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. Interestingly, a few annotated pseudogenes were indeed able to express peptides downstream of the inactivation site, suggesting the occurrence of recoding. Two mechanisms of recoding, namely, programmed frameshifting and codon redefinition, were both found. We believe that the phenomena of recoding are not rare in bacteria. More studies are required for a better understanding of bacterial translation and the implication of pseudogene recoding in Salmonella serovars.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Feng Y,Chien KY,Chen HL,Chiu CHdoi
10.1021/pr200904csubject
Has Abstractpub_date
2012-03-02 00:00:00pages
1715-9issue
3eissn
1535-3893issn
1535-3907journal_volume
11pub_type
杂志文章abstract：:Vascular endothelial growth factor receptor-2 (VEGFR-2) is an important receptor tyrosine kinase (RTK) that plays critical roles in both physiologic and pathologic angiogenesis. The extracellular domain of VEGFR-2 is composed of seven immunoglobulin-like domains, each with multiple potential N-glycosylation sites (seq...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00738
更新日期：2017-02-03 00:00:00
abstract：:Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00373
更新日期：2017-09-01 00:00:00
abstract：:Catechol estrogens (CEs) are known to be toxic metabolites and the initiators of the oncogenesis of breast cancers via forming covalent adducts with DNAs. CEs shall also react with proteins, but their cellular protein targets remain unexplored. Here, we reported the identification of protein targets of CEs in the solu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00578
更新日期：2021-01-01 00:00:00
abstract：:We have developed a high-throughput system for generating baculoviruses and testing the expression, solubility, and affinity column purification of encoded proteins. We have used this system to generate baculoviruses for and analyze the expression of 337 proteins from three different herpesviruses (HSV-1, EBV, and CMV...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050137u
更新日期：2005-11-01 00:00:00
abstract：:Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-thr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7008252
更新日期：2008-04-01 00:00:00
abstract：:Linear, short-chain polyfluorinated and perfluorinated alkyl compounds, often referred to as PFCs, have been in worldwide use as surfactants and polymer precursors for decades, and environmental dispersal of these highly persistent compounds represents a public health threat. Whereas ubiquitous low-level exposure to t...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr500990w
更新日期：2015-01-02 00:00:00
abstract：:In an attempt to find out the association of metabolic dysregulation with poor endometrial receptivity and pregnancy loss, serum metabonomic profiling of women with idiopathic recurrent spontaneous miscarriage (IRSM) is carried out and compared with fertile controls. (1)H nuclear magnetic resonance (NMR)-based metabon...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500379n
更新日期：2014-06-06 00:00:00
abstract：:Sardinian alcohol-preferring (sP) and Sardinian alcohol-non preferring (sNP) rats have been selectively bred for opposite alcohol preference and consumption. Aiming to verify possible differences at the proteomics level between sP and sNP rats, we investigated the salivary proteome by a a liquid chromatography-mass sp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00632
更新日期：2018-01-05 00:00:00
abstract：:Glutaredoxins (GRXs), small redox proteins that use reduced glutathione as an electron donor, are key components of the cellular antioxidant system. In this study, we used Saccharomyces cerevisiae as a model system to investigate the effects of GRX deletion on yeast chronological life span (CLS). Deletion of either Gr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00012
更新日期：2018-07-06 00:00:00
abstract：:Recently, we reported comparative analysis of glycoproteins which express cancer-specific N-glycans on various cancer cells and identified 24 glycoproteins having polylactosamine (polyLacNAc)-type N-glycans that are abundantly present in malignant cells [ Mitsui et al., J. Pharm. Biomed. Anal. 2012 , 70 , 718 - 726 ]....
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401015b
更新日期：2014-02-07 00:00:00
abstract：:The vast majority of human multiexon genes undergo alternative splicing and produce a variety of splice variant transcripts and proteins, which can perform different functions. These protein-coding splice variants (PCSVs) greatly increase the functional diversity of proteins. Most functional annotation algorithms have...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00883
更新日期：2016-06-03 00:00:00
abstract：:Oligomeric amyloid-β is currently of interest in amyloid-β mediated toxicity and the pathogenesis of Alzheimer's disease. Mapping the amyloid-β interaction partners could help to discover novel pathways in disease pathogenesis. To discover the amyloid-β interaction partners, we applied a protein array with more than 8...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1009096
更新日期：2011-04-01 00:00:00
abstract：:The chromatophore membrane of the photosynthetic diazotroph Rhodospirillum rubrum is of vital importance for a number of central processes, including nitrogen fixation. Using a novel amphiphile, we have identified protein complexes present under different nitrogen availability conditions by the use of two-dimensional ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100838x
更新日期：2011-06-03 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：:Individual proteomes typically differ from the reference human proteome at ∼10,000 single amino acid variants. When viewed on the population scale, this individual variation results in a wide variety of protein sequences. In targeted proteomics experiments, such variability can confound accurate protein quantification...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4011052
更新日期：2014-01-03 00:00:00
abstract：:Yeast two-hybridization (Y2H) is a classical method to study protein-protein interactions in organisms, and the top limitation of Y2H is the high ratio of false negatives and false positives. The most efficient way to reduce this error is to improve the quality of the library. The traditional library quality evaluatio...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00189
更新日期：2020-08-07 00:00:00
abstract：:Chronic Obstructive Pulmonary Disease (COPD), a lung disease related to smoking, is one of the leading causes of chronic morbidity and mortality around the world. One goal in COPD research is the identification of biomarkers for early diagnosis of the disease. Here, we sought COPD-specific changes in the proteome from...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800423x
更新日期：2008-12-01 00:00:00
abstract：:To understand bacterial reactions to environmental stress or infection-related processes, it is necessary to identify the involved proteins. In mass spectrometry-based proteomics, the method of choice for spectra-to-peptide-match is database search, but in recent times, spectral libraries have come into focus. Here, w...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00615
更新日期：2020-04-03 00:00:00
abstract：:Tropomyosins (Tm) constitute a family of ubiquitous and highly conserved actin-binding proteins, playing essential roles in a variety of biological processes. Tm isoforms produced by multiple Tm encoding genes and alternatively expressed exons along with post-translational modifications (PTMs) regulate Tm function. Th...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301054n
更新日期：2013-01-04 00:00:00
abstract：:Human milk is a rich source of bioactive proteins that support the early growth and development of the newborn. Although the major components of the protein fraction in human milk have been studied, the expression and relative abundance of minor components have received limited attention. We examined the expression of...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101028k
更新日期：2011-04-01 00:00:00
abstract：:The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyse...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900663d
更新日期：2009-11-01 00:00:00
abstract：:Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m (3) of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. T...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7006285
更新日期：2008-07-01 00:00:00
abstract：:Protein phosphorylation is the most abundant reversible covalent modification. Human protein kinases participate in almost all biological pathways, and approximately half of the kinases are associated with disease. PhoSigNet was designed to store and display human phosphorylation-mediated signal transduction networks,...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00249
更新日期：2015-07-02 00:00:00
abstract：:Coronary artery disease is one of the most frequent causes of morbidity and mortality worldwide. It is even more prevalent in patients with type 2 diabetes mellitus who suffer from obesity and increased accumulation of epicardial fat with a possible contributing role in the development of coronary artery disease. We p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00269
更新日期：2020-10-02 00:00:00
abstract：:Autosomal dominant polycystic liver disease (PCLD) is characterized by multiple liver cysts and is caused by mutations in PRKCSH (hepatocystin). Mechanisms of cystogenesis are unknown, but previous studies have shown that hepatocystin is secreted in vitro. The goal of this study was to determine the fate of hepatocyst...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8000282
更新日期：2008-06-01 00:00:00
abstract：:Immune recognition of nonself is coordinated through complex mechanisms involving both innate and adaptive responses. Circulating antibodies communicate with effector cells of the innate immune system through surface receptors known as Fcγ receptors (FcγRs). The FcγRs are single-pass transmembrane glycoproteins respon...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400344h
更新日期：2013-08-02 00:00:00
abstract：:Aberrant protein phosphorylation plays important roles in cancer-related cell signaling. With the goal of achieving multiplexed, comprehensive, and fully automated relative quantitation of site-specific phosphorylation, we present a simple label-free strategy combining an automated pH/acid-controlled IMAC procedure an...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100394u
更新日期：2010-11-05 00:00:00
abstract：:Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800169k
更新日期：2008-07-01 00:00:00
abstract：:Due to the increasing prevalence of nosocomial and community-acquired antibiotic resistant Staphylococcus aureus (SA), understanding the determinants of SA nasal carriage has become a major imperative. Previous research has revealed many host and bacterial factors that contribute to SA nasal carriage. To assess bacter...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200029r
更新日期：2011-04-01 00:00:00
abstract：:Large-scale identification of protein-protein interactions (PPIs) in functional complexes represents an efficient route to elucidate the regulatory rules of cellular functions. Whereas many methods have been developed to identify the PPIs associated with particular target/bait protein in complexes, little information ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800662x
更新日期：2009-05-01 00:00:00
