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PubMed2004

Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome.

The complete nucleotide sequence of the chloroplast genome of sugarcane (Saccharum officinarum) was determined. It consists of 141,182 base-pairs (bp), containing a pair of inverted repeat regions (IR(A), IR(B)) of 22,794 bp each. The IR(A) and IR(B) sequences separate a small single copy region (12,546 bp) and a large single copy (83,048 bp) region. The gene content and relative arrangement of the 116 identified genes (82 peptide-encoding genes, four ribosomal RNA genes, 30 tRNA genes), with the 16 ycf genes, are highly similar to maize. Editing events, defined as C-to-U transitions in the mRNA sequences, were comparable with those observed in maize, rice and wheat. The conservation of gene organization and mRNA editing suggests a common ancestor for the sugarcane and maize plastomes. These data provide the basis for functional analysis of plastid genes and plastid metabolism within the Poaceae. The sugarcane chloroplast DNA sequence is available at GenBank under accession NC005878.

Base Sequence↗
PubMedDate not supplied

Structural features of epithelial remodeling in usual interstitial pneumonia histologic pattern.

Epithelial remodeling probably contributes to parenchymal deterioration in usual interstitial pneumonia/idiopathic pulmonary fibrosis (UIP/IPF), but understanding its mechanisms is still a challenge. The aim of our study was to examine apoptosis and the epithelial changes in the histologic pattern of UIP. After immunohistochemical staining we quantified the content of type I cells, type II cells, surfactant-A protein, bcl-2, and Fas-ligand (Fas-L) in control and alveolar collapse, fibroblastic foci, and honeycomb in UIP areas of 23 open lung biopsies. A significant association was found between epithelial changes and parenchymal deterioration (p < 0.05). Type I epithelial cell density was similar between control (1.7 +/- 0.7%) and UIP alveolar collapse areas (1.8 +/- 0.6%) but decreased progressively in fibroblastic foci zones (0.8 +/- 0.4%) and honeycomb changes (0.4 +/- 0.3%). Type II cell density increased from control (25.6 +/- 8.3%) to areas of alveolar collapse (34.5 +/- 11.4%), then decreased toward fibroblastic foci (15.4 +/- 6.0%) and honeycomb change areas (23.1 +/- 8.6%). The surfactant-A protein increased from control (6.7 +/- 3.2%) to areas of alveolar collapse (31.1 +/- 9.5%) and decreased toward fibroblastic foci (14.5 +/- 4.9%) and honeycomb change areas (21.1 +/- 8.9%). Fas-L positive epithelial cell density presented a progressive decline from control (48.5 +/- 9.5%), alveolar collapse (37.9 +/- 12.4%), fibroblastic foci (27.4 +/- 6.8%), and honeycomb change areas (21.9 +/- 6.5%). A similar decline in density was found for bcl-2 positive epithelial cells from control (20.4 +/- 2.7%), alveolar collapse (18.9 +/- 5.1%), and fibroblastic foci areas (13.8 +/-2.9%), then increased honeycomb change areas (16.3 +/- 2.8%). We conclude that loss of the nuclear (bcl-2) and membrane (Fas-L) regulation of normal cell population density and suppression of cell death by apoptosis in UIP may be a determinant of the abnormal epithelial/parenchymal remodeling in UIP.

Aged↗
PubMed2002

Structural features and expression analysis of a linear mitochondrial plasmid in rapeseed (Brassica napus L.).

A linear plasmid molecule about 11 kb in length is present in the mitochondria of some varieties of rapeseed (Brassica napus L.). This plasmid can be inherited from the male parent, through the pollen, as well as by the usual maternal route, although the main mitochondrial genome is maternally inherited in rapeseed. We determined the complete nucleotide sequence of this plasmid DNA and clarified its genetic organization. The length of the linear plasmid is 11,640 bp. At the termini of the plasmid molecule are inverted repeats of 327 bp. The GC content of the plasmid DNA is 30.9%; thus, the plasmid is quite AT-rich compared to the main mitochondrial genome in higher plants. The plasmid has six ORFs, two of which encode a phage-type DNA polymerase and a phage-type RNA polymerase, respectively. RT-PCR analyses revealed that all six ORFs are transcribed, and all four ORFs on the minus strand are probably cotranscribed from a single promoter located in the terminal inverted repeat. We also show here that at least three of the six ORFs are translated into proteins in rapeseed mitochondria, and expressed at relatively high levels in flowers, as shown by Western analysis. These results suggest that this linear DNA molecule is able to replicate as an autonomous replicon and to express the genes it carries in rapeseed mitochondria.

Amino Acid Sequence↗
PubMed2006

Structural features of transiently modified beta-lactoglobulin relevant to the stable binding of large hydrophobic molecules.

Binding sites for hydrophobic molecules on bovine beta-lactoglobulin, and their susceptibility to temperature, were studied by using various spectroscopic probes. Binding of probes carrying a single fluorophore moiety, a single nitroxide moiety, or both moieties on the same molecule, was followed by EPR and fluorescence. The presence of a fatty acid side chain in the dual probes was found to be required for binding to beta-lactoglobulin. Binding occurred only after the protein was heated at temperatures below the threshold for its irreversible denaturation. Binding became extremely tight and stable upon cooling of the protein-probe mixture. Comparison among the various probes suggests that multiple binding sites for hydrophobes are present in the native protein, and in the partially-and reversibly-modified form of beta-lactoglobulin present in solution at neutral pH and subdenaturing temperatures. Thus, the specificity of hydrophobes binding to beta-lactoglobulin may be modulated by simple physical treatment of the protein.

Animals↗
PubMed1984

Structural features and some binding properties of proteoheparan sulfate enzymatically labeled by calf brain microsomes.

Previous studies established that brain microsomes catalyze the transfer of [35S]sulfate from 3'-phosphoadenosine 5'-phospho[35S]sulfate to an O-linked oligosaccharide chain of a membrane glycoprotein and sulfamino groups of a membrane-associated proteoheparan sulfate (R. R. Miller and C. J. Waechter (1979) Arch. Biochem. Biophys. 198, 31-41). A large fraction of the proteoheparan [35S]sulfate can be released by treating the enzymatically labeled membranes from calf brain with 1 M NaCl. The salt-extracted 35S-labeled proteoglycan has been partially purified by a combination of ion-exchange and gel filtration chromatography. Based on chromatographic analyses, the 35S-labeled proteoglycan labeled in vitro is proposed to be a family of proteoheparan [35S]sulfates having an average molecular weight estimated to be 55,000. Variation in the length of the 35S-labeled polysaccharide chains partially accounts for the differences in molecular size of the proteoheparan [35S]sulfates. Binding studies reveal that the intact proteoheparan [35S]sulfates, as well as the free 35S-labeled polysaccharides released by mild alkali treatment, rapidly reassociate with calf brain membrane preparations. The association with calf brain membranes is saturable and reversible. Consistent with the binding being a specific interaction, only iduronic acid-containing glycosaminoglycans inhibit the association of the 35S-labeled proteoglycan with calf brain membranes and facilitate the disassociation. Neither the binding of the 35S-labeled proteoglycan to membranes nor the displacement was affected by hyaluronic acid, chondroitin 4-sulfate, or chondroitin 6-sulfate. The binding of the enzymatically labeled proteoheparan sulfate is reduced by preincubating membranes with either trypsin or chymotrypsin, but not with neuraminidase or phospholipase D. These results suggest that at least one class of proteoheparan sulfates could be specifically bound to one or more brain membrane proteins. The results also suggest a role for iduronosyl residues, and perhaps the stereochemical relationship of the carboxyl group to the O-sulfate moiety at C-2, in the recognition process.

Animals↗
PubMed1986

Structural features of bovine fetuin revealed from analysis of the primary translation product: anomalous behavior on sodium dodecyl sulfate-polyacrylamide gel electrophoresis is due largely to peptide and not solely to carbohydrate.

Native bovine fetuin is a major alpha 1-glycoprotein in the serum and cerebrospinal fluid of fetal calves. We previously reported (Johnson, W.V., and Heath, E.C. (1986) Biochemistry 25, 5518-5525) the purification of the primary translation product for fetuin (prefetuin) from a rabbit reticulocyte cell-free translation system and showed that prefetuin contains an 18 amino acid signal peptide. Here we report that although the apparent sodium dodecyl sulfate (SDS) gel molecular weights of fetuin and prefetuin are 64,000 and 49,000, respectively, when analyzed by gel filtration chromatography under denaturing and reducing conditions, molecular weight values of 48,000 and 40,000 were found for native fetuin and the nonglycosylated prefetuin, respectively. These molecular weight values are in agreement with those expected on the basis of the sedimentation diffusion data of Spiro (Spiro, R.G. (1960) J. Biol. Chem. 235, 2860-2869) and indicate that the polypeptide moiety makes a major contribution toward the anomalous SDS gel electrophoretic mobility of fetuin. Therefore, the carbohydrate moiety is not solely responsible for this property. Edman degradation of [35S]methionine-labeled prefetuin indicated that the N-terminal residue is the only methionine present in prefetuin; native fetuin lacks methionine. Additionally, hydroxylamine cleavage of an Asn-Gly bond in prefetuin localized one of the N-linked carbohydrate side chains to the middle of the polypeptide chain of native fetuin.

Animals↗
PubMed1976

Structural features of luliberin (luteinising hormone-releasing factor) inferred from fluorescence measurements.

The fluorescence and excitation spectra of luliberin (luteinizing hormone-releasing factor) in 0.005 M aqueous ammonium acetate are identical in shape to those of N-acetyltryptophan amide and are related to the indole side chain of Trp3. The change of fluoresecence intensity of luliberin with pH was measured in the range of pH 4-11. The increase of pH from 4 to 7.5 is followed by about 50% increase in fluorescence intensity due to deprotonation of the imidazolium side chain of His2. The fluorimetric titration curve in this pH region reveals a pK value for His2 of 5.95. Increasing of pH from 8 to 11 results in about 40% quenching of the fluorescence due to electronic energy transfer from the excited indole of Trp3 to the phenolate side chain of Tyr5. The pK value of Tyr5, obtained independently from the fluorimetric and photometric titrations indicate that at pH 7-8 luliberin contains only one charged residue, Arg8, which is in close vicinity to both His2 and Tyr5. The side chains of His2, Tyr5 and Arg8 presumably form a combined unit which may play an active role in the hormone action. Trp3 is at a maximal distance from this unit and may thus act as an independent active unit.

Gonadotropin-Releasing Hormone↗
PubMed1983

Identification of a key structural feature of cobalt(III)-bleomycins: an exogenous ligand (e.g. hydroperoxide) bound to cobalt.

A series of cobalt(III) complexes of the anticancer antibiotic bleomycin has been prepared. Mass spectrometry and enzymatic analysis show that the green cobalt-bleomycin complex contains a hydroperoxide (-OOH) group bound to cobalt with unusual stability. Under appropriate conditions, cobalt-bleomycins containing other monodentate ligands to cobalt can be formed; fast-atom bombardment mass spectra of such complexes show peaks for cobalt-bleomycin at the expected mass, and also peaks for the intact complexes at the required higher mass.

Bleomycin↗
PubMed1988

Soluble lignin-carbohydrate complexes from sheep rumen fluid: their composition and structural features.

Lignin-carbohydrate complexes, isolated from cell-free rumen fluid of sheep, consisted of polyphenolic material in association with carbohydrate (5.5%) and protein (1.8%). No separation of carbohydrate from the other components could be effected. The complexes showed a bimodal distribution of molecular size with the higher-molecular-weight fraction richer in carbohydrate. Methylation analysis indicated a wide range of linkages and a high proportion of terminal sugars. Reducing sugars were found in the complexes, particularly in the low-molecular-weight fraction (approximately 25%), suggesting that ether linkages to the phenolics were also present.

Animals↗