The functional proteome landscape of Escherichia coli

Mateus, André; Hevler, Johannes F.; Bobonis, Jacob; Kurzawa, Nils; Shah, Malay B.; Mitosch, Karin; Goemans, Camille; Helm, Dominic; Stein, Frank; Typas, Athanasios; Savitski, Mikhail M.

doi:10.1038/s41586-020-3002-5

Cited by 81 publications

(104 citation statements)

References 62 publications

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“…Third, it would be interesting to experimentally test the hypothesis that protein and RNA chaperones evolve under more and more stringent purifying selection during long-term experimental evolution, which follows from the premise that hypermutator LTEE populations are affected by a mutation load that affects protein folding and stability. Studies on the existence and relevance of phenomena like evolutionary capacitance caused by the contributions that PPI make to folding stability ( Dixit and Maslov 2013 ; Jarzab et al 2020 ; Mateus et al 2020 ), including cryptic genetic variation hidden by protein and RNA chaperones ( Queitsch et al 2002 ; Bergman and Siegal 2003 ; Masel 2005 , 2006 , 2013 ; Trotter et al 2014 ; Geiler-Samerotte et al 2016 ; Zheng et al 2019 ) during experimental evolution, and the effects of such phenomena on rates of protein evolution may be especially valuable in this regard. Finally, it would be valuable to develop a better understanding of the temperature sensitivity of evolved LTEE populations ( Mongold et al 1996 , 1999 ; Leiby and Marx 2014 ), and to collect data on protein evolutionary rates in long-term experiments conducted at elevated temperatures ( Bennett et al 1990 ; Tenaillon et al 2012 ).…”

Section: Discussionmentioning

confidence: 99%

Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli

Maddamsetti

2021

Genome Biology and Evolution

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Although it is well known that abundant proteins evolve slowly across the tree of life, there is little consensus for why this is true. Here, I report that abundant proteins evolve slowly in the hypermutator populations of Lenski’s long-term evolution experiment with Escherichia coli (LTEE). Specifically, the density of all observed mutations per gene, as measured in metagenomic time series covering 60,000 generations of the LTEE, significantly anti-correlates with mRNA abundance, protein abundance, and degree of protein-protein interaction. The same pattern holds for nonsynonymous mutation density. However, synonymous mutation density, measured across the LTEE hypermutator populations, positively correlates with protein abundance. These results show that universal constraints on protein evolution are visible in data spanning three decades of experimental evolution. Therefore, it should be possible to design experiments to answer why abundant proteins evolve slowly.

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Section: Discussionmentioning

confidence: 99%

Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli

Maddamsetti

2021

Genome Biology and Evolution

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“…MS sample preparation and measurements were performed as described 25,46 . Protein digestion was performed using a modified SP3 protocol 46,47 .…”

Section: Methodsmentioning

confidence: 99%

Molecular mechanisms of stress-induced reactivation in mumps virus condensates

Zhang

Sridharan

Zagoriy

et al. 2021

Preprint

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SummaryViruses can establish both acute and persistent chronic infections, and some viruses have developed the ability to switch between the two. However, the molecular mechanisms that trigger a transition from a benign chronic infection into pathogenesis remain unknown. Here we investigated the role of the cellular stress response in provoking a chronic-to-acute transition in viral replication in a model of mumps virus infection. Using a combination of cell biology, whole-cell proteomics and cryo-electron tomography we show that stress induces phosphorylation of the disordered viral Phosphoprotein, which we suggest facilitates partitioning of the viral polymerase into preformed viral condensates, constituting the core components of the viral replication machinery. This occurs concomitantly with a conformational change in the viral nucleocapsids that exposes the viral genome and can further facilitate its replication. These changes in the viral condensate upon exogenous stress, accompanied by down-regulation of the host antiviral response, provide an environment that supports up-regulation of viral replication and virion release. Thus, we elucidate molecular and structural mechanisms of a stress-mediated switch that disrupts the equilibrium between the virome and the host in chronic infection.

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“…Genome-scale gene deletion ( 1 – 5 ) or knockdown ( 4 , 6 , 7 ) libraries have revolutionized high-throughput approaches for characterizing gene function and interactions in microbes ( 8 – 11 ). These libraries intend to disrupt the function of single genes but can inadvertently affect other genes.…”

Section: Observationmentioning

confidence: 99%