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  • 1
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 50 ( 2012-12-11)
    Abstract: Except for cystinosin, the molecular activity of other PQ-loop proteins remains unknown. The elucidation of PQLC2 function suggests that small-molecule transport is a conserved feature of the PQ-loop protein family, in agreement with the recent identification of SWEET sugar transporters ( 3 ) and of the mitochondrial pyruvate carrier ( 4 , 5 ) in related protein families. The characterization of PQLC2 also has clinical implications. Its role in cysteamine therapy of cystinosis should form the basis of rationales to improve this treatment and alleviate its constraints and side effects. For instance, allosteric or transcriptional activators of PQLC2 might potentiate cysteamine and help reduce the doses. The study of PQLC2 may also help clarify the origin of cationic amino acid abnormalities in Batten disease, another lysosomal disease characterized by early-onset neurodegeneration and the accumulation of “aging pigment” (lipofuscin) in lysosomes. We next showed that PQLC2 exports from lysosomes a key chemical intermediate (cysteamine-cysteine mixed disulfide) underlying the current drug therapy of cystinosis, a rare inherited disease caused by mutations in the cystinosin gene. In this condition, large amounts of cystine accumulate in the patient’s lysosomes ( Fig. P1 ) and progressively impair the function of multiple organs, including the kidney, endocrine glands, muscles, and CNS ( 1 ). The drug cysteamine (Cystagon) depletes cystine from cystinotic lysosomes and, with lifelong treatment, alleviates symptoms. According to an early biochemical model ( 1 ), cysteamine reacts with lysosomal cystine and forms a lysine-like mixed disulfide that exits lysosomes through an unknown lysosomal transporter of cationic amino acids ( Fig. P1 ). The elucidation of PQLC2 function prompted us to examine whether it corresponded to this mixed disulfide transporter. Using our frog oocyte assay, we found that PQLC2 efficiently transports the mixed disulfide. Moreover, silencing of the PQLC2 human gene in cultured cells of patients trapped this intermediate when cells were exposed to cysteamine. We concluded that PQLC2 plays a key role in the therapeutic action of cysteamine. We next identified PQLC2, a mammalian PQ-loop protein closely related to the yeast Ypq proteins, in purified lysosomal membranes. Because of the strong homology between PQLC2 and Ypq1–3, we reasoned that cationic amino acids are likely substrates. Indeed, frog oocytes expressing PQLC2 at their plasma membrane displayed robust transport activity that was strongly activated in acidic extracellular medium (mimicking the lysosomal lumen) and exhibited narrow selectivity for cationic amino acids, including arginine, histidine, and lysine. Moreover, heterologous expression of PQLC2 at the vacuole of the yeast ypq2 mutant restored canavanine sensitivity, and PQLC2 efficiently transported canavanine, suggesting that the increased canavanine sensitivity provided by PQLC2 results from increased vacuolar export. We concluded that PQLC2 and Ypq1–3 are evolutionarily conserved lysosomal/vacuolar exporters of cationic amino acids. We first showed that three yeast PQ-loop proteins of unknown function, Ypq1, Ypq2, and Ypq3, localize to the vacuolar membrane and are involved in homeostasis of cationic amino acids. Genetic inactivation of Ypq1 and Ypq2 decreases the sensitivity of yeast cells to canavanine, a natural toxic analog of arginine. This resistance phenotype requires prior accumulation of cationic amino acids in the vacuole. Moreover, transcription of the YPQ3 gene is activated by lysine starvation. We thus hypothesized that Ypq1–3 proteins export cationic amino acids from the yeast vacuole. Transport of solute across membranes is crucial to eukaryotic cell physiology, as illustrated by diverse diseases associated with defective transport and the presence of ∼400 solute transporter genes in humans. However, the function of many putative transporters remains unknown, such as the proteins responsible for lysosomal export of metabolites. Cystinosin, the lysosomal cystine exporter defective in cystinosis ( 1 ), is characterized by a duplicated motif termed the PQ loop. PQ-loop proteins are more frequent in eukaryotes than in prokaryotes, and, except for cystinosin, their molecular function remains unknown. The substrate-coupled proton-binding site is nested in the second PQ loop, suggesting that these motifs have functional significance ( 2 ). Here, we showed that another PQ-loop protein, PQLC2, is a lysosomal amino acid transporter that is relevant for the treatment of cystinosis.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
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  • 2
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 338, No. 6114 ( 2012-12-21), p. 1569-1575
    Abstract: The Higgs boson was postulated nearly five decades ago within the framework of the standard model of particle physics and has been the subject of numerous searches at accelerators around the world. Its discovery would verify the existence of a complex scalar field thought to give mass to three of the carriers of the electroweak force—the W + , W – , and Z 0 bosons—as well as to the fundamental quarks and leptons. The CMS Collaboration has observed, with a statistical significance of five standard deviations, a new particle produced in proton-proton collisions at the Large Hadron Collider at CERN. The evidence is strongest in the diphoton and four-lepton (electrons and/or muons) final states, which provide the best mass resolution in the CMS detector. The probability of the observed signal being due to a random fluctuation of the background is about 1 in 3 × 10 6 . The new particle is a boson with spin not equal to 1 and has a mass of about 125 giga–electron volts. Although its measured properties are, within the uncertainties of the present data, consistent with those expected of the Higgs boson, more data are needed to elucidate the precise nature of the new particle.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2012
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  • 3
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 32 ( 2020-08-11), p. 19168-19177
    Abstract: The emergence of superbugs developing resistance to antibiotics and the resurgence of microbial infections have led scientists to start an antimicrobial arms race. In this context, we have previously identified an active RiPP, the Ruminococcin C1, naturally produced by Ruminococcus gnavus E1, a symbiont of the healthy human intestinal microbiota. This RiPP, subclassified as a sactipeptide, requires the host digestive system to become active against pathogenic Clostridia and multidrug-resistant strains. Here, we report its unique compact structure on the basis of four intramolecular thioether bridges introduced post-translationally by a specific radical-SAM sactisynthase. This structure confers to the Ruminococcin C1 important clinical properties including stability to digestive conditions and physicochemical treatments, a higher affinity for bacteria than simulated intestinal epithelium, a valuable activity at therapeutic doses on a range of clinical pathogens, mediated by energy resources disruption, and finally safety for human gut tissues.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
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  • 4
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2014
    In:  Proceedings of the National Academy of Sciences Vol. 111, No. 4 ( 2014-01-28), p. 1385-1390
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 111, No. 4 ( 2014-01-28), p. 1385-1390
    Abstract: Modern scientific research produces datasets of increasing size and complexity that require dedicated numerical methods to be processed. In many cases, the analysis of spectroscopic data involves the denoising of raw data before any further processing. Current efficient denoising algorithms require the singular value decomposition of a matrix with a size that scales up as the square of the data length, preventing their use on very large datasets. Taking advantage of recent progress on random projection and probabilistic algorithms, we developed a simple and efficient method for the denoising of very large datasets. Based on the QR decomposition of a matrix randomly sampled from the data, this approach allows a gain of nearly three orders of magnitude in processing time compared with classical singular value decomposition denoising. This procedure, called urQRd (uncoiled random QR denoising), strongly reduces the computer memory footprint and allows the denoising algorithm to be applied to virtually unlimited data size. The efficiency of these numerical tools is demonstrated on experimental data from high-resolution broadband Fourier transform ion cyclotron resonance mass spectrometry, which has applications in proteomics and metabolomics. We show that robust denoising is achieved in 2D spectra whose interpretation is severely impaired by scintillation noise. These denoising procedures can be adapted to many other data analysis domains where the size and/or the processing time are crucial.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2014
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