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The proteome landscape of the kingdoms of life 期刊论文
NATURE, 2020
作者:  Arzi, Anat;  Rozenkrantz, Liron;  Gorodisky, Lior;  Rozenkrantz, Danit;  Holtzman, Yael;  Ravia, Aharon;  Bekinschtein, Tristan A.;  Galperin, Tatyana;  Krimchansky, Ben-Zion;  Cohen, Gal;  Oksamitni, Anna;  Aidinoff, Elena;  Sacher, Yaron;  Sobel, Noam
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported(1), advances in mass-spectrometry-based proteomics(2)have enabled increasingly comprehensive identification and quantification of the human proteome(3-6). However, there have been few comparisons across species(7,8), in stark contrast with genomics initiatives(9). Here we use an advanced proteomics workflow-in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system-for the in-depth study of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a large-scale case study for sequence-based machine learning, as we demonstrate by experimentally confirming the predicted properties of peptides fromBacteroides uniformis. Our results offer a comparative view of the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the biological challenge of maintaining protein structure in all branches of life. Likewise, a universally high fraction is involved in supplying energy resources, although these pathways range from photosynthesis through iron sulfur metabolism to carbohydrate metabolism. Generally, however, proteins and proteomes are remarkably diverse between organisms, and they can readily be explored and functionally compared at www.proteomesoflife.org.


  
Mechanism of adrenergic Ca(V)1.2 stimulation revealed by proximity proteomics 期刊论文
NATURE, 2020, 577 (7792) : 695-+
作者:  Peng, Guangdun;  Suo, Shengbao;  Cui, Guizhong;  Yu, Fang;  Wang, Ran;  Chen, Jun;  Chen, Shirui;  Liu, Zhiwen;  Chen, Guoyu;  Qian, Yun;  Tam, Patrick P. L.;  Han, Jing-Dong J.;  Jing, Naihe
收藏  |  浏览/下载:24/0  |  提交时间:2020/07/03

An in vivo approach to identify proteins whose enrichment near cardiac Ca(V)1.2 channels changes upon beta-adrenergic stimulation finds the G protein Rad, which is phosphorylated by protein kinase A, thereby relieving channel inhibition by Rad and causing an increased Ca2+ current.


Increased cardiac contractility during the fight-or-flight response is caused by beta-adrenergic augmentation of Ca(V)1.2 voltage-gated calcium channels(1-4). However, this augmentation persists in transgenic murine hearts expressing mutant Ca(V)1.2 alpha(1C) and beta subunits that can no longer be phosphorylated by protein kinase A-an essential downstream mediator of beta-adrenergic signalling-suggesting that non-channel factors are also required. Here we identify the mechanism by which beta-adrenergic agonists stimulate voltage-gated calcium channels. We express alpha(1C) or beta(2B) subunits conjugated to ascorbate peroxidase(5) in mouse hearts, and use multiplexed quantitative proteomics(6,7) to track hundreds of proteins in the proximity of Ca(V)1.2. We observe that the calcium-channel inhibitor Rad(8,9), a monomeric G protein, is enriched in the Ca(V)1.2 microenvironment but is depleted during beta-adrenergic stimulation. Phosphorylation by protein kinase A of specific serine residues on Rad decreases its affinity for beta subunits and relieves constitutive inhibition of Ca(V)1.2, observed as an increase in channel open probability. Expression of Rad or its homologue Rem in HEK293T cells also imparts stimulation of Ca(V)1.3 and Ca(V)2.2 by protein kinase A, revealing an evolutionarily conserved mechanism that confers adrenergic modulation upon voltage-gated calcium channels.


  
Nitrogen sourcing during viral infection of marine cyanobacteria 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2019, 116 (31) : 15590-15595
作者:  Waldbauer, Jacob R.;  Coleman, Maureen L.;  Rizzo, Adriana, I;  Campbell, Kathryn L.;  Lotus, John;  Zhang, Lichun
收藏  |  浏览/下载:4/0  |  提交时间:2019/11/27
biogeochemistry  proteomics  bacteriophage  
Metaproteomics Identifies the Protein Machinery Involved in Metal and Radionuclide Reduction in Subsurface Microbiomes and Elucidates Mechanisms and U(VI) Reduction Immobilization 科技报告
来源:US Department of Energy (DOE). 出版年: 2015
作者:  Pfiffner, Susan M.;  LĂśffler, Frank;  Ritalahti, Kirsti;  Sayler, Gary;  Layton, Alice;  Hettich, Robert
收藏  |  浏览/下载:4/0  |  提交时间:2019/04/05
Dissimilatory metal-reducing bacteria  proteomics  c-type cytochrome  radionuclide reduction  
Syntrophic interactions and mechanisms underpinning anaerobic methane oxidation: targeted metaproteogenomics, single-cell protein detection and quantitative isotope imaging of microbial consortia 科技报告
来源:US Department of Energy (DOE). 出版年: 2014
作者:  Orphan, Victoria Jeanne
收藏  |  浏览/下载:3/0  |  提交时间:2019/04/05
methane  syntrophy  stable isotope probing  nanoSIMS  proteomics  
Nitrate Enhanced Microbial Cr(VI) Reduction-Final Report 科技报告
来源:US Department of Energy (DOE). 出版年: 2011
作者:  Joel E. Kostka;  Lee Kerkhof;  Kuk-Jeong Chin;  Martin Keller;  Joseph W. Stucki
收藏  |  浏览/下载:13/0  |  提交时间:2019/04/05
nitrate reduction  chromate reduction  Geobacter metallireducens  Desulfovibrio desulfuricans  Sulfurospirillum barnesii  nitrite reductase  desulfoviridin  multi-heme cyctochrome C  proteomics  MALDI-TOF  LC/MS-MS