Individual and Collective Contributions of Chaperoning and Degradation to Protein Homeostasis in E. coli

Cho, Younhee; Zhang, Xin; Pobre, Kristine Faye R.; Liu, Yu; Powers, David L.; Gierasch, Lila M.; Powers, Evan T.

doi:10.1016/j.celrep.2015.03.018

Cited by 42 publications

(43 citation statements)

References 56 publications

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“…Why this should be is not clear. DnaJ is a cochaperone of DnaK that functions in proteostasis to limit misfolded proteins (74,75). Given that Trp limitation leads to a decrease in global translation rates (42), one would anticipate a decreased need for chaperone function under these conditions.…”

Section: Discussionmentioning

confidence: 99%

Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation

2016

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In evolving to an obligate intracellular niche, Chlamydia has streamlined its genome by eliminating superfluous genes as it relies on the host cell for a variety of nutritional needs like amino acids. However, Chlamydia can experience amino acid starvation when the human host cell in which the bacteria reside is exposed to interferon gamma (IFN-␥), which leads to a tryptophan (Trp)-limiting environment via induction of the enzyme indoleamine-2,3-dioxygenase (IDO). The stringent response is used to respond to amino acid starvation in most bacteria but is missing from Chlamydia. Thus, how Chlamydia, a Trp auxotroph, responds to Trp starvation in the absence of a stringent response is an intriguing question. We previously observed that C. pneumoniae responds to this stress by globally increasing transcription while globally decreasing translation, an unusual response. Here, we sought to understand this and hypothesized that the Trp codon content of a given gene would determine its transcription level. We quantified transcripts from C. pneumoniae genes that were either rich or poor in Trp codons and found that Trp codon-rich transcripts were increased, whereas those that lacked Trp codons were unchanged or even decreased. There were exceptions, and these involved operons or large genes with multiple Trp codons: downstream transcripts were less abundant after Trp codon-rich sequences. These data suggest that ribosome stalling on Trp codons causes a negative polar effect on downstream sequences. Finally, reassessing previous C. pneumoniae microarray data based on codon content, we found that upregulated transcripts were enriched in Trp codons, thus supporting our hypothesis. Chlamydia is an obligate intracellular bacterial pathogen that causes a range of illnesses in humans and animals (1-4). It alternates between functionally and morphologically distinct forms during its developmental cycle (see reference 5 for review). The elementary body (EB) mediates attachment and internalization into a susceptible host cell, whereas the reticulate body (RB) grows and divides within a membrane-bound pathogen-specified parasitic organelle termed an inclusion (6). In evolving to obligate intracellular parasitism, Chlamydia has streamlined its genome by eliminating superfluous pathways and genes (7). Conversely, if Chlamydia has maintained a set of genes, then it is likely important for the bacterium.There are two primary species of Chlamydia that cause significant disease in humans: C. pneumoniae and C. trachomatis. Many chlamydial infections are often unrecognized and asymptomatic, and failure to treat these infections can lead to chronic sequelae. For C. trachomatis, these sequelae can include pelvic inflammatory disease, tubal factor infertility, and reactive arthritis (8, 9). C. pneumoniae has been associated with a number of chronic conditions, including atherosclerosis and adult-onset asthma among others (10, 11). One possible explanation for asymptomatic chlamydial infections may be due to the ability of the organism to ente...

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Section: Discussionmentioning

confidence: 99%

Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation

2016

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“…These proteins have been divided into three classes depending on their extent of interaction with GroEL: class I (42 proteins), class II (126 proteins), and class III (84 proteins). Recent theoretical studies based on the FoldEco simulation model characterize these three classes of GroEL substrates (13,32). Here, we model the whole proteostasis machine of E. coli and its handling of these 252 proteins.…”

Section: Methodsmentioning

confidence: 99%

“…2). Under normal (nonstress) conditions, the flux through B is negligible (13). The Ln protease degrades proteins on a timescale that is slow enough that the protein has time to attempt to fold or be chaperoned first.…”

Section: Proteostasis Machine Performs Dynamical Sortingmentioning

confidence: 99%

Bacterial proteostasis balances energy and chaperone utilization efficiently

Santra

Farrell

Dill

2017

Proc. Natl. Acad. Sci. U.S.A.

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Chaperones are protein complexes that help to fold and disaggregate a cell's proteins. It is not understood how four major chaperone systems of Escherichia coli work together in proteostasis: the recognition, sorting, folding, and disaggregating of the cell's many different proteins. Here, we model this machine. We combine extensive data on chaperoning, folding, and aggregation rates with expression levels of proteins and chaperones measured at different growth rates. We find that the proteostasis machine recognizes and sorts a client protein based on two biophysical properties of the client's misfolded state (M state): its stability and its kinetic accessibility from its unfolded state (U state). The machine is energy-efficient (the sickest proteins use the most ATP-expensive chaperones), comprehensive (it can handle any type of protein), and economical (the chaperone concentrations are just high enough to keep the whole proteome folded and disaggregated but no higher). The cell needs higher chaperone levels in two situations: fast growth (when protein production rates are high) and very slow growth (to mitigate the effects of protein degradation). This type of model complements experimental knowledge by showing how the various chaperones work together to achieve the broad folding and disaggregation needs of the cell.proteostasis | chaperone | protein folding | shields up | shields down A major action of cells is proteostasis (1-4). A cell's proteostasis "machine" is the collection of chaperones and synthesis and degradation processes that maintain the homeostatic balance of the folding and disaggregation of the cell's proteins. It is a machine in the sense that it is an energy-driven cyclic device that has component parts that work together to create its action. Proteostasis can become unbalanced under stresses, such as temperature, osmotic shock, oxidation, or drugs, or different growth conditions. Proteome health can fail if the machine is pushed beyond its tipping point (for example, in cell aging, cancer, or neurodegenerative diseases, such as Alzheimer's and Parkinson's) (1, 2, 4, 5).Much is now understood about the component parts (i.e., the structures of some chaperones, the folding equilibria and kinetics of isolated proteins in vitro, and the rates at which particular chaperones help fold and disaggregate particular proteins). The organism in which this is best understood is arguably Escherichia coli. What is not yet known is how the component chaperones act together as a machine on the many different proteins to meet the cell's needs. It is not known how "decisions" are made for trafficking different proteins through different chaperones.Cells have multiple types of chaperones. Also, different classes of proteins have different relationships with each chaperone (6). E. coli has four major chaperone systems: GroEL/GroES (GroE), DnaK/DnaJ/GrpE (KJE), Trigger Factor (TF), and ClpB (B) (7). Complex cells have more (8). E. coli proteins fall into three classes of interaction with GroEL (7): class I protei...

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“…1–3 Molecular chaperones play an important role in regulating the proteome by facilitating the folding of nascent polypeptide chains, preventing protein aggregation under stress conditions, and helping proteins refold during and after stress. Despite the clear importance of chaperones, achieving a detailed understanding of the mechanisms by which chaperones interact with their substrate proteins has proven to be a particularly difficult endeavor.…”

Section: Introductionmentioning

confidence: 99%

Capturing a Dynamic Chaperone–Substrate Interaction Using NMR-Informed Molecular Modeling

et al. 2016

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Chaperones maintain a healthy proteome by preventing aggregation and by aiding in protein folding. Precisely how chaperones influence the conformational properties of their substrates, however, remains unclear. To achieve a detailed description of dynamic chaperone–substrate interactions, we fused site-specific NMR information with coarse-grained simulations. Our model system is the binding and folding of a chaperone substrate, immunity protein 7 (Im7), with the chaperone Spy. We first used an automated procedure in which NMR chemical shifts inform the construction of system-specific force fields that describe each partner individually. The models of the two binding partners are then combined to perform simulations on the chaperone–substrate complex. The binding simulations show excellent agreement with experimental data from multiple biophysical measurements. Upon binding, Im7 interacts with a mixture of hydrophobic and hydrophilic residues on Spy's surface, causing conformational exchange within Im7 to slow down as Im7 folds. Meanwhile, the motion of Spy's flexible loop region increases, allowing for better interaction with different substrate conformations, and helping offset losses in Im7 conformational dynamics that occur upon binding and folding. Spy then preferentially releases Im7 into a well-folded state. Our strategy has enabled a residue-level description of a dynamic chaperone–substrate interaction, improving our understanding of how chaperones facilitate substrate folding. More broadly, we validate our approach using two other binding partners, showing that this approach provides a general platform from which to investigate other flexible biomolecular complexes through the integration of NMR data with efficient computational models.

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Individual and Collective Contributions of Chaperoning and Degradation to Protein Homeostasis in E. coli

Cited by 42 publications

References 56 publications

Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation

Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation

Bacterial proteostasis balances energy and chaperone utilization efficiently

Capturing a Dynamic Chaperone–Substrate Interaction Using NMR-Informed Molecular Modeling

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