Multidimensional Protein Identification Technology Analysis Research Articles

Abstract 2571: DBC1, a novel CBP-interacting protein, promotes p53 stability by regulating CBP-dependent p53 polyubiquitination

Abstract The acetyltransferase CBP, in conjunction with the E3 ubiquitin ligase enzyme, Mdm2, maintains physiologic levels of the tumor suppressor protein p53 in the absence of cellular stress, via a cytoplasmic, but not nuclear, p53-directed E4 polyubiquitin activity. CBP also possesses cytoplasmic, but not nuclear, E3 ubiquitin ligase, autoubiquitination activity. To understand the mechanism by which the ubiquitin ligase activities of CBP are compartmentalized in the cell, we have employed Multidimensional Protein Identification Technology (MudPIT) to identify cytoplasmic and nuclear CBP interacting proteins. MudPIT analysis revealed that Cell Cycle and Apoptosis Regulator protein (CCAR2), also known as Deleted in Breast Cancer 1 protein (DBC1), is a novel CBP- interacting protein in both the nucleus and cytoplasm. The N-terminus of DBC1 bound to multiple CBP domains, including the putative E3/E4 domain of CBP located at the N-terminus. Interaction between DBC1 and CBP suppressed the in vitro E3 autoubiquitination activity of CBP. Functional studies demonstrated that DBC1 directly regulates the cellular compartmentalization of CBP E3 and p53-directed E4 ubiquitin ligase activities. Knockdown of DBC1 in U2OS cells stimulated normally absent nuclear p53 polyubiquitination, and also caused a decrease in p53-dependent and p53-independent apoptosis, rescued by CBP/DBC1 double knockdown. Further, over-expression of DBC1 rescued the increase in nuclear p53 polyubiquitination and decrease in p53 half-life observed in DBC1 depleted cells. Together, these results identify DBC1 as a novel binding partner of CBP and a critical regulator of CBP ubiquitin ligase activities. Based on our data that DBC1 loss inactivates p53 function through destabilization, we queried the TCGA database for co-occurrence of DBC1 loss with maintenance of wild-type p53 status which showed that 33% of breast, 40% of lung, and 96% of prostate cancer cases with DBC1 alterations maintained wild-type p53 status. Therefore, by restoring DBC1 function, this work could lead to reactivation of p53 tumor suppressor activity in tumors with DBC1 alterations maintaining wild-type p53 status. Citation Format: Oluwatoyin E. Akande, Priyadarshan K. Damle, Nicholas E. Sherman, Steven R. Grossman. DBC1, a novel CBP-interacting protein, promotes p53 stability by regulating CBP-dependent p53 polyubiquitination [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2571. doi:10.1158/1538-7445.AM2017-2571

Patterns of Proteins Removed with High-Flux Membranes on High-Volume Hemodiafiltration Detected with a MultiDimensional LC-MS/MS Strategy

Background: Aim of this prospective crossover study was to identify the nature of the middle-molecular weight solutes removed during high-volume post-dilution HDF. Methods: The efficiency in removing small molecules, protein-bound and middle-molecular proteins was evaluated in 16 chronic dialysis patients on post-dilution HDF with two high-flux dialyzer membranes (Amembris and Polyamix). Multidimensional Protein Identification Technology (MudPIT) was employed to identify middle-molecular weight solutes in spent dialysate. Results: Efficiency of post-dilution HDF in removing solutes of different MW was high with both membranes, but higher with Amembris than with Polyamix. With MudPIT analysis, 277 proteins were identified in the dialysate fluids. Although the protein-removal pattern was similar among patients and tested membranes, the total and protein-specific peptide spectral count (mass spectrometric quantitation criteria) of most proteins were higher using the Amembris membrane. Conclusions: The MudPIT approach showed to be a powerful tool to identify a broad molecular weight spectrum of proteins removed with post-dilution HDF. Short Summary: Aim of this prospective crossover study was to analyze the hydraulic properties of two high-flux dialyzer membranes (Amembris and Polyamix) during high-volume, post-dilution HDF and to evaluate the influence of these properties on the removal of proteins and peptides using an in-depth analysis of the spent dialysate. For this analysis, a liquid chromatography tandem mass spectrometry approach called MudPIT (Multidimensional Protein Identification Technology) was used to identify the middle molecular weight solutes present in the spent dialysate of patients. The capability of post-dilution HDF in removing solutes of different MW was very high with both dialyzers, but higher with the Amembris membrane. The proteomic MudPIT approach showed to be a powerful tool to identify a wide molecular spectrum of proteins removed from blood during post-dilution HDF. These results may contribute to address research toward a better knowledge of uremic toxins and the balance between the intended and unintended removal of undesired and beneficial proteins next to identification of new target proteins as potential candidates for uremic toxicity. i 2014 S. Karger AG, Basel

CS-08 * SONIC HEDGEHOG SIGNALING PROTECTS ATOH1 FROM DEGRADATION MEDIATED BY THE HECT DOMAIN E3 UBIQUITIN LIGASE HUWE1 IN CEREBELLAR GRANULE NEURON PROGENITORS

Cerebellar development requires a balance between several biological processes including proliferation, differentiation and migration. The pro-neural basic helix-loop-helix transcription factor Atoh1 was shown to be a key player controlling the formation of granule neuron progenitors (GNPs). Its uncontrolled levels in collaboration with Sonic Hedgehog (SHH) activation are critical for medulloblastoma (MB) formation, a devastating pediatric tumor that originates from the cerebellum. Because Atoh1 acts as a lineage dependency transcription factor in MB, mechanisms controlling Atoh1 expression are keen interest in the field. However, how this master transcription factor is regulated has remained poorly understood. In our study, we dissected the machinery that regulates Atoh1 in GNPs and in MB. We first identified two phosphorylation sites that regulate Atoh1 stability and function in GNPs. Second, combining tandem affinity purification with an Atoh1 phospho-deficient mutant and multidimensional protein identification technology analysis, we identified the E3 ubiquitin ligase Huwe1 as Atoh1 binding partner. We showed that Atoh1 physically interacted with Huwe1 in a phospho-dependent manner in GNPs, mediating its ubiquitylation whereas Cre-mediated deletion of Huwe1 from postnatal GNPs increased Atoh1 protein levels. Next, we uncovered that SHH regulates Atoh1 stability by preventing its phospho-dependent degradation by Huwe1. In the tumoral context, consistent with Atoh1 upregulation in MBs driven by SHH activation, Huwe1 was found downregulated in primary mouse tumors. In human SHH MB, low HUWE1 expression was found specifically associated with poor prognosis. Overall, our results reveal that SHH and Atoh1 contribute to a positive autoregulatory loop promoting neuronal precursor expansion. Consequently, Huwe1 alterations in SHH MB illustrate the disruption of this developmental mechanism in cancer. This crosstalk between SHH signaling and Atoh1 during cerebellar development highlights a new collaborative network that could be further targeted in MB.

Pupylated proteins in Corynebacterium glutamicum revealed by MudPIT analysis.

In a manner similar to ubiquitin, the prokaryotic ubiquitin-like protein (Pup) has been shown to target proteins for degradation via the proteasome in mycobacteria. However, not all actinobacteria possessing the Pup protein also contain a proteasome. In this study, we set out to study pupylation in the proteasome-lacking non-pathogenic model organism Corynebacterium glutamicum. A defined pup deletion mutant of C. glutamicum ATCC 13032 grew aerobically as the parent strain in standard glucose minimal medium, indicating that pupylation is dispensable under these conditions. After expression of a Pup derivative carrying an aminoterminal polyhistidine tag in the Δpup mutant and Ni(2+)-chelate affinity chromatography, pupylated proteins were isolated. Multidimensional protein identification technology (MudPIT) and MALDI-TOF-MS/MS of the elution fraction unraveled 55 proteins being pupylated in C. glutamicum and 66 pupylation sites. Similar to mycobacteria, the majority of pupylated proteins are involved in metabolism or translation. Our results define the first pupylome of an actinobacterial species lacking a proteasome, confirming that other fates besides proteasomal degradation are possible for pupylated proteins.

Abstract 434: LDL Apheresis Significantly Alters HDL Cargo and Function in Familial Hypercholesterolemia Subjects

In addition to cholesterol, HDL transports a wide-variety of cargo including vitamins, nucleic acids, and a diverse set of proteins. Outside of the reverse cholesterol transport pathway, HDL has alternative functions that contribute to its anti-atherogenicity, including anti-inflammatory, anti-oxidant, and signaling capacities. Recently, we found that HDL transports and delivers functional microRNAs to recipient cells, which likely confers HDL’s ability to suppress adhesion molecule expression in endothelial cells. As such, changes to HDL’s cargo impact many of these alternative functions, and thus its protective capacity. HDL dysfunction has been identified among patients with familial hypercholesterolemia (FH), an inherited disease due to mutations in the LDL receptor and associated with severe elevations in LDL-cholesterol (LDL-C) levels, which may necessitate LDL apheresis (LA) in management. Here we demonstrate that LA significantly alters HDL’s miRNA and protein signatures. We believe that these changes may have profound consequences on HDL’s protective capacity. Using density-gradient ultracentrifugation, we found 31 proteins to be significantly altered on HDL after LA, as determined by shotgun proteomics and multidimensional protein identification technology analysis. For example, vitamin D-binding protein (1.74-fold) was increased, while lipopolysaccharide-binding protein (-1.92-fold), platelet-activating factor acetylhydrolase (-2.06), and apolipoprotein A-V (-2.4-fold) were found to be decreased. Gene ontology and KEGG enrichment analysis demonstrated roles of these proteins in response to stress, coagulation, hemostasis, and vesicle-mediated transport. Fast-protein liquid chromatography was used to further purify HDL for miRNA profiling using TaqMan OpenArrays, and we found 8 HDL-miRNAs to be significantly altered -- 3 down (miR-302b -13.9-fold, miR-224 -1.8, miR-572 -2.4-fold) and 5 up (miR-7 9.8-fold, miR-208b 16.2-fold, miR-34a-3p 3-fold, miR-627 2.4-fold, miR-1183 4.8-fold). Both miR-302b and miR-224 decreased; these are miRNAs previously reported to suppress proliferation through targeting AKT2 and apoptosis, respectively. As such, these changes likely alter HDL’s function in FH subjects.

Proteomic Analysis of Pol II Preinitiation Complexes: The Roles of Mediator and SAGA

An important property of RNA polymerase II preinitiation complexes (PIC) is their ability to coordinate transcription initiation with chromatin modification and remodeling. We employed multidimensional protein identification technology (MuDPIT) to study the composition and assembly of PICs in HeLa and mouse embryonic stem (ES) cell nuclear extracts. Strikingly, most of the machinery necessary for transcription initiation on chromatin is part of the PIC. The PIC is nearly identical between ES and HeLa cells, and contains two major co‐activator complexes, Mediator and SAGA. Genomewide analysis of Mediator reveals a close correlation with Pol II, TBP and mRNA levels implying a major role in PIC assembly. Mechanistic analysis of the two co‐activators showed that they play distinct roles in PIC function. Mediator coordinates assembly of the Pol II initiation factors and chromatin machinery into a PIC, while SAGA acts after PIC assembly to allow transcription on chromatin. MuDPIT analysis of Mediator isolated from native chromatin, under conditions where the transcriptional machinery remains intact, suggests that PICs assembled in vitro and in vivo are similar.

Proteomics and Phosphoproteomics Analysis of Human Lens Fiber Cell Membranes

The human lens fiber cell insoluble membrane fraction contains important membrane proteins, cytoskeletal proteins, and cytosolic proteins that are strongly associated with the membrane. The purpose of this study was to characterize the lens fiber cell membrane proteome and phosphoproteome from human lenses. HPLC-mass spectrometry-based multidimensional protein identification technology (MudPIT), without or with phosphopeptide enrichment, was applied to study the proteome and phosphoproteome of lens fiber cell membranes, respectively. In total, 951 proteins were identified, including 379 integral membrane and membrane-associated proteins. Enriched gene categories and pathways based on the proteomic analysis include carbohydrate metabolism (glycolysis/gluconeogenesis, pentose phosphate pathway, pyruvate metabolism), proteasome, cell-cell signaling and communication (GTP binding, gap junction, focal adhesion), glutathione metabolism, and actin regulation. The combination of TiO(2) phosphopeptide enrichment and MudPIT analysis revealed 855 phosphorylation sites on 271 proteins, including 455 phosphorylation sites that have not been previously identified. PKA, PKC, CKII, p38MAPK, and RSK are predicted as the major kinases for phosphorylation on the sites identified in the human lens membrane fraction. The results presented herein significantly expand the characterized proteome and phosphoproteome of the human lens fiber cell and provide a valuable reference for future research in studies of lens development and disease.

Proteomic and Functional Annotation Analysis of Injured Peripheral Nerves Reveals ApoE as a Protein Upregulated by Injury that is Modulated by Metformin Treatment

BackgroundPeripheral nerve injury (PNI) results in a fundamental reorganization of the translational machinery in the injured peripheral nerve such that protein synthesis is increased in a manner linked to enhanced mTOR and ERK activity. We have shown that metformin treatment, which activates adenosine monophosphate-activated protein kinase (AMPK), reverses tactile allodynia and enhanced translation following PNI. To gain a better understanding of how PNI changes the proteome of the sciatic nerve and ascertain how metformin treatment may cause further change, we conducted a range of unbiased proteomic studies followed by biochemical experiments to confirm key results.ResultsWe used multidimensional protein identification technology (MUDPIT) on sciatic nerve samples taken from rats with sham surgery, spinal nerve ligation (SNL) surgery or SNL + 200 mg/kg metformin treatment. MUDPIT analysis on these complex samples yielded a wide variety of proteins that were sorted according to their peptide counts in SNL and SNL + metformin compared to sham. These proteins were then submitted to functional annotation analysis to identify potential functional networks altered by SNL and SNL + metformin treatment. Additionally, we used click-chemistry-based labeling and purification of nascently synthesized proteins followed by MUDPIT to further identify peptides that were synthesized within the injured nerve. With these methods, we identified apolipoprotein E (ApoE) as a protein profoundly increased by PNI and further increased by PNI and metformin. This result was confirmed by Western Blot of samples from SNL rats and spared nerve injury (SNI) mice. Furthermore, we show that 7-day treatment with metformin in naïve mice leads to an increase in ApoE expression in the sciatic nerve.ConclusionsThese proteomic findings support the hypothesis that PNI leads to a fundamental reorganization of gene expression within the injured nerve. Our data identify a key association of ApoE with PNI that is regulated by metformin treatment. We conclude from the known functions of ApoE in the nervous system that ApoE may be an intrinsic factor linked to nerve regeneration after PNI, an effect that is further enhanced by metformin treatment.

A new flow path design for multidimensional protein identification technology using nano-liquid chromatography electrospray ionization mass spectrometry

Multidimensional protein identification technology (MudPIT) is one of the most versatile methods for separating and identifying highly complex peptides or proteins. However, there are still inherent problems resulting from salt in eluent systems and instrumentation with MudPIT. We designed a novel and simple flow path using two-valve system and successfully performed a fully automated peptide analysis using MudPIT coupled with nano-liquid chromatography electrospray ionization mass spectrometry (nLC-ESI-MS). It enables to generate a remarkably stable nanospray during the MudPIT analysis and realize the fully automated MudPIT system. This column arrangement could be easily installed to avoid laborious loading steps and unstable ionization from discontinuous flow. Consequently, the new flow path design for MudPIT system guarantees the detection of more peptides and higher protein coverage in proteome analysis.

OS045. Multi-dimensional protein identification technology analysis of syncytiotrophoblast vesicles released from perfused preeclampsia placentas

In pre-eclampsia, the consequences of poor placentation lead to the second stage of pre-eclampsia, which involves activation of a maternal systemic inflammatory response (MSIR). Endothelial and other inflammatory cellular dysfunction cause the diverse features which characterise the disorder. We have previously shown that syncytiotrophoblast microvesicles (STBM) are pro-inflammatory and circulate in increased amounts in pre-eclamptic women. We hypothesise that multiple placental "danger signals" are carried by STBM into the maternal circulation in increased amounts in PE with pro-inflammatory, anti-angiogenic and pro-coagulant activity, implicating STBM in the pathophysiology of PE. To characterise the proteins carried by STBM from normal and PE placentas. For the first time multi-dimensional protein identification technology (MudPIT) was used to derive the proteome profiles of normal and PE placenta STBM. STBM were prepared from placentas (normal term: n=9 and PE: n=5) by dual lobe perfusion, isolated by ultracentrifugation and stored at -80°C. Normal and PE derived placenta STBM pools were then subjected to MudPIT analysis. 538 proteins unique to PE STBM, 604 proteins unique to normal STBM and 1421 proteins common to both preparations were found. Preliminary analysis indicates the presence of alarmins (HSP70, and galectin 3), exosomal proteins (CD63,CD9,CD81), immunoregulatory molecules (CD26,CD200,CD47,Galectin 1), complement and complement regulatory molecules (C1q,C3,CD55,CD59 and vitronectin), amino acid transporters (CD98) and anti-angiogenic molecules (endoglin). Our analysis also reveals that proteins known to be elevated in blood before, or at, the time of pre-eclampsia are elevated or unique in STBM from PE placentas, including Fetuin A, Inter-alpha (globulin) inhibitor H4, Serum amyloid P component, Apolipoprotein H (or B2GP1) and Apolipoprotein AII. Thus, as predicted, a large number of circulating molecules are associated with STBM. The inter-relationships between proteins that are unique to either PE or normal pregnancy and the processes in which they are involved are being determined by Ingenuity Pathways Analysis software. In terms of biofunctions, preliminary analysis shows that proteins unique to PE STBM have a highly significant association (p<10(-11)) with 6 disease pathways including inflammatory, immunological, cardiovascular and reproductive system diseases and organ injury, whereas for proteins unique to normal STBM only protein synthesis was significant at the same level. STBM contain a heterogeneous population of vesicles that convey a large repertoire of placental proteins into the maternal circulation. The profound differences between PE and normal STBM indicate their pro-inflammatory potential.

Single-Step Inline Hydroxyapatite Enrichment Facilitates Identification and Quantitation of Phosphopeptides from Mass-Limited Proteomes with MudPIT

Herein we report the characterization and optimization of single-step inline enrichment of phosphopeptides directly from small amounts of whole cell and tissue lysates (100-500 μg) using a hydroxyapatite (HAP) microcolumn and Multidimensional Protein Identification Technology (MudPIT). In comparison to a triplicate HILIC-IMAC phosphopeptide enrichment study, ∼80% of the phosphopeptides identified using HAP-MudPIT were unique. Similarly, analysis of the consensus phosphorylation motifs between the two enrichment methods illustrates the complementarity of calcium- and iron-based enrichment methods and the higher sensitivity and selectivity of HAP-MudPIT for acidic motifs. We demonstrate how the identification of more multiply phosphorylated peptides from HAP-MudPIT can be used to quantify phosphorylation cooperativity. Through optimization of HAP-MudPIT on a whole cell lysate we routinely achieved identification and quantification of ca. 1000 phosphopeptides from a ∼1 h enrichment and 12 h MudPIT analysis on small quantities of material. Finally, we applied this optimized method to identify phosphorylation sites from a mass-limited mouse brain region, the amygdala (200-500 μg), identifying up to 4000 phosphopeptides per run.

MudPIT analysis of alkaline tolerance by Listeria monocytogenes strains recovered as persistent food factory contaminants

Alkaline solutions are used to clean food production environments but the role of alkaline resistance in persistent food factory contamination by Listeria monocytogenes is unknown. We used shotgun proteomics to characterise alkaline adapted L. monocytogenes recovered as persistent and transient food factory contaminants. Three unrelated strains were studied including two persistent and a transient food factory contaminant determined using multilocus sequence typing (MLST). The strains were adapted to growth at pH 8.5 and harvested in exponential phase. Protein extracts were analysed using multidimensional protein identification technology (MudPIT) and protein abundance compared by spectra counting. The strains elicited core responses to alkaline growth including modulation of intracellular pH, stabilisation of cellular processes and reduced cell-division, independent to lineage, MLST or whether the strains were transient or persistent contaminants. Alkaline adaptation by all strains corresponded to that expected in stringent-response induced cells, with protein expression supporting metabolic shifts concordant with elevated alarmone production and indicating that the alkaline-stringent response results from energy rather than nutrient limitation. We believe this is the first report describing induction of a stringent response in different L. monocytogenes strains by alkaline pH under non-limiting growth conditions. The work emphasises the need for early intervention to avoid persistent food factory contamination by L. monocytogenes.

Mediator coordinates PIC assembly with recruitment of CHD1

Murine Chd1 (chromodomain helicase DNA-binding protein 1), a chromodomain-containing chromatin remodeling protein, is necessary for embryonic stem (ES) cell pluripotency. Chd1 binds to nucleosomes trimethylated at histone 3 Lys 4 (H3K4me3) near the beginning of active genes but not to bivalent domains also containing H3K27me3. To address the mechanism of this specificity, we reproduced H3K4me3- and CHD1-stimulated gene activation in HeLa extracts. Multidimensional protein identification technology (MuDPIT) and immunoblot analyses of purified preinitiation complexes (PICs) revealed the recruitment of CHD1 to naive chromatin but enhancement on H3K4me3 chromatin. Studies in depleted extracts showed that the Mediator coactivator complex, which controls PIC assembly, is also necessary for CHD1 recruitment. MuDPIT analyses of CHD1-associated proteins support the recruitment data and reveal numerous components of the PIC, including Mediator. In vivo, CHD1 and Mediator are recruited to an inducible gene, and genome-wide binding of the two proteins correlates well with active gene transcription in mouse ES cells. Finally, coimmunoprecipitation of CHD1 and Mediator from cell extracts can be ablated by shRNA knockdown of a specific Mediator subunit. Our data support a model in which the Mediator coordinates PIC assembly along with the recruitment of CHD1. The combined action of the PIC and H3K4me3 provides specificity in targeting CHD1 to active genes.

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes

The use of quantitative proteomics methods to study protein complexes has the potential to provide in-depth information on the abundance of different protein components as well as their modification state in various cellular conditions. To interrogate protein complex quantitation using shotgun proteomic methods, we have focused on the analysis of protein complexes using label-free multidimensional protein identification technology and studied the reproducibility of biological replicates. For these studies, we focused on three highly related and essential multi-protein enzymes, RNA polymerase I, II, and III from Saccharomyces cerevisiae. We found that label-free quantitation using spectral counting is highly reproducible at the protein and peptide level when analyzing RNA polymerase I, II, and III. In addition, we show that peptide sampling does not follow a random sampling model, and we show the need for advanced computational models to predict peptide detection probabilities. In order to address these issues, we used the APEX protocol to model the expected peptide detectability based on whole cell lysate acquired using the same multidimensional protein identification technology analysis used for the protein complexes. Neither method was able to predict the peptide sampling levels that we observed using replicate multidimensional protein identification technology analyses. In addition to the analysis of the RNA polymerase complexes, our analysis provides quantitative information about several RNAP associated proteins including the RNAPII elongation factor complexes DSIF and TFIIF. Our data shows that DSIF and TFIIF are the most highly enriched RNAP accessory factors in Rpb3-TAP purifications and demonstrate our ability to measure low level associated protein abundance across biological replicates. In addition, our quantitative data supports a model in which DSIF and TFIIF interact with RNAPII in a dynamic fashion in agreement with previously published reports.

The ATAC Acetyltransferase Complex Coordinates MAP Kinases to Regulate JNK Target Genes

In response to extracellular cues, signal transduction activates downstream transcription factors like c-Jun to induce expression of target genes. We demonstrate that the ATAC (Ada two A containing) histone acetyltransferase (HAT) complex serves as a transcriptional cofactor for c-Jun at the Jun N-terminal kinase (JNK) target genes Jra and chickadee. ATAC subunits are required for c-Jun occupancy of these genes and for H4K16 acetylation at the Jra enhancer, promoter, and transcribed sequences. Under conditions of osmotic stress, ATAC colocalizes with c-Jun, recruits the upstream kinases Misshapen, MKK4, and JNK, and suppresses further activation of JNK. Relocalization of these MAPKs and suppression of JNK activation by ATAC are dependent on the CG10238 subunit of ATAC. Thus, ATAC governs the transcriptional response to MAP kinase signaling by serving as both a coactivator of transcription and as a suppressor of upstream signaling.

Identification of a conserved F-box protein 6 interactor essential for endocytosis and cytokinesis in fission yeast

The F-box domain is a degenerated motif consisting of approximately 40 amino acid residues that specifically bind Skp1, a core component of the SCF (Skp1-Cdc53/Cullin 1-F-box protein) ubiquitin ligase. Recent work, mainly performed in budding yeast, indicates that certain F-box proteins form non-SCF complexes together with Skp1 in the absence of cullins and play various roles in cell cycle and signalling pathways. However, it is not established whether these non-SCF complexes are unique to budding yeast or common in other eukaryotes. In the present paper, using TAP (tandem affinity purification) coupled to MudPIT (Multidimensional Protein Identification Technology) analysis, we have identified a novel conserved protein, Sip1, in fission yeast, as an interacting partner of an essential F-box protein Pof6. Sip1 is a large HEAT (huntingtin, elongation factor 3, the PR65/A subunit of protein phosphatase 2A and the lipid kinase Tor)-repeats containing protein (217 kDa) and forms a complex with Pof6 and Skp1. This complex does not contain cullins, indicating that it is a novel non-SCF complex. Like Pof6 and Skp1, Sip1 is essential for cell viability and temperature-sensitive sip1 mutants display cell division arrest as binucleate cells with septa. Sip1 localizes to the nucleus and dynamic cytoplasmic dots, which are shown in the present study to be endocytic vesicles. Consistent with this, sip1 mutants are defective in endocytosis. Furthermore, towards the end of cytokinesis, constriction of the actomyosin ring and dissociation of type II myosin and septum materials are substantially delayed in the absence of functional Sip1. These results indicate that the conserved Sip1 protein comprises a novel non-SCF F-box complex that plays an essential role in endocytosis, cytokinesis and cell division.

Proteomic analysis of the secretome of rice calli

The cell wall and extracellular matrix in higher plants include secreted proteins that play critical roles in a wide range of cellular processes, such as structural integrity and biogenesis. Compared with the intensive cell wall proteomic studies in Arabidopsis, the list of cell wall proteins identified in monocot species is lacking. Therefore, we conducted a large-scale proteomic analysis of secreted proteins from rice. Highly purified secreted rice proteins were obtained from the medium of a suspension of callus culture and were analyzed with multidimensional protein identification technology (MudPIT). As a result, we could detect a total of 555 rice proteins by MudPIT analysis. Based on bioinformatic analyses, 27.7% (154 proteins) of the identified proteins are considered to be secreted proteins because they possess a signal peptide for the secretory pathway. Among the 154 identified proteins, 27% were functionally categorized as stress response proteins, followed by metabolic proteins (26%) and factors involved in protein modification (24%). Comparative analysis of cell wall proteins from Arabidopsis and rice revealed that one third of the secreted rice proteins overlapped with those of Arabidopsis. Furthermore, 25 novel rice-specific secreted proteins were found. This work presents the large scale of the rice secretory proteome from culture medium, which contributes to a deeper understanding of the rice secretome.

Multidimensional protein identification technology analysis highlights mitoxantrone-induced expression modulations in the primary prostate cancer cell proteome.

Chemotherapeutic agents as they are used today have limited effectiveness against prostate cancer, but may potentially be used in new combinations with more efficacious results. Mitoxantrone, used for palliation of prostate cancer, has recently been found by our group to improve the susceptibility of primary prostate cancer cells to killing through the Fas-mediated death pathway. Here we used a shotgun proteomics approach to first profile the entire prostate cancer proteome and then identify specific factors involved in this mitoxantrone response. Peptides derived from primary prostate cancer cells treated with or without 100 nM mitoxantrone were analyzed by multidimensional protein identification technology (MudPIT). Strict limits and data filtering hierarchies were applied to identify proteins with high confidence. We identified 1498 proteins belonging to the prostate cancer proteome, 83 of which were significantly upregulated and 27 of which were markedly downregulated following mitoxantrone treatment. These proteins perform diverse functions, including ceramide production, tumour suppression, and oxidative reduction. Detailed proteomic analyses of prostate cancer cells and their response to mitoxantrone will further our understanding of its mechanisms of action. Identification of proteins influenced by treatment with mitoxantrone or other compounds may lead to the development of more effective drug combinations against prostate cancer.

Non-Proteasomal Targets of Proteasome Inhibitors Bortezomib and Carfilzomib

The proteasome is a multicatalytic protease complex that has been validated as a therapeutic target in oncology with the approval of bortezomib for the treatment of multiple myeloma and mantle cell lymphoma. Carfilzomib is a next generation proteasome inhibitor that is structurally and mechanistically distinct from bortezomib and has entered clinical development in oncology. Both inhibitors target the chymotrypsin-like activity of the proteasome, but their mechanism of action differs due to their unique chemical pharmacores (or “warheads”): bortezomib is a boronate while carfilzomib is an epoxyketone. Phase 1 studies with carfilzomib suggest a clinical safety profile that has both commonalities and distinctions from bortezomib. Transient thrombocytopenia is observed with both molecules suggesting that this event is a proteasome inhibitor class effect. In contrast, the painful peripheral neuropathy that is commonly observed with bortezomib appears to be less severe and possibly less frequent with carfilzomib, raising the possibility that non-proteasome mechanisms may underlie this toxicity. To gain potential insight into the common and unique clinical toxicities of bortezomib and carfilzomib, we evaluated their propensity to act as inhibitors of non-proteasomal enzymes. Bortezomib and carfilzomib were initially screened in a panel of candidate cysteine, aspartyl, metallo-, and serine proteases. Bortezomib significantly inhibited the serine proteases cathepsin G (IC50= 0.3μM) and chymase (IC50= 1.1μM), while carfilzomib did not inhibit these enzymes (IC50>10μM). These effects were further validated in cell extracts prepared from the Thp1 monocyte cell line and peripheral blood mononuclear cells (PBMC), where the inhibition of cathepsin G and chymase by bortezomib was detected using FP-biotin, a serine hydrolase-specific fluorophosphonate activity-based probe. These results suggest that the boronic acid warhead of bortezomib has greater off-target activity than the epoxyketone warhead of carfilzomib. To further investigate this hypothesis, off-target binding of proteasome inhibitors with either the boronate (Cbz-LLL-boronate) or epoxyketone (Cbz-LLL-epoxyketone) warheads were tested in cell extracts and intact cells using FP-biotin detection. Several serine hydrolases in liver (HepG2), lung (A549), kidney (786-O), and leukemia (Thp1) tumor cell lines were found to bind the boronate inhibitor but not the epoxyketone inhibitor. This result suggests that the boronate warhead is more “promiscuous” than the expoxyketone warhead. To obtain a global inhibition profile of the serine hydrolases that are targeted by bortezomib, multidimensional protein identification technology (MudPIT) analysis was performed on FP-biotin-reactive proteins from HepG2 cell extracts. Bortezomib was found to bind several serine hydrolases, including cathepsin A and dipeptidyl peptidase IV (DPP IV) and we have further validated these targets using specific antibodies. Taken together, these data demonstrate that non-proteasomal enzymes can be targeted by bortezomib (cathepsin G, cathepsin A, DPP IV and chymase), whereas carfilzomib does not appear to inhibit non-proteasomal targets in our assays. Work in progress includes biochemical and cell-based characterization for non-proteasomal targets, further global proteomic inhibition profiling using MudPIT analyses, and assessing the potential contribution of non-proteasomal targets to the differential toxicity profiles of the two proteasome inhibitor classes.

High Quality Catalog of Proteotypic Peptides from Human Heart

Proteomics research is beginning to expand beyond the more traditional shotgun analysis of protein mixtures to include targeted analyses of specific proteins using mass spectrometry. Integral to the development of a robust assay based on targeted mass spectrometry is prior knowledge of which peptides provide an accurate and sensitive proxy of the originating gene product (i.e., proteotypic peptides). To develop a catalog of "proteotypic peptides" in human heart, TRIzol extracts of left-ventricular tissue from nonfailing and failing human heart explants were optimized for shotgun proteomic analysis using Multidimensional Protein Identification Technology (MudPIT). Ten replicate MudPIT analyses were performed on each tissue sample and resulted in the identification of 30 605 unique peptides with a q-value < or = 0.01, corresponding to 7138 unique human heart proteins. Experimental observation frequencies were assessed and used to select over 4476 proteotypic peptides for 2558 heart proteins. This human cardiac data set can serve as a public reference to guide the selection of proteotypic peptides for future targeted mass spectrometry experiments monitoring potential protein biomarkers of human heart diseases.