Thomas Arnesen

Repost appreciated:
Open #PhDposition in structural virology in my group! Join us in Umeå, Sweden to uncover how arboviruses remodel infected cells. In situ #cryoET and #cryoEM combined with #virology, #cellbiology, and #biophysics.
Deadline 7 September. More info: www.carlsonlab.se/join/

💡Interested in our recently advertised @embl.org-style group leader positions but still not sure about it? Maybe this clip will convince you to join us👇!

The evolutionary rise of oxygen sensing in land plants Land plants evolved from aquatic green algal ancestors to dominate terrestrial ecosystems approximately 480 million years ago during the Ordovician period (Hammarlund et al., 2020). This major event i...

Our 'Spotlight' discussing an excellent recent paper by @lauradc.bsky.social @n-end-rules.bsky.social & @syno2xis.bsky.social et al on the evolution of oxygen signalling in land plants is now online at Molecular Plant.

Spotlight: tinyurl.com/7ydn6p4a

Original paper: tinyurl.com/yw5yd4f8

📢 Our August issue is online!

🎨 The cover highlights a Feature Review from Stephanie Rosswag de Souza, @gzaffagnini.bsky.social, and @bokelab.bsky.social on how proteostasis functions in cellular dormancy across a number of examples, from yeast to adult quiescent stem cells and vertebrate oocytes.

Zebrafish model shows that NAA15 and N-terminal acetylation defects cause heart disease | Independently confirms the causal link between pathogenic NAA15 variants and congenital heart disease | Burns lab @bostonchildrens.bsky.social www.biorxiv.org/content/10.1...

Mechanism for voltage-gated channel inactivation uncovered | N-terminal acetylation of the intracellular domain of the Shaker potassium channel is key for plugging the pore | By Kenton Swartz lab in @nature.com @ispt-proteinterm.bsky.social www.nature.com/articles/s41...

How to define degrons and E3 ligase specificities by peptide pulldowns | Methods in Enzymology | Kwon and Ji labs | #KCMF1 #Cysteine #Arg/N-degron @ispt-proteinterm.bsky.social www.sciencedirect.com/science/arti...

Using a specific antibody to detect proteins carrying N-terminal formylation | Methods in Enzymology | Hwang lab @ispt-proteinterm.bsky.social www.sciencedirect.com/science/arti...

Assessing protein N-terminal myristoylation. Detailed protocols by Ed Tate's group in Methods in Enzymology. #lipidation @ispt-proteinterm.bsky.social @imperialcollegeldn.bsky.social www.sciencedirect.com/science/arti...

NAC controls nascent chain fate through tunnel sensing and chaperone action The nascent polypeptide-associated complex (NAC) is a conserved ribosome-bound factor with essential yet incompletely understood roles in protein biogenesis. Here, we show that NAC is a multifaceted r...

www.biorxiv.org/content/10.1...

I am excited to share a big part of my thesis in preprint form, where we analysed the determinants of NAC-binding to translating ribosomes using selective ribosome profiling in C. elegans.

Making sense of oxygen sensing - Thomas Keeley & Peter Ratcliffe describe challenges encountered in measuring and manipulating cell monolayer oxygenation in vitro, and innovative approaches to overcome them
www.embopress.org/doi/full/10....

Expression and purification of ribosome associated factors: Methionine aminopeptidases and N-terminal acetyltransferases | Methods in Enzymology | Marius Klein and Irmgard Sinning @uniheidelberg.bsky.social @ispt-proteinterm.bsky.social www.sciencedirect.com/science/arti...

How to express, purify and assess the activity of the ATE1 arginyltransferase | Methods in Enzymology | Yi Zhang lab @ispt-proteinterm.bsky.social www.sciencedirect.com/science/arti...

Method to determine the identity and modification state of plastid precursor protein N-termini in the cytosol by combining protoplast protein import assays with targeted mass spectrometry | Methods in Enzymology | Baginsky lab. @ispt-proteinterm.bsky.social www.sciencedirect.com/science/arti...

Engineering reduced activity in the oxygen-sensing Arabidopsis thaliana plant cysteine oxidase 4 enzyme results in improved flood resilience Plant cysteine oxidases (PCOs) are oxygen-sensing enzymes that play an important role in plant responses to low oxygen (hypoxia). PCO-catalysed dioxygenation of the N-terminal Cys of substrates, inclu...

Engineered mutations in the AtPCO4 active site reduce its activity and improve plant submergence resilience! Our new preprint: tinyurl.com/2ydj7qx5, 1 of 2 preprints out this week from the @emilyflashman.bsky.social and @syno2xis.bsky.social labs to link PCO function in plants with flood tolerance!

Bidirectional control of a metabolic transition by the GID ubiquitin ligase The GID/CTLH ubiquitin ligase is a multisubunit E3 conserved across eukaryotes. GID/CTLH has been implicated in a variety of processes, including metabolic regulation, cell proliferation, embryonic de...

Gid11 is a substrate receptor of the GID multisubunit E3 ligase during a metabolic switch. Specific degradation of proteins linked to glycolysis via their N-terminal threonine lacking N-terminal acetylation. #N-degron Khmelinskii lab @ispt-proteinterm.bsky.social
www.biorxiv.org/content/10.1...

Engineering reduced activity in the oxygen-sensing Arabidopsis thaliana plant cysteine oxidase 4 enzyme results in improved flood resilience Plant cysteine oxidases (PCOs) are oxygen-sensing enzymes that play an important role in plant responses to low oxygen (hypoxia). PCO-catalysed dioxygenation of the N-terminal Cys of substrates, inclu...

Engineering reduced activity in the oxygen-sensing Arabidopsis thaliana plant cysteine oxidase 4 enzyme results in improved flood resilience. By Dirr et al. Licausi and Flashman labs @syno2xis.bsky.social @emilyflashman.bsky.social www.biorxiv.org/content/10.1...

Manipulating plant oxygen sensing through NCO substitution reveals trade-offs between growth and flooding tolerance The oxygen-dependent degradation of Ethylene Response Factors VII (ERFVIIs) through the N-degron pathway is central to regulating the transcriptional responses to hypoxia in vascular plants. Plant Cys...

Manipulating plant oxygen sensing through NCO substitution reveals trade-offs between growth and flooding tolerance. Perri et al. - another preprint from the Licausi and Flashman labs. @monicaperri1.bsky.social @emilyflashman.bsky.social @syno2xis.bsky.social www.biorxiv.org/content/10.1...

Excited to announce our new methods paper in Methods in Enzymology!

We share our pipeline for building high-diversity DNA libraries & exploring protein stability in E. coli.

Free access until Sept 4: authors.elsevier.com/a/1lRkeHRzCX...
Updated, companion preprint: www.biorxiv.org/content/10.1...

New paper out in Mol Cell, where we show how N-myristolytransferases lipidate proteins on the translating ribosome!
Continuing our successful collaboration with DeuerlingLab @uni-konstanz.de & Shu-ou Chan @caltech.edu
@snsf.ch @ethz.ch
www.cell.com/molecular-ce...

DEGRONOPEDIA - a web server for identifying and predicting protein degradation signals across eukaryotic proteomes. Detailed guide by Natalia Szulc @lumirare.com and Wojciech Pokrzywa @wpokrzywa.bsky.social in Methods in Enzymology. @ispt-proteinterm.bsky.social www.sciencedirect.com/science/arti...

How to use bacteria for arginylation assessment. Co-expression of ATE1 and substrate outlined by Yi Zhang and colleagues in Methods in Enzymology. @ispt-proteinterm.bsky.social www.sciencedirect.com/science/arti...

How to detect protein N-terminal arginylation - a key step of protein degradation via the Arg/N-degron pathway. By Jasper Eising and @ndissmeyer.bsky.social in Methods in Enzymology. @ispt-proteinterm.bsky.social www.sciencedirect.com/science/arti...

How to assess protein stability and N-degrons via the Ubiquitin reference technique. From the Protein Metabolism Lab (Yong Tae Kwon) at SNU Seoul ups.snu.ac.kr in Methods in Enzymology @ispt-proteinterm.bsky.social www.sciencedirect.com/science/arti...

📣 Our July issue is live!

Inside, you'll find a variety of articles focused on #mitochondrialbiochemistry, plus an interview with many of the authors! The cover (by @brischigliaro.bsky.social) emphasizes one of these reviews from Antoni Barrientos et al.

Find it here 👉 www.cell.com/biochemical-...

Acetylhistidine in our blood can prevent kidney disease and is produced by the HisAT (NAT16) enzyme displaying a rare double-GNAT structure. Great efforts by Matti Myllykoski and the rest of the team at @unibergen.bsky.social to get this published. #acetyltransferase www.nature.com/articles/s41...

Celebrating 35 years of Trends in Cell Biology and introducing our special issue on ribosomal dynamics and cellular homeostasis As Trends in Cell Biology marks its 35th anniversary, we pause to reflect on the incredible journey this journal has taken since its launch. Over three and a half decades, Trends in Cell Biology has chronicled the evolving landscape of cellular research, providing a platform for pioneering insights that have shaped our understanding of fundamental biological processes. From early explorations of cellular architecture to today’s sophisticated molecular and systemic analyses, the journal has continually embraced scientific innovation and fostered a vibrant community of researchers.

Celebrating 35 years of Trends in Cell Biology and introducing our special issue on ribosomal dynamics and cellular homeostasis

A genetically encoded fluorescent biosensor for visualization of acetyl-CoA in live cells Smith et al. engineered a “turn on” fluorescent biosensor (dubbed “PancACe”) for acetyl-CoA from a fusion of the proteins PanZ and circularly permuted GFP. PancACe measures changes in acetyl-CoA level...

A genetically encoded fluorescent biosensor for visualization of acetyl-CoA in live cells: Cell Chemical Biology www.cell.com/cell-chemica...

📣 Our June issue is live!

Inside, you'll find three Reviews focused on #PeptideBiochemistry, plus an accompanying interview with the authors! The cover emphasizes one of these reviews from the group of Katrin Svnensson on peptide hormones.

Find the issue here 👉 www.cell.com/issue/S0968-...

GID4 recognition of Pro/N-degron peptides: Conformational selection and induced fit The N-degron pathway is essential for protein quality control and cellular homeostasis. GID4, a subunit of the GID ubiquitin ligase, is the main recog…

GID4 recognition of Pro/N-degron peptides: Conformational selection and induced fit www.sciencedirect.com/science/arti...