Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA. Crystal structure of an oligomeric complex of yeast SmF

Sm and Sm-like proteins are key components of small ribonucleoproteins involved in many RNA and DNA processing pathways. In eukaryotes, these complexes contain seven unique Sm or Sm-like (Lsm) proteins assembled as hetero-heptameric rings, whereas in Archaea and bacteria six or seven-membered rings are made from only a single polypeptide chain. Here we show that single Sm and Lsm proteins from yeast also have the capacity to assemble into homo-oligomeric rings. Formation of homo-oligomers by the spliceosomal small nuclear ribonucleoprotein components SmE and SmF preclude hetero-interactions vital to formation of functional small nuclear RNP complexes in vivo. To better understand these unusual complexes, we have determined the crystal structure of the homomeric assembly of the spliceosomal protein SmF. Like its archaeal/bacterial homologs, the SmF complex forms a homomeric ring but in an entirely novel arrangement whereby two heptameric rings form a co-axially stacked dimer via interactions mediated by the variable loops of the individual SmF protein chains. Furthermore, we demonstrate that the homomeric assemblies of yeast Sm and Lsm proteins are capable of binding not only to oligo(U) RNA but, in the case of SmF, also to oligo(dT) single-stranded DNA.     

Time-resolved magnetic circular dichroism spectroscopy of photolyzed carbonmonoxy cytochrome c oxidase (cytochrome aa3).

Nanosecond time-resolved magnetic circular dichroism (TRMCD) and time-resolved natural circular dichroism (TRCD) measurements of photolysis products of the CO complex of eukaryotic cytochrome c oxidase (CcO-CO) are presented. TRMCD spectra obtained at 100 ns and 10 microseconds after photolysis are diagnostic of pentacoordinate cytochrome a3Fe2+, as would be expected for simple photodissociation. Other time-resolved spectroscopies (UV-visible and resonance Raman), however, show evidence for unusual Fea3(2+) coordination after CO photolysis (Woodruff, W. H., O. Einarsdóttir, R. B. Dyer, K. A. Bagley, G. Palmer, S. J. Atherton, R. A. Goldbeck, T. D. Dawes, and D. S. Kliger. 1991. Proc. Nat. Acad. Sci. U.S.A. 88:2588-2592). Furthermore, time-resolved IR experiments have shown that photodissociated CO binds to CuB+ prior to recombining with Fea3(2+) (Dyer, R. B., O. Einarsdóttir, P. M. Killough, J. J. López-Garriga, and W. H. Woodruff. 1989. J. Am. Chem. Soc. 111:7657-7659). A model of the CcO-CO photolysis cycle which is consistent with all of the spectroscopic results is presented. A novel feature of this model is the coordination of a ligand endogenous to the protein to the Fe axial site vacated by the photolyzed CO and the simultaneous breaking of the Fe-imidazole(histidine) bond.     

The purification and characterization of acetoacetyl-coenzyme A reductase from Azotobacter beijerinckii

A soluble acetoacetyl-CoA reductase (EC 1.1.1.36) was purified 54-fold from Azotobacter beijerinckii N.C.I.B. 9067 and the reaction product identified as d(-)-beta-hydroxybutyryl-CoA. The Michaelis constants for acetoacetyl-CoA, NADPH and NADH were determined and the reaction rate was found to be some fivefold greater with NADPH than with NADH. At neutral pH the equilibrium greatly favours the formation of the reduced product. Substrate specificity was in the order: acetoacetyl-CoA>acetoacetylpantetheine>acetoacetyl-(acyl-carrier protein). The enzyme possesses a functional thiol group, suffers inactivation by oxygen and is inhibited by thiol-blocking reagents. Inhibition by p-chloromercuribenzoate is reversed by excess of dithiothreitol, which also protects the enzyme from inactivation by oxygen.     

STUDIES ON SARGASSUM. I. A LIGHT MICROSCOPIC EXAMINATION OF THE WOUND REGENERATION PROCESS IN MATURE STIPES OF S. FILIPENDULA

Regrowth from wounded stipe explants of Sargassum can be divided into four stages based on cytological changes. The first stage involves changes associated with the wound reactions and the formation of a wound epidermis. The second stage includes the formation of a well defined medullary pit with meristematically active cells around its periphery. Several “bud primordia” are also formed which begin to grow by cell division towards the wound surface. The third stage involves a period of internal tissue differentiation in the “bud primordia” such that mitotic activity is localized in the bud tip and the basal cells grow by cell elongation. The fourth stage marks a major change in the morphology of the regeneration branch from a tubular structure to that of a flattened blade. This change in morphology is preceded by the formation of an apical pit around which the flattened growth appears to be organized.     

Abnormal amino acid metabolism in mutants of Saccharomyces cerevisiae affected in the initiation of sporulation

Amino acid metabolism was examined during sporulation in a wild-type strain of Saccharomyces cerevisiae and in a mutant homozygous for the spd1 mutation (derepression of sporulation). In the wild-type initiation of sporulation involves a rise in intracellular glutamate. In the derepressed mutant there was no further increase of intracellular glutamate: glutamate was already present at a greater concentration than in the wild-type. These elevated glutamate levels are apparently due to reduction in the activity of 2-oxoglutarate dehydrogenase. One consequence of the elevated glutamate levels in diploids homozygous for the spd1 mutation is the production of considerable amounts of glycyl-L-proline, glutathione and saccharopine.     

The Endosomal Protein-Sorting Receptor Sortilin Has a Role in Trafficking α-1 Antitrypsin

Up to 1 in 3000 individuals in the United States have α-1 antitrypsin deficiency, and the most common cause of this disease is homozygosity for the antitrypsin-Z variant (ATZ). ATZ is inefficiently secreted, resulting in protein deficiency in the lungs and toxic polymer accumulation in the liver. However, only a subset of patients suffer from liver disease, suggesting that genetic factors predispose individuals to liver disease. To identify candidate factors, we developed a yeast ATZ expression system that recapitulates key features of the disease-causing protein. We then adapted this system to screen the yeast deletion mutant collection to identify conserved genes that affect ATZ secretion and thus may modify the risk for developing liver disease. The results of the screen and associated assays indicate that ATZ is degraded in the vacuole after being routed from the Golgi. In fact, one of the strongest hits from our screen was Vps10, which can serve as a receptor for the delivery of aberrant proteins to the vacuole. Because genome-wide association studies implicate the human Vps10 homolog, sortilin, in cardiovascular disease, and because hepatic cell lines that stably express wild-type or mutant sortilin were recently established, we examined whether ATZ levels and secretion are affected by sortilin. As hypothesized, sortilin function impacts the levels of secreted ATZ in mammalian cells. This study represents the first genome-wide screen for factors that modulate ATZ secretion and has led to the identification of a gene that may modify disease severity or presentation in individuals with ATZ-associated liver disease.