Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

Newman, J. Robert; Ghaemmaghami, Sina; Ihmels, Jan; Breslow, David K.; Noble, Matthew; DeRisi, Joseph L.; Weissman, Jonathan S.

doi:10.1038/nature04785

Cited by 1,454 publications

(1,997 citation statements)

References 44 publications

Supporting

145

Mentioning

1,796

Contrasting

Unclassified

Order By: Relevance

“…Importantly, as local dynamics can then propagate through biomolecular networks-for example, via signal transduction pathways [26][27][28][29][30][31] , potentially expressing themselves in species that are otherwise directly involved only in strictly classical kinetics-the presence of just one such mechanism within a larger biological process may lead to a variety of system-wide nonclassical behavior modes 22,[32][33][34][35][36][37][38][39][40] . Given such potentially global implications of locally deviant pathway dynamics, we hope that this work may offer biologists involved with kinetic analysis or molecular modeling additional tools and intuition to help decide whether their work requires the use of discrete and stochastic chemical master equation-based methods or whether the simpler classical chemical kinetics framework is sufficient.…”

Section: Discussionmentioning

confidence: 99%

Deviant effects in molecular reaction pathways

2006

View full text Add to dashboard Cite

In biological networks, any manifestations of behaviors substantially 'deviant' from the predictions of continuousdeterministic classical chemical kinetics (CCK) are typically ascribed to systems with complex dynamics and/or a small number of molecules. Here we show that in certain cases such restrictions are not obligatory for CCK to be largely incorrect. By systematically identifying properties that may cause significant divergences between CCK and the more accurate discrete-stochastic chemical master equation (CME) system descriptions, we comprehensively characterize potential CCK failure patterns in biological settings, including consequences of the assertion that CCK is closer to the 'mode' rather than the 'average' of stochastic reaction dynamics, as generally perceived. We demonstrate that mechanisms underlying such nonclassical effects can be very simple, are common in cellular networks and result in often unintuitive system behaviors. This highlights the importance of deviant effects in biotechnologically or biomedically relevant applications, and suggests some approaches to diagnosing them in situ.Although the temporal evolution of a spatially homogeneous molecular system subject to a set of (bio)chemical reactions is often described macroscopically via the classical chemical kinetics (CCK) formalism through a set of deterministic differential equations (ODEs) 1 -otherwise referred to as 'reaction rate equations' or 'mass action kinetics'-this approach does not substantially reflect the fundamentally random and discrete nature of individual molecular interactions. The latter is well described by the chemical master equation (CME) 2-4 . Although this makes CME an intrinsically much more accurate description of biological or chemical molecular system dynamics, CCK is significantly more efficient computationally and could be viewed as derived from CME via a set of limiting approximations 5 .The conditions under which these approximations hold are often considered to be broadly valid for biological and/or simple chemical systems. However, as shown here, neither is guaranteed to be the case. Breakdowns in the limiting approximations can occur in some of the most basic processes owing to mechanisms that are particularly common in biological systems. These breakdowns then manifest themselves as various 'deviant nonclassical effects'-distinctive behaviors not accounted for by the classical molecular kinetic description-whereby the discrete and/or stochastic nature of reaction events conspires to drive the characteristic behavior of the system substantially away from that predicted by classical kinetics.Notably, we demonstrate that although deviant effects may be stochastic in origin, this is by no means a requirement. The behavior of the system might be accurately characterized by a deterministic formalism, albeit not by CCK. In particular, although CCK dynamics is at times casually interpreted as describing the evolution of CME averages-this is only strictly accurate for purely linear (unimolecular and consta...

show abstract

Section: Discussionmentioning

confidence: 99%

Deviant effects in molecular reaction pathways

2006

View full text Add to dashboard Cite

show abstract

“…2a). GFP fluorescence was used as a proxy for the relative abundance of the resulting fusion proteins (Chong et al, 2012;Newman et al, 2006). Interestingly, the Erg9p-yEGFP strain exhibited a dramatic decrease in GFP fluorescence level in the post-exponential growth phase (Fig.…”

Section: Erg9p Signal Peptidementioning

confidence: 99%

A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae

Peng

Plan

Chrysanthopoulos

et al. 2017

Metabolic Engineering

101

128

View full text Add to dashboard Cite

A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae, Metabolic Engineering, http://dx.doi.org/10. 1016/j.ymben.2016.12.003 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. AbstractSesquiterpenes are C15 isoprenoids with utility as fragrances, flavours, pharmaceuticals, and potential biofuels. Microbial fermentation is being examined as a competitive approach for bulk production of these compounds. Competition for carbon allocation between synthesis of endogenous sterols and production of the introduced sesquiterpene limits yields. Achieving balance between endogenous sterols and heterologous sesquiterpenes is therefore required to achieve economical yields. In the current study, the yeast Saccharomyces cerevisiae was used to produce the acyclic sesquiterpene alcohol, trans-nerolidol. Nerolidol production was first improved by enhancing the upstream mevalonate pathway for the synthesis of the precursor farnesyl pyrophosphate (FPP). However, excess FPP was partially directed towards squalene by squalene synthase (Erg9p), resulting in squalene accumulation to 1 % biomass; moreover, the specific growth rate declined. In order to redirect carbon away from sterol production and towards the desired heterologous sesquiterpene, a novel protein destabilisation approach was developed for Erg9p. It was shown that Erg9p is located on endoplasmic reticulum and lipid droplets through a C-terminal ER-targeted transmembrane peptide. 2A PEST (rich in Pro, Glu/Asp, Ser, and Thr) sequence-dependent endoplasmic reticulum-associated protein degradation (ERAD) mechanism was established to decrease cellular levels of Erg9p without relying on inducers, repressors or specific repressing conditions. This improved nerolidol titre by 86 % to ~100 mg L -1 . In this strain, squalene levels were similar to the wild-type control strain, and downstream ergosterol levels were slightly decreased relative to the control, indicating redirection of carbon away from sterols and towards sesquiterpene production. There was no negative effect on cell growth under these conditions. Protein degradation is an efficient mechanism to control carbon allocation at flux-competing nodes in metabolic engineering applications. This study demonstrates that an engineered ERAD mechanism can be used to balance flux competition between the endogenous sterol pathway and an introduced bio-product pathways at the FPP node. The approach of protein degradation in general might be more widely applied to improve metabolic engineering outcomes.

show abstract

“…It is thus likely that the functionality and operation of chemical circuits involving low copy numbers of some species may considerably differ from standard predictions based on the LNA or REs. In addition, a detailed understanding of how extrinsic noise influences a circuit's low-copy-number properties is desirable because experimental studies suggest that extrinsic noise is frequently comparable to, or larger than, intrinsic noise 26 .…”

mentioning

confidence: 99%

Discreteness-induced concentration inversion in mesoscopic chemical systems

et al. 2012

View full text Add to dashboard Cite

molecular discreteness is apparent in small-volume chemical systems, such as biological cells, leading to stochastic kinetics. Here we present a theoretical framework to understand the effects of discreteness on the steady state of a monostable chemical reaction network. We consider independent realizations of the same chemical system in compartments of different volumes. Rate equations ignore molecular discreteness and predict the same average steadystate concentrations in all compartments. However, our theory predicts that the average steady state of the system varies with volume: if a species is more abundant than another for large volumes, then the reverse occurs for volumes below a critical value, leading to a concentration inversion effect. The addition of extrinsic noise increases the size of the critical volume. We theoretically predict the critical volumes and verify, by exact stochastic simulations, that rate equations are qualitatively incorrect in sub-critical volumes.

show abstract

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

Cited by 1,454 publications

References 44 publications

Deviant effects in molecular reaction pathways

Deviant effects in molecular reaction pathways

A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae

Discreteness-induced concentration inversion in mesoscopic chemical systems

Contact Info

Product

Resources

About