Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems.

Current techniques for quantitative proteomics focus mainly on measuring overall protein dynamics, which is the net result of protein synthesis and degradation. Understanding the rate of this synthesis/degradation is essential to fully appreciate cellular dynamics and bridge the gap between transcriptome and proteome data. Protein turnover rates can be estimated through "label-chase" experiments employing stable isotope-labeled precursors; however, the implicit assumption of steady-state in such analyses may not be applicable for many intrinsically dynamic systems. In this study, we present a novel extension of the "label-chase" concept using SILAC and a secondary labeling step with iTRAQ reagents to estimate protein turnover rates in Streptomyces coelicolor cultures undergoing transition from exponential growth to stationary phase. Such processes are of significance in Streptomyces biology as they pertain to the onset of synthesis of numerous therapeutically important secondary metabolites. The dual labeling strategy enabled decoupling of labeled peptide identification and quantification of degradation dynamics at MS and MS/MS scans respectively. Tandem mass spectrometry analysis of these multitagged proteins enabled estimation of degradation rates for 115 highly abundant proteins in S. coelicolor. We compared the rate constants obtained using this dual labeling approach with those from a SILAC-only analysis (assuming steady-state) and show that significant differences are generally observed only among proteins displaying considerable temporal dynamics and that the directions of these differences are largely consistent with theoretical predictions.

Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor.

Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels. Systems analyses of such processes incorporating large-scale transcriptome or proteome profiling can be quite revealing. Although consistency between mRNA and proteins is often implicitly assumed in many studies, examples of divergent trends are frequently observed. Here, we present a comparative transcriptome and proteome analysis of growth and stationary phase adaptation in Streptomyces coelicolor, taking the time-dynamics of process into consideration. These processes are of immense interest in microbiology as they pertain to the physiological transformations eliciting biosynthesis of many naturally occurring therapeutic agents. A shotgun proteomics approach based on mass spectrometric analysis of isobaric stable isotope labeled peptides (iTRAQ) enabled identification and rapid quantification of approximately 14% of the theoretical proteome of S. coelicolor. Independent principal component analyses of this and DNA microarray-derived transcriptome data revealed that the prominent patterns in both protein and mRNA domains are surprisingly well correlated. Despite this overall correlation, by employing a systematic concordance analysis, we estimated that over 30% of the analyzed genes likely exhibited significantly divergent patterns, of which nearly one-third displayed even opposing trends. Integrating this data with biological information, we discovered that certain groups of functionally related genes exhibit mRNA-protein discordance in a similar fashion. Our observations suggest that differences between mRNA and protein synthesis/degradation mechanisms are prominent in microbes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level.

Selection against undifferentiated human embryonic stem cells by a cytotoxic antibody recognizing podocalyxin-like protein-1.

Future therapeutic applications of differentiated human embryonic stem cells (hESC) carry a risk of teratoma formation by contaminating undifferentiated hESC. We generated 10 monoclonal antibodies (mAbs) against surface antigens of undifferentiated hESC, showing strong reactivity against undifferentiated, but not differentiated hESC. The mAbs did not cross react with mouse fibroblasts and showed weak to no reactivity against human embryonal carcinoma cells. Notably, one antibody (mAb 84) is cytotoxic to undifferentiated hESC and NCCIT cells in a concentration-dependent, complement-independent manner. mAb 84 induced cell death of undifferentiated, but not differentiated hESC within 30 minutes of incubation, and immunoprecipitation of the mAb-antigen complex revealed that the antigen is podocalyxin-like protein-1. Importantly, we observed absence of tumor formation when hESC and NCCIT cells were treated with mAb 84 prior to transplantation into severe combined immunodeficiency mice. Our data indicate that mAb 84 may be useful in eliminating residual hESC from differentiated cells populations for clinical applications. Disclosure of potential conflicts of interest is found at the end of this article.

Genomic and proteomic exploration of CHO and hybridoma cells under sodium butyrate treatment.

Sodium butyrate has been known to increase the specific productivity of recombinant proteins in mammalian cells. In quest of physiological mechanisms leading to the increased productivity, DNA microarray and two dimensional gel electrophoresis (2DE) were used to assess the response of Chinese hamster ovary (CHO) and a mouse hybridoma cell (MAK) to butyrate treatment at the transcriptome and proteome level. The expression of the orthologous genes represented on both CHO cDNA and mouse Affymetrix microarray, as well as genes in the same ontological class were compared. Only a relatively small number of orthologs changed their expression consistently between the two cell lines, however, at a functional class level many genes involved in cell cycle and apoptosis were affected in both cell lines. Furthermore, a large number of genes involved in protein processing, secretion and redox activity were upregulated in both CHO and MAK cells. More genes showed a consistent trend of change at both transcript and protein levels than those which showed opposite trend in MAK cells. Overall the results suggested that the changes arising in the protein processing machinery may be responsible for the increased productivity upon butyrate treatment in both CHO and MAK cells.

Direct binding of PP2A to Sprouty2 and phosphorylation changes are a prerequisite for ERK inhibition downstream of fibroblast growth factor receptor stimulation.

In the context of fibroblast growth factor (FGF) signaling, Sprouty2 (Spry2) is the most profound inhibitor of the Ras/ERK pathway as compared with other Spry isoforms. An exclusive, necessary, but cryptic PXXPXR motif in the C terminus of Spry2 is revealed upon stimulation. The activation of Spry2 appears to be linked to sequences in the N-terminal half of the protein and correlated with a bandshifting seen on SDS-PAGE. The band-shifting is likely caused by changes in the phosphorylation status of key Ser and Thr residues following receptor stimulation. Dephosphorylation of at least two conserved Ser residues (Ser-112 and Ser-115) within a conserved Ser/Thr sequence is accomplished upon stimulation by a phosphatase that binds to Spry2 around residues 50-60. We show that human Spry2 co-immunoprecipitates with both the catalytic and the regulatory subunits of protein phosphatase 2A (PP2A-C and PP2A-A, respectively) in cells upon FGF receptor (FGFR) activation. PP2A-A binds directly to Spry2, but not to Spry2Delta50-60 (Delta50-60), and the activity of PP2A increases with both FGF treatment and FGFR1 overexpression. c-Cbl and PP2A-A compete for binding centered around Tyr-55 on Spry2. We show that there are at least two distinct pools of Spry2, one that binds PP2A and another that binds c-Cbl. c-Cbl binding likely targets Spry2 for ubiquitin-linked destruction, whereas the phosphatase binding and activity are necessary to dephosphorylate specific Ser/Thr residues. The resulting change in tertiary structure enables the Pro-rich motif to be revealed with subsequent binding of Grb2, a necessary step for Spry2 to act as a Ras/ERK pathway inhibitor in FGF signaling.

Molecular portrait of high productivity in recombinant NS0 cells.

Many important therapeutic proteins are produced in recombinant mammalian cells. Upon the introduction of the product gene, the isolated clones typically exhibit a wide range of productivity and high producers are subsequently selected for use in production. Using DNA microarray, two-dimensional gel electrophoresis (2DE), and iTRAQ as global surveying tools, we examined the transcriptome and proteome profiles of 11 lines of NS0 cells producing the same antibody molecule. Genes that are significantly differentially expressed between high and low producer groups statistically fall into a number of functional classes. Their distribution among the functional classes differs somewhat between transcriptomic and proteomic results. Overall, a high degree of consistency between transcriptome and proteome analysis are seen, although some genes exhibiting inconsistent trends between transcript and protein levels were observed as expected. In a novel approach, functional gene networks were retrieved using computational pathway analysis tools and their association with productivity was tested by physiological comprehension of the possible pathways involved in high recombinant protein production. Network analysis indicates that protein synthesis pathways were altered in high producers at both transcriptome and proteome levels, whereas the effect on cell growth/death pathways was more prominent only at the transcript level. The results suggest a common mechanism entailing the alteration of protein synthesis and cell growth control networks leading to high productivity. However, alternate routes with different sets of genes may be invoked to give rise to the same mechanistic outcomes. Such systematic approaches, combining transcriptomic and proteomic tools to examine high and low producers of recombinant mammalian cells will greatly enhance our capability to rationally design high producer cells. This work is a first step towards shedding a new light on the global physiological landscape of hyper productivity of recombinant cells.

PKC delta phosphorylates p52ShcA at Ser29 to regulate ERK activation in response to H2O2.

Both PKC delta and ShcA have been implicated in cell response to oxidative stress [Y. Hu, X. Wang, L. Zeng, D.Y. Cai, K. Sabapathy, S.P. Goff, E.J. Firpo, B. Li, Mol Biol Cell., 16 (2005) 3705-3718, B. Li, X. Wang, N. Rasheed, Y. Hu, S. Boast, T. Ishii, K. Nakayama, K.I. Nakayama, S.P., Goff, Genes Dev, 18 (2004) 1824-1837, E. Migliaccio, M. Giorgio, S. Mele, G. Pelicci, P. Reboldi, P.P. Pandolfi, L. Lanfrancone, P.G. Pelicci, Nature, 402 (1999) 309-313], yet their relationship in the response has not been studied. Here we report that PKC delta interacts with ShcA and this interaction is promoted by H(2)O(2). PKC delta and ShcA are also colocalized in the cytoplasm and displayed co-translocation in response to H(2)O(2). Activated PKC delta was able to phosphorylate ShcA at Ser29, as determined by mass spectrometry. These results suggest that ShcA, p66 and p52, are substrates that interact with PKC delta. This phosphorylation is critical in H(2)O(2) induced ERK activation as reconstitution with ShcA Ser29A failed to rescue ERK activation of ShcA-/- MEFs, while ShcA could. In line with this conclusion, inhibition of PKC delta with inhibitors is able to diminish H(2)O(2) induced ERK activation in MEFs. These results suggest that the interaction between PKC delta and ShcA and the phosphorylation of ShcA at Ser29 play important roles in ERK activation in cell response to H(2)O(2).

Large-scale gene expression analysis of cholesterol dependence in NS0 cells.

NS0, a nonsecreting mouse myeloma cell, is a major host line used for recombinant antibody production. These cells have a cholesterol-dependent phenotype and rely on an exogenous supply of cholesterol for their survival and growth. To better understand the physiology underlying cholesterol dependence, we compared NS0 cells, cultivated under standard cholesterol-dependent growth conditions (NS0), to cells adapted to cholesterol-independent conditions (NS0 revertant, NS0_r). Large-scale transcriptional analyses were done using the Affymetrix GeneChip array, MG-U74Av2. The transcripts expressed differentially across the two cell lines were identified. Additionally, proteomic tools were employed to analyze cell lysates from these two cell lines. Cellular proteins from both NS0 and NS0_r were subjected to 2D gel electrophoresis. MALDI-TOF mass spectrometry was performed to determine the identity of the differentially expressed spots. We examined the expression level of mouse genes directly involved in cholesterol biosynthesis, lipid metabolism, and central energy metabolism. Most of these genes were downregulated in the revertant cell type, NS0_r, compared to NS0. Overall, a large number of genes are expressed differentially, indicating that the reversal of cholesterol dependency has a profound effect on cell physiology. It is probable that a single gene mutation, activation, or inactivation is responsible for cholesterol auxotrophy. However, the wide-ranging changes in gene expression point to the distinct possibility of a regulatory event affecting the reversibility of auxotrophy, either directly or indirectly.