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Tagwerker C, et al.  (2006) A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking. Mol Cell Proteomics 5(4):737-48

Abstract: Tandem-affinity strategies reach exceptional protein purification grades and have considerably improved the outcome of mass spectrometry-based proteomics experiments. However, current tandem-affinity tags are incompatible with two-step purification under fully denaturing conditions. Such stringent purification conditions are desirable for mass spectrometric analyses of protein modifications as they result in maximal preservation of posttranslational modifications. Here we describe the HB-tag, a new tandem-affinity tag for two-step purification under denaturing conditions. The HB-tag consists of a hexahistidine-tag and a bacterially-derived in vivo biotinylation signal peptide, that induces efficient biotin attachment to the HB-tag in yeast and mammalian cells. HB-tagged proteins can be sequentially purified under fully denaturing conditions, such as 8M urea, by Ni(2+)-chelate chromatography and binding to streptavidin resins. The stringent separation conditions compatible with the HB-tag prevent loss of protein modifications, and the high purification grade achieved by the tandem affinity strategy facilitates mass spectrometric analysis of posttranslational modifications. Ubiquitination is a particular sensitive protein modification that is rapidly lost during purification under native conditions due to ubiquitin-hydrolase activity. The HB-tag is ideal to study ubiquitination because the denaturing conditions inhibit hydrolase activity and the tandem-affinity strategy greatly reduces non-specific background. We tested the HB-tag in proteome-wide ubiquitin profiling experiments in yeast and identified a number of known ubiquitinated proteins as well as so far unidentified candidate ubiquitination targets. In addition, the stringent purification conditions compatible with the HB-tag allow effective mass spectrometric identification of in vivo cross-linked protein complexes, thereby expanding proteomics analyses to the description of weakly or transiently associated protein complexes.

Status: Published Type: Journal Article PubMed ID: 16432255

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AAC1 AAC3 ACB1 ACC1 ACS2 ADE3 ADE5,7 ADE6 ADH4 ADO1
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RPS30A RPS30B RPS31 RPS4A RPS4B RPS5 RPS6A RPS6B RPS7A RPS7B
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RPS8A RPS8B RSP5 RVS167 SAC6 SAH1 SAM1 SAM2 SAN1 SCS2
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SKP1 SKP2 SNA3 SNF1 SPC42 SPO75 SPS1 SPT23 SRP1 SSA1
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SSA2 SSA3 SSA4 SSB1 SSB2 SSF1 SSH4 SSS1 STI1 SUB2
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TOM70 TPI1 TPN1 TPS1 TSA1 TSL1 TYS1 UBA1 UBC1 UBC4
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UBC8 UBI4 UBX5 UFO1 UGP1 URA2 URA3 VAC17 VAS1 VDE
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YHR097C YIL108W YJR027W YKL066W YMR046C YPR003C YPT52 ZEO1 ZRT1 ZRT2
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