The Functions of the N Terminus of the φX174 Internal Scaffolding Protein, a Protein Encoded in an Overlapping Reading Frame in a Two Scaffolding Protein System

2004 ◽  
Vol 335 (1) ◽  
pp. 383-390 ◽  
Author(s):  
Christopher R Novak ◽  
Bentley A Fane
Keyword(s):  
Protein A ◽  
Scaffolding Protein ◽  
Reading Frame ◽  
Protein System ◽  
N Terminus

scholarly journals Functionalization of Cellulose-Based Hydrogels with Bi-Functional Fusion Proteins Containing Carbohydrate-Binding Modules

Materials ◽  
2021 ◽  
Vol 14 (12) ◽  
pp. 3175
Author(s):  
Mariana Barbosa ◽  
Hélvio Simões ◽  
Duarte Miguel F. Prazeres
Keyword(s):  
Fusion Proteins ◽  
Fluorescent Protein ◽  
Protein A ◽  
Chemical Properties ◽  
Main Idea ◽  
Bioactive Molecules ◽  
Scaffolding Protein ◽  
Carbohydrate Binding ◽  
Biological Interactions ◽  
Carbohydrate Binding Modules

Materials with novel and enhanced functionalities can be obtained by modifying cellulose with a range of biomolecules. This functionalization can deliver tailored cellulose-based materials with enhanced physical and chemical properties and control of biological interactions that match specific applications. One of the foundations for the success of such biomaterials is to efficiently control the capacity to combine relevant biomolecules into cellulose materials in such a way that the desired functionality is attained. In this context, our main goal was to develop bi-functional biomolecular constructs for the precise modification of cellulose hydrogels with bioactive molecules of interest. The main idea was to use biomolecular engineering techniques to generate and purify different recombinant fusions of carbohydrate binding modules (CBMs) with significant biological entities. Specifically, CBM-based fusions were designed to enable the bridging of proteins or oligonucleotides with cellulose hydrogels. The work focused on constructs that combine a family 3 CBM derived from the cellulosomal-scaffolding protein A from Clostridium thermocellum (CBM3) with the following: (i) an N-terminal green fluorescent protein (GFP) domain (GFP-CBM3); (ii) a double Z domain that recognizes IgG antibodies; and (iii) a C-terminal cysteine (CBM3C). The ability of the CBM fusions to bind and/or anchor their counterparts onto the surface of cellulose hydrogels was evaluated with pull-down assays. Capture of GFP-CBM3 by cellulose was first demonstrated qualitatively by fluorescence microscopy. The binding of the fusion proteins, the capture of antibodies (by ZZ-CBM3), and the grafting of an oligonucleotide (to CBM3C) were successfully demonstrated. The bioactive cellulose platform described here enables the precise anchoring of different biomolecules onto cellulose hydrogels and could contribute significatively to the development of advanced medical diagnostic sensors or specialized biomaterials, among others.

scholarly journals Saccharomyces cerevisiae ubiquitin-like protein Rub1 conjugates to cullin proteins Rtt101 and Cul3 in vivo

2004 ◽  
Vol 377 (2) ◽  
pp. 459-467 ◽  
Author(s):  
Jose M. LAPLAZA ◽  
Magnolia BOSTICK ◽  
Derek T. SCHOLES ◽  
M. Joan CURCIO ◽  
Judy CALLIS
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein A ◽  
Fold Increase ◽  
Lysine Residue ◽  
Reading Frame ◽  
E3 Ligases ◽  
C Terminus ◽  
Dependent Modification ◽  
F Box Protein

In Saccharomyces cerevisiae, the ubiquitin-like protein Rub1p (related to ubiquitin 1 protein) covalently attaches to the cullin protein Cdc53p (cell division cycle 53 protein), a subunit of a class of ubiquitin E3 ligases named SCF (Skp1–Cdc53–F-box protein) complex. We identified Rtt101p (regulator of Ty transposition 101 protein, where Ty stands for transposon of yeast), initially found during a screen for proteins to confer retrotransposition suppression, and Cul3p (cullin 3 protein), a protein encoded by the previously uncharacterized open reading frame YGR003w, as two new in vivo targets for Rub1p conjugation. These proteins show significant identity with Cdc53p and, therefore, are cullin proteins. Modification of Cul3p is eliminated by deletion of the Rub1p pathway through disruption of either RUB1 or its activating enzyme ENR2/ULA1. The same disruptions in the Rub pathway decreased the percentage of total Rtt101p that is modified from approx. 60 to 30%. This suggests that Rtt101p has an additional RUB1- and ENR2-independent modification. All modified forms of Rtt101p and Cul3p were lost when a single lysine residue in a conserved region near the C-terminus was replaced by an arginine residue. These results suggest that this lysine residue is the site of Rub1p-dependent and -independent modifications in Rtt101p and of Rub1p-dependent modification in Cul3p. An rtt101Δ strain was hypersensitive to thiabendazole, isopropyl (N-3-chlorophenyl) carbamate and methyl methanesulphonate, but rub1Δ strains were not. Whereas rtt101Δ strains exhibited a 14-fold increase in Ty1 transposition, isogenic rub1Δ strains did not show statistically significant increases. Rtt101K791Rp, which cannot be modified, complemented for Rtt101p function in a transposition assay. Altogether, these results suggest that neither the RUB1-dependent nor the RUB1-independent form of Rtt101p is required for Rtt101p function. The identification of additional Rub1p targets in S. cerevisiae suggests an expanded role for Rub in this organism.

scholarly journals Chemical modifications of a recombinant bovine stress-inducible 70 kDa heat-shock protein (Hsp70) mimics Hsp70 isoforms from tissues

1995 ◽  
Vol 305 (1) ◽  
pp. 197-203 ◽  
Author(s):  
J A Gutierrez ◽  
V Guerriero
Keyword(s):  
Skeletal Muscle ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Expression System ◽  
Protein A ◽  
Two Dimensional Gel Electrophoresis ◽  
Calculated Molecular Mass ◽  
Reading Frame ◽  
Heat Shock Protein Hsp70 ◽  
Bovine Skeletal Muscle

A cDNA clone for the stress-inducible 70 kDa heat-shock protein (Hsp70) has been isolated from a bovine skeletal-muscle cDNA library. This mRNA encodes a protein with a calculated molecular mass of 70250 Da. The cDNA has one continuous open reading frame capable of encoding a 641-amino-acid protein. Expression of this cDNA in a bacterial expression system produced a protein with a mobility identical with that of the inducible Hsp70 protein from bovine skeletal muscle as determined by SDS/PAGE. Two-dimensional gel electrophoresis demonstrated this protein to have focusing properties identical with that of a minor isoform from bovine skeletal muscle. Upon carbamylation of this bacterially expressed protein, a train of charged proteins with charge differences of -1 were produced. These carbamylated proteins were shown to have similar focusing mobilities to the Hsp70 isoforms isolated from bovine skeletal muscle. These results demonstrate the identification of a skeletal-muscle inducible Hsp70 gene and suggest that the presence of multiple Hsp70 isoforms may be the product of post-translational modifications to the Hsp70 proteins.

scholarly journals Proteasome-Dependent Degradation of Daxx by the Viral E1B-55K Protein in Human Adenovirus-Infected Cells

2010 ◽  
Vol 84 (14) ◽  
pp. 7029-7038 ◽  
Author(s):  
Sabrina Schreiner ◽  
Peter Wimmer ◽  
Hüseyin Sirma ◽  
Roger D. Everett ◽  
Paola Blanchette ◽  
...  
Keyword(s):  
Viral Protein ◽  
Protein A ◽  
Human Adenovirus ◽  
Nuclear Bodies ◽  
Virus Growth ◽  
Reading Frame ◽  
Early Region ◽  
Early Protein ◽  
Antiviral Activities ◽  
Infected Cells

ABSTRACT The death-associated protein Daxx found in PML (promyelocytic leukemia protein) nuclear bodies (PML-NBs) is involved in transcriptional regulation and cellular intrinsic antiviral resistence against incoming viruses. We found that knockdown of Daxx in a nontransformed human hepatocyte cell line using RNA interference (RNAi) techniques results in significantly increased adenoviral (Ad) replication, including enhanced viral mRNA synthesis and viral protein expression. This Daxx restriction imposed upon adenovirus growth is counteracted by early protein E1B-55K (early region 1B 55-kDa protein), a multifunctional regulator of cell-cycle-independent Ad5 replication. The viral protein binds to Daxx and induces its degradation through a proteasome-dependent pathway. We show that this process is independent of Ad E4orf6 (early region 4 open reading frame 6), known to promote the proteasomal degradation of cellular p53, Mre11, DNA ligase IV, and integrin α3 in combination with E1B-55K. These results illustrate the importance of the PML-NB-associated factor Daxx in virus growth restriction and suggest that E1B-55K antagonizes innate antiviral activities of Daxx and PML-NBs to stimulate viral replication at a posttranslational level.

scholarly journals Molecular Characterization of Plasmid pBM300 from Bacillus megaterium QM B1551

2005 ◽  
Vol 71 (6) ◽  
pp. 3068-3076 ◽  
Author(s):  
Muthusamy Kunnimalaiyaan ◽  
Patricia S. Vary
Keyword(s):  
Bacillus Megaterium ◽  
Protein A ◽  
Coding Region ◽  
Rolling Circle ◽  
Rep Protein ◽  
Reading Frame ◽  
Germination Ability ◽  
Rep Proteins ◽  
A Cell ◽  
Complete Sequencing

ABSTRACT Strain QM B1551 of Bacillus megaterium contains seven compatible plasmids: two small rolling circle plasmids and five theta-replicating plasmids with cross-hybridizing replicons. To expand our understanding of these plasmids, the replicon region (6.7 kb) from pBM300 was cloned, sequenced, and functionally characterized. Sequence analysis showed that the replication protein (RepM300) was highly homologous to two other plasmid Rep proteins of the same strain but to no other known proteins. Furthermore, the location of the replication origin was within the RepM300 coding region, and the origin contained three 12-base direct repeats. Deletion analysis of the replicon confirmed the role of the Rep protein and showed that open reading frame 2 (ORF2) was required for stability. However, the protein encoded by ORF2 is entirely different from the replicon stability proteins encoded by the other two replicons. The entire plasmid was isolated from the plasmid array by integrating a spectinomycin resistance gene and transforming a plasmidless strain, PV361. Complete sequencing showed that pBM300 was 26,300 bp long, had a G+C content of 35.2%, and contained 20 ORFs, two of which encoded proteins that had no similarity to other proteins in the database. The proteins encoded by the plasmid ORFs had similarity to proteins for mobilization and transfer, an integrase, a rifampin resistance protein, a cell wall hydrolase, glutathione synthase, and a biotin carboxylase. The similarities were to several gram-positive genera and a few gram-negative genera and archaea. oriT and ssoT-like regions were detected near two mob genes. These results suggest that pBM300 is a mobilizable hybrid plasmid that confers increased metabolic and germination ability on its host. Its replicon also helps define a new plasmid family.

scholarly journals Extensive alternative splicing and dual promoter usage generate Tcf-1 protein isoforms with differential transcription control properties.

1996 ◽  
Vol 16 (3) ◽  
pp. 745-752 ◽  
Author(s):  
M Van de Wetering ◽  
J Castrop ◽  
V Korinek ◽  
H Clevers
Keyword(s):  
T Cell ◽  
Pcr Amplification ◽  
Cell Receptor ◽  
Protein Isoforms ◽  
Striking Similarity ◽  
Cdna Clones ◽  
Transcription Control ◽  
Reading Frame ◽  
N Terminus

Previously, we reported the isolation of cDNA clones representing four alternative splice forms of TCF-1, a T-cell-specific transcription factor. In the present study, Western blotting (immunoblotting) yielded a multitude of TCF-1 proteins ranging from 25-55 kDa, a pattern not simply explained from the known splice alternatives. Subsequent cDNA cloning, PCR amplification, and analysis by rapid amplification of 5' cDNA ends revealed (i) the presence of an alternative upstream promoter, which extended the known N terminus by 116 amino acids, (ii) the presence of four alternative exons, and (iii) the existence of a second reading frame in the last exon encoding an extended C terminus. Inclusion of the extended N terminus into the originally reported protein resulted in a striking similarity to the lymphoid factor Lef-1. Several of the TCF-1 isoforms, although less potent, mimicked Lef-1 in transactivating transcription through the T-cell receptor alpha-chain (TCR-alpha) enhancer. These data provide a molecular basis for the complexity of the expressed TCF-1 proteins and establish the existence of functional differences between these isoforms. Furthermore, the functional redundancy between Tcf-1 and Lef-1 explains the apparently normal TCR-alpha expression in single Tcf-1 or Lef-1 knockout mice despite the firm in vitro evidence for the importance of the Tcf/Lef site in the TCR-alpha enhancer.

scholarly journals Study of the Myb-factor polymorphism based on comparative genomics of vegetable Solanaceae crops (tomato, pepper, eggplant) to search for DNA markers that differentiate samples by the anthocyans accumulation

2020 ◽  
Vol 63 (6) ◽  
pp. 721-729
Author(s):  
O. G. Babak ◽  
N. A. Nekrashevich ◽  
T. V. Nikitinskaya ◽  
K. K. Yatsevich ◽  
A. V. Kilchevsky
Keyword(s):  
Protein A ◽  
Close Correlation ◽  
Anthocyanin Synthesis ◽  
Allelic Polymorphism ◽  
Biotic And Abiotic Stress ◽  
Caps Marker ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Mrna Maturation ◽  
New Varieties

Anthocyanins are high-value plant antioxidants; they also determine biotic and abiotic stress resistance. The aim of our research was to study the allelic polymorphism of Antocyanin 1 orthologs in the vegetable Solanaceae crops of C. annuum and S. melongena. The search revealed the following closest genes in C. annuum: Myb113-like1 TF and Myb113like2 transcription factors and Myb1 in S. melongena. Exon amplicons of those genes were obtained and then sequenced in the pepper and eggplant samples with contrasting anthocyanin fruit coloration. Primers to the identified polymorphisms were developed and their correlation with the anthocyanin accumulation in fruits was studied. A close correlation was found between a minimum accumulation or the complete absence of anthocyanin synthesis in fruits with a single nucleotide deletion (Myb113-like1), and in the pepper samples, 2 SNP (Myb113-like2) was detected using the CAPS marker Myb 113-AccI. In the eggplant samples, the deletions of 6 and 26 bp were detected using the SCAR marker MybMel and the CAPS marker MybmelPst1. The disturbance of anthocyanin synthesis in pepper forms with 1Indel in Myb113-like1 TF was determined by a shift in the reading frame and SNPs in Myb113-like2 TF lead to amino acid substitutions: Lys → Arg and Thr → Lys. In the eggplant, a deletion of 6 bp leads to the loss of ala and arg in the protein; a deletion of 26 bp causes disorder during the mRNA maturation. The developed markers allow identifying the Myb-like TF alleles under study, resulting in anthocyanin synthesis disturbance in fruits. C. annuum and S. melongena samples with different alleles were selected for a further study and new varieties in agriculture. 

Evolutionarily conserved regions in Caenorhabditis transposable elements deduced by sequence comparison

Genome ◽  
1991 ◽  
Vol 34 (1) ◽  
pp. 6-12 ◽  
Author(s):  
Shiv S. Prasad ◽  
Linda J. Harris ◽  
David L. Baillie ◽  
Ann M. Rose
Keyword(s):  
Amino Acid ◽  
Transposable Element ◽  
Sequence Comparison ◽  
Horizontal Transmission ◽  
Protein A ◽  
Open Reading Frame ◽  
Single Open Reading Frame ◽  
Major Open Reading Frame ◽  
Reading Frame ◽  
Caenorhabditis Species

In this paper we present the sequence of an intact Caenorhabditis briggsae transposable element, Tcb2. Tcb2 is 1606 base pairs in length and contains 80 base pair imperfect terminal repeats and a single open reading frame. We have identified blocks of T-rich repeats in the regions 150–200 and 1421–1476 of this element which are conserved in the Caenorhabditis elegans element Tc1. The sequence conservation of these regions in elements from different Caenorhabditis species suggests that they are of functional importance. A single open reading frame corresponding to the major open reading frame of Tc1 is conserved among Tc1, Tcb1, and Tcb2. Comparison of the first 550 nucleotides of the sequence among the three elements has allowed the evaluation of a model proposing an extension of the major open reading frame. Our data support the suggestion that Tc1 is capable of producing a 335 amino acid protein. A comparison of the sequence coding for the amino and carboxy termini of the 273 amino acid transposase from Caenorhabditis Tc1-like elements and Drosophila HB1 showed different amounts of divergence for each of these regions, indicating that the two functional domains have undergone different amounts of selection. Our data are not compatible with the proposal that Tc1-related sequences have been acquired via horizontal transmission. The divergence of Tc1 from the two C. briggsae elements, Tcb1 and Tcb2, indicated that all three elements have been diverging from each other for approximately the same amount of time as the genomes of the two species.Key words: Caenorhabditis, transposable element, sequence comparison.

scholarly journals The Canine Papillomavirus E5 Protein Signals from the Endoplasmic Reticulum

2009 ◽  
Vol 83 (24) ◽  
pp. 12833-12841 ◽  
Author(s):  
Rachel Condjella ◽  
Xuefeng Liu ◽  
Frank Suprynowicz ◽  
Hang Yuan ◽  
Sawali Sudarshan ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Growth Inhibition ◽  
Er Stress ◽  
Protein A ◽  
Keratinocyte Differentiation ◽  
Keratinocyte Proliferation ◽  
Reading Frame ◽  
E5 Protein

ABSTRACT The recently discovered Canis familiaris papillomavirus (PV) type 2 (CfPV2) provides a unique opportunity to study PV gene functions in vitro and in vivo. Unlike the previously characterized canine oral PV, CfPV2 contains an E5 open reading frame and is associated with progression to squamous cell carcinoma. In the current study, we have expressed and characterized the CfPV2-encoded E5 protein, a small, hydrophobic, 41-amino-acid polypeptide. We demonstrate that, similar to the E5 protein from high-risk human PV type 16, the CfPV2 E5 protein is localized in the endoplasmic reticulum (ER) and that its expression decreases keratinocyte proliferation and cell life span. E5 expression also increases the percentage of cells in the G1 phase of the cell cycle, with a concomitant decrease in the percentage of cells in S phase. To identify a potential mechanism for E5-mediated growth inhibition from the ER, we developed a real-time PCR method to quantify the splicing of XBP1 mRNA as a measure of ER stress. We found that the CfPV2 E5 protein induced ER stress and that this, as well as the observed growth inhibition, is tempered significantly by coexpression of the CfPV2 E6 and E7 genes. It is possible that the spatial/temporal regulation of E6/E7 gene expression during keratinocyte differentiation might therefore modulate E5 activity and ER stress.

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