Erik Jönsson

As the endpoint for the ubiquitin-proteasome system, the 26S proteasome is the principal proteolytic machine responsible for regulated protein degradation in eukaryotic cells. The proteasome's cellular functions range from general protein homeostasis and stress response to the control of vital processes such as cell division and signal transduction. To reliably process all the proteins presented to it in the complex cellular environment, the proteasome must combine high promiscuity with exceptional substrate selectivity. Recent structural and biochemical studies have shed new light on the many steps involved in proteasomal substrate processing, including recognition, deubiquitination, and ATP-driven translocation and unfolding. In addition, these studies revealed a complex conformational landscape that ensures proper substrate selection before the proteasome commits to processive degradation. These advances in our understanding of the proteasome's intricate machinery set the stage for future studies on how the proteasome functions as a major regulator of the eukaryotic proteome.

The effect of four biogas digestates (BD-A, BD-B, BD-C, and BD-D) and pig slurry (PS) on soil microbial functions was assessed at application rates corresponding to 0–1120 kg<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:msup><mml:mrow><mml:mtext>N</mml:mtext><mml:msub><mml:mrow><mml:mtext>H</mml:mtext></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>-N ha −1 . At dose corresponding to 140 kg<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mrow><mml:msup><mml:mrow><mml:mtext>N</mml:mtext><mml:msub><mml:mrow><mml:mtext>H</mml:mtext></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>-N ha −1 , 30.9–32.5% of the carbon applied in BD-A, BD-C, and PS was utilized during 12 days, while for BD-B and BD-D corresponding utilization was 19.0 and 16.9%, respectively. All BDs resulted in net nitrogen assimilation at low rates (17.5–140 kg<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M3"><mml:mrow><mml:msup><mml:mrow><mml:mtext>N</mml:mtext><mml:msub><mml:mrow><mml:mtext>H</mml:mtext></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>-N ha −1 ) but net mineralization dominated at higher rates. PS resulted in net mineralization at all application rates. All residues inhibited potential ammonium oxidation (PAO), with EC 50 -values ranging between 45 and 302 kg<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M4"><mml:mrow><mml:msup><mml:mrow><mml:mtext>N</mml:mtext><mml:msub><mml:mrow><mml:mtext>H</mml:mtext></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>-N ha −1 . Low rates of BDs appeared to weakly stimulate potential denitrification activity (PDA), while higher rates resulted in logarithmic decrease. The EC 50 -values for PDA were between 238 and 347 kg<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M5"><mml:mrow><mml:msup><mml:mrow><mml:mtext>N</mml:mtext><mml:msub><mml:mrow><mml:mtext>H</mml:mtext></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>-N ha −1 . No inhibition of PDA was observed after amendment with PS. In conclusion, biogas digestates inhibited ammonia oxidation and denitrification, which could be an early warning of potential hazardous substances in the digestates. However, this effect can also be regarded as positive, since it may reduce nitrogen losses.

proteasome recognizes thousands of appropriate protein substrates in eukaryotic cells through attached ubiquitin chains and uses its adenosine triphosphatase (ATPase) motor for mechanical unfolding and translocation into a proteolytic chamber. Here, we used single-molecule Förster resonance energy transfer measurements to monitor the conformational dynamics of the proteasome, observe individual substrates during their progression toward degradation, and elucidate how these processes are regulated by ubiquitin chains. Rapid transitions between engagement- and processing-competent proteasome conformations control substrate access to the ATPase motor. Ubiquitin chain binding functions as an allosteric regulator to slow these transitions, stabilize the engagement-competent state, and aid substrate capture to accelerate degradation initiation. Upon substrate engagement, the proteasome remains in processing-competent states for translocation and unfolding, except for apparent motor slips when encountering stably folded domains. Our studies revealed how ubiquitin chains allosterically regulate degradation initiation, which ensures substrate selectivity in a crowded cellular environment.