Toward Understanding the Biochemical Determinants of Protein Degradation Rates

Marrero, Miguel; Barrio-Hernandez, Iñigo

doi:10.1021/acsomega.0c05318

Cited by 14 publications

(9 citation statements)

References 35 publications

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“…Protein lifetime can be influenced by both sequence‐encoded features and environmental factors (Marrero & Barrio‐Hernandez, 2021 ). For instance, proteins with long disordered segments are generally more short‐lived than proteins that adopt a stable structure (van der Lee et al , 2014 ; Fishbain et al , 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes

Hasper

Welle

Hryhorenko

et al. 2023

Molecular Systems Biology

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The lifespans of proteins range from minutes to years within mammalian tissues. Protein lifespan is relevant to organismal aging, as long‐lived proteins accrue damage over time. It is unclear how protein lifetime is shaped by tissue context, where both cell turnover and proteolytic degradation contribute to protein turnover. We develop t urnover and r eplication a nalysis by 15 N i sotope l abeling (TRAIL) to quantify protein and cell lifetimes with high precision and demonstrate that cell turnover, sequence‐encoded features, and environmental factors modulate protein lifespan across tissues . Cell and protein turnover flux are comparable in proliferative tissues, while protein turnover outpaces cell turnover in slowly proliferative tissues. Physicochemical features such as hydrophobicity, charge, and disorder influence protein turnover in slowly proliferative tissues, but protein turnover is much less sequence‐selective in highly proliferative tissues. Protein lifetimes vary nonrandomly across tissues after correcting for cell turnover. Multiprotein complexes such as the ribosome have consistent lifetimes across tissues, while mitochondria, peroxisomes, and lipid droplets have variable lifetimes. TRAIL can be used to explore how environment, aging, and disease affect tissue homeostasis.

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Section: Introductionmentioning

confidence: 99%

Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes

Hasper

Welle

Hryhorenko

et al. 2023

Molecular Systems Biology

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“…Next, we determined the kinetics of degradation by this concatenated degron. In general, the ubiquitin-proteasome system (UPS) can react fairly quickly to the changing environment and can degrade targeted proteins in a matter of minutes. − Ideally, a system of inducible degradation of proteins can take advantage of this property of UPS and allow similarly fast degradation and thus enable rapid temporal control of protein stability. We observed that the substrate degradation using concatenated SSD degron was very fast at higher concentrations of rapamycin, achieving near-plateau levels after only 30 min (Figure c).…”

Section: Resultsmentioning

confidence: 99%

Subunits of an E3 Ligase Complex as Degrons for Efficient Degradation of Cytosolic, Nuclear, and Membrane Proteins

Verbič,

Lebar,

Praznik

et al. 2024

ACS Synth. Biol.

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Protein degradation is a highly regulated cellular process crucial to enable the high dynamic range of the response to external and internal stimuli and to balance protein biosynthesis to maintain cell homeostasis. Within mammalian cells, hundreds of E3 ubiquitin ligases target specific protein substrates and could be repurposed for synthetic biology. Here, we present a systematic analysis of the four protein subunits of the multiprotein E3 ligase complex as scaffolds for the designed degrons. While all of them were functional, the fusion of a fragment of Skp1 with the target protein enabled the most effective degradation. Combination with heterodimerizing peptides, protease substrate sites, and chemically inducible dimerizers enabled the regulation of protein degradation. While the investigated subunits of E3 ligases showed variable degradation efficiency of the membrane and cytosolic and nuclear proteins, the bipartite SSD (SOCSbox-Skp1(ΔC111)) degron enabled fast degradation of protein targets in all tested cellular compartments, including the nucleus and plasma membrane, in different cell lines and could be chemically regulated. These subunits could be employed for research as well as for diverse applications, as demonstrated in the regulation of Cas9 and chimeric antigen receptor proteins.

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“…This suggested that the N-terminus is generally evolutionarily optimized for expression efficiency, which also supports why it is widely used for protein expression optimization [86][87][88] . A short hotspot at the very last position in the C-terminus was frequently mutated, which is known as a signal involved in protein degradation 5,6 . Besides the Cterminus, however, most of the amino acids were substituted uniformly across the entire sequence length, mainly with the hydrophobic amino acids A (alanine), G (glycine) and V (valine) (Figure 2G).…”

Section: Discussionmentioning

confidence: 99%

“…For instance, protein synthesis is strongly regulated at the initiation step 1,2 , whose rate varies broadly between mRNAs, depending not only on the transcript sequence features but also on the amino acids at the N-terminal 3,4 . In bacteria, the amino acid composition of the C-terminal is a strong determinant of protein degradation rates, explaining a wide range of protein abundances 5,6 . These, along with the multiple mechanisms of post-translational regulation 7,8 , suggest that this rather tight regulation occurs at the degradation level and is encoded, at least partially, in the amino acid sequence.…”

Section: Introductionmentioning

confidence: 99%

The amino acid sequence determines protein abundance through its conformational stability and reduced synthesis cost

Buric,

Viknander,

et al. 2023

Preprint

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Understanding what drives protein abundance is essential to biology, medicine, and biotechnology. Driven by evolutionary selection, the amino acid sequence is tailored to meet the required abundance of proteomes, underscoring the intricate relationship between sequence and functional demand. Yet, the specific role of amino acid sequences in determining proteome abundance remains elusive. Here, we demonstrate that the amino acid sequence predicts abundance by shaping a protein’s conformational stability. We show that increasing the abundance provides metabolic cost benefits, underscoring the evolutionary advantage of maintaining a highly abundant and stable proteome. Specifically, using a deep learning model (BERT), we predict 56% of protein abundance variation inSaccharomyces cerevisiaesolely based on amino acid sequence. The model reveals latent factors linking sequence features to protein stability. To probe these relationships, we introduce MGEM (Mutation Guided by an Embedded Manifold), a methodology for guiding protein abundance through sequence modifications. We find that mutations increasing abundance significantly alter protein polarity and hydrophobicity, underscoring a connection between protein stability and abundance. Through molecular dynamics simulations andin vivoexperiments in yeast, we confirm that abundance-enhancing mutations result in longer-lasting and more stable protein expression. Importantly, these sequence changes also reduce metabolic costs of protein synthesis, elucidating the evolutionary advantage of cost-effective, high-abundance, stable proteomes. Our findings support the role of amino acid sequence as a pivotal determinant of protein abundance and stability, revealing an evolutionary optimization for metabolic efficiency.

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Toward Understanding the Biochemical Determinants of Protein Degradation Rates

Cited by 14 publications

References 35 publications

Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes

Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes

Subunits of an E3 Ligase Complex as Degrons for Efficient Degradation of Cytosolic, Nuclear, and Membrane Proteins

The amino acid sequence determines protein abundance through its conformational stability and reduced synthesis cost

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