Lausanne: Following the day-night cycle, the liver has its own metabolic rhythm. Using cutting-edge proteomics, scientists at EPFL and Nestlé Institute of Health Sciences have now identified over 500 liver proteins that change in abundance over the course of the day in the cell nucleus, opening a new dimension of metabolism. Biological processes occurring in our bodies are far from static, but instead the rhythm of most of them is dictated by an internal, 24-hour biological metronome called the ‘circadian clock’. During each day-night cycle, many physiological processes follow oscillatory waves orchestrated by this clock, allowing them to adapt and anticipate the body’s demands at a given time of day. EPFL scientists have now used cutting-edge proteomics to monitor the temporal accumulation of over 5,000 different proteins in the nucleus of mouse liver cells, and have identified over 500 that are connected to the 24-hours cycle. The study, published in Cell Metabolism, is the first in this field in terms of scale and resolution, and has significant implications regarding our understanding of the interconnections between rhythmic metabolism and nutrition.
Biology is affected by time
bodies follow the day-night, or “diurnal”, cycle, by finely tuning
metabolic processes to time of day — this is why we can sleep for hours
without going hungry through the night but can barely stand eight hours
after breakfast, or why jet lag can sometimes cause digestive problems.
Such oscillations are the focus of “chronobiology” a research field that
looks at how biological functions are organized in time and how disease
could arise when this time organization is disturbed.
regulation of metabolism is connected to how our genes produce proteins.
Many genes follow our circadian clock by adjusting the rate at which
they produce proteins, and knowing which genes do this would help us
understand how metabolism changes over the course of a day.
Unfortunately, even though the human genome was mapped out more than a
decade ago, investigating how genes control the production of proteins
on a time-dependent scale is still difficult, mostly because of the
sheer number of proteins present in a cell.
500 liver proteins affected by the day-night cycle
Felix Naef at EPFL and Frédéric Gachon at the Nestlé Institute of Health Sciences,
have now made a breakthrough in our understanding of time-dependent
metabolism. Working only the nuclei of liver cells, the scientists
identified 5000 proteins of which more than 500 were affected during the
diurnal cycle; more specifically, the proteins entered and left the
nucleus over the course of the day. In addition, they found that key
cellular functions such as DNA repair, ribosome biogenesis, cell cycle
and chromosome regulation (polyploidy) were also affected by diurnal
To counteract the huge complexity of the proteome, the
researchers only focused on the cell’s nucleus instead of the entire
cell. The nucleus is where genes produce proteins that are then sent to
various locations around the cell. As such, the nucleus is very
sensitive to environmental and biochemical signals, and can translate
these into molecular responses by controlling protein production.
scientists used biochemical techniques to isolate the nuclei from liver
cells taken from mice with and without a functioning circadian clock.
Having isolated the nuclei, they extracted all the proteins from them
and analyzed them with mass spectrometry.
genomics for genes, proteomics is the field of digital biology where
computers are used to create detailed databases and maps of the complete
set of an organism’s proteins. The scientists used a technique called
SILAC coupled with high-resolution proteomics, which can efficiently
quantify proteins — in this case, the proteins are quantified in the
nucleus at different time-points throughout a 24-hour cycle. By doing
this, they were able to get a global picture of how the diurnal cycle
affects protein accumulation in the liver-cell nucleus.
many studies approach physiological functions statically, our temporal
approach gave us unprecedented insights into how metabolism cycles over a
day,” says Felix Naef. “We were surprised by how pervasively nuclear
functions in liver are influenced by the day and night and feeding
“The study also shows that this quantitative proteomics
approach is an excellent tool for systematic analysis of cell
functions,” says Frédéric Gachon. “This would not be feasible
with conventional proteomic techniques.”
This work involves a
collaboration between EPFL’s Institute of Bioengineering and the Nestlé
Institute of Health Sciences, with contributions from the University of
Lausanne, and the Institut de Génétique Moléculaire de Montpellier. It
was funded by the Swiss National Science Foundation, EPFL, the European
Research Council (ERC), and the Leenaards Foundation.
Wang, Daniel Mauvoisin, Eva Martin, Florian Atger, Antonio Núñes
Galindo, Loïc Dayon, Federico Sizzano, Alessio Palini, Martin Kussmann,
Patrice Waridel, Manfredo Quadroni, Vjekoslav Dulić, Felix Naef, and
Frédéric Gachon. Nuclear proteomics uncovers diurnal regulatory landscapes in mouse liver.Cell Metabolism 03 November 2016. DOI: 10.1016/j.cmet.2016.10.003