The poly(C)-binding proteins: A multiplicity of functions and a search for mechanisms

Makeyev, Aleksandr V.; Liebhaber, Stephen A.

doi:10.1017/s1355838202024627

Cited by 413 publications

(427 citation statements)

References 95 publications

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“…It is also believed that BAG3 could be responsible for impairing response to therapy, and could represent a novel therapeutic target [57]. The other up-regulated protein, Poly(rC)-binding protein 1, is a nucleic acid binding protein that functions as an accelerator of mRNA metabolic processes and has roles in mRNA stabilization, translational activation and translational silencing [58,59]. In addition, several proteins with role in cell proliferation and tumorigenesis that are up-regulated in cancerous cell states have been found to be down-regulated in the Tam treated cells.…”

Section: Biological Relevance Of Differentially Expressed Proteinsmentioning

confidence: 99%

Differential protein expression analysis using stable isotope labeling and PQD linear ion trap MS technology

Armenta

Hoeschele

Lazar

2009

J. Am. Soc. Mass Spectrom.

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An isotope tags for relative and absolute quantitation (iTRAQ)-based reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) method was developed for differential protein expression profiling in complex cellular extracts. The estrogen positive MCF-7 cell line, cultured in the presence of 17␤-estradiol (E2) and tamoxifen (Tam), was used as a model system. MS analysis was performed with a linear trap quadrupole (LTQ) instrument operated by using pulsed Q dissociation (PQD) detection. Optimization experiments were conducted to maximize the iTRAQ labeling efficiency and the number of quantified proteins. MS data filtering criteria were chosen to result in a false positive identification rate of Ͻ4%. The reproducibility of protein identifications was ϳ60%-67% between duplicate, and ϳ50% among triplicate LC-MS/MS runs, respectively. The run-to-run reproducibility, in terms of relative standard deviations (RSD) of global mean iTRAQ ratios, was better than 10%. The quantitation accuracy improved with the number of peptides used for protein identification. From a total of 530 identified proteins (P Ͻ 0.001) in the E2/Tam treated MCF-7 cells, a list of 255 proteins (quantified by at least two peptides) was generated for differential expression analysis. A method was developed for the selection, normalization, and statistical evaluation of such datasets. An approximate ϳ2-fold change in protein expression levels was necessary for a protein to be selected as a biomarker candidate. According to this data processing strategy, ϳ16 proteins involved in biological processes such as apoptosis, RNA processing/metabolism, DNA replication/transcription/repair, cell proliferation and metastasis, were found to be up-or down-regulated. R ecently, two-dimensional liquid chromatography (2DLC) with tandem MS detection has emerged as an attractive technology for quantitative proteomic profiling of complex cellular extracts [1][2][3][4]. Stable isotope labeling and label-free quantitation strategies have been explored [4 -13]. Isotope labeling approaches rely on the covalent attachment of stable isotope tags to specific amino acid residues of proteins or peptides during metabolic, enzymatic, or chemical processes. Label-free quantitation methods rely on measuring peak areas, intensities, or spectral counts, and benefit from not having to chemically alter the sample. Throughput, however, is lower, and quantitation errors are higher, as the samples are processed independently. Among chemical labeling techniques, isotope tags for relative and absolute quantitation (iTRAQ) has received much attention [14 -30]. In this approach, peptides are labeled with isobaric tags at the N-terminus and the lysine side chains. MS/MS fragmentation produces signature ions that can be used to obtain quantitative information. Perhaps the most attractive advantage of this approach is that it can be used for the simultaneous quantification (relative or absolute) of up to four/eight different samples. Simplicity, of course, is an added benefit.A...

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Section: Biological Relevance Of Differentially Expressed Proteinsmentioning

confidence: 99%

Differential protein expression analysis using stable isotope labeling and PQD linear ion trap MS technology

Armenta

Hoeschele

Lazar

2009

J. Am. Soc. Mass Spectrom.

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“…The repeat sequence is highly C-rich and many KH-domain RNAbinding proteins can bind to such sequences and are known to be involved in various post-transcriptional controls. 26 Indeed, a scan of the D4 sequence for sequences that may modify RNA stability and translational efficiency 27 identified hnRNP K and E binding sites, known as DICE, that are present as a tandem repeated sequence in the 15-lipoxygenase 3 0 untranslated region and suppress translation. 28,29 This identified consensus sequence is present in the region analyzed and includes sequences in the first repeat unit (a sequence).…”

Section: O Schoots and Hhm Van Tolmentioning

confidence: 99%

The human dopamine D4 receptor repeat sequences modulate expression

2003

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Genetic studies have implicated a polymorphic repeat sequence in exon 3 of the human dopamine D4 receptor in various behavioral and psychiatric disorders. Functionally various repeat variants are nearly identical, but whether these have different effects on gene expression has not been studied. To study the role of the repeat sequences on expression independently from its structural and functional effects at the protein level, we introduced these sequences immediately upstream of the promoter and in the 3 0 untranslated region of a luciferase reporter vector. In this report, we demonstrate that the repeat sequence can both modulate promoter activity and alter expression post-transcriptionally. The repeat sequence can serve as a substrate for a nuclear binding factor and all the three repeat variants can suppress promoter activity. Placement of the three repeat variants downstream from the luciferase gene in the expression vector shows, however, that the D4.7 repeat sequence has significantly suppressed expression of the reporter compared to the D4.2 and D4.4 repeats, likely via mechanisms involving RNA stability or translational efficiency. These data indicate that the various D4 repeat sequences have different effects on expression, which may explain its potential role in behavioral disorders.

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“…As a result of alternative splicing, there are several known isoforms of K protein (Dejgaard et al, 1994;Makeyev and Liebhaber, 2002). To explore the possibility that there are isoforms of K protein enriched in cancer, we sequenced cDNA encoding K protein from colorectal adenocarcinoma and compared it to the cDNAs from the surrounding normal mucosa.…”

mentioning

confidence: 99%

Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa

et al. 2006

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The heterogeneous nuclear ribonucleoprotein K (hnRNP K) protein is an RNA-binding protein involved in many processes that compose gene expression. K protein is upregulated in the malignant processes and has been shown to modulate the expression of genes involved in mitogenic responses and tumorigenesis. To explore the possibility that there are alternative isoforms of K protein expressed in colon cancer, we amplified and sequenced K protein mRNA that was isolated from colorectal cancers as well as from normal tissues surrounding the tumours. Sequencing revealed a single G-to-A base substitution at position 274 that was found in tumours and surrounding mucosa, but not in individuals that had no colorectal tumour. This substitution most likely reflects an RNA editing event because it was not found in the corresponding genomic DNAs. Sequencing of RNA from normal colonic mucosa of patients with prior resection of colorectal cancer revealed only the wild-type K protein transcript, indicating that G274A isoform is tumour related. To our knowledge, this is the first example of an RNA editing event in cancer and its surrounding tissue, a finding that may offer a new diagnostic and treatment marker.

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The poly(C)-binding proteins: A multiplicity of functions and a search for mechanisms

Cited by 413 publications

References 95 publications

Differential protein expression analysis using stable isotope labeling and PQD linear ion trap MS technology

Differential protein expression analysis using stable isotope labeling and PQD linear ion trap MS technology

The human dopamine D4 receptor repeat sequences modulate expression

Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa

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