genome ◽  
1991 ◽  
Vol 34 (4) ◽  
pp. 644-651 ◽  
Author(s):  
Kenneth Koo ◽  
W. Dorsey Stuart
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Neurospora Crassa ◽  
Rna Binding ◽  
Signal Sequence ◽  
Average Length ◽  
Open Reading Frame ◽  
Mrna Transcript ◽  
S1 Nuclease ◽  
Reading Frame

The gene product of the mtr locus of Neurospora crassa is required for the transport of neutral aliphatic and aromatic amino acids via the N system. We have previously cloned three cosmids containing Neurospora DNA that complement the mtr-6(r) mutant allele. The cloned DNAs were tightly linked to restriction fragment length polymorphisms that flank the mtr locus. A 2.9-kbp fragment from one cosmid was subcloned and found to complement the mtr-6(r) allele. Here we report the sequence of the fragment that hybridized to a poly(A)+ mRNA transcript of about 2300 nucleotides. We have identified an 845-bp open reading frame (ORF) having a 59-bp intron as the potential mtr ORF. S1 nuclease analysis of the transcript confirmed the transcript size and the presence of the intron. A second open reading frame was found upstream in the same reading frame as the mtr ORF and appears to be present in the mRNA transcript. The mtr ORF is predicted to encode a 261 amino acid polypeptide with a molecular mass of 28 613 Da. The proposed polypeptide exhibits six potential α-helical transmembrane domains with an average length of 23 amino acids, does not have a signal sequence, and contains amino acid sequence homologous to an RNA binding motif.Key words: sequence, membranes, ribonucleoprotein.

Sequence and expression of the dCMP deaminase gene (DCD1) of Saccharomyces cerevisiae

1986 ◽  
Vol 6 (5) ◽  
pp. 1711-1721
Author(s):  
E M McIntosh ◽  
R H Haynes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Open Reading Frame ◽  
Northern Analysis ◽  
Hindiii Site ◽  
Reading Frame ◽  
Hindiii Restriction Site ◽  
Cycle Dependent

The dCMP deaminase gene (DCD1) of Saccharomyces cerevisiae has been isolated by screening a Sau3A clone bank for complementation of the dUMP auxotrophy exhibited by dcd1 dmp1 haploids. Plasmid pDC3, containing a 7-kilobase (kb) Sau3A insert, restores dCMP deaminase activity to dcd1 mutants and leads to an average 17.5-fold overproduction of the enzyme in wild-type cells. The complementing activity of the plasmid was localized to a 4.2-kb PvuII restriction fragment within the Sau3A insert. Subcloning experiments demonstrated that a single HindIII restriction site within this fragment lies within the DCD1 gene. Subsequent DNA sequence analysis revealed a 936-nucleotide open reading frame encompassing this HindIII site. Disruption of the open reading frame by integrative transformation led to a loss of enzyme activity and confirmed that this region constitutes the dCMP deaminase gene. Northern analysis indicated that the DCD1 mRNA is a 1.15-kb poly(A)+ transcript. The 5' end of the transcript was mapped by primer extension and appears to exhibit heterogeneous termini. Comparison of the amino acid sequence of the T2 bacteriophage dCMP deaminase with that deduced for the yeast enzyme revealed a limited degree of homology which extends over the entire length of the phage polypeptide (188 amino acids) but is confined to the carboxy-terminal half of the yeast protein (312 amino acids). A potential dTTP-binding site in the yeast and phage enzymes was identified by comparison of homologous regions with the amino acid sequences of a variety of other dTTP-binding enzymes. Despite the role of dCMP deaminase in dTTP biosynthesis, Northern analysis revealed that the DCD1 gene is not subject to the same cell cycle-dependent pattern of transcription recently found for the yeast thymidylate synthetase gene (TMP1).

scholarly journals Cloning, Nucleotide Sequence, and Expression of the Gene Encoding the Bacteriocin Boticin B from Clostridium botulinum Strain 213B

2000 ◽  
Vol 66 (12) ◽  
pp. 5480-5483 ◽  
Author(s):  
Sean S. Dineen ◽  
Marite Bradshaw ◽  
Eric A. Johnson
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Clostridium Botulinum ◽  
Shuttle Vector ◽  
Open Reading Frame ◽  
Gene Encoding ◽  
Reading Frame ◽  
Heat Stable ◽  
Group I

ABSTRACT Boticin B is a heat-stable bacteriocin produced byClostridium botulinum strain 213B that has inhibitory activity against various strains of C. botulinum and related clostridia. The gene encoding the bacteriocin was localized to a 3.0-kb HindIII fragment of an 18.8-kb plasmid, cloned, and sequenced. DNA sequencing revealed the boticin B structural gene,btcB, to be an open reading frame encoding 50 amino acids. A C. botulinum strain 62A transconjugant containing theHindIII fragment inserted into a clostridial shuttle vector expressed boticin B, although at much lower levels than those observed in C. botulinum 213B. To our knowledge, this is the first demonstration and characterization of a bacteriocin from toxigenic group I C. botulinum.

scholarly journals The Wuhan Pneumonia Outbreak: High Isoleucine and High Valine Plus Glycine Contents Are Features of the Proteins of 2019-nCoV Virus

2020 ◽  
Author(s):  
Sirui Yan ◽  
Yulin Wan ◽  
Ying Zhang ◽  
Shanshan An ◽  
Kaiqiao Yang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Animal Studies ◽  
Viral Infections ◽  
Underlying Mechanism ◽  
Essential Amino Acids ◽  
Global Scale ◽  
Open Reading Frame ◽  
Cell Swelling ◽  
Reading Frame ◽  
Short Period

The current pneumonia epidemic in China could evolve into a pandemic on a global scale if not effectively contained. The 2019-nCoV possesses a 61-amino acid open reading frame resembling SARS-CoV virulence factor - ORF6 peptide. The isoleucine content is 15.9% in ORF6 of SARS-CoV versus 16.4% of that in 2019-nCoV. Given the proton affinity in the carbonyl oxygen in isoleucine, augmented proton traffic can enhance proton-ion antiport and prompt cell swelling. As the content of essential amino acids in the open reading frame of 2019-nCoV reaches 57.4%, a starch/vitamin diet served for short period of time does not give rise to essential amino acids and halts virion production, which could be adopted as prophylactic approach of many viral infections. Plant-based diet or fasting/boiled rice water can also minimize the intake of essential amino acids or all amino acids respectively. Calorie restriction has been confirmed in animal studies to extend lifespan, and its underlying mechanism is not fully known. Furthermore, several proteins of 2019-nCoV possess high valine plus glycine content, which is implicated in heart disease.

Pax-6, a murine paired box gene, is expressed in the developing CNS

Development ◽  
1991 ◽  
Vol 113 (4) ◽  
pp. 1435-1449 ◽  
Author(s):  
C. Walther ◽  
P. Gruss
Keyword(s):  
Amino Acids ◽  
Neural Tube ◽  
Multigene Family ◽  
Ventricular Zone ◽  
Open Reading Frame ◽  
Cdna Clones ◽  
Coding Region ◽  
Paired Domain ◽  
Reading Frame ◽  
Pax Genes

A multigene family of paired-box-containing genes (Pax genes) has been identified in the mouse. In this report, we describe the expression pattern of Pax-6 during embryogenesis and the isolation of cDNA clones spanning the entire coding region. The Pax-6 protein consists of 422 amino acids as deduced from the longest open reading frame and contains, in addition to the paired domain, a paired-type homeodomain. Beginning with day 8 of gestation, Pax-6 is expressed in discrete regions of the forebrain and the hindbrain. In the neural tube, expression is mainly confined to mitotic active cells in the ventral ventricular zone along the entire anteroposterior axis starting at day 8.5 of development. Pax-6 is also expressed in the developing eye, the pituitary and the nasal epithelium.

scholarly journals Genomic Characterization of an Echovirus 7 Isolate of Southeast Asian Ancestry Recovered from a Child in Nigeria with Acute Flaccid Paralysis

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
T. O. C. Faleye ◽  
O. M. Adewumi ◽  
J. A. Adeniji
Keyword(s):  
Amino Acids ◽  
Acute Flaccid Paralysis ◽  
Southeast Asian ◽  
Open Reading Frame ◽  
Flaccid Paralysis ◽  
Reading Frame ◽  
Asian Ancestry ◽  
Genomic Characterization

Here, we describe the genome of an echovirus 7 (E7) isolate of Southeast Asian ancestry recovered from a child in Nigeria with acute flaccid paralysis (AFP). The genome has 7,295 nucleotides (nt) and an open reading frame (ORF) with 2,195 amino acids.

DNA vaccination of pigs with open reading frame 1–7 of PRRS virus

Vaccine ◽  
2004 ◽  
Vol 22 (27-28) ◽  
pp. 3628-3641 ◽  
Author(s):  
Annette Malene Barfoed ◽  
Merete Blixenkrone-Møller ◽  
Merethe Holm Jensen ◽  
Anette Bøtner ◽  
Søren Kamstrup
Keyword(s):  
Dna Vaccination ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Prrs Virus ◽  
Open Reading Frame 1

Mutagenesis of hexon “FX” hepatic tropism

Blood ◽  
2009 ◽  
Vol 114 (5) ◽  
pp. 929-930 ◽  
Author(s):  
Eric J. Kremer
Keyword(s):  
Amino Acids ◽  
Gene Transfer ◽  
Capsid Protein ◽  
Major Capsid Protein ◽  
Coagulation Factor ◽  
Factor X ◽  
Hypervariable Regions

In this issue of Blood, Alba and colleagues identify key amino acids in adenovirus hexon hypervariable regions that interact with coagulation factor X. By mutating these residues on the adenovirus's major capsid protein in Ad-based vectors, the authors succeed in retargeting gene transfer away from hepatocytes. The advances achieved in this study may create a vector platform that can be used to develop Ad-based therapeutics for nonliver-targeted diseases.

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