Here we describe Rev immunoprecipitation in the presence of HIV-1 replication for mass spectrometry. The methods described can be used for the identification of nucleolar factors involved in the HIV-1 infectious cycle and are applicable to other disease models for the characterization of understudied pathways.
The HIV-1 infectious cycle requires viral protein interactions with host factors to facilitate viral replication, packaging, and release. The infectious cycle further requires the formation of viral/host protein complexes with HIV-1 RNA to regulate the splicing and enable nucleocytoplasmic transport. The HIV-1 Rev protein accomplishes the nuclear export of HIV-1 mRNAs through multimerization with intronic cis-acting targets – the Rev response element (RRE). A nucleolar localization signal (NoLS) exists within the COOH-terminus of the Rev arginine-rich motif (ARM), allowing the accumulation of Rev/RRE complexes in the nucleolus. Nucleolar factors are speculated to support the HIV-1 infectious cycle through various other functions in addition to mediating mRNA-independent nuclear export and splicing. We describe an immunoprecipitation method of wild-type (WT) Rev in comparison to Rev nucleolar mutations (deletion and single-point Rev-NoLS mutations) in the presence of HIV-1 replication for mass spectrometry. Nucleolar factors implicated in the nucleocytoplasmic transport (nucleophosmin B23 and nucleolin C23), as well as cellular splicing factors, lose interaction with Rev in the presence of Rev-NoLS mutations. Various other nucleolar factors, such as snoRNA C/D box 58, are identified to lose interaction with Rev mutations, yet their function in the HIV-1 replication cycle remain unknown. The results presented here demonstrate the use of this approach for the identification of viral/host nucleolar factors that maintain the HIV-1 infectious cycle. The concepts used in this approach are applicable to other viral and disease models requiring the characterization of understudied pathways.
The nucleolus is postulated as the interaction ground of various cellular host and viral factors required for viral replication. The nucleolus is a complex structure subdivided into three different compartments: the fibrillar compartment, the dense fibrillar compartment, and the granular compartment. The HIV-1 Rev protein localizes specifically within granular compartments; however, the reason for this localization pattern is unknown. In the presence of single-point mutations within the NoLS sequence (Rev mutations 4, 5, and 6), Rev maintains a nucleolar pattern and has previously been shown to rescue HIV-1HXB2 replication, however, with reduced efficiency compared to WT Rev1. All single-point mutations are unable to sustain the HIV-1NL4-3 infectious cycle. In the presence of multiple single-point mutations within the NoLS sequence (Rev-NoLS mutations 2 and 9), Rev has been observed to disperse throughout the nucleus and cytoplasm and has not been able to rescue HIV-1HXB2 replication1. The goal of this proteomics study is to decipher nucleolar as well as nonnucleolar cellular factors involved in the Rev-mediated HIV-1 infectious pathway. Rev immunoprecipitation conditions are optimized through interaction with the nucleolar B23 phosphoprotein, which has previously been shown to lose interaction with Rev in the presence of nucleolar mutations.
Rev cellular factors have been extensively studied in the past; however, this has been done in the absence of viral pathogenesis. One protein, in particular, that is characterized in this study through Rev interaction during HIV-1 replication is the nucleolar phosphoprotein B23 – also called nucleophosmin (NPM), numatrin, or NO38 in amphibians2,3,4. B23 is expressed as three isoforms (NPM1, NPM2, and NPM3) – all members of the nucleophosmin/nucleoplasmin nuclear chaperone family5,6. The NPM1 molecular chaperone functions in the proper assembly of nucleosomes, in the formation of protein/nucleic acid complexes involved in chromatin higher-order structures7,8, and in the prevention of aggregation and misfolding of target proteins through an N-terminal core domain (residues 1-120)9. NPM1 functionality extends to ribosome genesis through the transport of preribosomal particles between the nucleus and cytoplasm10,11, the processing of preribosomal RNA in the internal transcribed spacer sequence12,13, and arresting the nucleolar aggregation of proteins during ribosomal assembly14,15. NPM1 is implicated in the inhibition of apoptosis16 and in the stabilization of tumor suppressors ARF17,18 and p5319, revealing its dual role as an oncogenic factor and tumor suppressor. NPM1 participates in the cellular activities of genome stability, centrosome replication, and transcription. NPM1 is found in nucleoli during cell cycle interphase, along the chromosomal periphery during mitosis, and in prenucleolar bodies (PNB) at the conclusion of mitosis. NPM2 and NPM3 are not as well-studied as NPM1, which undergoes altered expression levels during malignancy20.
NPM1 is documented in the nucleocytoplasmic shuttling of various nuclear/nucleolar proteins through an internal NES and NLS9,21 and was previously reported to drive the nuclear import of HIV-1 Tat and Rev proteins. In the presence of B23-binding-domain-β-galactosidase fusion proteins, Tat mislocalizes within the cytoplasm and loses transactivation activity; this demonstrates a strong affinity of Tat for B232. Another study established a Rev/B23 stable complex in the absence of RRE-containing mRNAs. In the presence of RRE mRNA, Rev dissociates from B23 and binds preferably to the HIV RRE, leading to the displacement of B2322. It is unknown where, at the subnuclear level, Tat transactivation and the Rev exchange process of B23 for HIV mRNA take place. Both proteins are postulated to enter the nucleolus simultaneously through B23 interaction. The involvement of other host cellular proteins in the HIV nucleolar pathway is expected. The methods described in this proteomics investigation will help elucidate the interplay of the nucleolus with host cellular factors involved during HIV-1 pathogenesis.
The proteomics investigation was initiated through the expression of Rev NoLS single-point mutations (M4, M5, and M6) and multiple arginine substitutions (M2 and M9) for HIV-1HXB2 production. In this model, a HeLa cell line stably expressing Rev-deficient HIV-1HXB2 (HLfB) is transfected with WT Rev and Rev nucleolar mutations containing a flag tag at the 3' end. The presence of WT Rev will allow viral replication to occur in HLfB culture, in comparison to Rev-NoLS mutations that do not rescue Rev deficiency (M2 and M9), or allow viral replication to occur but not as efficiently as WT Rev (M4, M5, and M6)1. The cell lysate is collected 48 h later after viral proliferation in the presence of Rev expression and subjected to immunoprecipitation with a lysis buffer optimized for Rev/B23 interaction. Lysis buffer optimization using varying salt concentrations is described, and protein elution methods for HIV-1 Rev are compared and analyzed in silver-stained or Coomassie-stained SDS-PAGE gels. The first proteomics approach involves the direct analysis of an eluted sample from expressed WT Rev, M2, M6, and M9 by tandem mass spectrometry. A second approach by which the eluates of WT Rev, M4, M5, and M6 underwent a gel extraction process is compared to the first approach. Peptide affinity to Rev-NoLS mutations in comparison to WT Rev is analyzed and the protein identification probability displayed. These approaches reveal potential factors (nucleolar and nonnucleolar) that participate in HIV-1 mRNA transport and splicing with Rev during HIV-1 replication. Overall, the cell lysis, IP, and elution conditions described are applicable to viral proteins of interest for the understanding of host cellular factors that activate and regulate infectious pathways. This is also applicable to the study of cellular host factors required for the persistence of various disease models. In this proteomics model, HIV-1 Rev IP is optimized for B23 interaction to elucidate nucleolar factors involved in nucleocytoplasmic shuttling activity and HIV-1 mRNA binding. Additionally, cell lines stably expressing infectious disease models that are deficient for key proteins of interest can be developed, similar to the HLfB cell line, to study infectious pathways of interest.
1. Cell culture
2. Expression of Rev-NoLS-3'flag mutations during HIV-1 replication
3. Collection of viral protein lysate
4. Bradford assay
NOTE: Prepare 10x bovine serum albumin (BSA) from 100x BSA stock before generating protein standard curves.
5. Coimmunoprecipitation of Rev-NoLS-3'flag
6. Preparation of SDS-PAGE gels
7. Western blot transfer
8. Immunoblotting
9. Coomassie staining
10. Silver staining
11. In-gel reduction, alkylation, and digestion of Coomassie-stained gel bands
12. Liquid chromatography/mass spectrometry
NOTE: The samples were analyzed using a mass spectrometer equipped with ultra HPLC, a nanospray source, and a column (see the Table of Materials). Solvents A and B are 0.1% formic acid in water and acetonitrile, respectively.
13. Data analysis for mass spectrometry
Rev-NoLS single- and multiple-point arginine mutations, corresponding to a variety of subcellular localization patterns, were examined in their ability to interact with cellular host factors in comparison to WT Rev. WT Rev-3'flag and pcDNA-flag vector were expressed in HLfB culture. Protein complexes were processed from total cell lysate and stained with silver stain reagent. Rev-NoLS-3'flag is detectable (approximately 18 kDa) in three different lysis buffer conditions containing various concentrations of NaCl (137 mM, 200 mM, and 300 mM) in Figure 1. B23 was detectable (37 kDa) in lysis buffer containing lower salt concentration (137 mM, lanes 2–4), barely detectable in lysis buffer containing 200 mM NaCl, and undetectable in lysis buffer containing a high salt concentration (300 mM NaCl). In Figure 2, WT Rev-3'flag, Rev-NoLS M1-3'flag, and pcDNA-flag vector were expressed in HLfB culture. Protein complexes were processed from total cell lysates prepared from two lysis buffer conditions (137 mM and 200 mM NaCl). M2 mouse monoclonal IgG1 was used in the detection of Rev-3'flag expression from cell lysates. B23 detection was optimal in lysis buffer containing 137 mM NaCl with WT Rev-3'flag (input and α-flag-Rev IP) but lost affinity with Rev-NoLS M1-3'flag. B23 affinity with WT Rev-3'flag decreased with a higher salt concentration in lysis buffer containing 200 mM NaCl. pcDNA negative control did not yield nonspecific immunodetection in input and α-flag-Rev IP of all lysis buffer conditions.
Elution conditions were optimized for Rev-NoLS-3'flag IP in Figure 3. WT Rev-3'flag and pcDNA-flag vector were expressed in HLfB culture. Protein complexes were processed from total cell lysates and eluted using three different conditions to eradicate light and heavy chain background (25 and 50 kDa) – 2x sample loading buffer at 37 °C for 15 min, 2x sample loading buffer at 95 °C for 3 min, and 3x flag peptide at 4 °C for 30 min. Rev NoLS-3'flag (~18 kDa) was most detectable after elution through boiling in 2x sample loading buffer. B23 (~37 kDa) was detectable under two conditions – 37 °C incubation in 2x sample loading buffer for 15 min and 95 °C incubation in 2x sample loading buffer for 3 min.
M2 (nuclear/nucleolar in localization, nonfunctional in HIV-1HXB2 production), M6 (nucleolar in pattern, functional in HIV-1HXB2 production), and M9 (dispersed in the cytoplasm/nucleus, nonfunctional in viral production) were expressed in HLfB culture. Protein complexes were processed from total cell lysate, eluted through 95 °C incubation in 2x sample loading buffer for 3 min, and resolved in silver stain reagent (Figure 4). WT Rev was detectable after IP flag reaction. Rev-NoLS M2, M6, and M9 were also detectable at 18 kDa. Bands corresponding to B23 protein were observed at the 37 kDa marker. Protein complexes were further observed in each lane corresponding to IP reactions of WT Rev, M2, M6, M9, and pcDNA negative background control. Protein lysates were analyzed by immunodetection for α-flag-Rev and B23. Abundant WT Rev and moderate levels of M6 were expressed (α-flag input) and detectable after flag IP (α-flag-Rev IP, Figure 5). M2 and M9 were not highly expressed from 20 μg of protein lysate input but detectable at low intensity after flag IP from 5 mg of protein lysate. pcDNA negative control did not yield nonspecific immunodetection in input and α-flag-Rev IP. B23 affinity with WT Rev was observed after IP flag reaction (B23 co-IP). B23 affinity was slightly observed with M2 (two single-point mutations R48,50G) and M6 (single-point mutation R50G). B23 affinity was lost in the presence of three single-point mutations of M9 (R46,48,50G) within Rev-NoLS.
Total lysates from immunoprecipitated WT Rev and Rev-NoLS-3'flag mutations (4, 5, 6, and 8) were processed, stained with Coomassie reagent, and visualized in comparison to BSA serial dilutions (right panel). Rev-NoLS-3'flag is detectable (12.5-25 µg) in the presence and absence of mutations at 18 kDa (Figure 6). Protein complexes processed from IP reactions of WT Rev-3'flag, nucleolar-localizing Rev-NoLS-3'flag mutations (M4, M5, and M6), and negative control pcDNA-flag were visualized in SDS-PAGE gels stained with Coomassie reagent (Figure 7). WT Rev (WT1 and WT2) was detectable after IP flag reaction at 18 kDa. Rev-NoLS mutations were slightly detectable after expression in HLfB and IP flag reaction. pcDNA negative control did not yield nonspecific background at 18 kDa.
Immunoprecipitated lysates prepared from WT Rev-3'flag, M2, M6, M9, and negative control pcDNA-flag (shown in Figure 4) were analyzed by tandem mass spectrometry. Protein identification probability (in percentages) is displayed for comparison of protein interactions occurring with each nucleolar-localizing Rev-NoLS mutation versus WT Rev (Table 1). Cellular proteins, some of which are nucleolar in localization pattern (ribosomal isoforms, eukaryotic translation initiation factor 48, snoRNA C/D box 58B, and nucleophosmin B23), were identified as direct/indirect binding partners of WT Rev. These nucleolar factors lost binding affinity to M2 (two single-point mutations R48,50G), M6 (single-point mutation R50G), and M9 (three single-point mutation R46,48,50G), similar to pcDNA negative control. Each lane of the Coomassie-stained gel in Figure 6 was processed for tandem mass spectrometry (Table 2). Peptide affinity to Rev-NoLS mutations was analyzed and displayed using protein identification probability (in percentages). A variety of cellular proteins, some of which are nucleolar in localization pattern (nucleolin C23, nucleophosmin B23, and nucleosome assembly protein), were identified as direct/indirect protein binding factors of WT Rev. These nucleolar factors were not identified to bind with M4, M5, and M6. Transport factors ARHGEF1 (rho guanine nucleotide exchange factor 1) and TBC1D24 (TCB1 domain family, member 24) were lost in affinity in the presence of Rev-NoLS mutations. Splicing factors hnRNPC (heterogeneous ribonuclear protein C) and PNN (pinin, desmosome-associated protein) were additionally observed to bind to WT Rev, which lost interaction with Rev single-point nucleolar mutations.
Figure 1: Optimization of cell lysis conditions for Rev-3'flag co-IP during HIV-1 production. WT Rev-NoLS-3'flag and negative control pcDNA-flag IP conditions were optimized in three different NaCl concentrations (137 mM, 200 mM, and 300 mM) in lysis buffer. As observed through silver staining, 137 mM NaCl was the optimal salt concentration for Rev immunoprecipitation and B23 binding. Please click here to view a larger version of this figure.
Figure 2: Optimization of lysis conditions for Rev-3'flag co-IP and B23 immunodetection during HIV-1 production. WT Rev-NoLS-3'flag, M1-3'flag, and negative control pcDNA-flag IP conditions were optimized in two different NaCl concentrations (137 mM and 200 mM) in lysis buffer. As observed through immunodetection, 137 mM NaCl was the optimal salt concentration for Rev immunoprecipitation and B23 binding. Please click here to view a larger version of this figure.
Figure 3: Optimization of Rev-3'flag co-IP elution during HIV-1 production, visualized by silver staining. Protein complexes were processed from total cell lysates prepared during WT Rev-3'flag and pcDNA-flag IP. Three different elution conditions were tested – 2x sample loading buffer at 37 °C for 15 min, 2x sample loading buffer at 95 °C for 3 min, and 3x flag peptide at 4 °C for 30 min. The optimal elution conditions of WT Rev occurred after the 15 min incubation period in 2x sample loading buffer at 37 °C and after the 3 min incubation period in 2x sample loading buffer at 95 °C. Please click here to view a larger version of this figure.
Figure 4: Immunoprecipitation of Rev-3'flag mutations 2, 6, and 9 during HIV-1 production. Protein complexes that bound directly/indirectly with WT Rev, M2 (R48,50G), M6 (R50G), M9 (R46,48,50G), and negative control pcDNA-flag in the presence of HIV-1 replication are shown in a silver-stained SDS-PAGE gel. Please click here to view a larger version of this figure.
Figure 5: Rev-3'flag co-IP of mutations 2, 6, and 9 for B23 immunodetection during HIV-1 production. The protein lysates and IP reactions prepared from WT Rev, M2, M6, M9, and negative control pcDNA-flag in Figure 4 were further analyzed by immunodetection for α-flag-Rev and B23. WT Rev and mutant expression, as well as interaction with B23 nucleocytoplasmic protein, are observed. Please click here to view a larger version of this figure.
Figure 6: Quantification of Rev-NoLS mutations 4, 5, 6, and 8 after flag IP reaction. IP reactions from HLfB expressing WT Rev and nucleolar-localizing M4 (R46G), M5 (R48G), M6 (R50G), M8 (ΔRQ), and negative control pcDNA-flag were measured for protein concentration using BSA serial dilutions. A protein concentration of 12.5-25 µg was observed for each sample. Please click here to view a larger version of this figure.
Figure 7: Immunoprecipitation of nucleolar-localizing Rev-NoLS mutations 4, 5, and 6 during HIV-1 production. Coomassie-stained SDS-PAGE gel containing immunoprecipitated protein complexes of WT Rev (1 and 2), M4, M5, and M6 are shown. Please click here to view a larger version of this figure.
Identified Proteins | Molecular Weight | WT Rev | M2 | M6 | M9 |
signal recognition particle 14kDa (homologous Alu RNA binding protein) | 15 kDa | 95% | 0 | 0 | 0 |
ribosomal protein S3A | 30 kDa | 95% | 0 | 0 | 0 |
eukaryotic translation initiation factor 4B | 69 kDa | 95% | 0 | 0 | 0 |
ribosomal protein L31 | 14 kDa | 91% | 0 | 0 | 0 |
ribosomal protein L12 | 18 kDa | 93% | 0 | 0 | 0 |
ribosomal protein L22 | 15 kDa | 91% | 0 | 0 | 0 |
small nucleolar RNA, C/D box 58B | 15 kDa | 87% | 0 | 0 | 0 |
zinc finger, CCHC domain containing 11 | 185 kDa | 87% | 0 | 0 | 0 |
actin binding LIM protein 1 | 79 kDa | 79% | 0 | 0 | 0 |
ribosomal protein S13 | 17 kDa | 78% | 0 | 0 | 0 |
nucleophosmin (nucleolar phosphoprotein B23, numatrin) | 33 kDa | 73% | 0 | 0 | 0 |
Table 1: Identification of cellular host factors that interact with WT Rev during HIV-1 production. Protein eluates prepared from WT Rev, M2, M6, and M9 were directly analyzed by tandem mass spectrometry. Protein interactions that are directly/indirectly bound to WT Rev versus M2, M6, and M9 are summarized by protein identification probability (in percentages).
Identified Proteins | Molecular Weight | M4 | M5 | M6 | WT | pCDNA |
poly(A) binding protein, cytoplasmic 1 | 61 kDa | 98% | 0 | 100% | 100% | 0 |
heat shock 70kDa protein 1B | 70 kDa | 100% | 100% | 100% | 100% | 0 |
ribosomal protein L7 | 29 kDa | 91% | 0 | 100% | 100% | 0 |
histone cluster 1, H1e | 22 kDa | 0 | 0 | 100% | 100% | 0 |
ribosomal protein L4 | 48 kDa | 95% | 0 | 100% | 100% | 0 |
ribosomal protein L13 | 24 kDa | 99% | 0 | 100% | 100% | 0 |
complement component 1, q subcomponent binding protein | 31 kDa | 100% | 100% | 100% | 100% | 0 |
Y box binding protein 1 | 36 kDa | 0 | 0 | 100% | 100% | 0 |
nucleosome assembly protein 1-like 1 | 45 kDa | 0 | 0 | 0 | 100% | 0 |
ribosomal protein L8 | 28 kDa | 89% | 36% | 100% | 100% | 0 |
ribosomal protein L18 | 22 kDa | 27% | 0 | 100% | 100% | 0 |
heat shock 70kDa protein 8 | 71 kDa | 5% | 99% | 100% | 100% | 0 |
ribosomal protein L19 | 23 kDa | 10% | 0 | 81% | 100% | 0 |
ribosomal protein L27 | 16 kDa | 92% | 0 | 100% | 100% | 0 |
ribosomal protein L7a | 30 kDa | 0 | 0 | 100% | 100% | 0 |
ribosomal protein L24 | 18 kDa | 0 | 0 | 100% | 99% | 0 |
tubulin, beta class I | 50 kDa | 92% | 69% | 100% | 100% | 0 |
ribosomal protein L6 | 33 kDa | 0 | 0 | 100% | 100% | 0 |
heat shock 70kDa protein 9 (mortalin) | 74 kDa | 33% | 99% | 100% | 100% | 0 |
ribosomal protein S2 | 31 kDa | 87% | 0 | 100% | 100% | 0 |
casein kinase 2, alpha 1 polypeptide | 45 kDa | 0 | 0 | 50% | 100% | 0 |
ribosomal protein L14 | 23 kDa | 0 | 0 | 81% | 100% | 0 |
ribosomal protein, large, P0 | 34 kDa | 0 | 0 | 100% | 100% | 0 |
histone cluster 1, H1b | 23 kDa | 0 | 0 | 73% | 100% | 0 |
heat shock 70kDa protein 5 (glucose-regulated protein) | 72 kDa | 99% | 0 | 100% | 100% | 0 |
ribosomal protein S4, X-linked | 30 kDa | 0 | 0 | 100% | 100% | 0 |
ribosomal protein S20 | 13 kDa | 98% | 94% | 99% | 99% | 0 |
ribosomal protein L28 | 16 kDa | 0 | 0 | 100% | 99% | 0 |
ribosomal protein S14 | 16 kDa | 0 | 0 | 100% | 100% | 0 |
ribosomal protein S3A | 30 kDa | 0 | 0 | 100% | 100% | 0 |
ribosomal protein L21 | 19 kDa | 0 | 0 | 100% | 100% | 0 |
zinc finger CCCH-type, antiviral 1 | 101 kDa | 0 | 0 | 97% | 100% | 0 |
histone cluster 1, H1c | 21 kDa | 0 | 0 | 0 | 98% | 0 |
ribosomal protein L36 | 12 kDa | 0 | 0 | 100% | 100% | 0 |
ribosomal protein S18 | 18 kDa | 90% | 0 | 100% | 100% | 0 |
modulator of apoptosis 1 | 40 kDa | 42% | 88% | 34% | 0 | 0 |
ribosomal protein L17 | 21 kDa | 0 | 0 | 100% | 100% | 0 |
ribosomal protein S26 | 13 kDa | 91% | 0 | 99% | 98% | 0 |
ribosomal protein L32 | 18 kDa | 0 | 0 | 48% | 100% | 0 |
ribosomal protein L35 | 15 kDa | 0 | 0 | 97% | 100% | 0 |
ribosomal protein L29 | 18 kDa | 0 | 0 | 57% | 94% | 0 |
ribosomal protein S9 | 23 kDa | 0 | 0 | 100% | 100% | 0 |
heterogeneous nuclear ribonucleoprotein H1 (H) | 51 kDa | 98% | 0 | 100% | 100% | 0 |
ribosomal protein S8 | 22 kDa | 0 | 0 | 78% | 100% | 0 |
ribosomal protein L10 | 25 kDa | 0 | 0 | 100% | 100% | 0 |
ribosomal protein L23a | 18 kDa | 0 | 0 | 68% | 100% | 0 |
ribosomal protein S6 | 29 kDa | 0 | 0 | 100% | 100% | 0 |
ribosomal protein L31 | 14 kDa | 0 | 0 | 95% | 100% | 0 |
ribosomal protein S13 | 17 kDa | 0 | 0 | 100% | 99% | 0 |
ribosomal protein L10a | 25 kDa | 45% | 0 | 81% | 100% | 0 |
poly(A) binding protein, cytoplasmic 4 (inducible form) | 70 kDa | 0 | 0 | 100% | 100% | 0 |
transmembrane emp24 protein transport domain containing 1 | 25 kDa | 0 | 0 | 0 | 100% | 0 |
EBNA1 binding protein 2 | 35 kDa | 0 | 0 | 69% | 100% | 0 |
conserved helix-loop-helix ubiquitous kinase | 85 kDa | 74% | 92% | 65% | 83% | 0 |
ribosomal protein L12 | 18 kDa | 0 | 0 | 57% | 100% | 0 |
ribosomal protein S24 | 15 kDa | 0 | 0 | 100% | 100% | 0 |
cold shock domain protein A | 40 kDa | 0 | 0 | 0 | 100% | 0 |
ribosomal protein L27a | 17 kDa | 0 | 0 | 89% | 99% | 0 |
heterogeneous nuclear ribonucleoprotein F | 46 kDa | 0 | 0 | 99% | 99% | 0 |
ribosomal protein L11 | 20 kDa | 0 | 0 | 99% | 100% | 0 |
ribosomal protein L26-like 1 | 17 kDa | 0 | 0 | 100% | 100% | 0 |
casein kinase 2, alpha prime polypeptide | 41 kDa | 0 | 0 | 0 | 100% | 0 |
tubulin, alpha 1a | 50 kDa | 33% | 0 | 100% | 0 | 0 |
ribosomal protein L3 | 46 kDa | 0 | 0 | 86% | 94% | 0 |
mitochondrial ribosomal protein L15 | 33 kDa | 0 | 0 | 100% | 99% | 0 |
nucleolin | 77 kDa | 0 | 0 | 25% | 100% | 0 |
mitochondrial ribosomal protein S21 | 11 kDa | 0 | 0 | 93% | 94% | 0 |
KRR1, small subunit (SSU) processome component, homolog (yeast) | 44 kDa | 89% | 0 | 76% | 99% | 0 |
mitochondrial ribosomal protein S7 | 28 kDa | 0 | 0 | 0 | 100% | 0 |
chloride channel, nucleotide-sensitive, 1A | 22 kDa | 0 | 0 | 97% | 86% | 0 |
cyclin B3 | 158 kDa | 0 | 0 | 67% | 49% | 0 |
guanine nucleotide binding protein-like 3 (nucleolar) | 61 kDa | 0 | 0 | 99% | 98% | 0 |
mitochondrial ribosomal protein S23 | 22 kDa | 0 | 0 | 100% | 50% | 0 |
mitochondrial ribosomal protein S22 | 41 kDa | 0 | 0 | 0 | 99% | 0 |
nucleophosmin (nucleolar phosphoprotein B23, numatrin) | 33 kDa | 0 | 0 | 52% | 97% | 0 |
ribosomal protein S19 | 16 kDa | 0 | 0 | 0 | 99% | 0 |
glyceraldehyde-3-phosphate dehydrogenase | 36 kDa | 0 | 0 | 100% | 0 | 0 |
histone cluster 1, H2bg | 14 kDa | 0 | 0 | 53% | 72% | 0 |
ribosomal protein S23 | 16 kDa | 0 | 0 | 68% | 0 | 0 |
Rho guanine nucleotide exchange factor (GEF) 1 | 104 kDa | 0 | 0 | 0 | 94% | 0 |
death associated protein 3 | 46 kDa | 0 | 0 | 87% | 87% | 0 |
mitochondrial ribosomal protein S6 | 14 kDa | 0 | 0 | 52% | 84% | 0 |
ribosomal protein L39 | 6 kDa | 0 | 0 | 0 | 87% | 0 |
mitochondrial ribosomal protein S28 | 21 kDa | 0 | 0 | 85% | 99% | 0 |
histone cluster 1, H4h | 11 kDa | 0 | 0 | 0 | 93% | 0 |
mitochondrial ribosomal protein L43 | 23 kDa | 0 | 0 | 0 | 97% | 0 |
ribosomal protein S15 | 17 kDa | 0 | 0 | 0 | 85% | 0 |
ribosomal protein S12 | 15 kDa | 0 | 0 | 68% | 39% | 0 |
ribosomal protein L35a | 13 kDa | 0 | 0 | 0 | 96% | 0 |
mitochondrial ribosomal protein L38 | 45 kDa | 0 | 0 | 42% | 98% | 0 |
mitochondrial ribosomal protein S14 | 15 kDa | 0 | 0 | 45% | 76% | 0 |
phosphodiesterase 5A, cGMP-specific | 95 kDa | 14% | 0 | 0 | 72% | 0 |
ribosomal protein L15 | 24 kDa | 0 | 0 | 0 | 56% | 0 |
heterogeneous nuclear ribonucleoprotein C (C1/C2) | 22 kDa | 0 | 0 | 0 | 100% | 0 |
mitochondrial ribosomal protein S16 | 11 kDa | 0 | 0 | 0 | 92% | 0 |
ribosomal protein S15a | 15 kDa | 0 | 0 | 0 | 91% | 0 |
neurexin 2 | 185 kDa | 0 | 50% | 0 | 0 | 0 |
autism susceptibility candidate 2 | 139 kDa | 0 | 0 | 46% | 0 | 0 |
mitochondrial ribosomal protein L17 | 20 kDa | 0 | 0 | 0 | 92% | 0 |
splicing factor 3a, subunit 1, 120kDa | 89 kDa | 0 | 0 | 56% | 89% | 0 |
La ribonucleoprotein domain family, member 1 | 116 kDa | 0 | 0 | 65% | 66% | 0 |
leprecan-like 2 | 62 kDa | 0 | 0 | 0 | 68% | 0 |
ribosomal protein L18a | 21 kDa | 0 | 0 | 0 | 86% | 0 |
ribosomal protein L23 | 15 kDa | 0 | 0 | 60% | 47% | 0 |
transmembrane emp24 protein transport domain containing 9 | 27 kDa | 0 | 0 | 0 | 78% | 0 |
signal recognition particle 72kDa | 75 kDa | 0 | 0 | 0 | 100% | 0 |
lectin, galactoside-binding, soluble, 3 | 26 kDa | 0 | 71% | 28% | 0 | 0 |
mitochondrial ribosomal protein L1 | 37 kDa | 0 | 0 | 0 | 69% | 0 |
H1 histone family, member X | 22 kDa | 0 | 0 | 0 | 96% | 0 |
casein kinase 2, beta polypeptide | 25 kDa | 0 | 0 | 0 | 89% | 0 |
solute carrier family 4, sodium bicarbonate cotransporter, member 7 | 118 kDa | 82% | 0 | 0 | 0 | 0 |
WD repeat domain 13 | 54 kDa | 0 | 81% | 0 | 0 | 0 |
transcription elongation factor A (SII), 3 | 17 kDa | 0 | 0 | 0 | 38% | 0 |
ribosomal protein S16 | 16 kDa | 0 | 0 | 75% | 0 | 0 |
SP140 nuclear body protein | 92 kDa | 0 | 0 | 0 | 64% | 0 |
otoferlin | 227 kDa | 62% | 0 | 0 | 0 | 0 |
golgi transport 1B | 15 kDa | 0 | 0 | 0 | 33% | 0 |
mitochondrial ribosomal protein S34 | 26 kDa | 0 | 0 | 0 | 33% | 0 |
ribosomal protein L30 | 13 kDa | 0 | 0 | 0 | 49% | 0 |
actin binding LIM protein 1 | 96 kDa | 0 | 0 | 0 | 43% | 0 |
guanine nucleotide binding protein-like 2 (nucleolar) | 84 kDa | 40% | 0 | 0 | 0 | 0 |
high density lipoprotein binding protein | 141 kDa | 0 | 0 | 34% | 0 | 0 |
adenosine deaminase, RNA-specific, B2 | 81 kDa | 0 | 0 | 28% | 0 | 0 |
cystatin E/M | 17 kDa | 0 | 27% | 0 | 0 | 0 |
zinc finger protein 786 | 80 kDa | 0 | 0 | 23% | 0 | 0 |
pleckstrin homology-like domain, family B, member 1 | 145 kDa | 0 | 0 | 0 | 95% | 0 |
protein phosphatase methylesterase 1 | 44 kDa | 0 | 0 | 94% | 0 | 0 |
janus kinase and microtubule interacting protein 2 | 95 kDa | 0 | 0 | 0 | 94% | 0 |
signal recognition particle 68kDa | 67 kDa | 0 | 0 | 0 | 93% | 0 |
TBC1 domain family, member 24 | 63 kDa | 0 | 0 | 0 | 89% | 0 |
mitochondrial ribosomal protein L27 | 16 kDa | 0 | 0 | 0 | 89% | 0 |
mitochondrial ribosomal protein L2 | 24 kDa | 0 | 0 | 0 | 88% | 0 |
mitochondrial ribosomal protein S2 | 33 kDa | 0 | 0 | 0 | 87% | 0 |
Pentatricopeptide repeat domain 3 | 79 kDa | 0 | 0 | 0 | 84% | 0 |
ribosomal protein, large, P2 | 12 kDa | 0 | 0 | 0 | 76% | 0 |
IMP (inosine 5'-monophosphate) dehydrogenase 2 | 56 kDa | 0 | 0 | 76% | 0 | 0 |
tubulin, beta 4B class IVb | 50 kDa | 0 | 0 | 76% | 0 | 0 |
mitochondrial ribosomal protein L23 | 19 kDa | 0 | 0 | 0 | 74% | 0 |
mitochondrial ribosomal protein S31 | 45 kDa | 0 | 0 | 0 | 74% | 0 |
galactose-3-O-sulfotransferase 1 | 49 kDa | 74% | 0 | 0 | 0 | 0 |
suppressor of variegation 4-20 homolog 1 (Drosophila) | 99 kDa | 0 | 72% | 0 | 0 | 0 |
mitochondrial ribosomal protein S25 | 20 kDa | 0 | 0 | 0 | 70% | 0 |
ribosomal L1 domain containing 1 | 55 kDa | 0 | 0 | 0 | 70% | 0 |
family with sequence similarity 110, member D | 29 kDa | 69% | 0 | 0 | 0 | 0 |
ribosomal protein L36a-like | 12 kDa | 0 | 0 | 0 | 66% | 0 |
cerebellin 4 precursor | 22 kDa | 0 | 0 | 0 | 64% | 0 |
N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits | 144 kDa | 64% | 0 | 0 | 0 | 0 |
RAD51 homolog B (S. cerevisiae) | 38 kDa | 0 | 0 | 0 | 64% | 0 |
transcription elongation regulator 1 | 124 kDa | 63% | 0 | 0 | 0 | 0 |
homeobox A1 | 15 kDa | 0 | 0 | 0 | 62% | 0 |
phospholipid transfer protein | 49 kDa | 0 | 0 | 0 | 62% | 0 |
Rho GTPase activating protein 33 | 137 kDa | 0 | 0 | 54% | 0 | 0 |
mitochondrial ribosomal protein S18B | 29 kDa | 0 | 0 | 0 | 52% | 0 |
endoplasmic reticulum aminopeptidase 2 | 106 kDa | 51% | 0 | 0 | 0 | 0 |
tripartite motif containing 28 | 89 kDa | 0 | 50% | 0 | 0 | 0 |
immature colon carcinoma transcript 1 | 24 kDa | 0 | 0 | 0 | 50% | 0 |
AT rich interactive domain 1A (SWI-like) | 242 kDa | 0 | 0 | 49% | 0 | 0 |
mitochondrial ribosomal protein S17 | 15 kDa | 0 | 0 | 0 | 48% | 0 |
pinin, desmosome associated protein | 82 kDa | 0 | 0 | 0 | 48% | 0 |
protein phosphatase, Mg2+/Mn2+ dependent, 1G | 59 kDa | 0 | 0 | 0 | 45% | 0 |
G patch domain and ankyrin repeats 1 | 39 kDa | 45% | 0 | 0 | 0 | 0 |
mitochondrial ribosomal protein L3 | 39 kDa | 0 | 0 | 0 | 44% | 0 |
budding uninhibited by benzimidazoles 3 homolog (yeast) | 37 kDa | 0 | 44% | 0 | 0 | 0 |
WD and tetratricopeptide repeats 1 | 76 kDa | 0 | 0 | 0 | 44% | 0 |
protein disulfide isomerase family A, member 2 | 58 kDa | 0 | 0 | 0 | 42% | 0 |
kazrin, periplakin interacting protein | 86 kDa | 0 | 41% | 0 | 0 | 0 |
coiled-coil-helix-coiled-coil-helix domain containing 2 | 16 kDa | 0 | 0 | 40% | 0 | 0 |
heat shock protein 90kDa alpha (cytosolic), class A member 1 | 85 kDa | 0 | 0 | 40% | 0 | 0 |
retinitis pigmentosa GTPase regulator | 83 kDa | 0 | 0 | 40% | 0 | 0 |
CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1 |
104 kDa | 0 | 39% | 0 | 0 | 0 |
mitochondrial ribosomal protein L37 | 48 kDa | 0 | 0 | 0 | 39% | 0 |
C2CD2-like | 76 kDa | 0 | 38% | 0 | 0 | 0 |
DnaJ (Hsp40) homolog, subfamily C, member 6 | 106 kDa | 0 | 0 | 38% | 0 | 0 |
mitochondrial ribosomal protein L51 | 15 kDa | 0 | 0 | 0 | 38% | 0 |
bystin-like | 50 kDa | 0 | 0 | 0 | 38% | 0 |
huntingtin-associated protein 1 | 76 kDa | 0 | 0 | 0 | 37% | 0 |
zinc finger protein 263 | 77 kDa | 0 | 36% | 0 | 0 | 0 |
cell division cycle and apoptosis regulator 1 | 133 kDa | 0 | 0 | 34% | 0 | 0 |
protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase) |
256 kDa | 0 | 0 | 34% | 0 | 0 |
KRAB-A domain containing 2 | 56 kDa | 0 | 0 | 0 | 31% | 0 |
activating signal cointegrator 1 complex subunit 2 | 28 kDa | 0 | 0 | 0 | 31% | 0 |
centrosomal protein 76kDa | 74 kDa | 0 | 30% | 0 | 0 | 0 |
polymerase (RNA) III (DNA directed) polypeptide C (62kD) | 61 kDa | 0 | 0 | 0 | 30% | 0 |
5-hydroxytryptamine (serotonin) receptor 6 | 47 kDa | 0 | 0 | 0 | 29% | 0 |
T cell receptor alpha joining 56 | 2 kDa | 0 | 26% | 0 | 0 | 0 |
biorientation of chromosomes in cell division 1-like | 330 kDa | 0 | 0 | 0 | 25% | 0 |
Ras association and DIL domains | 114 kDa | 0 | 0 | 25% | 0 | 0 |
WD repeat domain 66 | 130 kDa | 0 | 0 | 0 | 24% | 0 |
chromosome 6 open reading frame 25 | 13 kDa | 0 | 0 | 22% | 0 | 0 |
transmembrane protein 177 | 34 kDa | 0 | 0 | 0 | 21% | 0 |
neural precursor cell expressed, developmentally down-regulated 4-like | 101 kDa | 0 | 20% | 0 | 0 | 0 |
Table 2: Identification of cellular host factors complexed with nucleolar-localizing Rev mutations 4, 5, and 6 during HIV-1 production. The Coomassie-stained SDS-PAGE gel in Figure 6 was processed for tandem mass spectrometry. Protein interaction results of WT Rev versus nucleolar mutations M4, M5, and M6 are summarized by protein identification probability (in percentages).
Mass spectrometric analyses comparing Rev-NoLS mutations and WT Rev in the presence of HIV-1 were assessed to understand nucleolar factors involved in the viral replication cycle. This would identify nucleolar components required for viral infectivity. Nucleolar B23 has a high affinity to Rev-NoLS and functions in the nucleolar localization of Rev3 and nucleocytoplasmic transport of Rev-bound HIV mRNAs22. The affinity of B23 with Rev-NoLS mutations, which contained single or multiple arginine substitutions, was assessed through immunoprecipitation of Rev-3'flag during viral production (Figure 2; WT and mutations M2, M6, and M9). B23 affinity to single-point Rev-NoLS mutations M4, M5, and M6 were previously examined in the presence of HIV-1 replication. In the previous study, IP eluates of M4, M5, and M6 were subjected to western immunoblotting with an antibody specific to α-flag for Rev and B23 affinity1. In the background of Rev single-point mutations, B23 binding affinity was significantly reduced. B23 maintained affinity with WT Rev during HIV replication. Single-point mutations induced within Rev-NoLS were expected to decrease binding affinity to other cellular host factors facilitating HIV mRNA binding and transport. Rev-NoLS single- and multiple-point mutations in this model abolished nucleophosmin B23 affinity to Rev, indicating a disruption in nucleocytoplasmic shuttling and HIV mRNA transport. It is likely that nucleolar factors (nucleolin C23 and nucleosome assembly protein 1), transport factors (ARHGEF1 and TCB1D24), and splicing factors (hnRNPC and PNN) are involved in the HIV-1 infectious cycle through interaction with Rev protein complexes. Table 1 and Table 2 reveal various other cellular factors, both nucleolar and nonnucleolar in pattern, that are potentially involved in the HIV-1 replication cycle through Rev. The nucleolar factor – snoRNA C/D box 58, implicated in snoRNA processing, snoRNA transport to the nucleolus, and 2'-O-methylation of ribosomal RNA – was identified yet the function of this protein in the HIV-1 replication cycle remains unknown. The specific roles of these cellular factors in the HIV-1 infectious cycle are currently being investigated.
The results presented here demonstrate the use of this approach for the identification of viral/host nucleolar factors that maintain the HIV-1 infectious cycle. Viral/host nucleolar factors that participate in other disease models could be identified using this approach. It is further likely that one nucleolar factor could involve multifunctional roles in various disease models. For example, B23 has been implicated in the transport of nucleolar viral proteins, viral assembly, encapsidation, replication, and latency in other viral infectious models. B23 is characterized in interactions with NoLS of cellular factors for nucleocytoplasmic transport – p120 growth factor (amino acids 40-57)23 and C23 pre-rRNA processor (amino acids 540–628)24. B23 is also documented to interact with the human T-cell lymphotropic virus (HTLV-1) protein Rex (amino acids 1-22)25, HIV-1 Tat (amino acids 49–57)2, and HIV-1 Rev (amino acids 37-47)26. The Japanese encephalitis virus (JEV) genome encodes a nucleolar-localizing core protein, through which amino acids Gly42 and Pro43 interact with the N-terminal region of B23 during JEV infection, resulting in the transportation of viral core protein/B23 into the nucleus27. The single-stranded RNA genome of the Hepatitis B virus (HBV) is composed partially of double-stranded DNA, which encodes a nucleolar core protein. The HBV core protein associates with nucleolin and B23 in the nucleolus28; B23 was demonstrated in the HBV assembly through interaction with the core protein N-terminal domain. Specifically, B23 amino acids 259-294 bind to the N-terminal domain of the HBV core protein to allow viral encapsidation29. The negative-sense, single-stranded RNA hepatitis D virus (HDV) expresses HDVAg antigen in two isoforms; the small isoform aids in RNA replication, and the large isoform facilitates viral assembly. RNA replication takes place within the nucleolus and requires B23 interaction with HDVAg30,31. HDV infection causes an upregulation of B23, which interacts mostly with the small HDVAg isoform and less with the large HDVAg isoform. Interactions take place through the small HDVAg NLS domain, through which B23 binds and achieves nuclear accumulation. Upon deletion of the HDV binding site to B23, RNA replication was impaired. HDVAg was shown to colocalize with B23 and nucleolin in the nucleolus. Nucleolin was discovered to possess transcriptional properties as a repressor32, revealing the nucleolus as a compartment for regulation of HDV replication. B23 is also involved in the latency of the Kaposi’s sarcoma-associated herpesvirus (KSHV) genome. KSHV latent protein – v-cyclin – with host CDK6 kinase, phosphorylates B23 at Thr199, facilitating B23 interaction with latency-associated nuclear antigen33. The latency-associated nuclear antigen acts to prevent viral lytic replication. Depletion of B23 leads to KSHV reactivation, revealing B23 as a regulator of KSHV latency. B23 function in the HIV-1 replication cycle is characterized in the nucleocytoplasmic transport activity of Tat and Rev, and it is unknown if B23 can induce latency during HIV infection. B23’s involvement in the replication, encapsidation, and assembly of HIV-1 is currently unknown.
Adaptation of this method to other disease models would require much effort and time for the generation of protein-deficient infectious backbones expressed in the appropriate cell lines. The advantage of this Rev-deficient HIV-1HXB2 backbone is the ability to examine Rev-NoLS mutations in the presence of the full viral backbone, viral infectious factors, and host factors involved in the HIV-1 replication cycle. Other studies have examined Rev nucleolar function in the absence of the full HIV-1 infectious system. Thorough characterization of infectious and disease pathways must include representative environments that support the natural course of disease progression. Two different types of analyses were conducted and compared in the ability to identify nucleolar factors. Table 1 lists factors that remained bound to WT Rev as a result of direct mass spectrometry analysis of protein eluate. This analysis yielded several known factors of HIV-1 Rev. This direct method was compared to another process involving the extraction of protein separated within SDS-PAGE gels and mass spectrometry analysis of such proteins. This second method yielded a variety of known and potential factors that are bound to the Rev protein complex but lacked the following proteins previously identified in Table 1: signal recognition particle 14 kDa, eukaryotic translation initiation factor 4B, ribosomal protein L22, small nucleolar RNA C/D box 58B, and zinc finger CCHC domain containing 11. Ultimately, the superior method chosen for mass spectrometry analyses in this protocol involved the extraction of peptides from SDS-PAGE gels. The first direct method included 2x sample buffer in the eluate without bromophenol blue; the remaining components of the 2x sample buffer could interfere with complete trypsin treatment and could yield incompletely processed peptides for mass spectrometry analysis. The second indirect method was able to purify trypsin-treated peptides from potential contaminants of SDS-PAGE.
The mass spectrometry preparation methods described here could be utilized for the identification of therapeutic interventions to eradicate HIV-1 infection through targeting Rev. All deletion and single-point Rev-NoLS mutations could be examined for dominant-negative activity and utilized in the arrest of Rev function. Dominant negative characteristics of interest for Rev functional arrest are the following: Rev/RRE binding affinity; relocalization of nucleolar WT Rev through multimerization with Rev mutants; loss in affinity to key cellular factors involved in HIV-1 mRNA transport and splicing. Rev multimerization involving the coexpression of Rev-NoLS mutations with WT Rev could be examined. Dominant negative mutations in this model are expected to multimerize with WT Rev and shift nucleolar patterns toward the nucleus and cytoplasm, leading to a Rev functional arrest. Mass spectrometry could be used to identify the loss of key cellular factors involved in HIV-1 mRNA splicing and transport. The identification of missing interactions with WT Rev as a result of coexpression with dominant-negative Rev-NoLS mutations would reveal the involvement of nucleolar-specific pathways in HIV-1 pathogenesis. Alternatively, viral HIV-1NL4-3 particles generated in the background of Rev-NoLS mutations could be investigated for all packaged cellular factors. Cellular and viral factors packaged within viral particles may be further identified through mass spectrometry. This would reveal the presence of nucleolar factors within viral particles and the role of identified nucleolar factors in viral infection. The methods described are applicable to other viral and disease models for the identification and characterization of understudied pathways. This would allow the development of therapeutic interventions against diseases by which limited treatments are available.
The authors have nothing to disclose.
The authors acknowledge Dr. Barbara K. Felber and Dr. George N. Pavlakis for the HLfB adherent culture provided by the National Institutes of Health (NIH) AIDS Research and Reference Reagent Program, Division of AIDS, National Institute of Allergy and Infectious Diseases (NIAID), NIH. The authors also acknowledge financial sources provided by the NIH, Grants AI042552 and AI029329.
Acetic acid | Fisher Chemical | A38S-212 | |
Acetonitrile | Fisher Chemical | A955-500 | |
Acrylamide:Bisacrylamide | BioRad | 1610158 | |
Ammonium bicarbonate | Fisher Chemical | A643-500 | |
Ammonium persulfate | Sigma-Aldrich | 7727-54-0 | |
ANTI-Flag M2 affinity gel | Sigma-Aldrich | A2220 | |
anti-Flag M2 mouse monoclonal IgG | Sigma-Aldrich | F3165 | |
BioMax MS film | Carestream | 8294985 | |
Bio-Rad Protein Assay Dye Reagent Concentrate, 450 mL | Bio-Rad | 5000006 | |
B23 mouse monoclonal IgG | Santa Cruz Biotechnologies | sc-47725 | |
Bromophenol blue | Sigma-Aldrich | B0126 | |
Carnation non-fat powdered milk | Nestle | N/A | |
Cell scraper | ThermoFisher Scientific | 179693PK | |
C18IonKey nanoTile column | Waters | 186003763 | |
Corning 100-mm TC-treated culture dishes | Fisher Scientific | 08-772-22 | |
Dithiothreitol | Thermo Scientific | J1539714 | |
1 x DPBS | Corning | 21-030-CVRS | |
ECL Estern blotting substrate | Pierce | 32106 | |
Ethanol, 200 proof | Fisher Chemical | A409-4 | |
FBS | Gibco | 16000044 | |
Formic Acid | Fisher Chemical | A117-50 | |
GelCode blue stain reagent | ThermoFisher | 24590 | |
Glycerol | Fisher Chemical | 56-81-5 | |
goat-anti-mouse IgG-HRP | Santa Cruz Biotechnologies | sc-2005 | |
Iodoacetamide | ACROS Organics | 122270050 | |
KimWipe delicate task wiper | Kimberly Clark Professional | 34120 | |
L-glutamine | Gibco | 25030081 | |
Methanol | Fisher Chemical | 67-56-1 | |
NanoAcuity UPLC | Waters | N/A | |
Pierce Silver Stain Kit | Thermo Scientific | 24600df | |
15-mL Polypropylene conical tube | Falcon | 352097 | |
Prestained Protein Ladder, 10 to 180 kDa | Thermo Scientific | 26616 | |
Protease inhibitor cocktail | Roche | 4693132001 | |
Purified BSA | New England Biolabs | B9001 | |
PVDF Western blotting membrane | Roche | 3010040001 | |
Sodium Pyruvate | Gibco | 11360070 | |
10 x TBS | Fisher Bioreagents | BP2471500 | |
TEMED | BioRad | 1610880edu | |
Triton X-100 detergent solution | BioRad | 1610407 | |
Trizaic source | Waters | N/A | |
trypsin-EDTA | Corning | 25-051-CIS | |
Tween 20 | BioRad | 1706531 | |
Synapt G2 mass spectrometer | Waters | N/A | |
Whatman filter paper | Tisch Scientific | 10427813 |