Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii

BACKGROUND: The cellular proteome and metabolome are underlying dynamic regulation allowing rapid adaptation to changes in the environment. System-wide analysis of these dynamics will provide novel insights into mechanisms of stress adaptation for higher photosynthetic organisms. We applied pulsed-SILAC labeling to a photosynthetic organism for the first time and we established a method to study proteome dynamics in the green alga chlamydomonas reinhardtii, an emerging model system for plant biology. In addition, we combined the analysis of protein synthesis with metabolic profiling to study the dynamic changes of metabolism and proteome turnover under salt stress conditions. RESULTS: To study de novo protein synthesis an arginine auxotroph Chlamydomonas strain was cultivated in presence of stable isotope-labeled arginine for 24 hours. From the time course experiment in 3 salt concentrations we could identify more than 2500 proteins and their H/L ratio in at least one experimental condition; for 998 proteins at least 3 ratio counts were detected in the 24 h time point (0 mM NaCl). After fractionation we could identify 3115 proteins and for 1765 of them we determined their de novo synthesis rate. Consistently with previous findings we showed that RuBisCO is among the most prominent proteins in the cell; and similar abundance and turnover for the small and large RuBisCO subunit could be calculated. The D1 protein was identified among proteins with a high synthesis rates. A global median half-life of 45 h was calculated for Chlamydomonas proteins under the chosen conditions. CONCLUSION: To investigate the temporal co-regulation of the proteome and metabolome, we applied salt stress to chlamydomonas and studied the time dependent regulation of protein expression and changes in the metabolome. The main metabolic response to salt stress was observed within the amino acid metabolism. In particular, proline was up-regulated manifold and according to that an increased carbon flow within the proline biosynthetic pathway could be measured. In parallel the analysis of abundance and de novo synthesis of the corresponding enzymes revealed that metabolic rearrangements precede adjustments of protein abundance

Proteomics quality control : a quality control software for MaxQuant results

Mass spectrometry-based proteomics coupled to liquid chromatography has matured into an automatized, high-throughput technology, producing data on the scale of multiple gigabytes per instrument per day. Consequently, an automated quality control (QC) and quality analysis (QA), capable of detecting measurement bias, verifying consistency and avoiding propagation of error is paramount for instrument operators and scientists in charge of downstream analysis. We have developed an R-based quality control pipeline called Proteomics Quality Control (PTXQC) for bottom-up LC-MS data generated by the MaxQuant software pipeline. PTXQC creates a quality control report containing a comprehensive and powerful set of quality control metrics, augmented with automated scoring functions. The automated scores are collated to create an overview heatmap at the beginning of the report, giving valuable guidance also to non-specialists. Our software supports a wide range of experimental designs, including stable isotope labeling by amino acids in cell culture (SILAC), Tandem Mass Tags (TMT) and label-free data. Furthermore, we introduce new metrics to score MaxQuant's Match-between-runs (MBR) functionality by which peptide identifications can be transferred across Raw files based on accurate RT and m/z. Last but not least, PTXQC is easy to install and use and represents the first QC software capable of processing MaxQuant result tables. PTXQC is freely available at https://github.com/cbielow/PTXQC

Splicing factor Rbm10 facilitates heterochromatin assembly in fission yeast

Splicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpression of Rbm10 in fission yeast leads to strong global intron retention. Rbm10 also interacts with splicing factors in a pattern resembling that of human RBM10, suggesting that the function of Rbm10 as a splicing regulator is conserved. Surprisingly, our deep-sequencing data showed that deletion of Rbm10 caused only minor effect on genome-wide gene expression and splicing. However, the mutant displays severe heterochromatin defects. Further analyses confirmed that the heterochromatin defects in the mutant did not result from mis-splicing of heterochromatin factors. Our proteomic data revealed that Rbm10 associates with the histone deacetylase Clr6 complex and chromatin remodeling complexes known to be essential for heterochromatin silencing. Our work together with previous findings further suggests that different splicing subunits may play distinct roles in heterochromatin regulation

Localized inhibition of protein phosphatase 1 by NUAK1 promotes spliceosome activity and reveals a MYC-sensitive feedback control of transcription.

Deregulated expression of MYC induces a dependence on the NUAK1 kinase, but the molecular mechanisms underlying this dependence have not been fully clarified. Here, we show that NUAK1 is a predominantly nuclear protein that associates with a network of nuclear protein phosphatase 1 (PP1) interactors and that PNUTS, a nuclear regulatory subunit of PP1, is phosphorylated by NUAK1. Both NUAK1 and PNUTS associate with the splicing machinery. Inhibition of NUAK1 abolishes chromatin association of PNUTS, reduces spliceosome activity, and suppresses nascent RNA synthesis. Activation of MYC does not bypass the requirement for NUAK1 for spliceosome activity but significantly attenuates transcription inhibition. Consequently, NUAK1 inhibition in MYC-transformed cells induces global accumulation of RNAPII both at the pause site and at the first exon-intron boundary but does not increase mRNA synthesis. We suggest that NUAK1 inhibition in the presence of deregulated MYC traps non-productive RNAPII because of the absence of correctly assembled spliceosomes

Valoración global del corazón en el paciente con transplante cardiaco mediante tomografía computarizada de doble fuente

In routine clinical practice surveillance of heart transplant recipients is usually performed using echocardiography and conventional coronary angiography. The latter permits diagnosis and follow-up of coronary allograft vasculopathy. However, this procedure is invasive and is not free of complications. Conventional multislice computed tomography (MSCT) has been shown to be a useful non-invasive tool for ruling out coronary artery disease and evaluating cardiac function. However, due to its limited temporal resolution betablocker administration is required, and its usefulness in certain patient populations with restricted response to this medication, such as heart transplant recipients, may therefore be limited. Dual-source CT (DSCT) allows evaluation of the coronary arteries in all individuals independent of their heart rate. In the case presented here, we demonstrate that DSCT may be useful for evaluating cardiac function and ruling out coronary allograft vasculopathy in heart transplant recipients

Alterations of mTOR signaling impact metabolic stress resistance in colorectal carcinomas with BRAF and KRAS mutations

Metabolic reprogramming is as a hallmark of cancer, and several studies have reported that BRAF and KRAS tumors may be accompanied by a deregulation of cellular metabolism. We investigated how BRAF(V600E) and KRAS(G12V) affect cell metabolism, stress resistance and signaling in colorectal carcinoma cells driven by these mutations. KRAS(G12V) expressing cells are characterized by the induction of glycolysis, accumulation of lactic acid and sensitivity to glycolytic inhibition. Notably mathematical modelling confirmed the critical role of MCT1 designating the survival of KRAS(G12V) cells. Carcinoma cells harboring BRAF(V600E) remain resistant towards alterations of glucose supply or application of signaling or metabolic inhibitors. Altogether these data demonstrate that an oncogene-specific decoupling of mTOR from AMPK or AKT signaling accounts for alterations of resistance mechanisms and metabolic phenotypes. Indeed the inhibition of mTOR in BRAF(V600E) cells counteracts the metabolic predisposition and demonstrates mTOR as a potential target in BRAF(V600E)-driven colorectal carcinomas

Dual-source CT for visualization of the coronary arteries in heart transplant patients with high heart rates

OBJECTIVE. The purpose of this study was to evaluate the quality of dual-source CT images of the coronary arteries in heart transplant recipients with high heart rates. SUBJECTS AND METHODS. Contrast-enhanced dual-source CT coronary angiography was performed on 23 heart transplant recipients (20 men, three women; mean age, 61.1 ± 12.8 years). Data sets were reconstructed in 5% steps from 30% to 80% of the R-R interval. Two blinded independent readers using a 5-point scale (0, not evaluative; 4, excellent quality) assessed the quality of images of coronary segments. RESULTS. The mean heart rate during scanning was 89.2 ± 10.4 beats/min. Interobserver agreement on the quality of images of the whole coronary tree was a kappa value of 0.78 and for selection of the optimal reconstruction interval was a kappa value of 0.82. The optimal reconstruction interval was systole in 17 (74%) of the 23 of heart transplant recipients. At the best reconstruction interval, diagnostic image quality (score ≥ 2) was obtained in 92.1% (303 of 329) of the coronary artery segments. The mean image quality score for the whole coronary tree was 3.1 ± 1.01. No significant correlation between mean heart rate (ρ = 0.31) or heart rate variability (ρ = 0.23) and overall image quality score was observed (p = not significant). CONCLUSION. Dual-source CT acquisition yields coronary angiograms of diagnostic quality in heart transplant recipients. Mean heart rate and heart rate variability during scanning do not have a negative effect on the overall quality of images of the coronary arteries

Trasplante de homoinjertos valvulares cardiacos y vasculares

The advances in the manipulation of human tissues, the development of cryobiology, paediatric cardiac surgery, the impossibility of obtaining an ideal prosthetic cardiac valve and the surgical treatment of cardiovascular infections have revived interest in the use of homografts. The donors of these homografts can be: a) Live donors: aortic and pulmonary valve of the recipient of a heart transplant; b) Multiorgan donors with a diagnosis of death according to neurological criteria, whose heart is rejected for heart transplant; c) Cadaver donors with asystolia of less than 8 hours. Homograft cardiac valves are the substitute of choice in aortic valve endocarditis, patients with counter-indications for anticoagulation, reconstruction of the outflow tract of the right ventricle, aortic valve replacement in children and young adults through the Ross operation, and an optional indication is the aortic valve and/or rising aorta replacement in patients over 60 years of age. Although there are not sufficiently broad series of homogratfs with arterial substitutes, with respect to the number of patients and time of evolution, the results suggest that this can benefit patients with vascular infection, immunodepressed patients or complex patients whose technique during the operation might require a homograft

The pro-neurotrophin receptor sortilin is a major neuronal apolipoprotein E receptor for catabolism of amyloid-β peptide in the brain

Apolipoprotein E (APOE) is the major risk factor for sporadic Alzheimer's disease. Among other functions, APOE is proposed to sequester neurotoxic amyloid-{beta} (A{beta}) peptides in the brain, delivering them to cellular catabolism via neuronal APOE receptors. Still, the receptors involved in this process remain controversial. Here, we identified the pro-neurotrophin receptor sortilin as major endocytic pathway for clearance of APOE/A{beata} complexes in neurons. Sortilin binds APOE with high affinity. Lack of receptor expression in mice results in accumulation of APOE and of A{beta} in the brain and in aggravated plaque burden. Also, primary neurons lacking sortilin exhibit significantly impaired uptake of APOE/A{beta} complexes despite proper expression of other APOE receptors. Despite higher than normal brain APOE levels, sortilin-deficient animals display anomalies in brain lipid metabolism (e.g., accumulation of sulfatides) seen in APOE-deficient mice, indicating functional deficiency in cellular APOE uptake pathways. Together, our findings identified sortilin as an essential neuronal pathway for APOE-containing lipoproteins in vivo and suggest an intriguing link between A{beta} catabolism and pro-neurotrophin signaling converging on this receptor