Principles of cellular resource allocation revealed by condition-dependent proteome profiling
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TLDR
It is suggested that steadily growing cells prepare for conditions that demand increased translation by producing excess ribosomes, at the expense of lower steady-state growth rate, which is currently the limit of full ribosomal usage.Abstract:
Growing cells coordinate protein translation with metabolic rates. Central to this coordination is ribosome production. Ribosomes drive cell growth, but translation of ribosomal proteins competes with production of non-ribosomal proteins. Theory shows that cell growth is maximized when all expressed ribosomes are constantly translating. To examine whether budding yeast function at this limit of full ribosomal usage, we profiled the proteomes of cells growing in different environments. We find that cells produce excess ribosomal proteins, amounting to a constant ≈8% of the proteome. Accordingly, ≈25% of ribosomal proteins expressed in rapidly growing cells does not contribute to translation. Further, this fraction increases as growth rate decreases and these excess ribosomal proteins are employed when translation demands unexpectedly increase. We suggest that steadily growing cells prepare for conditions that demand increased translation by producing excess ribosomes, at the expense of lower steady-state growth rate.read more
Citations
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Journal ArticleDOI
Homeostasis of protein and mRNA concentrations in growing cells
Jie Lin,Ariel Amir +1 more
TL;DR: A minimal gene expression model is constructed that predicts a transition from exponential to linear growth of cell volume as the protein-to-DNA ratio increases and shows that this result emerges naturally when ribosomes and RNAPs limit expression.
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Root of the Tree: The Significance, Evolution, and Origins of the Ribosome.
TL;DR: The ribosome shows that protein folding initiated with intrinsic disorder, supported through a short, primitive exit tunnel, and was enabled by a long, mature exit tunnel that partially offset the general thermodynamic tendency of all polypeptides to form β-sheets.
Journal ArticleDOI
Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions.
Sophia Hsin-Jung Li,Zhiyuan Li,Junyoung O. Park,Christopher G. King,Joshua D. Rabinowitz,Ned S. Wingreen,Zemer Gitai +6 more
TL;DR: Bacteria tune ribosome usage across different limiting nutrients to enable balanced nutrient-limited growth while also preparing for future nutrient upshifts.
Journal ArticleDOI
Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate
Ze Cheng,Christopher F Mugler,Abdurrahman Keskin,Stefanie Hodapp,Leon Y. Chan,Karsten Weis,Philipp Mertins,Aviv Regev,Marko Jovanovic,Gloria A. Brar +9 more
TL;DR: Two distinct signatures of protein synthesis suggest intriguing and currently mysterious differences in the cellular consequences of deficiency for small and large ribosomal subunits.
Journal ArticleDOI
Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness
Blake Tye,Nicoletta Commins,Lillia V. Ryazanova,Martin Wühr,Michael Springer,David Pincus,David Pincus,L. Stirling Churchman +7 more
TL;DR: It is proposed that ribosome assembly is a key vulnerability of proteostasis maintenance in proliferating cells that may be compromised by diverse genetic, environmental, and xenobiotic perturbations that generate orphan r-proteins.
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