scholarly journals Mouse aggrecan, a large cartilage proteoglycan: protein sequence, gene structure and promoter sequence

1995 ◽  
Vol 308 (2) ◽  
pp. 433-440 ◽  
Author(s):  
H Watanabe ◽  
L Gao ◽  
S Sugiyama ◽  
K Doege ◽  
K Kimata ◽  
...  
Keyword(s):  
Amino Acid ◽  
Core Protein ◽  
Chondroitin Sulphate ◽  
Promoter Sequence ◽  
Type Ii Collagen ◽  
Start Codon ◽  
Structural Domains ◽  
Exon 2 ◽  
Link Protein ◽  
Untranslated Sequence

Seven genomic clones for mouse aggrecan core protein have been isolated including 3 kb of 5′- and 7 kb of 3′-flanking sequences. All exon sequences and their intron boundary sequences in these clones were identified and mapped by DNA sequencing. The gene spans at least 61 kb and contains 18 exons. Exon 1 encodes 5′-untranslated sequence and exon 2 contains a translation start codon, methionine. The coding sequence is 6545 bp for a 2132-amino-acid protein with calculated M(r) = 259,131 including an 18-amino-acid signal peptide. There is a strong correlation between structural domains and exons. Notably, the chondroitin sulphate domain consisting of 1161 amino acids is encoded by a single exon of 3.6 kb. Although link protein has similar structural domains and subdomains, the sequence identity and the organization of exons encoding the subdomains B and B′ of G1 and G2 domains revealed a strong similarity of mouse aggrecan to both human versican and rat neurocan. Primer extension analysis identified four transcription start sites which are close together. The promoter sequence showed high G/C content (65%) and contained several consensus binding motifs for transcription factors including Sp-1 and the glucocorticoid receptor. There are stretches of sequences similar to the promoter region of both the type-II collagen and link protein genes. These sequences may be important for cartilage gene expression.

The Formation of Cartilage Extracellular Matrix

1988 ◽  
Vol 46 ◽  
pp. 230-231
Author(s):  
B.M. Vertel
Keyword(s):  
Extracellular Matrix ◽  
Hyaline Cartilage ◽  
Core Protein ◽  
Type Ii Collagen ◽  
Type Ii ◽  
Structural Components ◽  
Normal Cartilage ◽  
Link Protein ◽  
Cartilage Extracellular Matrix ◽  
Compression Type

Normal cartilage function is dependent upon the unique structural properties of the extensive extracellular matrix (ECM). In final assembled form, the ECM of hyaline cartilage is composed of abundant amounts of proteoglycan (PG) and type II collagen. Additional collagens and glycoproteins may be important structural components as well. Through their concentration of negative charges, PGs confer upon the cartilage ECM the ability to retain high levels of hydration and thereby resist compression. Type II collagen fibers contribute to the tensile strength of cartilage.In the cartilage ECM, PG monomers associate with hyaluronic acid and link protein to form large aggregates. In turn, PG aggregates are associated with the fibrous meshwork of type II collagen. Interactions with other ECM molecules may occur as well. The cartilage matrix constituents are themselves large and complex. For example, the PG monomer is 1-5 x 106 daltons in size and contains a core protein of Mr >300K (comprising only 8-10% of the complete monomer).

scholarly journals Metalloproteinase digestion of cartilage proteoglycan. Pattern of cleavage by stromelysin and susceptibility to collagenase

1991 ◽  
Vol 279 (3) ◽  
pp. 733-739 ◽  
Author(s):  
C Hughes ◽  
G Murphy ◽  
T E Hardingham
Keyword(s):  
Core Protein ◽  
Chondroitin Sulphate ◽  
Relative Viscosity ◽  
Gel Chromatography ◽  
High Concentration ◽  
Link Protein ◽  
Rapid Fall ◽  
Sds Page ◽  
Proteoglycan Aggregates ◽  
Rabbit Bone

The action of purified rabbit bone stromelysin was investigated on proteoglycan aggregates from pig laryngeal cartilage. The enzyme caused a rapid fall in viscosity of proteoglycan aggregate solution (6 mg/ml), and the products of a partial digest (60% loss of relative viscosity) and a complete digest (95% loss of relative viscosity) were characterized. Analysis by gel chromatography on Sepharose 2B under associative conditions showed that 95% of the glycosaminoglycans in the complete digest were in small-sized fragments, whereas most of the hyaluronan-binding G1 domain and link protein remained intact and bound to hyaluronan. In contrast, there was extensive digestion of the G2 domain which resulted in 76% loss in its detection by immunoassay. Analysis of the partial digest also showed considerable loss (40%) of detection of the G2 domain, but the glycosaminoglycan-rich fragments were much larger than in the complete digest. There was also much less cleavage to create small fragments containing the G1 domain. This was evident on SDS/PAGE analysis where a 58 kDa G1 domain fragment was abundant in the complete digest, but was only present in small amounts in the partial digest. There was also only very limited conversion of link protein from a 44 kDa form to a 40 kDa form. The digestion of proteoglycan aggregate (6 mg/ml) by stromelysin was unaffected by the addition of a high concentration of extra chondroitin sulphate chains (14 mg/ml), and the digestion of proteoglycan monomer showed that the G1 domain was resistant to stromelysin digestion even when not bound to hyaluronan and link protein. The results show that stromelysin degrades the proteoglycan protein core with major cleavages close to, but not within, the G1 domain, and extensive cleavage in other regions. Experiments with purified collagenase, a metalloproteinase structurally related to stromelysin, showed that it too cleaved proteoglycan at several sites within the glycosaminoglycan-rich region of the core protein. Metalloproteinase attack on proteoglycan thus not only occurs with stromelysin but also with collagenase.

scholarly journals Molecular cloning and sequence analysis of the cDNA for small proteoglycan II of bovine bone

1987 ◽  
Vol 248 (3) ◽  
pp. 801-805 ◽  
Author(s):  
A A Day ◽  
C I McQuillan ◽  
J D Termine ◽  
M R Young
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue ◽  
Core Protein ◽  
Chondroitin Sulphate ◽  
Homologous Sequence ◽  
Bovine Bone ◽  
Amino Acid Homology ◽  
Core Proteins ◽  
Attachment Sites

The cDNA for the full-length core protein of the small chondroitin sulphate proteoglycan II of bovine bone was cloned and sequenced. A 1.3 kb clone (lambda Pg28) was identified by plaque hybridization with a previously isolated 1.0 kb proteoglycan cDNA clone (lambda Pg20), positively identified previously by polyclonal and monoclonal antibody reactivity and by hybrid-selected translation in vitro [Day, Ramis, Fisher, Gehron Robey, Termine & Young (1986) Nucleic Acids Res. 14, 9861-9876]. The cDNA sequences of both clones were identical in areas of overlap. The 360-amino-acid-residue protein contains a 30-residue propeptide of which the first 15 residues are highly hydrophobic. The mature protein consists of 330 amino acid residues corresponding to an Mr of 36,383. The core protein contains three potential glycosaminoglycan-attachment sites (Ser-Gly), only one of which is within a ten-amino-acid-residue homologous sequence seen at the known attachment sites of related small proteoglycans. Comparisons of the published 24-residue N-terminal protein sequence of bovine skin proteoglycan II core protein with the corresponding region in the deduced sequence of the bovine core protein reveals complete homology. Comparison of the cDNA-derived sequences of bovine bone and human embryonic fibroblast proteoglycans shows a hypervariable region near the N-terminus. Nucleotide homology between bone and fibroblast core proteins was 87% and amino acid homology was 90%.

Gene regulation during cartilage differentiation: temporal and spatial expression of link protein and cartilage matrix protein in the developing limb

Development ◽  
1989 ◽  
Vol 107 (1) ◽  
pp. 23-33
Author(s):  
N.S. Stirpe ◽  
P.F. Goetinck
Keyword(s):  
Matrix Protein ◽  
Core Protein ◽  
Type Ii Collagen ◽  
Cartilage Matrix ◽  
Type Ii ◽  
Spatial Expression ◽  
Link Protein ◽  
Genes Encoding ◽  
Temporal And Spatial ◽  
And Cartilage

The temporal and spatial expression of link protein and cartilage matrix protein genes was defined during chondrogenesis in the developing chick embryonic wing bud, using RNA in situ hybridization. For comparison, the expression of genes encoding type II collagen and cartilage proteoglycan core protein was also examined. Link protein transcripts are first detected at stage 25 of Hamburger and Hamilton, together with proteoglycan core protein transcripts. Type II collagen transcripts were first detected as early as stage 23 whereas cartilage matrix protein transcripts could not be detected before stage 26. The results of the study indicate that the temporal expression of the genes for cartilage matrix protein and type II collagen are independent of each other and also independent of that for link protein and proteoglycan core protein.

scholarly journals Genetic Organization and Mode of Action of a Novel Bacteriocin, Bacteriocin 51: Determinant of VanA-Type Vancomycin-Resistant Enterococcus faecium

2011 ◽  
Vol 55 (9) ◽  
pp. 4352-4360 ◽  
Author(s):  
Hitoshi Yamashita ◽  
Haruyoshi Tomita ◽  
Takako Inoue ◽  
Yasuyoshi Ike
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Enterococcus Faecium ◽  
Promoter Sequence ◽  
Signal Peptidase ◽  
Start Codon ◽  
Content Type ◽  
Acid Protein ◽  
Vancomycin Resistant ◽  
Amino Acid Protein

ABSTRACTBacteriocin 51 (Bac 51) is encoded on the mobile plasmid pHY (6,037 bp), which was isolated from vancomycin-resistantEnterococcus faeciumVRE38. Bacteriocin 51 is active againstE. faecium,E. hirae, andE. durans. Sequence analysis of pHY showed that it encodes nine open reading frames (ORFs) from ORF1 to ORF9 (in that order). Genetic analysis suggested that ORF1 and ORF2, which were designatedbacAandbacB, respectively, are the bacteriocin and immunity genes.bacAencodes a 144-amino-acid protein. The deduced BacA protein has a typical signal sequence at its amino terminus, and a potential signal peptidase-processing site corresponding to the V-E-A sequence is located between the 37th and 39th amino acids. The predicted mature BacA protein consists of 105 amino acids. A potential promoter sequence was identified upstream of the start codon.bacBencodes a 55-amino-acid protein. No obvious promoter or terminator sequence was identified betweenbacAandbacB. Northern blot analysis ofbacAandbacBwith abacARNA probe produced a transcript of approximately 700 nucleotides, which corresponded to the combined nucleotide sizes ofbacAandbacB, indicating that transcription was initiated from the promoter upstream ofbacA, continued throughbacB, and was terminated at the terminator downstream ofbacB. The transcription start site was determined to be the T nucleotide located 6 nucleotides downstream from the −10 promoter sequence. These results indicate thatbacAandbacBconstitute an operon and thatbacAis the bacteriocin structural gene whilebacBis the immunity gene. The purified C-terminally His tagged BacA protein of Bac 51 showed bacteriostatic activity against the indicator strain. The purified C-terminally His tagged BacA protein of Bac 32 (whose mature BacA protein has 54 amino acids) and the culture filtrates of the Bac 31- and Bac 43-producingE. faecalisstrain FA2-2 showed bactericidal activity. Bac 31 and Bac 43 are pore-forming bacteriocins, unlike the newly characterized bacteriocin Bac 51.

scholarly journals Kinetics of intracellular processing of chondroitin sulfate proteoglycan core protein and other matrix components.

1988 ◽  
Vol 106 (6) ◽  
pp. 2191-2202 ◽  
Author(s):  
S C Campbell ◽  
N B Schwartz
Keyword(s):  
Core Protein ◽  
Type Ii Collagen ◽  
Subcellular Fractionation ◽  
Type Ii ◽  
Link Protein ◽  
The Core ◽  
Intracellular Processing ◽  
Collagen Secretion ◽  
Golgi Region ◽  
Kinetics Of

Pulse-chase labeling techniques are used in conjunction with subcellular fractionation and quantitative immunoprecipitation to define the kinetics of intracellular translocation and secretion of proteoglycan core protein, along with link protein and type II collagen. In embryonic chick chondrocytes the core protein is processed very rapidly, exhibiting a t 1/2 in both the rough endoplasmic reticulum and golgi region of less than 10 min. Link protein appears to be processed as rapidly as the core protein, but the kinetics of type II collagen secretion is 3-4 times slower. These results are consistent with possible segregation and coordinate intracellular processing of link protein and core protein, macromolecules which are known to associate extracellularly. In contrast, rat chondrosarcoma chondrocytes translocated and secreted the core protein much more slowly (t 1/2 = 40 min) than the chick cells, perhaps due to the significantly reduced levels of galactosyltransferase I observed in the transformed chondrocytes.

Healing of Circular Defects in the Rabbit Medial Meniscus Can Occur Spontaneously and Is not Improved by Intra-Articular Hyaluronic Acid

1996 ◽  
Vol 09 (02) ◽  
pp. 60-5 ◽  
Author(s):  
N. Hope ◽  
P. Ghosh ◽  
S. Collier
Keyword(s):  
Hyaluronic Acid ◽  
Medial Meniscus ◽  
Chondroitin Sulphate ◽  
Rabbit Model ◽  
Type Ii Collagen ◽  
Type Ii ◽  
Keratan Sulphate ◽  
Meniscal Healing ◽  
Meniscus Healing ◽  
Made In

SummaryThe aim of this study was to determine the effects of intra-articular hyaluronic acid on meniscal healing. Circular defects, 1.0 mm in diameter, were made in the anterior third of the medial meniscus in rabbits. In one joint, 0.4 ml hyaluronic acid (Healon®) was instilled, and in the contralateral (control) joint, 0.4 ml Ringer’s saline. Four rabbits were killed after four, eight and 12 weeks and the menisci examined histologically. By eight weeks most of the lesions had healed by filling with hyaline-like cartilage. Healing was not improved by hyaluronic acid treatment. The repair tissue stained strongly with alcian blue, and the presence of type II collagen, keratan sulphate, and chondroitin sulphate was demonstrated by immunohistochemical localisation. In contrast to the circular defects, longitudinal incisions made in the medial menisci of a further six rabbits did not show any healing after 12 weeks, indicating that the shape of the lesion largely determined the potential for healing.The effect of hyaluronic acid on meniscal healing was tested in a rabbit model. With one millimeter circular lesions in the medial meniscus, healing by filling with hyalinelike cartilage was not significantly affected by the application of hyaluronic acid intra-articularly at the time of surgery, compared to saline controls, as assessed histologically four, eight and 12 weeks after the operation.

scholarly journals A Single Point Mutation, Asn16→Lys, Dictates the Temperature-Sensitivity of the Reovirus tsG453 Mutant

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 289
Author(s):  
Kathleen K. M. Glover ◽  
Danica M. Sutherland ◽  
Terence S. Dermody ◽  
Kevin M. Coombs
Keyword(s):  
Amino Acid ◽  
Temperature Sensitivity ◽  
Reverse Genetics ◽  
Core Protein ◽  
Single Point ◽  
Single Amino Acid ◽  
Single Point Mutation ◽  
Temperature Sensitive ◽  
Amino Acid Substitutions ◽  
Gene Encoding

Studies of conditionally lethal mutants can help delineate the structure-function relationships of biomolecules. Temperature-sensitive (ts) mammalian reovirus (MRV) mutants were isolated and characterized many years ago. Two of the most well-defined MRV ts mutants are tsC447, which contains mutations in the S2 gene encoding viral core protein σ2, and tsG453, which contains mutations in the S4 gene encoding major outer-capsid protein σ3. Because many MRV ts mutants, including both tsC447 and tsG453, encode multiple amino acid substitutions, the specific amino acid substitutions responsible for the ts phenotype are unknown. We used reverse genetics to recover recombinant reoviruses containing the single amino acid polymorphisms present in ts mutants tsC447 and tsG453 and assessed the recombinant viruses for temperature-sensitivity by efficiency-of-plating assays. Of the three amino acid substitutions in the tsG453 S4 gene, Asn16-Lys was solely responsible for the tsG453ts phenotype. Additionally, the mutant tsC447 Ala188-Val mutation did not induce a temperature-sensitive phenotype. This study is the first to employ reverse genetics to identify the dominant amino acid substitutions responsible for the tsC447 and tsG453 mutations and relate these substitutions to respective phenotypes. Further studies of other MRV ts mutants are warranted to define the sequence polymorphisms responsible for temperature sensitivity.

scholarly journals Plasmodium vivax Cysteine-Rich Protective Antigen Polymorphism at Exon-1 Shows Recombination and Signatures of Balancing Selection

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 29
Author(s):  
Lilia González-Cerón ◽  
José Cebrián-Carmona ◽  
Concepción M. Mesa-Valle ◽  
Federico García-Maroto ◽  
Frida Santillán-Valenzuela ◽  
...  
Keyword(s):  
Amino Acid ◽  
B Cell ◽  
Plasmodium Vivax ◽  
Nucleotide Diversity ◽  
Protective Antigen ◽  
Balancing Selection ◽  
Southern Mexico ◽  
Exon 2 ◽  
Exon 1 ◽  
Tajima’S D

Plasmodium vivax Cysteine-Rich Protective Antigen (CyRPA) is a merozoite protein participating in the parasite invasion of human reticulocytes. During natural P. vivax infection, antibody responses against PvCyRPA have been detected. In children, low anti-CyRPA antibody titers correlated with clinical protection, which suggests this protein as a potential vaccine candidate. This work analyzed the genetic and amino acid diversity of pvcyrpa in Mexican and global parasites. Consensus coding sequences of pvcyrpa were obtained from seven isolates. Other sequences were extracted from a repository. Maximum likelihood phylogenetic trees, genetic diversity parameters, linkage disequilibrium (LD), and neutrality tests were analyzed, and the potential amino acid polymorphism participation in B-cell epitopes was investigated. In 22 sequences from Southern Mexico, two synonymous and 21 nonsynonymous mutations defined nine private haplotypes. These parasites had the highest LD-R2 index and the lowest nucleotide diversity compared to isolates from South America or Asia. The nucleotide diversity and Tajima’s D values varied across the coding gene. The exon-1 sequence had greater diversity and Rm values than those of exon-2. Exon-1 had significant positive values for Tajima’s D, β-α values, and for the Z (HA: dN > dS) and MK tests. These patterns were similar for parasites of different origin. The polymorphic amino acid residues at PvCyRPA resembled the conformational B-cell peptides reported in PfCyRPA. Diversity at pvcyrpa exon-1 is caused by mutation and recombination. This seems to be maintained by balancing selection, likely due to selective immune pressure, all of which merit further study.

Likelihood Models of Somatic Mutation and Codon Substitution in Cancer Genes

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 695-705 ◽  
Author(s):  
Ziheng Yang ◽  
Simon Ro ◽  
Bruce Rannala
Keyword(s):  
Amino Acid ◽  
Gene Mutation ◽  
Somatic Mutation ◽  
Mutation Rates ◽  
Functional Domains ◽  
Cancer Gene ◽  
Structural Domains ◽  
Specific Amino Acid ◽  
Silent Substitution ◽  
Codon Substitution

Abstract The role of somatic mutation in cancer is well established and several genes have been identified that are frequent targets. This has enabled large-scale screening studies of the spectrum of somatic mutations in cancers of particular organs. Cancer gene mutation databases compile the results of many studies and can provide insight into the importance of specific amino acid sequences and functional domains in cancer, as well as elucidate aspects of the mutation process. Past studies of the spectrum of cancer mutations (in particular genes) have examined overall frequencies of mutation (at specific nucleotides) and of missense, nonsense, and silent substitution (at specific codons) both in the sequence as a whole and in a specific functional domain. Existing methods ignore features of the genetic code that allow some codons to mutate to missense, or stop, codons more readily than others (i.e., by one nucleotide change, vs. two or three). A new codon-based method to estimate the relative rate of substitution (fixation of a somatic mutation in a cancer cell lineage) of nonsense vs. missense mutations in different functional domains and in different tumor tissues is presented. Models that account for several potential influences on rates of somatic mutation and substitution in cancer progenitor cells and allow biases of mutation rates for particular dinucleotide sequences (CGs and dipyrimidines), transition vs. transversion bias, and variable rates of silent substitution across functional domains (useful in detecting investigator sampling bias) are considered. Likelihood-ratio tests are used to choose among models, using cancer gene mutation data. The method is applied to analyze published data on the spectrum of p53 mutations in cancers. A novel finding is that the ratio of the probability of nonsense to missense substitution is much lower in the DNA-binding and transactivation domains (ratios near 1) than in structural domains such as the linker, tetramerization (oligomerization), and proline-rich domains (ratios exceeding 100 in some tissues), implying that the specific amino acid sequence may be less critical in structural domains (e.g., amino acid changes less often lead to cancer). The transition vs. transversion bias and effect of CpG dinucleotides on mutation rates in p53 varied greatly across cancers of different organs, likely reflecting effects of different endogenous and exogenous factors influencing mutation in specific organs.

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