Uncovering the proteome response of the master circadian clock to light using an AutoProteome system

Mol Cell Proteomics. 2011 Nov;10(11):M110.007252. doi: 10.1074/mcp.M110.007252. Epub 2011 Aug 22.


In mammals, the suprachiasmatic nucleus (SCN) is the central circadian pacemaker that governs rhythmic fluctuations in behavior and physiology in a 24-hr cycle and synchronizes them to the external environment by daily resetting in response to light. The bilateral SCN is comprised of a mere ~20,000 neurons serving as cellular oscillators, a fact that has, until now, hindered the systematic study of the SCN on a global proteome level. Here we developed a fully automated and integrated proteomics platform, termed AutoProteome system, for an in-depth analysis of the light-responsive proteome of the murine SCN. All requisite steps for a large-scale proteomic study, including preconcentration, buffer exchanging, reduction, alkylation, digestion and online two-dimensional liquid chromatography-tandem MS analysis, are performed automatically on a standard liquid chromatography-MS system. As low as 2 ng of model protein bovine serum albumin and up to 20 μg and 200 μg of SCN proteins can be readily processed and analyzed by this system. From the SCN tissue of a single mouse, we were able to confidently identify 2131 proteins, of which 387 were light-regulated based on a spectral counts quantification approach. Bioinformatics analysis of the light-inducible proteins reveals their diverse distribution in different canonical pathways and their heavy connection in 19 protein interaction networks. The AutoProteome system identified vasopressin-neurophysin 2-copeptin and casein kinase 1 delta, both of which had been previously implicated in clock timing processes, as light-inducible proteins in the SCN. Ras-specific guanine nucleotide-releasing factor 1, ubiquitin protein ligase E3A, and X-linked ubiquitin specific protease 9, none of which had previously been implicated in SCN clock timing processes, were also identified in this study as light-inducible proteins. The AutoProteome system opens a new avenue to systematically explore the proteome-wide events that occur in the SCN, either in response to light or other stimuli, or as a consequence of its intrinsic pacemaker capacity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Automation, Laboratory*
  • Cattle
  • Chromatography, Liquid / standards
  • Circadian Clocks*
  • Gene Expression / radiation effects
  • Light*
  • Male
  • Metabolic Networks and Pathways
  • Mice
  • Mice, Inbred C57BL
  • Protein Interaction Maps
  • Proteome / genetics
  • Proteome / isolation & purification
  • Proteome / metabolism*
  • Serum Albumin, Bovine / standards
  • Suprachiasmatic Nucleus / metabolism*
  • Suprachiasmatic Nucleus / radiation effects
  • Tandem Mass Spectrometry / standards


  • Proteome
  • Serum Albumin, Bovine