Proteogenomics analysis of CUG codon translation in the human pathogen Candida albicans.

Background: Yeasts of the CTG-clade lineage, which includes the human-infecting Candida albicans, Candida parapsilosis and Candida tropicalis species, are characterized by an altered genetic code. Instead of translating CUG codons as leucine, as happens in most eukaryotes, these yeasts, whose ancestors are thought to have lost the relevant leucine-tRNA gene, translate CUG codons as serine using a serine-tRNA with a mutated anticodon, [Formula: see text]. Previously reported experiments have suggested that 3-5% of the CTG-clade CUG codons are mistranslated as leucine due to mischarging of the [Formula: see text].

Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu-tRNAs in Ascoidea asiatica.

Although the "universal" genetic code is now known not to be universal, and stop codons can have multiple meanings, one regularity remains, namely that for a given sense codon there is a unique translation. Examining CUG usage in yeasts that have transferred CUG away from leucine, we here report the first example of dual coding: Ascoidea asiatica stochastically encodes CUG as both serine and leucine in approximately equal proportions. This is deleterious, as evidenced by CUG codons being rare, never at conserved serine or leucine residues, and predominantly in lowly expressed genes.

Serum uromodulin-a marker of kidney function and renal parenchymal integrity.

Background: An ELISA to analyse uromodulin in human serum (sUmod) was developed, validated and tested for clinical applications.

Methods: We assessed sUmod, a very stable antigen, in controls, patients with chronic kidney disease (CKD) stages 1-5, persons with autoimmune kidney diseases and recipients of a renal allograft by ELISA.

Results: Median sUmod in 190 blood donors was 207 ng/mL (women: men, median 230 versus 188 ng/mL, P = 0.

Corrigendum: Coat/Tether Interactions-Exception or Rule?

[This corrects the article on p. 44 in vol. 4, PMID: 27243008.

ER arrival sites for COPI vesicles localize to hotspots of membrane trafficking.

COPI-coated vesicles mediate retrograde membrane traffic from the cis-Golgi to the endoplasmic reticulum (ER) in all eukaryotic cells. However, it is still unknown whether COPI vesicles fuse everywhere or at specific sites with the ER membrane. Taking advantage of the circumstance that the vesicles still carry their coat when they arrive at the ER, we have visualized active ER arrival sites (ERAS) by monitoring contact between COPI coat components and the ER-resident Dsl tethering complex using bimolecular fluorescence complementation (BiFC).

Coat/Tether Interactions-Exception or Rule?

Coat complexes are important for cargo selection and vesicle formation. Recent evidence suggests that they may also be involved in vesicle targeting. Tethering factors, which form an initial bridge between vesicles and the target membrane, may bind to coat complexes.

Clinical characterization of a presenilin 1 mutation (F177S) in a family with very early-onset Alzheimer's disease in the third decade of life.

Background: Early-onset familial Alzheimer disease (AD) is an autosomal dominant disorder caused by mutations in the amyloid precursor protein, presenilin 1 (PSEN1), or presenilin 2 gene. The objective of this study was to characterize the phenotype in a large family with a PSEN1 F177S mutation by performing detailed clinical assessments, neuroimaging, and neuropathological analysis.

Methods: In two subjects, clinical and neuropsychological assessments, structural magnetic resonance imaging, F-18-2-fluoro-2-deoxy-D-glucose positron emission tomographic imaging, AD biomarkers in cerebrospinal fluid and genetic analysis were available.

The Dsl1 protein tethering complex is a resident endoplasmic reticulum complex, which interacts with five soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein receptors (SNAREs): implications for fusion and fusion regulation.

Retrograde vesicular transport from the Golgi to the ER requires the Dsl1 tethering complex, which consists of the three subunits Dsl1, Dsl3, and Tip20. It forms a stable complex with the SNAREs Ufe1, Use1, and Sec20 to mediate fusion of COPI vesicles with the endoplasmic reticulum. Here, we analyze molecular interactions between five SNAREs of the ER (Ufe1, Use1, Sec20, Sec22, and Ykt6) and the Dsl1 complex in vitro and in vivo.

Dsl1p/Zw10: common mechanisms behind tethering vesicles and microtubules.

Fusion of Golgi-derived COP (coat protein)-I vesicles with the endoplasmic reticulum (ER) is initiated by specific tethering complexes: the Dsl1 (depends on SLY1-20) complex in yeast and the syntaxin 18 complex in mammalian cells. Both tethering complexes are firmly associated with soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) at the ER. The structure of the Dsl1 tethering complex has been determined recently.

A tethering complex recruits SNAREs and grabs vesicles.

Protein tethers can bridge gaps between membranes. Ren et al. (2009) now provide evidence that the yeast Dsl1 complex tethers vesicles to the endoplasmic reticulum (ER) by binding ER SNARE proteins at its base and capturing vesicles using a loop region that extends 20 nm from the ER membrane.

A link between ER tethering and COP-I vesicle uncoating.

The yeast Dsl1p vesicle tethering complex, comprising the three subunits Dsl1p, Dsl3p, and Tip20p, is stably associated with three endoplasmic reticulum-localized Q-SNAREs and is believed to play a central role in the tethering and fusion of Golgi-derived COP-I transport vesicles. Dsl1p also interacts directly with COP-I subunits. We now show that binding of Dsl1p to COP-I subunits involves binding sites identical to those involved in interactions between COP-I subunits that stabilize the COP-I coat.

The GET complex mediates insertion of tail-anchored proteins into the ER membrane.

Tail-anchored (TA) proteins, defined by the presence of a single C-terminal transmembrane domain (TMD), play critical roles throughout the secretory pathway and in mitochondria, yet the machinery responsible for their proper membrane insertion remains poorly characterized. Here we show that Get3, the yeast homolog of the TA-interacting factor Asna1/Trc40, specifically recognizes TMDs of TA proteins destined for the secretory pathway. Get3 recognition represents a key decision step, whose loss can lead to misinsertion of TA proteins into mitochondria.

Mutations of the SM protein Sly1 resulting in bypass of GTPase requirement in vesicular transport are confined to a short helical region.

Ypt/Rab GTPases and Sec1/Munc18 (SM) proteins are key components of the membrane fusion machinery. Here, we describe new mutants of the yeast SM protein Sly1 that specifically bypass the need for GTPases Ypt1 and Ypt6 in vesicular transport. All sequence alterations are confined to a short alpha-helix (alpha-20), which is conserved in fungal Sly1 proteins and, when deleted, results in GTPase suppression.

Dsl1p, Tip20p, and the novel Dsl3(Sec39) protein are required for the stability of the Q/t-SNARE complex at the endoplasmic reticulum in yeast.

The "Dsl1p complex" in Saccharomyces cerevisiae, consisting of Dsl1p and Tip20p, is involved in Golgi-ER retrograde transport and it is functionally conserved from yeast to mammalian cells. To further characterize this complex, we analyzed the function of Dsl3p, a protein that interacts with Dsl1p in yeast two hybrids screens. DSL3, recently identified in a genome wide analysis of essential genes as SEC39, encodes a cytosolic protein of 82 kDa that is peripherally associated with membranes derived from the ER.

Identification of functionally interacting SNAREs by using complementary substitutions in the conserved '0' layer.

Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes form bundles of four parallel alpha-helices. The central '0' layer of interacting amino acid side chains is highly conserved and contains one arginine and three glutamines, leading to the classification of SNAREs into R, Qa, Qb, and Qc-SNAREs. Replacing one of the glutamines with arginine in the yeast exocytotic SNARE complex is either lethal or causes a conditional growth defect that is compensated by replacing the R-SNARE arginine with glutamine.

Dsl1p, an essential component of the Golgi-endoplasmic reticulum retrieval system in yeast, uses the same sequence motif to interact with different subunits of the COPI vesicle coat.

Dsl1p is required for Golgi-endoplasmic reticulum (ER) retrograde transport in yeast. It interacts with the ER resident protein Tip20p and with delta-COP, a subunit of coatomer, the coat complex of COPI vesicles. To test the significance of these interactions, we mapped the different binding sites and created mutant versions of Dsl1p and delta-COP, which are unable to bind directly to each other.

Use1p is a yeast SNARE protein required for retrograde traffic to the ER.

SNAREs on transport vesicles and target membranes are required for vesicle targeting and fusion. Here we describe a novel yeast protein with a typical SNARE motif but with low overall amino acid homologies to other SNAREs. The protein localized to the endoplasmic reticulum (ER) and was therefore named Use1p (unconventional SNARE in the ER).

ARF-GAP-mediated interaction between the ER-Golgi v-SNAREs and the COPI coat.

In eukaryotic cells, secretion is achieved by vesicular transport. Fusion of such vesicles with the correct target compartment relies on SNARE proteins on both vesicle (v-SNARE) and the target membranes (t-SNARE). At present it is not clear how v-SNAREs are incorporated into transport vesicles.