Abstract：
:Mutagenesis through fast neutron (FN) radiation of soybean resulted in a mutant with a 15% increase in seed protein content. A comparative genomic hybridization analysis confirmed that the mutant is lacking 24 genes located at chromosomes 5 and 10. A tandem mass tag-based proteomic profiling of the wild type and the FN mutant revealed 3,502 proteins, of which 206 proteins exhibited increased abundance and 214 proteins showed decreased abundance. Among the abundant proteins, basic 7S globulin increased fourfold, followed by vacuolar-sorting receptor and protein transporters. The differentially expressed proteins were mapped on the global metabolic pathways. It was observed that there was an enrichment of 29 ribosomal proteins, 16 endoplasmic reticular proteins, and several proteins in export metabolic pathways. The deletion of the sequence-specific DNA binding transcription factor along with 23 other genes may have altered the negative regulation of protein syntheses processes, resulting in an increase in the overall protein content of the mutant seed. This mutant is a valuable resource for researchers to understand the metabolic pathways that may affect an increase in seed protein content (the mass spectrometry data files were submitted to massive.ucsd.edu # MassIVE MSV000084228).
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Islam N,Krishnan HB,Natarajan Sdoi
10.1021/acs.jproteome.0c00160subject
Has Abstractpub_date
2020-10-02 00:00:00pages
3936-3944issue
10eissn
1535-3893issn
1535-3907journal_volume
19pub_type
杂志文章abstract：:Stress in the form of moderate periods of maternal separation of newborn rats has been postulated to cause permanent changes in the central nervous system and diseases in later life. It is also considered that dietary supplementation with long chain polyunsaturated fatty acids (LC-PUFAs) can potentially ameliorate the...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0504182
更新日期：2006-07-01 00:00:00
abstract：:Protein cleavage coupled with isotope dilution mass spectrometry (PC-IDMS) has the potential to provide the absolute concentration of a specific protein, or multiple proteins, in complex mixtures. However, PC-IDMS differs from standard IDMS since the internal standard is a different molecule than the analyte at the st...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr034124x
更新日期：2004-05-01 00:00:00
abstract：:Mass spectrometry (MS) has become an accessible tool for whole proteome quantitation with the ability to characterize protein expression across thousands of proteins within a single experiment. A subset of MS quantification methods (e.g., SILAC and label-free) monitor the relative intensity of intact peptides, where t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00699
更新日期：2018-01-05 00:00:00
abstract：:Phosphorylation enhances IGFBP-1 binding to IGF-I, thereby limiting the bioavailability of IGF-I that may be important in fetal growth. Our goal in this study was to determine whether changes in site-specific IGFBP-1 phosphorylation were unique to fetal growth restriction. To establish a link, we compared IGFBP-1 phos...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900987n
更新日期：2010-04-05 00:00:00
abstract：:Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00165
更新日期：2018-06-01 00:00:00
abstract：:Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results....
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00113
更新日期：2019-01-04 00:00:00
abstract：:Endothelial cells (ECs) form the inner layer of blood vessels and physically separate the blood from the surrounding tissue. To support tissues with nutrients and oxygen, the endothelial monolayer is semipermeable. When EC permeability is altered, blood vessels are not functional, and this is associated with disease. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00166
更新日期：2016-07-01 00:00:00
abstract：:The balance between comprehensively analyzing the proteome and using valuable mass spectrometry time is a genuine challenge in the field of proteomics. Multidimensional fractionation strategies have significantly increased proteome coverage, but often at the cost of increased mass analysis time, despite advances in ma...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00082
更新日期：2019-05-03 00:00:00
abstract：:Monoassociation of germfree Interleukin 10 gene deficient (IL-10-/-) 129SvEv but not wild-type mice with Enterococcus faecalis induces severe chronic colitis. Bacterial strain-specific effects on the development of chronic intestinal inflammation are not understood. We investigated the molecular mechanisms of E. faeca...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800785m
更新日期：2009-03-01 00:00:00
abstract：:Cellular functions are largely carried out by noncovalent protein complexes that may exist within the cell as stable modules or as assemblies of dynamically changing composition, whose formation and decomposition are triggered in response to extracellular stimuli. The protein constituents of complexes often exhibit po...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1003888
更新日期：2010-10-01 00:00:00
abstract：:Proteins and peptides present within clinical samples represent a valuable library of information regarding the ongoing processes within cells and tissues in health and disease. We have developed and validated novel technology applications that can be used to characterize the patterns of global protein expression in t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050122w
更新日期：2005-07-01 00:00:00
abstract：:A common animal model of chemical hepatocarcinogenesis was used to demonstrate the potential identification of carcinogenicity related protein signatures/biomarkers. Therefore, an animal study in which rats were treated with the known liver carcinogen N-nitrosomorpholine (NNM) or the corresponding vehicle was evaluate...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050279o
更新日期：2006-02-01 00:00:00
abstract：:Bacillus Amyloliquefaciens SQR9 is a well-investigated plant growth-promoting rhizobacteria with strong root colonization capability. To identify the key proteins involved in in situ root colonization and biofilm formation, the proteomic profiles of planktonic and root colonized SQR9 cells were compared. A total of 75...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500565m
更新日期：2014-12-05 00:00:00
abstract：:To identify proteins that are involved in the molecular mechanisms of oxygen-induced retinopathy (OIR), a well-established model of blinding ischemic retinopathy, we quantitatively analyzed the retinal proteome in a mouse model of OIR. OIR was induced by exposing C57BL/6 mice on postnatal day 7 (P7) to 75% hyperoxia f...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300389r
更新日期：2012-11-02 00:00:00
abstract：:A selective method for the enrichment of O-GlcNAcylated peptides using a novel CLICK chemistry reagent is described. Peptides modified by O-GlcNAc were enzymatically labeled with N-azidoacetylgalactosamine. The azide was then reacted with a phospho-alkyne using CLICK chemistry and O-GlcNAcGalNAzPO(4)-containing peptid...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100565j
更新日期：2011-04-01 00:00:00
abstract：:Akt1 is a serine/threonine kinase that promotes cell growth and survival. Previously, Akt1 activation in a double transgenic (DTG) mouse model fed a high-fat/high-sucrose (HF/HS) diet was found to promote type IIb muscle growth and to lead to a significant reduction in obesity. Here, we have used metabolomics to exami...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500756u
更新日期：2015-01-02 00:00:00
abstract：:A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragm...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00184
更新日期：2015-06-05 00:00:00
abstract：:The Human Proteome Project (HPP) has made great efforts to clarify the existing evidence of human proteins since 2012. However, according to the recent release of neXtProt (2019-1), approximately 10% of all human genes still have inadequate or no experimental evidence of their translation at the protein level. They we...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00355
更新日期：2019-12-06 00:00:00
abstract：:We recently developed a novel method for analysis of collagen O-glycosylations, which include galactosyl-hydroxylysine (GHL) and glucosyl-galactosyl-hydroxylysine (GGHL), using hydrazide chemistry (Taga, Y., Mol. Cell. Proteomics 2012, 11 (6), M111.010397). Here we investigated an overglycosylation model of collagen p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400079d
更新日期：2013-05-03 00:00:00
abstract：:Wilson's Disease (WD), a copper transport disorder caused by a genetic defect in the ATP7B gene, has been a long time strong candidate for newborn screening (NBS), since early interventions can give better results by preventing irreversible neurological disability or liver cirrhosis. Several previous pilot studies mea...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00828
更新日期：2017-02-03 00:00:00
abstract：:Compartment proteomics enable broad characterization of target tissues. We employed a simple fractionation method and filter-aided sample preparation (FASP) to characterize the cytosolic and membrane fractions of white perch ovary tissues by semiquantitative tandem mass spectrometry using label-free quantitation based...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401067g
更新日期：2014-03-07 00:00:00
abstract：:Streptococcus agalactiae causes severe systemic infections in human and fish. In the present study, we established a pathogen-plasma interaction model by which we explored how S. agalactiae evaded serum-mediated killing. We found that S. agalactiae grew faster in the presence of yellow grouper plasma than in the absen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00215
更新日期：2016-07-01 00:00:00
abstract：:We undertook an unbiased metabolite profiling of fibroblasts from schizophrenia patients and healthy controls to identify metabolites and pathways that are dysregulated in disease, seeking to gain new insights into the disease biology of schizophrenia and to discover potential disease-related biomarkers. We measured p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00628
更新日期：2017-02-03 00:00:00
abstract：:Protein turnover is an important aspect of the regulation of cellular processes for organisms when responding to developmental or environmental cues. The measurement of protein turnover in plants, in contrast to that of rapidly growing unicellular organismal cultures, is made more complicated by the high degree of ami...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00772
更新日期：2016-03-04 00:00:00
abstract：:Several high-throughput statistical methods were evaluated for processing data generated by two-dimensional polyacrylamide gel electrophoresis, including how to handle missing data, normalization, and statistical analysis of data obtained from 2-D gels. Quantile normalization combined with a nonparametric permutation ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049886m
更新日期：2004-11-01 00:00:00
abstract：:A biphasic monolithic capillary column with 10 cm segment of strong-cation exchange monolith and 65 cm segment of reversed-phase monolith was prepared within a single 100 microm i.d. capillary. Separation performance of this column was evaluated by a five-cycle online multidimensional separation of 10 microg tryptic d...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr700562b
更新日期：2008-01-01 00:00:00
abstract：:A rate-limiting and costly step in many proteomics analyses is the cloning of all of the ORFs for an organism into technique-specific vectors. Here, we describe the generation of a Campylobacter jejuni expression clone set using a high-throughput cloning approach based on recombination in E. coli. The approach uses na...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0341134
更新日期：2004-05-01 00:00:00
abstract：:Starting in 2007, we have grown soybean (Glycine max [L.] Merr. variety Soniachna) and flax (Linum usitatissimum, L. variety Kyivskyi) in the radio-contaminated Chernobyl area and analyzed the seed proteomes. In the second-generation flax seeds, we detected a 12% increase in oil content. To characterize the bases for ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400528m
更新日期：2013-11-01 00:00:00
abstract：:Mass spectrometry is being used to identify protein biomarkers that can facilitate development of drug treatment. Mass spectrometry-based labeling proteomic experiments result in complex proteomic data that is hierarchical in nature often with small sample size studies. The generalized linear model (GLM) is the most p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b01050
更新日期：2017-09-01 00:00:00
abstract：:Recoding refers to the reprogramming of mRNA translation by nonstandard read-out rules. In this study, we used stable isotope labeling with amino acids in cell culture (SILAC) technology to investigate the proteome of host-adapted Salmonella serovars, which are characteristic of accumulation of pseudogenes. Interestin...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200904c
更新日期：2012-03-02 00:00:00
