Nav: Home

New protein-sensing mechanism discovered

July 31, 2019

New research published in Molecular Cell on 31 July 2019 conducted by researchers from the University of Konstanz's Collaborative Research Centre 969 "Chemical and Biological Principles of Cellular Proteostasis" shows that the nascent polypeptide-associated complex (NAC) acts as a major protein identifying and, possibly, sorting device inside the cell. Working closely with Professor Nenad Ban, an expert for resolving ribosomal structures from ETH Zurich, the team led by Professor Elke Deuerling and Dr Martin Gamerdinger from the University of Konstanz's Department of Biology - including co-workers Annalena Wallisch, Dr Stefan Kreft, Nadine Sachs and Renate Schlömer as well as Junior Professor Florian Stengel and doctoral researcher Carolin Sailer - has discovered that NAC inserts the N-terminal domain of its β-subunit (N-βNAC) deep into the ribosomal tunnel to sense substrates directly upon synthesis and to escort growing polypeptides to the cytosol.

"No other factor we know does that, which is why we were so utterly surprised by our findings. Although NAC was discovered as long as 25 years ago, we are only now beginning to understand how crucial it is for proper cell function. Our study shows that, besides acting as a chaperone both on and off the ribosome, NAC is also able to recognize nascent polypeptide chains deep inside the ribosomal tunnel", says Professor Elke Deuerling, lead author on the study and Professor of Molecular Microbiology at the University of Konstanz. "We already knew NAC to transiently interact with translating ribosomes. But we did not understand how exactly NAC interacts with the ribosome and with nascent substrates to regulate protein folding and transport to the endoplasmic reticulum (ER), which is essential for organismal viability".

The researchers performed biochemical, genetic and structural analyses in the model system C. elegans to attain a more detailed understanding of how NAC identifies and sorts nascent polypeptide chains inside the ribosomal tunnel. "Until quite recently, we assumed that the earliest point of interaction between ribosome-associated factors such as chaperones, enzymes and transport proteins was when the nascent polypeptide chains exit the ribosomal tunnel", explains Dr Martin Gamerdinger, first author on the study alongside Kan Kobayashi, formerly of ETH Zurich and currently an assistant professor at the University of Tokyo. "Usually, at that point, the chains have a length of about 40 amino acids. What we have discovered is that NAC binds to nascent chains as short as ten amino acids or even shorter, and it is doing it inside the tunnel. This makes NAC the very first factor to contact newly synthesized proteins. We even suspect it to be able to sense when the first two amino acids of a nascent protein connect with each other".

As the researchers have been able to show using a combination of cryo-electron microscopy, mass spectrometry and biochemical analyses, including a series of site-specific crosslink experiments, NAC inserts the positively charged and highly flexible N-terminal domain of its β-subunit (N-βNAC) into the ribosomal tunnel, which is for the most part lined by negatively charged ribosomal RNA. "What our study demonstrates is that NAC is able to sense translation activity inside the tunnel and, more importantly, that it is able to sense the character of the proteins that are being synthesized. At least that is our current hypothesis", says Elke Deuerling.

Once they exit the ribosomal tunnel, nascent protein chains can continue down a range of different biogenesis pathways: Some are passed on to other factors that escort these chains to their intended destinations somewhere else inside the cell. Some are modified by enzymes, others require chaperone support to attain their native structural fold. As Martin Gamerdinger comments: "If what we are assuming about the early sensing-mechanism of NAC is correct, then this complex is the single most important protein sorting mechanism that we know of. It would explain how cells manage the complex processes and reactions that take place in connection with nascent polypeptide chains once they exit the ribosomal tunnel". Accordingly, what the researchers plan to verify next is whether the N-βNAC domain can identify the character of nascent proteins inside the ribosomal tunnel and how it prompts them to enter the correct protein biogenesis pathways.

"What we further found is that NAC acts as a molecular filter, preventing inactive ribosomes or ribosomes in the early translational stages from interacting with the translocon of the ER, i.e. with the complex that transports nascent polypeptides with a targeting signal sequence into the endoplasmic reticulum. Unregulated ribosome-translocon interactions could lead to the wrong proteins entering the endoplasmic reticulum on the one hand, and to depletion of protein factors that are in fact needed elsewhere on the other", says Elke Deuerling. "NAC is thus responsible for making the various steps involved in protein biogenesis much more efficient and specific".

While the N-βNAC domain seems to be responsible for sensing and possibly for sorting nascent polypeptide chains, another NAC domain, N-αNAC, interacts with the β-domain and with itself in order to regulate NAC activity on ribosomes. "This, too, is something that we did not know about before", explains Martin Gamerdinger. "Without N-αNAC, NAC would bind too strongly to the ribosome, interfering with the essential protein translation processes taking place there. We have yet to understand how exactly this auto-inhibitory function of NAC works, but what seems clear is that N-αNAC downregulates ribosome binding". As in vivo experiments with C. elegans clearly showed, worms expressing a NAC variant that lacks the auto-inhibition and shows enhanced ribosome binding were developmentally delayed due to reduced protein synthesis rates and impaired translation, clearly showing defects caused by NAC-ribosome misregulation.
-end-
Facts:
  • International team of researchers from the University of Konstanz and ETH Zurich identifies nascent chain recognition mechanism deep inside the ribosomal tunnel that is driven by the essential eukaryotic chaperone NAC (nascent polypeptide-associated complex).
  • NAC tunnel-sensing activity is essential for organismal viability and critical for the regulation of protein transport to the endoplasmic reticulum; major implications for general understanding of protein translation and maturation in cells.
  • Original publication: Martin Gamerdinger, Kan Kobayashi, Annalena Wallisch, Stefan G. Kreft, Carolin Sailer, Renate Schlömer, Nadine Sachs, Ahmad Jomaa, Florian Stengel, Nenad Ban, Elke Deuerling. Early scanning of nascent polypeptides inside the ribosomal tunnel by NAC. Molecular Cell. 31 July 2019. DOI: https://doi.org/10.1016/j.molcel.2019.06.030 (DOI becomes active shortly after 11:00 US Eastern Time, after the embargo has lifted).
  • The research carried out at the University of Konstanz was supported by the Collaborative Research Centre 969 "Chemical and Biological Principles of Cellular Proteostasis", funded by the German Research Foundation (DFG) since 2012.
Note to editors:

Images are available for download here:

Image 1: https://cms.uni-konstanz.de/fileadmin/pi/fileserver/2019/Bilder/new_protein-sensing.jpg

Caption: Ribosome binding of NAC is mediated by a ribosome binding regulatory arm (N-αNAC, blue) and a translation sensor domain (N-βNAC, green). N-βNAC senses short nascent chains already deep inside the ribosomal tunnel close to the peptidyl-transferase centre (orange) where amino acids are assembled into proteins. The tunnel-sensing activity of NAC is believed to orchestrate general cotranslational protein folding and transport processes in the cell.

Copyright: Martin Gamerdinger

Image 2: https://cms.uni-konstanz.de/fileadmin/pi/fileserver/2019/Bilder/new_protein_sensing_team.jpg

Caption: The University of Konstanz team, from left to right: Nadine Sachs, Martin Gamerdinger, Renate Schlömer, Elke Deuerling, Carolin Sailer, Stefan Kreft

Copyright: University of Konstanz

Contact:

University of Konstanz
Communications and Marketing
Phone: +49 7531 88-3603
Email: kum@uni-konstanz.de

University of Konstanz

Related Science Articles:

75 science societies urge the education department to base Title IX sexual harassment regulations on evidence and science
The American Educational Research Association (AERA) and the American Association for the Advancement of Science (AAAS) today led 75 scientific societies in submitting comments on the US Department of Education's proposed changes to Title IX regulations.
Science/Science Careers' survey ranks top biotech, biopharma, and pharma employers
The Science and Science Careers' 2018 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.
Science in the palm of your hand: How citizen science transforms passive learners
Citizen science projects can engage even children who previously were not interested in science.
Applied science may yield more translational research publications than basic science
While translational research can happen at any stage of the research process, a recent investigation of behavioral and social science research awards granted by the NIH between 2008 and 2014 revealed that applied science yielded a higher volume of translational research publications than basic science, according to a study published May 9, 2018 in the open-access journal PLOS ONE by Xueying Han from the Science and Technology Policy Institute, USA, and colleagues.
Prominent academics, including Salk's Thomas Albright, call for more science in forensic science
Six scientists who recently served on the National Commission on Forensic Science are calling on the scientific community at large to advocate for increased research and financial support of forensic science as well as the introduction of empirical testing requirements to ensure the validity of outcomes.
World Science Forum 2017 Jordan issues Science for Peace Declaration
On behalf of the coordinating organizations responsible for delivering the World Science Forum Jordan, the concluding Science for Peace Declaration issued at the Dead Sea represents a global call for action to science and society to build a future that promises greater equality, security and opportunity for all, and in which science plays an increasingly prominent role as an enabler of fair and sustainable development.
PETA science group promotes animal-free science at society of toxicology conference
The PETA International Science Consortium Ltd. is presenting two posters on animal-free methods for testing inhalation toxicity at the 56th annual Society of Toxicology (SOT) meeting March 12 to 16, 2017, in Baltimore, Maryland.
Citizen Science in the Digital Age: Rhetoric, Science and Public Engagement
James Wynn's timely investigation highlights scientific studies grounded in publicly gathered data and probes the rhetoric these studies employ.
Science/Science Careers' survey ranks top biotech, pharma, and biopharma employers
The Science and Science Careers' 2016 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.
Three natural science professors win TJ Park Science Fellowship
Professor Jung-Min Kee (Department of Chemistry, UNIST), Professor Kyudong Choi (Department of Mathematical Sciences, UNIST), and Professor Kwanpyo Kim (Department of Physics, UNIST) are the recipients of the Cheong-Am (TJ Park) Science Fellowship of the year 2016.
More Science News and Science Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Climate Mindset
In the past few months, human beings have come together to fight a global threat. This hour, TED speakers explore how our response can be the catalyst to fight another global crisis: climate change. Guests include political strategist Tom Rivett-Carnac, diplomat Christiana Figueres, climate justice activist Xiye Bastida, and writer, illustrator, and artist Oliver Jeffers.
Now Playing: Science for the People

#562 Superbug to Bedside
By now we're all good and scared about antibiotic resistance, one of the many things coming to get us all. But there's good news, sort of. News antibiotics are coming out! How do they get tested? What does that kind of a trial look like and how does it happen? Host Bethany Brookeshire talks with Matt McCarthy, author of "Superbugs: The Race to Stop an Epidemic", about the ins and outs of testing a new antibiotic in the hospital.
Now Playing: Radiolab

Speedy Beet
There are few musical moments more well-worn than the first four notes of Beethoven's Fifth Symphony. But in this short, we find out that Beethoven might have made a last-ditch effort to keep his music from ever feeling familiar, to keep pushing his listeners to a kind of psychological limit. Big thanks to our Brooklyn Philharmonic musicians: Deborah Buck and Suzy Perelman on violin, Arash Amini on cello, and Ah Ling Neu on viola. And check out The First Four Notes, Matthew Guerrieri's book on Beethoven's Fifth. Support Radiolab today at Radiolab.org/donate.