Two novel proteins in the mitochondrial outer membrane mediate β-barrel protein assembly

Mitochondrial outer and inner membranes contain translocators that achieve protein translocation across and/or insertion into the membranes. Recent evidence has shown that mitochondrial β-barrel protein assembly in the outer membrane requires specific translocator proteins in addition to the components of the general translocator complex in the outer membrane, the TOM40 complex. Here we report two novel mitochondrial outer membrane proteins in yeast, Tom13 and Tom38/Sam35, that mediate assembly of mitochondrial β-barrel proteins, Tom40, and/or porin in the outer membrane. Depletion of Tom13 or Tom38/Sam35 affects assembly pathways of the β-barrel proteins differently, suggesting that they mediate different steps of the complex assembly processes of β-barrel proteins in the outer membrane

Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer

<p>Abstract</p> <p>Background</p> <p>Serum is an ideal source of biomarker discovery and proteomic profiling studies are continuously pursued on serum samples. However, serum is featured by high level of protein glycosylations that often cause ionization suppression and confound accurate quantification analysis by mass spectrometry. Here we investigated the effect of N-glycan and sialic acid removal from serum proteins on the performance of label-free quantification results.</p> <p>Results</p> <p>Serum tryptic digests with or without deglycosylation treatment were analyzed by LC-MALDI MS and quantitatively compared on the Expressionist Refiner MS module. As a result, 345 out of 2,984 peaks (11.6%) showed the specific detection or the significantly improved intensities in deglycosylated serum samples (<it>P </it>< 0.01). We then applied this deglycosylation-based sample preparation to the identification of lung cancer biomarkers. In comparison between 10 healthy controls and 20 lung cancer patients, 40 peptides were identified to be differentially presented (<it>P </it>< 0.01). Their quantitative accuracies were further verified by multiple reaction monitoring. The result showed that deglycosylation was needed for the identification of some unique candidates, including previously unreported O-linked glycopeptide of complement component C9.</p> <p>Conclusions</p> <p>We demonstrated here that sample deglycosylation improves the quantitative performance of shotgun proteomics, which can be effectively applied to any samples with high glycoprotein contents.</p

Identification of Tam41 maintaining integrity of the TIM23 protein translocator complex in mitochondria

Newly synthesized mitochondrial proteins are imported into mitochondria with the aid of protein translocator complexes in the outer and inner mitochondrial membranes. We report the identification of yeast Tam41, a new member of mitochondrial protein translocator systems. Tam41 is a peripheral inner mitochondrial membrane protein facing the matrix. Disruption of the TAM41 gene led to temperature-sensitive growth of yeast cells and resulted in defects in protein import via the TIM23 translocator complex at elevated temperature both in vivo and in vitro. Although Tam41 is not a constituent of the TIM23 complex, depletion of Tam41 led to a decreased molecular size of the TIM23 complex and partial aggregation of Pam18 and -16. Import of Pam16 into mitochondria without Tam41 was retarded, and the imported Pam16 formed aggregates in vitro. These results suggest that Tam41 facilitates mitochondrial protein import by maintaining the functional integrity of the TIM23 protein translocator complex from the matrix side of the inner membrane

Occurrence of silk stitch abscess after surgery in patients with oral squamous cell carcinoma

Objectives: To elucidate the predisposing factors and clinical characteristics related to the occurrence of stitch abscess after surgery in patients with oral squamous cell carcinoma (SCC). Patients and Methods: The subjects were 232 patients who underwent excision and/or reconstruction and/or neck dissection for oral SCC using silk sutures for high ligation of the blood vessels. Detection rates and characteristics of patients with stitch abscess were retrospectively evaluated by comparing patients with and without stitch abscesses after surgery diagnosed by ultrasonography and findings of various modalities in 232 patients. Several echogenic dots with subtle acoustic shadows in a hypoechoic mass were identified as the characteristic findings of stitch abscess on US. The patient groups with and without stitch abscess were compared with respect to various factors to identify those that predispose to the occurrence of stitch abscess. The factors analyzed included patients' sex and age, chemotherapy treatment, radiotherapy treatment, the presence of a history of allergy, and blood test results. Results: A significant correlation was found between the occurrence of stitch abscess and age, liver function abnormalities on blood tests, and the presence of a history of allergy. Multiple stitch abscesses clearly tended to occur more often than single ones in patients with stitch abscess. Conclusions: The occurrence of stitch abscesses was related to age, liver dysfunction, and/or the presence of allergies. When diagnosing stitch abscess, the occurrence of multiple stitch abscesses is important

Production of domoic acid by laboratory culture of the red alga Chondria armata

To clarify the production mechanisms and biologic functions of domoic acid (DA) by the red alga Chondria armata, we established a laboratory culture of C. armata. The alga grew better in modified PES medium (mPES) without trace metals or manganese than in unmodified mPES (seawater + nitrate, phosphate, iron, trace metals, vitamins, and 2-[4-(2-hydroxyethyl)-1-piperazinyl]-ethanesulfonic acid), suggesting that C. armata is especially hypersensitive to the toxicity of excessive manganese. C. armata cultured in N・P・Fe medium (seawater + nitrate, phosphate, and iron) grew best (mean growth rate 828.4%) at a relative nutrient concentration of 50%. Liquid chromatography-mass spectrometry analysis of the algal extracts revealed that the DA content of the cultured explants (2273-3308 ppm) was 4-5 fold higher than that of wild specimens. The extract of pooled explants (60 g) was purified by activated charcoal treatment and several types of column chromatography to afford ca. 10 mg DA. The 1H-nuclear magnetic resonance spectrum of the preparation was indistinguishable from the previously reported spectrum of DA, indicating that C. armata itself has an ability to produce DA

A Comprehensive Peptidome Profiling Technology for the Identification of Early Detection Biomarkers for Lung Adenocarcinoma

The mass spectrometry-based peptidomics approaches have proven its usefulness in several areas such as the discovery of physiologically active peptides or biomarker candidates derived from various biological fluids including blood and cerebrospinal fluid. However, to identify biomarkers that are reproducible and clinically applicable, development of a novel technology, which enables rapid, sensitive, and quantitative analysis using hundreds of clinical specimens, has been eagerly awaited. Here we report an integrative peptidomic approach for identification of lung cancer-specific serum peptide biomarkers. It is based on the one-step effective enrichment of peptidome fractions (molecular weight of 1,000–5,000) with size exclusion chromatography in combination with the precise label-free quantification analysis of nano-LC/MS/MS data set using Expressionist proteome server platform. We applied this method to 92 serum samples well-managed with our SOP (standard operating procedure) (30 healthy controls and 62 lung adenocarcinoma patients), and quantitatively assessed the detected 3,537 peptide signals. Among them, 118 peptides showed significantly altered serum levels between the control and lung cancer groups (p<0.01 and fold change >5.0). Subsequently we identified peptide sequences by MS/MS analysis and further assessed the reproducibility of Expressionist-based quantification results and their diagnostic powers by MRM-based relative-quantification analysis for 96 independently prepared serum samples and found that APOA4 273–283, FIBA 5–16, and LBN 306–313 should be clinically useful biomarkers for both early detection and tumor staging of lung cancer. Our peptidome profiling technology can provide simple, high-throughput, and reliable quantification of a large number of clinical samples, which is applicable for diverse peptidome-targeting biomarker discoveries using any types of biological specimens

DLEC1 and MLH1 promoter methylation are associated with poor prognosis in non-small cell lung carcinoma

The significance of chromosome 3p gene alterations in lung cancer is poorly understood. This study set out to investigate promoter methylation in the deleted in lung and oesophageal cancer 1 (DLEC1), MLH1 and other 3p genes in 239 non-small cell lung carcinomas (NSCLC). DLEC1 was methylated in 38.7%, MLH1 in 35.7%, RARβ in 51.7%, RASSF1A in 32.4% and BLU in 35.3% of tumours. Any two of the gene alterations were associated with each other except RARβ. DLEC1 methylation was an independent marker of poor survival in the whole cohort (P=0.025) and in squamous cell carcinoma (P=0.041). MLH1 methylation was also prognostic, particularly in large cell cancer (P=0.006). Concordant methylation of DLEC1/MLH1 was the strongest independent indicator of poor prognosis in the whole cohort (P=0.009). However, microsatellite instability and loss of MLH1 expression was rare, suggesting that MLH1 promoter methylation does not usually lead to gene silencing in lung cancer. This is the first study describing the prognostic value of DLEC1 and MLH1 methylation in NSCLC. The concordant methylation is possibly a consequence of a long-range epigenetic effect in this region of chromosome 3p, which has recently been described in other cancers