Higher‐order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle

Selective autophagy is the mechanism by which large cargos are specifically sequestered for degradation. The structural details of cargo and receptor assembly giving rise to autophagic vesicles remain to be elucidated. We utilize the yeast cytoplasm‐to‐vacuole targeting (Cvt) pathway, a prototype of selective autophagy, together with a multi‐scale analysis approach to study the molecular structure of Cvt vesicles. We report the oligomeric nature of the major Cvt cargo Ape1 with a combined 2.8 Å X‐ray and negative stain EM structure, as well as the secondary cargo Ams1 with a 6.3 Å cryo‐EM structure. We show that the major dodecameric cargo prApe1 exhibits a tendency to form higher‐order chain structures that are broken upon interaction with the receptor Atg19 in vitro. The stoichiometry of these cargo–receptor complexes is key to maintaining the size of the Cvt aggregate in vivo. Using correlative light and electron microscopy, we further visualize key stages of Cvt vesicle biogenesis. Our findings suggest that Atg19 interaction limits Ape1 aggregate size while serving as a vehicle for vacuolar delivery of tetrameric Ams1.     

On the oxidation of 3,4-dihydroxyphenethyl alcohol and 3,4-dihydroxyphenyl glycol by cuticular enzyme(s) from Sarcophaga bullata

The catabolic fate of 3,4-dihydroxyphenethyl alcohol (DHPA) and 3,4-dihydroxyphenylethyl glycol (DHPG) in insect cuticle was determined for the first time using cuticular enzyme(s) from Sarcophaga bullata and compared with mushroom tyrosinase-medicated oxidation. Mushroom tyrosinase converted both DHPA and DHPG to their corresponding quinone derivatives, while cuticular enzyme(s) partly converted DHPA to DHPG. Cuticular enzyme(s)-mediated oxidation of DHPA also accompanied the covalent binding of DHPA to the cuticle. Cuticle-DHPA adducts, upon pronase digestion, released peptides that had bound catechols. 3,4-Dihydroxyphenyl-acetaldehyde, the expected product of side chain desaturation of DHPA, was not formed at all. The presence of N-acetylcysteine, a quinone trap, in the reaction mixture containing DHPA and cuticle resulted in the generation of DHPA-quinone-N-acetylcysteine adduct and total inhibition of DHPG formation. The insect enzyme(s) converted DHPG to its quinone at high substrate concentration and to 2-hydroxy-3′,4′-dihydroxyacetophenone at low concentration. They converted exogenously added DHPA-quinone to DHPG, but acted sluggishly on DHPG-quinone. These results are consistent with the enzymatic transformations of phenoloxidase-generated quinones to quinone methides and subsequent nonenzymatic transformation of the latter to the observed products. Thus, quinone methide formation in insect cuticle seems to be caused by the combined action of two enzymes, phenoloxidase and quinone tautomerase, rather than the action of quinone methide-generating phenoloxidase (Sugumaran: Arch Insect Biochem Physiol 8, 73–88, 1988). It is proposed that DHPA and DHPG in combination can be used effectively to examine the participation of (1) quinone, (2) quinone methide, and (3) dehydro derivative intermediates in the metabolism of 4-alkylcatechols for cuticular sclerotization.     

Water quality studies on Buckingham Canal (Madras,India) — A discriminant analysis

Stepwise multiple discriminant analysis was applied to a two year water quality monitoring study of the Buckingham Canal at Madras, India. The variables were divided into

1. physical and chemical
2. pollutants; and
3. biological

to test which group is efficient in discriminating stations which differ in water quality. Biological variables obtained higher loadings on the discriminant functions than the other two groups. The derived discriminant functions were tested for their discriminating power through the classification phase with the same raw data. The \lsHit and Misses\rs tables of classification indicate that 81.660% of the samples were correctly classified by the biological variables, against only 46.660% of the samples in the case of physical and chemical variables and 48.33% in the case of pollutants.     

Efficient translation of long-lived messengers in extracts from dry pea primary axes

Extracts prepared from dry pea (Pisum sativum, L; cv oberon) primary axes translate efficiently their endogenous messengers in an in vitro protein synthesizing system. The native long-lived messengers are biologically fully active and direct the synthesis of a whole range of polypeptides with MW ranging up to 130,000. About 0.5% of the total in vitro synthesized polypeptides are recovered in the immunoprecipitate obtained with pea lectin antiserum. Since about one-fourth of the radioactivity in the immunoprecipitate comigrates with authentic pea lectin it is concluded that about 0.1% of the long-lived messengers code for the lectin.Abbreviations mRNA messenger RNA - mRNP messenger ribonucleoprotein - SDS sodium dodecyl sulphate - HEPES N-2-hydroxyethylpiperazine-N-ethanesulphonic acid - S.A specific activity     

Ion pairs in alpha helices

A survey of 47 globular proteins was made to determine the probability of occurrence of ion pairs separated by 1,2,3,... and 8 residues in the alpha helices. As a control, the probability of occurrence of like charged pairs was also determined. The survey showed that ion pairs of the type i,i +/- 3 and i, i +/- 4 are the most predominant. Such a preference was not observed for like charged pairs. The observed frequency of ion pairs is significantly greater than their expected frequency. The normalized frequencies of occurrence of the ion pairs were also found to increase generally with the helix length. These results indicate that the ion pairs may contribute to the stability of solvent-exposed alpha helices. Since the stabilization of protein secondary structure enhances the stability of protein tertiary structure, these results may throw light on the mechanism of protein folding.     

Eighteen new polymorphic markers in the multiple endocrine neoplasia type 1 (MEN1) region

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder in which affected individuals develop tumors primarily in the parathyroids, anterior pituitary, endocrine pancreas, and duodenum. The locus for MEN1 is tightly linked to the marker PYGM on chromosome 11q13, and linkage analysis has previously placed the MEN1 gene within a 2-Mb interval flanked by markers D11S1883 and D11S449. Loss of heterozygosity (LOH) studies in MEN1 and sporadic tumors have helped narrow the location of the gene to a 600-kb interval between PYGM and D11S449. Eighteen new polymerase chain reaction (PCR)-based polymorphic markers were generated for the MEN1 region, with ten mapping to the PYGM-D11S449 interval. These new markers, along with 14 previously known polymorphic markers, were precisely mapped on a 2.8-Mb (D11S480–D11S913) high-density clone contig-based, physical map generated for the MEN1 region. Received: 21 February 1997 / Accepted: 5 June 1997     

Unexpected Phenotype of Mice Lacking Shcbp1, a Protein Induced during T Cell Proliferation

T cell development and activation are highly regulated processes, and their proper execution is important for a competent immune system. Shc SH2-domain binding protein-1 (Shcbp1) is an evolutionarily conserved protein that binds to the adaptor protein ShcA. Studies in Drosophila and in cell lines have strongly linked Shcbp1 to cell proliferation, embryonic development, growth factor signaling, and tumorigenesis. Here we show that Shcbp1 expression is strikingly upregulated during the β-selection checkpoint in thymocytes, and that its expression tightly correlates with proliferative stages of T cell development. To evaluate the role for Shcbp1 during thymic selection and T cell function in vivo, we generated mice with global and conditional deletion of Shcbp1. Surprisingly, the loss of Shcbp1 expression did not have an obvious effect during T cell development. However, in a mouse model of experimental autoimmune encephalomyelitis (EAE), which depends on CD4⁺ T cell function and mimics multiple features of the human disease multiple sclerosis, Shcbp1 deficient mice had reduced disease severity and improved survival, and this effect was T cell intrinsic. These data suggest that despite the striking upregulation of Shcbp1 during T cell proliferation, loss of Shcbp1 does not directly affect T cell development, but regulates CD4⁺ T cell effector function in vivo.     

Target highlights in CASP13: Experimental target structures through the eyes of their authors

The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.     

Chemical-induced formation of BZ-junction with base extrusion

The crystal structure of BZ-junction reveals that left-handed Z-DNA stabilized by Z-DNA binding domain (Zα) is continuously stacked to right-handed B-DNA with AT bases’ extrusion in the junction site. However, this structure might not fully represent the BZ-junction in solution due to the possibility of the junction formation either by crystal packing or Zα interaction. Therefore, we investigated BZ-junction in solution with chemical Z-DNA inducers using CD and 2-aminopurine base-extrusion assay. We confirmed the formation of Z-DNA and BZ-junction with base-extrusion by chemical Z-DNA inducers. However, neither typical Z-DNA nor base-extrusion could be detected with some inducers such as spermine, suggesting that the energy barrier for the formation of the BZ junction might vary depending on the Z-DNA induction conditions.