The in Silicon Cloning ILF2 Gene and Prediction of ILF2 Protein Structure in Sheep

2011 ◽  
Vol 345 ◽  
pp. 423-428
Author(s):  
Ying Ning Sun ◽  
Yu Zhao ◽  
Wei Yu Wang
Keyword(s):  
Amino Acids ◽  
Gene Sequence ◽  
Rna Binding ◽  
Binding Domain ◽  
Nucleic Acid Binding ◽  
Zebra Fish ◽  
Probe Sequence ◽  
Base Pairs ◽  
Reading Frame ◽  
Cloned Cdna

In silicon cloning, we obtained ILF2 gene by using human ILF2 gene sequence (NM_004515) to be probe. Sequence analysis showed that the in silicon cloned cDNA was 1662 base pairs long with an open reading frame (ORF) containing 1173 nucleotides encoding a protein of 390 amino acids. 5’-untranslated region (UTR) was 74 bp, and 3’-UTR was 413 bp. A comparison of the sheep ILF2 with cow, horse, human, mouse, xenopus and zebra fish ILF2 amino acids had 96%, 91%, 91%, 81%, 61%, and 54% identity. The PI was 5.19, and molecular weight of the deduced protein was 43 050.12 Da. The pig ILF2 contained a RGG-rich single-stranded RNA-binding domain and a DZF zinc-finger nucleic acid binding domain. This study laid a foundation for further analysis of structure, expression and regulation of ILF2 gene in sheep.

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.

scholarly journals Mapping the RNA-binding domain on the Apple chlorotic leaf spot virus movement protein

2005 ◽  
Vol 86 (1) ◽  
pp. 225-229 ◽  
Author(s):  
Masamichi Isogai ◽  
Nobuyuki Yoshikawa
Keyword(s):  
Leaf Spot ◽  
Rna Binding ◽  
Movement Protein ◽  
Binding Domain ◽  
Sequence Specificity ◽  
Nucleic Acid Binding ◽  
Spot Virus ◽  
Uv Crosslinking ◽  
Chlorotic Leaf ◽  
Rna Binding Domain

The RNA-binding properties of the cell-to-cell movement protein (MP) of Apple chlorotic leaf spot virus were analysed. MP was expressed in Escherichia coli and was used in UV-crosslinking analysis, using a digoxigenin–UTP-labelled RNA probe and gel-retardation analysis. The analyses demonstrated that MP bound cooperatively to single-stranded RNA (ssRNA). When analysed for NaCl dependence of the RNA-binding activity, the majority of the MP could bind ssRNA even in binding buffer with 1 M NaCl. Furthermore, competition binding experiments showed that the MP bound preferentially to ssRNA and single-stranded DNA without sequence specificity. MP deletion mutants were used to identify the RNA-binding domain by UV-crosslinking analysis. Amino acid residues 82–126 and 127–287 potentially contain two independently active, single-stranded nucleic acid-binding domains.

Three new components contained in the vitelline coat of Tegula pfeifferi

Zygote ◽  
1999 ◽  
Vol 8 (S1) ◽  
pp. S61-S61 ◽  
Author(s):  
Kazu Haino-Fukushima ◽  
Xuxi Fan ◽  
Shouka Nakamura
Keyword(s):  
Amino Acids ◽  
Polyacrylamide Gel Electrophoresis ◽  
Enzymatic Reaction ◽  
Base Pairs ◽  
Sulphated Polysaccharides ◽  
Reading Frame ◽  
Glycosylation Sites ◽  
Long Time ◽  
Protein Components ◽  
Vitelline Coat

The vitelline coat (VC) lysin of Tegula, a marine molluscan genus, is released from the acrosome of sperm during fertilisation and can lyse the VC of only the same species. The lytic action of this lysin against the VC is not an enzymatic reaction, but a stoichiometric and irreversible one (Haino-Fukushima, 1974).The VC of Tegula pfeifferi consists of glycoproteins containing sulphated polysaccharides, which account for roughly two-thirds of the entire weight of the VC. The presence of a large quantity of polysaccharides in the VC had prevented rapid progress in the analysis of its protein components. Last year, we succeeded in a complete solubilisation of the VC by boiling for a long time in 1% SDS solution, and determined the cDNA sequence coding for a mature 41 kDa glycoprotein, which appears to be the major component of the VC from the results of SDS-polyacrylamide gel electrophoresis (PAGE). The cDNA, referred to as vcp41, comprises 1072 base pairs and contains one open reading frame with a sequence for 319 amino acids containing 19 amino acids of a signal peptide. The deduced amino acid sequence has five N-glycosylation sites and ten cysteine residues. It seems that almost 7 kDa in this 41kDa glycoprotein is polysaccharide constituents (Fan & Haino-Fukushima, 1998).

scholarly journals Identification of the RNA-Binding, Dimerization, and eIF4GI-Binding Domains of Rotavirus Nonstructural Protein NSP3

1999 ◽  
Vol 73 (7) ◽  
pp. 5411-5421 ◽  
Author(s):  
Maria Piron ◽  
Thierry Delaunay ◽  
Jeanne Grosclaude ◽  
Didier Poncet
Keyword(s):  
Amino Acids ◽  
Hybrid System ◽  
Rna Binding ◽  
Nonstructural Protein ◽  
Binding Domain ◽  
Initiation Factor ◽  
Yeast Two Hybrid ◽  
Dimerization Domain ◽  
Yeast Two Hybrid System ◽  
Two Hybrid

ABSTRACT The rotavirus nonstructural protein NSP3 is a sequence-specific RNA binding protein that binds the nonpolyadenylated 3′ end of the rotavirus mRNAs. NSP3 also interacts with the translation initiation factor eIF4GI and competes with the poly(A) binding protein. Deletion mutations and point mutations of NSP3 from group A rotavirus (NSP3A), expressed in Escherichia coli, indicate that the RNA binding domain lies between amino acids 4 and 149. Similar results were obtained with NSP3 from group C rotaviruses. Data also indicate that a dimer of NSP3A binds one molecule of RNA and that dimerization is necessary for strong RNA binding. The dimerization domain of NSP3 was mapped between amino acids 150 and 206 by using the yeast two-hybrid system. The eukaryotic initiation factor 4 GI subunit (eIF-4GI) binding domain of NSP3A has been mapped in the last 107 amino acids of its C terminus by using a pulldown assay and the yeast two-hybrid system. NSP3 is composed of two functional domains separated by a dimerization domain.

scholarly journals The 54-kD protein of signal recognition particle contains a methionine-rich RNA binding domain.

1990 ◽  
Vol 111 (5) ◽  
pp. 1793-1802 ◽  
Author(s):  
K Römisch ◽  
J Webb ◽  
K Lingelbach ◽  
H Gausepohl ◽  
B Dobberstein
Keyword(s):  
Amino Acids ◽  
Rna Binding ◽  
Signal Sequence ◽  
Signal Recognition Particle ◽  
Binding Domain ◽  
Secretory Proteins ◽  
Signal Recognition ◽  
Rna Binding Domain ◽  
Necessary And Sufficient

Signal recognition particle (SRP) plays the key role in targeting secretory proteins to the membrane of the endoplasmic reticulum (Walter, P., and V. R. Lingappa. 1986. Annu. Rev. Cell Biol. 2:499-516). It consists of SRP7S RNA and six proteins. The 54-kD protein of SRP (SRP54) recognizes the signal sequence of nascent polypeptides. The 19-kD protein of SRP (SRP19) binds to SRP7S RNA directly and is required for the binding of SRP54 to the particle. We used deletion mutants of SRP19 and SRP54 and an in vitro assembly assay in the presence of SRP7S RNA to define the regions in both proteins which are required to form a ribonucleoprotein particle. Deletion of the 21 COOH-terminal amino acids of SRP19 does not interfere with its binding to SRP7S RNA. Further deletions abolish SRP19 binding to SRP7S RNA. The COOH-terminal 207 amino acids of SRP54 (M domain) were found to be necessary and sufficient for binding to the SRP19/7S RNA complex in vitro. Limited protease digestion of purified SRP confirmed our results for SRP54 from the in vitro binding assay. The SRP54M domain could also bind to Escherichia coli 4.5S RNA that is homologous to part of SRP7S RNA. We suggest that the methionine-rich COOH terminus of SRP54 is a RNA binding domain and that SRP19 serves to establish a binding site for SRP54 on the SRP7S RNA.

scholarly journals Bamboo Mosaic Potexvirus Satellite RNA (satBaMV RNA)-Encoded P20 Protein Preferentially Binds to satBaMV RNA

1999 ◽  
Vol 73 (4) ◽  
pp. 3032-3039 ◽  
Author(s):  
Ming-Shiun Tsai ◽  
Yau-Heiu Hsu ◽  
Na-Sheng Lin
Keyword(s):  
Nucleic Acids ◽  
Protein Interactions ◽  
Rna Binding ◽  
Nonstructural Protein ◽  
Deletion Analysis ◽  
Nucleic Acid Binding ◽  
Satellite Rna ◽  
Reading Frame ◽  
C Terminus ◽  
Arginine Rich Motif

ABSTRACT A satellite RNA of 836 nucleotides [excluding the poly(A) tail] depends on the bamboo mosaic potexvirus (BaMV) for its replication and encapsidation. The BaMV satellite RNA (satBaMV) contains a single open reading frame encoding a 20-kDa nonstructural protein (P20). The P20 protein with eight histidine residues at the C terminus was overexpressed in Escherichia coli. Experiments of gel retardation, UV cross-linking, and Northwestern hybridization demonstrated that purified P20 was a nucleic-acid-binding protein. The binding of P20 to nucleic acids was strong and highly cooperative. P20 preferred binding to satBaMV- or BaMV-related sequences rather than to nonrelated sequences. By deletion analysis, the P20 binding sites were mainly located at the 5′ and 3′ untranslated regions of satBaMV RNA, and the RNA-protein interactions could compete with the poly(G) and, less efficiently, with the poly(U) homopolymers. The N-terminal arginine-rich motif of P20 was the RNA binding domain, as shown by in-frame deletion analysis. This is the first report that a plant virus satellite RNA-encoded nonstructural protein preferentially binds with nucleic acids.

A comparison of GABAC and ρ subunit receptors from the white perch retina

1997 ◽  
Vol 14 (5) ◽  
pp. 843-851 ◽  
Author(s):  
Aohua Qian ◽  
George Hyatt ◽  
Andres Schanzer ◽  
Rohan Hazra ◽  
Abigail S. Hackam ◽  
...  
Keyword(s):  
Amino Acids ◽  
White Perch ◽  
Partial Agonist ◽  
Reversal Potential ◽  
Open Reading Frame ◽  
Retinal Neurons ◽  
Base Pairs ◽  
Reading Frame ◽  
A Value ◽  
Gabac Receptors

AbstractThere is increasing evidence that GABAC receptors are composed of GABA ρ subunits. In this study, we compared the properties of native GABAC receptors with those of receptors composed of a GABA ρ subunit. A homologue of the GABA ρ gene was cloned from a white perch (Roccus americana) retinal cDNA library. The clone (perch-s) has an open reading frame of 1422 nucleotide base pairs and encodes a predicted protein of 473 amino acids. It is highly homologous to GABA ρ subunits cloned from human and rat retinas. The receptors (perch-s receptor) expressed by this gene in Xenopus oocytes show properties similar to those of the GABAC receptors present on white perch retinal neurons. GABA induced a sustained response that had a reversal potential of –27.1 +minus; 3.6 mV. The EC50 for the response was 1.74 +− 1.25 μM, a value similar to that reported for GABAC receptors. Pharmacologically, the responses were bicuculline insensitive and not modulated by either diazepam or pentobarbital as is the case for GABAc receptors. There were, however, some distinct differences between native GABAc and perch-s receptors. I4AA acts as a partial agonist on perch-s receptors whereas it is strictly an antagonist on native GABAC receptors. Picrotoxin inhibition is noncompetitive on perch-s receptors, but both competitive and noncompetitive on GABAC receptors. We conclude that GABAC receptors are formed by GABA p subunits but that native GABAc receptors probably consist of a mixture of GABA ρ subunits.

Sequence Analysis of the Riemerella anatipestifer OmpAMotB Gene(ORF 648bp) by Bioinformatics

2013 ◽  
Vol 647 ◽  
pp. 381-385
Author(s):  
Pan Xu ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Xiao Jia Wang
Keyword(s):  
Amino Acids ◽  
Protein Sequence ◽  
Gene Sequence ◽  
Gc Content ◽  
Gene Bank ◽  
Open Reading Frame ◽  
High Similarity ◽  
Reading Frame ◽  
Bioinformatics Software ◽  
Very High

The OmpA/MotB gene from RA by our lab was sequenced. And the molecular characteristic of this gene was analyzed with bioinformatics software. The result indicated that an open reading frame(ORF) containing 648bp nucleotides was preliminarily identified by aligning with gene bank database by software of BlastN and ORF Finder. The GC content of RA OmpA/MotB gene was 36.88% and encoded a 215 amino acids in this peptide. And from the analysis results we know that this gene sequence didn’t contain a successive at least two rare codons string. Phylogenetic tree of the amino acids sequences showed this gene has not very high similarity with the other 15 OmpA/MotB protein sequence.

Transient Structural Ordering of the RNA-Binding Domain of Carnation Mottle Virus p7 Movement Protein Modulates Nucleic Acid Binding

ChemBioChem ◽  
2005 ◽  
Vol 6 (8) ◽  
pp. 1391-1396 ◽  
Author(s):  
Marçal Vilar ◽  
Ana Saurí ◽  
Jose F. Marcos ◽  
Ismael Mingarro ◽  
Enrique Pérez-Payá
Keyword(s):  
Nucleic Acid ◽  
Rna Binding ◽  
Movement Protein ◽  
Binding Domain ◽  
Mottle Virus ◽  
Nucleic Acid Binding ◽  
Structural Ordering ◽  
Rna Binding Domain ◽  
Carnation Mottle Virus

scholarly journals Characterization and In Silico Analysis of Pregnancy-Associated Glycoprotein-1 Gene of Buffalo (Bubalus bubalis)

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Jerome A. ◽  
S. K. Singh ◽  
S. K. Agarwal ◽  
Mohini Saini ◽  
Ashwin Raut
Keyword(s):  
Amino Acids ◽  
Mammalian Species ◽  
Evolutionary Relationship ◽  
In Silico Analysis ◽  
Bubalus Bubalis ◽  
Phylogenetic Study ◽  
Base Pairs ◽  
Reading Frame ◽  
Genes Encoding ◽  
Amino Acid Signal Peptide

Pregnancy-Associated Glycoproteins (PAGs) are trophoblastic proteins belonging to the Aspartic proteinase family secreted by different placental cells of many mammalian species. They play a pivotal role in placentogenesis, foetomaternal unit remodeling, and implantation. The identification of the genes encoding those proteins will be helpful to unravel the intricate embryogenomic functions during pregnancy establishment. Considering importance of these proteins, the present study was undertaken to characterize the pregnancy associated glycoprotein-1 gene of buffalo. An 1181 base pairs buffalo Pregnancy-Associated Glycoprotein PAG-1 gene was PCR amplified from the RNA obtained from the fetal cotyledons. BLAST analysis of the buffalo PAG-1 sequence retrieved a total of 20 cattle, 5 goat, and 4 sheep PAG sequences, exhibiting more than 80% similarity. Buffalo PAG-1 gene contained an uninterrupted open reading frame of 1140 base pairs encoding 380 amino acids that possess a 15 amino acid signal peptide and mature peptide of 365 amino acids. The phylogenetic study of the buffalo PAG-1 gene revealed buffalo PAG-1 is more related to cattle, goat, and sheep PAG-1 sequences. By this study characterization of buffalo PAG-1 gene and its evolutionary relationship was deduced for the first time.

Sign in / Sign up

Export Citation Format

Share Document