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Azaharuddin M, Pal A, Mitra S, Dasgupta R, Basu T. A review on oligomeric polydispersity and oligomers-dependent holding chaperone activity of the small heat-shock protein IbpB of Escherichia coli. Cell Stress Chaperones 2023; 28:689-696. [PMID: 37910345 PMCID: PMC10746692 DOI: 10.1007/s12192-023-01392-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023] Open
Abstract
Inclusion body-associated proteins IbpA and IbpB of MW 16 KDa are the two small heat-shock proteins (sHSPs) of Escherichia coli, and they have only holding, but not folding, chaperone activity. In vitro holdase activity of IbpB is more than that of IbpA, and in combination, they synergise. Both IbpA and IbpB monomers first form homodimers, which as building blocks subsequently oligomerize to make heavy oligomers with MW of MDa range; for IbpB, the MW range of heavy oligomers is 2.0-3.0 MDa, whereas for IbpA oligomers, the values in MDa are not so specified/reported. By temperature upshift, such large oligomers of IbpB, but not of IbpA, dissociate to make relatively small oligomeric assemblies of MW around 600-700KDa. The larger oligomers of IbpB are assumed to be inactive storage form, which on facing heat or oxidative stress dissociate into smaller oligomers of ATP-independent holding chaperone activity. These smaller oligomers bind with stress-induced partially denatured/unfolded and thereby going to be aggregated proteins, to give them protection against permanent damage and aggregation. On withdrawal of stress, IbpB transfers the bound substrate protein to the ATP-dependent bi-chaperone system DnaKJE-ClpB, having both holdase and foldase properties, to finally refold the protein. Of the two sHSPs IbpA and IbpB of E. coli, this review covers the recent advances in research on IbpB only.
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Affiliation(s)
- Md Azaharuddin
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Anabadya Pal
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Sangeeta Mitra
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Rakhi Dasgupta
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Tarakdas Basu
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India.
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Tashjian TF, Zeinert RD, Eyles SJ, Chien P. Proteomic survey of the DNA damage response in Caulobacter crescentus. J Bacteriol 2023; 205:e0020623. [PMID: 37730540 PMCID: PMC10601758 DOI: 10.1128/jb.00206-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 09/22/2023] Open
Abstract
The bacterial DNA damage response is a critical, coordinated response to endogenous and exogenous sources of DNA damage. Response dynamics are dependent on coordinated synthesis and loss of relevant proteins. While much is known about its global transcriptional control, changes in protein abundance that occur upon DNA damage are less well characterized at the system level. Here, we perform a proteome-wide survey of the DNA damage response in Caulobacter crescentus. We find that while most protein abundance changes upon DNA damage are readily explained by changes in transcription, there are exceptions. The survey also allowed us to identify the novel DNA damage response factor, YaaA, which has been overlooked by previously published, transcription-focused studies. A similar survey in a ∆lon strain was performed to explore lon's role in DNA damage survival. The ∆lon strain had a smaller dynamic range of protein abundance changes in general upon DNA damage compared to the wild-type strain. This system-wide change to the dynamics of the response may explain this strain's sensitivity to DNA damage. Our proteome survey of the DNA damage response provides additional insight into the complex regulation of stress response and nominates a novel response factor that was overlooked in prior studies. IMPORTANCE The DNA damage response helps bacteria to react to and potentially survive DNA damage. The mutagenesis induced during this stress response contributes to the development of antibiotic resistance. Understanding how bacteria coordinate their response to DNA damage could help us to combat this growing threat to human health. While the transcriptional regulation of the bacterial DNA damage response has been characterized, this study is the first to our knowledge to assess the proteomic response to DNA damage in Caulobacter.
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Affiliation(s)
- Tommy F. Tashjian
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Rilee D. Zeinert
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Stephen J. Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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3
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Chernova LS, Vishnyakov IE, Börner J, Bogachev MI, Thormann KM, Kayumov AR. The Functionality of IbpA from Acholeplasma laidlawii Is Governed by Dynamic Rearrangement of Its Globular-Fibrillar Quaternary Structure. Int J Mol Sci 2023; 24:15445. [PMID: 37895124 PMCID: PMC10607609 DOI: 10.3390/ijms242015445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Small heat shock proteins (sHSPs) represent a first line of stress defense in many bacteria. The primary function of these molecular chaperones involves preventing irreversible protein denaturation and aggregation. In Escherichia coli, fibrillar EcIbpA binds unfolded proteins and keeps them in a folding-competent state. Further, its structural homologue EcIbpB induces the transition of EcIbpA to globules, thereby facilitating the substrate transfer to the HSP70-HSP100 system for refolding. The phytopathogenic Acholeplasma laidlawii possesses only a single sHSP, AlIbpA. Here, we demonstrate non-trivial features of the function and regulation of the chaperone-like activity of AlIbpA according to its interaction with other components of the mycoplasma multi-chaperone network. Our results show that the efficiency of the A. laidlawii multi-chaperone system is driven with the ability of AlIbpA to form both globular and fibrillar structures, thus combining functions of both IbpA and IbpB when transferring the substrate proteins to the HSP70-HSP100 system. In contrast to EcIbpA and EcIbpB, AlIbpA appears as an sHSP, in which the competition between the N- and C-terminal domains regulates the shift of the protein quaternary structure between a fibrillar and globular form, thus representing a molecular mechanism of its functional regulation. While the C-terminus of AlIbpA is responsible for fibrils formation and substrate capture, the N-terminus seems to have a similar function to EcIbpB through facilitating further substrate protein disaggregation using HSP70. Moreover, our results indicate that prior to the final disaggregation process, AlIbpA can directly transfer the substrate to HSP100, thereby representing an alternative mechanism in the HSP interaction network.
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Affiliation(s)
- Liliya S. Chernova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia;
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia;
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; (J.B.); (K.M.T.)
| | - Innokentii E. Vishnyakov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia;
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; (J.B.); (K.M.T.)
| | - Mikhail I. Bogachev
- Centre for Digital Telecommunication Technologies, St. Petersburg Electrotechnical University, Professora Popova 5, 197376 St. Petersburg, Russia;
| | - Kai M. Thormann
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; (J.B.); (K.M.T.)
| | - Airat R. Kayumov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia;
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Miwa T, Taguchi H. Escherichia coli small heat shock protein IbpA plays a role in regulating the heat shock response by controlling the translation of σ 32. Proc Natl Acad Sci U S A 2023; 120:e2304841120. [PMID: 37523569 PMCID: PMC10410725 DOI: 10.1073/pnas.2304841120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/23/2023] [Indexed: 08/02/2023] Open
Abstract
Small heat shock proteins (sHsps) act as ATP-independent chaperones that prevent irreversible aggregate formation by sequestering denatured proteins. IbpA, an Escherichia coli sHsp, functions not only as a chaperone but also as a suppressor of its own expression through posttranscriptional regulation, contributing to negative feedback regulation. IbpA also regulates the expression of its paralog, IbpB, in a similar manner, but the extent to which IbpA regulates other protein expressions is unclear. We have identified that IbpA down-regulates the expression of many Hsps by repressing the translation of the heat shock transcription factor σ32. The IbpA regulation not only controls the σ32 level but also contributes to the shutoff of the heat shock response. These results revealed an unexplored role of IbpA to regulate heat shock response at a translational level, which adds an alternative layer for tightly controlled and rapid expression of σ32 on demand.
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Affiliation(s)
- Tsukumi Miwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama226-8503, Japan
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama226-8503, Japan
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5
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Tashjian TF, Zeinert RD, Eyles SJ, Chien P. Proteomic survey of the DNA damage response in Caulobacter crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534141. [PMID: 36993274 PMCID: PMC10055390 DOI: 10.1101/2023.03.24.534141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
The bacterial DNA damage response is a critical, coordinated response to endogenous and exogenous sources of DNA damage. Response dynamics are dependent on coordinated synthesis and loss of relevant proteins. While much is known about its global transcriptional control, changes in protein abundance that occur upon DNA damage are less well characterized at the system level. Here, we perform a proteome-wide survey of the DNA damage response in Caulobacter crescentus . We find that while most protein abundance changes upon DNA damage are readily explained by changes in transcription, there are exceptions. The survey also allowed us to identify the novel DNA damage response factor, YaaA, which has been overlooked by previously published, transcription- focused studies. A similar survey in a Δ lon strain was performed to explore lon's role in DNA damage survival. The Δ lon strain had a smaller dynamic range of protein abundance changes in general upon DNA damage compared to the wild type strain. This system-wide change to the dynamics of the response may explain this strain's sensitivity to DNA damage. Our proteome survey of the DNA damage response provides additional insight into the complex regulation of stress response and nominates a novel response factor that was overlooked in prior studies. IMPORTANCE The DNA damage response helps bacteria to react to and potentially survive DNA damage. The mutagenesis induced during this stress response contributes to the development of antibiotic resistance. Understanding how bacteria coordinate their response to DNA damage could help us to combat this growing threat to human health. While the transcriptional regulation of the bacterial DNA damage response has been characterized, this study is the first to our knowledge to assess the proteomic response to DNA damage in Caulobacter .
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Affiliation(s)
- Tommy F. Tashjian
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Stephen J. Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
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6
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Structure, Substrate Specificity and Role of Lon Protease in Bacterial Pathogenesis and Survival. Int J Mol Sci 2023; 24:ijms24043422. [PMID: 36834832 PMCID: PMC9961632 DOI: 10.3390/ijms24043422] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Proteases are the group of enzymes that carry out proteolysis in all forms of life and play an essential role in cell survival. By acting on specific functional proteins, proteases affect the transcriptional and post-translational pathways in a cell. Lon, FtsH, HslVU and the Clp family are among the ATP-dependent proteases responsible for intracellular proteolysis in bacteria. In bacteria, Lon protease acts as a global regulator, governs an array of important functions such as DNA replication and repair, virulence factors, stress response and biofilm formation, among others. Moreover, Lon is involved in the regulation of bacterial metabolism and toxin-antitoxin systems. Hence, understanding the contribution and mechanisms of Lon as a global regulator in bacterial pathogenesis is crucial. In this review, we discuss the structure and substrate specificity of the bacterial Lon protease, as well as its ability to regulate bacterial pathogenesis.
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Branco LAC, Souza PFN, Neto NAS, Aguiar TKB, Silva AFB, Carneiro RF, Nagano CS, Mesquita FP, Lima LB, Freitas CDT. New Insights into the Mechanism of Antibacterial Action of Synthetic Peptide Mo-CBP 3-PepI against Klebsiella pneumoniae. Antibiotics (Basel) 2022; 11:antibiotics11121753. [PMID: 36551410 PMCID: PMC9774128 DOI: 10.3390/antibiotics11121753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae is a multidrug-resistant opportunistic human pathogen related to various infections. As such, synthetic peptides have emerged as potential alternative molecules. Mo-CBP3-PepI has presented great activity against K. pneumoniae by presenting an MIC50 at a very low concentration (31.25 µg mL-1). Here, fluorescence microscopy and proteomic analysis revealed the alteration in cell membrane permeability, ROS overproduction, and protein profile of K. pneumoniae cells treated with Mo-CBP3-PepI. Mo-CBP3-PepI led to ROS overaccumulation and membrane pore formation in K. pneumoniae cells. Furthermore, the proteomic analysis highlighted changes in essential metabolic pathways. For example, after treatment of K. pneumoniae cells with Mo-CBP3-PepI, a reduction in the abundance of protein related to DNA and protein metabolism, cytoskeleton and cell wall organization, redox metabolism, regulation factors, ribosomal proteins, and resistance to antibiotics was seen. The reduction in proteins involved in vital processes for cell life, such as DNA repair, cell wall turnover, and protein turnover, results in the accumulation of ROS, driving the cell to death. Our findings indicated that Mo-CBP3-PepI might have mechanisms of action against K. pneumoniae cells, mitigating the development of resistance and thus being a potent molecule to be employed in producing new drugs against K. pneumoniae infections.
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Affiliation(s)
- Levi A. C. Branco
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
| | - Pedro F. N. Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
- Correspondence: or
| | - Nilton A. S. Neto
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
| | - Tawanny K. B. Aguiar
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
| | - Ayrles F. B. Silva
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
| | - Rômulo F. Carneiro
- Department of Fisheries Engineering, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
| | - Celso S. Nagano
- Department of Fisheries Engineering, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
| | - Felipe P. Mesquita
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
| | - Luina B. Lima
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
| | - Cleverson D. T. Freitas
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
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Shotgun Proteomics Revealed Preferential Degradation of Misfolded In Vivo Obligate GroE Substrates by Lon Protease in Escherichia coli. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123772. [PMID: 35744894 PMCID: PMC9228906 DOI: 10.3390/molecules27123772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022]
Abstract
The Escherichia coli chaperonin GroEL/ES (GroE) is one of the most extensively studied molecular chaperones. So far, ~80 proteins in E. coli are identified as GroE substrates that obligately require GroE for folding in vivo. In GroE-depleted cells, these substrates, when overexpressed, tend to form aggregates, whereas the GroE substrates expressed at low or endogenous levels are degraded, probably due to misfolded states. However, the protease(s) involved in the degradation process has not been identified. We conducted a mass-spectrometry-based proteomics approach to investigate the effects of three ATP-dependent proteases, Lon, ClpXP, and HslUV, on the E. coli proteomes under GroE-depleted conditions. A label-free quantitative proteomic method revealed that Lon protease is the dominant protease that degrades the obligate GroE substrates in the GroE-depleted cells. The deletion of DnaK/DnaJ, the other major E. coli chaperones, in the ∆lon strain did not cause major alterations in the expression or folding of the obligate GroE substrates, supporting the idea that the folding of these substrates is predominantly dependent on GroE.
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9
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Piróg A, Cantini F, Nierzwicki Ł, Obuchowski I, Tomiczek B, Czub J, Liberek K. Two Bacterial Small Heat Shock Proteins, IbpA and IbpB, Form a Functional Heterodimer. J Mol Biol 2021; 433:167054. [PMID: 34022209 DOI: 10.1016/j.jmb.2021.167054] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 01/29/2023]
Abstract
Small heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones which in stress conditions bind to unfolded protein substrates and prevent their irreversible aggregation. Substrates trapped in sHsps-containing aggregates are efficiently refolded into native structures by ATP-dependent Hsp70 and Hsp100 chaperones. Most γ-proteobacteria possess a single sHsp (IbpA), while in a subset of Enterobacterales, as a consequence of ibpA gene duplication event, a two-protein sHsp (IbpA and IbpB) system has evolved. IbpA and IbpB are functionally divergent. Purified IbpA, but not IbpB, stably interacts with aggregated substrates, yet both sHsps are required to be present at the substrate denaturation step for subsequent efficient Hsp70-Hsp100-dependent substrate refolding. IbpA and IbpB interact with each other, influence each other's expression levels and degradation rates. However, the crucial information on how these two sHsps interact and what is the basic building block required for proper sHsps functioning was missing. Here, based on NMR, mass spectrometry and crosslinking studies, we show that IbpA-IbpB heterodimer is a dominating functional unit of the two sHsp system in Enterobacterales. The principle of heterodimer formation is similar to one described for homodimers of single bacterial sHsps. β-hairpins formed by strands β5 and β7 of IbpA or IbpB crystallin domains associate with the other one's β-sandwich in the heterodimer structure. Relying on crosslinking and molecular dynamics studies, we also propose the orientation of two IbpA-IbpB heterodimers in a higher order tetrameric structure.
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Affiliation(s)
- Artur Piróg
- Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Łukasz Nierzwicki
- Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Igor Obuchowski
- Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Bartłomiej Tomiczek
- Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.
| | - Krzysztof Liberek
- Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland.
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Obuchowski I, Karaś P, Liberek K. The Small Ones Matter-sHsps in the Bacterial Chaperone Network. Front Mol Biosci 2021; 8:666893. [PMID: 34055885 PMCID: PMC8155344 DOI: 10.3389/fmolb.2021.666893] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/28/2021] [Indexed: 11/22/2022] Open
Abstract
Small heat shock proteins (sHsps) are an evolutionarily conserved class of ATP-independent chaperones that form the first line of defence during proteotoxic stress. sHsps are defined not only by their relatively low molecular weight, but also by the presence of a conserved α-crystallin domain, which is flanked by less conserved, mostly unstructured, N- and C-terminal domains. sHsps form oligomers of different sizes which deoligomerize upon stress conditions into smaller active forms. Activated sHsps bind to aggregation-prone protein substrates to form assemblies that keep substrates from irreversible aggregation. Formation of these assemblies facilitates subsequent Hsp70 and Hsp100 chaperone-dependent disaggregation and substrate refolding into native species. This mini review discusses what is known about the role and place of bacterial sHsps in the chaperone network.
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Affiliation(s)
- Igor Obuchowski
- Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
| | | | - Krzysztof Liberek
- Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
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Abstract
The Borrelia spp. are tick-borne pathogenic spirochetes that include the agents of Lyme disease and relapsing fever. As part of their life cycle, the spirochetes traffic between the tick vector and the vertebrate host, which requires significant physiological changes and remodeling of their outer membranes and proteome. This crucial proteome resculpting is carried out by a diverse set of proteases, adaptor proteins, and related chaperones. Despite its small genome, Borrelia burgdorferi has dedicated a large percentage of its genome to proteolysis, including a full complement of ATP-dependent proteases. Energy-driven proteolysis appears to be an important physiological feature of this dual-life-cycle bacterium. The proteolytic arsenal of Borrelia is strategically deployed for disposal of proteins no longer required as they move from one stage to another or are transferred from one host to another. Likewise, the Borrelia spp. are systemic organisms that need to break down and move through host tissues and barriers, and so their unique proteolytic resources, both endogenous and borrowed, make movement more feasible. Both the Lyme disease and relapsing fever Borrelia spp. bind plasminogen as well as numerous components of the mammalian plasminogen-activating system. This recruitment capacity endows the spirochetes with a borrowed proteolytic competency that can lead to increased invasiveness.
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Stromberg ZR, Masonbrink RE, Mellata M. Transcriptomic Analysis of Shiga Toxin-Producing Escherichia coli during Initial Contact with Cattle Colonic Explants. Microorganisms 2020; 8:microorganisms8111662. [PMID: 33120988 PMCID: PMC7693793 DOI: 10.3390/microorganisms8111662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 01/10/2023] Open
Abstract
Foodborne pathogens are a public health threat globally. Shiga toxin-producing Escherichia coli (STEC), particularly O26, O111, and O157 STEC, are often associated with foodborne illness in humans. To create effective preharvest interventions, it is critical to understand which factors STEC strains use to colonize the gastrointestinal tract of cattle, which serves as the reservoir for these pathogens. Several colonization factors are known, but little is understood about initial STEC colonization factors. Our objective was to identify these factors via contrasting gene expression between nonpathogenic E. coli and STEC. Colonic explants were inoculated with nonpathogenic E. coli strain MG1655 or STEC strains (O26, O111, or O157), bacterial colonization levels were determined, and RNA was isolated and sequenced. STEC strains adhered to colonic explants at numerically but not significantly higher levels compared to MG1655. After incubation with colonic explants, flagellin (fliC) was upregulated (log2 fold-change = 4.0, p < 0.0001) in O157 STEC, and collectively, Lon protease (lon) was upregulated (log2 fold-change = 3.6, p = 0.0009) in STEC strains compared to MG1655. These results demonstrate that H7 flagellum and Lon protease may play roles in early colonization and could be potential targets to reduce colonization in cattle.
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Affiliation(s)
- Zachary R. Stromberg
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA;
| | - Rick E. Masonbrink
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA;
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA;
- Correspondence: ; Tel.: +1-515-294-9220
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13
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Miwa T, Chadani Y, Taguchi H. Escherichia coli small heat shock protein IbpA is an aggregation-sensor that self-regulates its own expression at posttranscriptional levels. Mol Microbiol 2020; 115:142-156. [PMID: 32959419 DOI: 10.1111/mmi.14606] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 11/28/2022]
Abstract
Aggregation is an inherent characteristic of proteins. Risk management strategies to reduce aggregation are critical for cells to survive upon stresses that induce aggregation. Cells cope with protein aggregation by utilizing a variety of chaperones, as exemplified by heat-shock proteins (Hsps). The heat stress-induced expression of IbpA and IbpB, small Hsps in Escherichia coli, is regulated by the σ32 heat-shock transcriptional regulator and the temperature-dependent translational regulation via mRNA heat fluctuation. We found that, even without heat stress, either the expression of aggregation-prone proteins or the ibpA gene deletion profoundly increases the expression of IbpA. Combined with other evidence, we propose novel mechanisms for the regulation of the small Hsps expression. Oligomeric IbpA self-represses the ibpA/ibpB translation, and mediates its own mRNA degradation, but the self-repression is relieved by sequestration of IbpA into the protein aggregates. Thus, the function of IbpA as a chaperone to form co-aggregates is harnessed as an aggregation sensor to tightly regulate the IbpA level. Since the excessive preemptive supply of IbpA in advance of stress is harmful, the prodigious and rapid expression of IbpA/IbpB on demand is necessary for IbpA to function as a first line of defense against acute protein aggregation.
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Affiliation(s)
- Tsukumi Miwa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuhei Chadani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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14
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Muselius B, Sukumaran A, Yeung J, Geddes-McAlister J. Iron Limitation in Klebsiella pneumoniae Defines New Roles for Lon Protease in Homeostasis and Degradation by Quantitative Proteomics. Front Microbiol 2020; 11:546. [PMID: 32390954 PMCID: PMC7194016 DOI: 10.3389/fmicb.2020.00546] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/12/2020] [Indexed: 01/24/2023] Open
Abstract
Nutrient adaptation is key in limiting environments for the promotion of microbial growth and survival. In microbial systems, iron is an essential component for many cellular processes, and bioavailability varies greatly among different conditions. In the bacterium, Klebsiella pneumoniae, the impact of iron limitation is known to alter transcriptional expression of iron-acquisition pathways and influence secretion of iron-binding siderophores, however, a comprehensive view of iron limitation at the protein level remains to be defined. Here, we apply a mass-spectrometry-based quantitative proteomics strategy to profile the global impact of iron limitation on the cellular proteome and extracellular environment (secretome) of K. pneumoniae. Our data define the impact of iron on proteins involved in transcriptional regulation and emphasize the modulation of a vast array of proteins associated with iron acquisition, transport, and binding. We also identify proteins in the extracellular environment associated with conventional and non-conventional modes of secretion, as well as vesicle release. In particular, we demonstrate a new role for Lon protease in promoting iron homeostasis outside of the cell. Characterization of a Lon protease mutant in K. pneumoniae validates roles in bacterial growth, cell division, and virulence, and uncovers novel degradation candidates of Lon protease associated with improved iron utilization strategies in the absence of the enzyme. Overall, we provide evidence of unique connections between Lon and iron in a bacterial system and suggest a new role for Lon protease in the extracellular environment during nutrient limitation.
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15
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Chernova LS, Bogachev MI, Chasov VV, Vishnyakov IE, Kayumov AR. N- and C-terminal regions of the small heat shock protein IbpA from Acholeplasma laidlawii competitively govern its oligomerization pattern and chaperone-like activity. RSC Adv 2020; 10:8364-8376. [PMID: 35497866 PMCID: PMC9050003 DOI: 10.1039/c9ra10172a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/18/2020] [Indexed: 12/11/2022] Open
Abstract
Small heat shock proteins (sHSPs) are ubiquitous molecular chaperones preventing the irreversible denaturation of proteins. While in Escherichia coli two sHSPs IbpA and IbpB work in strong cooperation, the sole Mollicute with free-living ability Acholeplasma laidlawii carries a single gene encoding the sHSP protein AlIbpA. In vitro, independently of the temperature, AlIbpA forms a heterogeneous mixture of approximately 24-mer globules, fibrils and huge protein aggregates. The removal of either 12 or 25 N-terminal amino acids led to the formation of fibrils and enhanced the protein ability to prevent the temperature-induced aggregation of insulin, assuming the fibrillar form as an active protein. In turn, the deletion of the C-terminus or substitution of C-terminal LEL motif by SEP decreased the temperature stability of AlIbpA and eliminated its chaperone function completely, although the protein remained predominantly in a globular state. This suggests that the C-terminal LEL motif is necessary for the chaperon-like activity of AlIbpA and fibril formation. Double N- and C-terminal truncations abolished both the chaperone-like activity and huge oligomer formation. Since the globular form of sHSPs is considered as their inactive form, our data suggest that the N-terminus of AlIbpA is responsible for the huge globule (low-active form) formation and behaves as an intramolecular inhibitor of the fibrils (active form) formation and substrates binding. Taken together these data demonstrate non-trivial properties of AlIbpA, in which the competitive action of N- and C-termini governs the equilibrium between either fibrillar or globular structures representing a possible molecular mechanism of the AlIbpA activity regulation. The CTD provides fibrils (active form) formation. The NTD leads to globules formation and behaves as an intramolecular inhibitor of CTD. Their competition governs the equilibrium between either fibrills or globules regulating the AlIbpA activity.![]()
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Affiliation(s)
- Liliya S Chernova
- Kazan Federal University 18 Kremlevskaya street 420008 Kazan Russia +7-843-233-78-02.,Institute of Cytology, Russian Academy of Sciences 4 Tikhoretsky Avenue 194064 St-Petersburg Russia +7-812-297-03-28
| | - Mikhail I Bogachev
- St. Petersburg Electrotechnical University 5 Professor Popov street 197376 St. Petersburg Russia
| | - Vitaly V Chasov
- Kazan Federal University 18 Kremlevskaya street 420008 Kazan Russia +7-843-233-78-02
| | - Innokentii E Vishnyakov
- Institute of Cytology, Russian Academy of Sciences 4 Tikhoretsky Avenue 194064 St-Petersburg Russia +7-812-297-03-28.,Peter the Great St.Petersburg Polytechnic University 29 Polytechnicheskaya street 195251 St-Petersburg Russia
| | - Airat R Kayumov
- Kazan Federal University 18 Kremlevskaya street 420008 Kazan Russia +7-843-233-78-02.,Institute of Cytology, Russian Academy of Sciences 4 Tikhoretsky Avenue 194064 St-Petersburg Russia +7-812-297-03-28
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16
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Babin BM, Kasperkiewicz P, Janiszewski T, Yoo E, Drąg M, Bogyo M. Leveraging Peptide Substrate Libraries to Design Inhibitors of Bacterial Lon Protease. ACS Chem Biol 2019; 14:2453-2462. [PMID: 31464417 PMCID: PMC6858493 DOI: 10.1021/acschembio.9b00529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lon is a widely conserved housekeeping protease found in all domains of life. Bacterial Lon is involved in recovery from various types of stress, including tolerance to fluoroquinolone antibiotics, and is linked to pathogenesis in a number of organisms. However, detailed functional studies of Lon have been limited by the lack of selective, cell-permeant inhibitors. Here, we describe the use of positional scanning libraries of hybrid peptide substrates to profile the primary sequence specificity of bacterial Lon. In addition to identifying optimal natural amino acid binding preferences, we identified several non-natural residues that were leveraged to develop optimal peptide substrates as well as a potent peptidic boronic acid inhibitor of Lon. Treatment of Escherichia coli with this inhibitor promotes UV-induced filamentation and reduces tolerance to ciprofloxacin, phenocopying established lon-deletion phenotypes. It is also nontoxic to mammalian cells due to its selectivity for Lon over the proteasome. Our results provide new insight into the primary substrate specificity of Lon and identify substrates and an inhibitor that will serve as useful tools for dissecting the diverse cellular functions of Lon.
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Affiliation(s)
- Brett M. Babin
- Department of Pathology Stanford University School of Medicine, Stanford, CA, USA
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Tomasz Janiszewski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Euna Yoo
- Department of Pathology Stanford University School of Medicine, Stanford, CA, USA
| | - Marcin Drąg
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Matthew Bogyo
- Department of Pathology Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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17
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Obuchowski I, Piróg A, Stolarska M, Tomiczek B, Liberek K. Duplicate divergence of two bacterial small heat shock proteins reduces the demand for Hsp70 in refolding of substrates. PLoS Genet 2019; 15:e1008479. [PMID: 31652260 PMCID: PMC6834283 DOI: 10.1371/journal.pgen.1008479] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 11/06/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
Small heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones that bind to aggregation-prone polypeptides at stress conditions. sHsps encage these polypeptides in assemblies, shielding them from further aggregation. To facilitate their subsequent solubilization and refolding by Hsp70 (DnaK) and Hsp100 (ClpB) chaperones, first, sHsps need to dissociate from the assemblies. In most γ-proteobacteria, these functions are fulfilled by a single sHsp (IbpA), but in a subset of Enterobacterales, a two-protein sHsp (IbpA and IbpB) system has evolved. To gain insight into the emergence of complexity within this chaperone system, we reconstructed the phylogeny of γ-proteobacteria and their sHsps. We selected proteins representative of systems comprising either one or two sHsps and analysed their ability to form sHsps-substrate assemblies. All the tested IbpA proteins, but not IbpBs, stably interact with an aggregating substrate. Moreover, in Escherichia coli cells, ibpA but not ibpB suppress the growth defect associated with low DnaK level, which points to the major protective role of IbpA during the breakdown of protein quality control. We also examined how sHsps affect the association of Hsp70 with the assemblies at the initial phase of disaggregation and how they affect protein recovery after stress. Our results suggest that a single gene duplication event has given rise to the sHsp system consisting of a strong canonical binder, IbpA, and its non-canonical paralog IbpB that enhances sHsps dissociation from the assemblies. The cooperation between the sHsps reduces the demand for Hsp70 needed to outcompete them from the assemblies by promoting sHsps dissociation without compromising assembly formation at heat shock. This potentially increases the robustness and elasticity of sHsps protection against irreversible aggregation. Small heat shock proteins (sHsps) are a class of molecular chaperones playing an important role in maintaining cell proteostasis. Their most widespread and evolutionarily conserved function is binding to denaturing polypeptides. Small Hsps shield their substrates from further aggregation until conditions are favourable for their refolding by chaperones from the Hsp70 and Hsp100 families. To exert this function, at stress conditions, oligomeric sHsps dissociate into dimers and scavenge partially unfolded substrates, forming assemblies containing both substrate proteins and sHsps. Substrate proteins in such assemblies are refolding-competent. Later, when a cell recovers from stress, sHsps need to dissociate from the assemblies to make the substrates available for the disaggregating and refolding chaperones. Most bacteria possess one sHsp-encoding gene. However, their single sHsp is burdened with a trade-off: on one hand, it has to rapidly associate with the misfolding proteins, on the other, it needs to dissociate from them to allow effective disaggregation. With phylogenetic and biochemical approaches, we analysed a two-sHsp system distinctive of the Enterobacterales order, unravelling a potential evolutionary advantage granted by functional cooperation between the two sHsps. Our results indicate that after a gene duplication event, one sHsp specialized in tight substrate binding, whereas another sHsp became important for efficient dissociation of both sHsps to enable recovery of proteins trapped in the assemblies.
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Affiliation(s)
- Igor Obuchowski
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
| | - Artur Piróg
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
| | - Milena Stolarska
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
| | - Bartłomiej Tomiczek
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
| | - Krzysztof Liberek
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
- * E-mail:
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18
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Elucidation of the molecular mechanism of heat shock proteins and its correlation with the effects of double mutations S679A & K722Q in the catalytic dyad residues of Lon protease. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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19
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Mogk A, Ruger-Herreros C, Bukau B. Cellular Functions and Mechanisms of Action of Small Heat Shock Proteins. Annu Rev Microbiol 2019; 73:89-110. [PMID: 31091419 DOI: 10.1146/annurev-micro-020518-115515] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Small heat shock proteins (sHsps) constitute a diverse chaperone family that shares the α-crystallin domain, which is flanked by variable, disordered N- and C-terminal extensions. sHsps act as the first line of cellular defense against protein unfolding stress. They form dynamic, large oligomers that represent inactive storage forms. Stress conditions cause a rapid increase in cellular sHsp levels and trigger conformational rearrangements, resulting in exposure of substrate-binding sites and sHsp activation. sHsps bind to early-unfolding intermediates of misfolding proteins in an ATP-independent manner and sequester them in sHsp/substrate complexes. Sequestration protects substrates from further uncontrolled aggregation and facilitates their refolding by ATP-dependent Hsp70-Hsp100 disaggregases. Some sHsps with particularly strong sequestrase activity, such as yeast Hsp42, are critical factors for forming large, microscopically visible deposition sites of misfolded proteins in vivo. These sites are organizing centers for triaging substrates to distinct quality control pathways, preferentially Hsp70-dependent refolding and selective autophagy.
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Affiliation(s)
- Axel Mogk
- Center for Molecular Biology of the University of Heidelberg and German Cancer Research Center, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; ,
| | - Carmen Ruger-Herreros
- Center for Molecular Biology of the University of Heidelberg and German Cancer Research Center, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; ,
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg and German Cancer Research Center, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; ,
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20
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Brown BL, Vieux EF, Kalastavadi T, Kim S, Chen JZ, Baker TA. N domain of the Lon AAA+ protease controls assembly and substrate choice. Protein Sci 2018; 28:1239-1251. [PMID: 30461098 DOI: 10.1002/pro.3553] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 11/09/2022]
Abstract
The protein quality control network (pQC) plays critical roles in maintaining protein and cellular homeostasis, especially during stress. Lon is a major pQC AAA+ protease, conserved from bacteria to human mitochondria. It is the principal enzyme that degrades most unfolded or damaged proteins. Degradation by Lon also controls cellular levels of several key regulatory proteins. Recently, our group determined that Escherichia coli Lon, previously thought to be an obligate homo-hexamer, also forms a dodecamer. This larger assembly has decreased ATPase activity and displays substrate-specific alterations in degradation compared with the hexamer. Here we experimentally probe the physical hexamer-hexamer interactions and the biological roles of the Lon dodecamer. Using structure prediction methods coupled with mutagenesis, we identified a key interface and specific residues within the Lon N domain that participates in an intermolecular coiled coil unique to the dodecamer. With this knowledge, we made a Lon variant (LonVQ ) that forms a dodecamer with increased stability, as determined by analytical ultracentrifugation and electron microscopy. Using this altered Lon, we characterize the Lon dodecamer's activities using a panel of substrates. Lon dodecamers are clearly functional, and complement critical lon- phenotypes but also exhibit altered substrate specificity. For example, the small heat shock proteins IbpA and IbpB are only efficiently degraded well by the hexamer. Thus, by elucidating the intermolecular contacts connecting the hexamers, we are starting to illuminate how dodecamer formation versus disassembly can alter Lon function under conditions where controlling specific activities and substrate preferences of this key protease may be advantageous.
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Affiliation(s)
- Breann L Brown
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ellen F Vieux
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Tejas Kalastavadi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - SaRa Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - James Z Chen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
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21
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He L, Luo D, Yang F, Li C, Zhang X, Deng H, Zhang JR. Multiple domains of bacterial and human Lon proteases define substrate selectivity. Emerg Microbes Infect 2018; 7:149. [PMID: 30120231 PMCID: PMC6098112 DOI: 10.1038/s41426-018-0148-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/16/2018] [Accepted: 06/23/2018] [Indexed: 02/05/2023]
Abstract
The Lon protease selectively degrades abnormal proteins or certain normal proteins in response to environmental and cellular conditions in many prokaryotic and eukaryotic organisms. However, the mechanism(s) behind the substrate selection of normal proteins remains largely unknown. In this study, we identified 10 new substrates of F. tularensis Lon from a total of 21 candidate substrates identified in our previous work, the largest number of novel Lon substrates from a single study. Cross-species degradation of these and other known Lon substrates revealed that human Lon is unable to degrade many bacterial Lon substrates, suggestive of a “organism-adapted” substrate selection mechanism for the natural Lon variants. However, individually replacing the N, A, and P domains of human Lon with the counterparts of bacterial Lon did not enable the human protease to degrade the same bacterial Lon substrates. This result showed that the “organism-adapted” substrate selection depends on multiple domains of the Lon proteases. Further in vitro proteolysis and mass spectrometry analysis revealed a similar substrate cleavage pattern between the bacterial and human Lon variants, which was exemplified by predominant representation of leucine, alanine, and other hydrophobic amino acids at the P(−1) site within the substrates. These observations suggest that the Lon proteases select their substrates at least in part by fine structural matching with the proteins in the same organisms.
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Affiliation(s)
- Lihong He
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Dongyang Luo
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Fan Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Chunhao Li
- Philip Research Institute for Oral Health, School of Dentistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China. .,Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.
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22
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Arends J, Griego M, Thomanek N, Lindemann C, Kutscher B, Meyer HE, Narberhaus F. An Integrated Proteomic Approach Uncovers Novel Substrates and Functions of the Lon Protease in Escherichia coli. Proteomics 2018; 18:e1800080. [PMID: 29710379 DOI: 10.1002/pmic.201800080] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/20/2018] [Indexed: 01/29/2023]
Abstract
Controlling the cellular abundance and proper function of proteins by proteolysis is a universal process in all living organisms. In Escherichia coli, the ATP-dependent Lon protease is crucial for protein quality control and regulatory processes. To understand how diverse substrates are selected and degraded, unbiased global approaches are needed. We employed a quantitative Super-SILAC (stable isotope labeling with amino acids in cell culture) mass spectrometry approach and compared the proteomes of a lon mutant and a strain producing the protease to discover Lon-dependent physiological functions. To identify Lon substrates, we took advantage of a Lon trapping variant, which is able to translocate substrates but unable to degrade them. Lon-associated proteins were identified by label-free LC-MS/MS. The combination of both approaches revealed a total of 14 novel Lon substrates. Besides the identification of known pathways affected by Lon, for example, the superoxide stress response, our cumulative data suggests previously unrecognized fundamental functions of Lon in sulfur assimilation, nucleotide biosynthesis, amino acid and central energy metabolism.
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Affiliation(s)
- Jan Arends
- Department of Microbial Biology, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Marcena Griego
- Department of Microbial Biology, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Nikolas Thomanek
- Medical Proteome Center, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Claudia Lindemann
- Medical Proteome Center, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Blanka Kutscher
- Department of Microbial Biology, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Helmut E Meyer
- Medical Proteome Center, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany.,Department of Biomedical Research, Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Bunsen-Kirchhoff-Straße 11, D-44139, Dortmund, Germany
| | - Franz Narberhaus
- Department of Microbial Biology, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
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23
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Varas MA, Riquelme-Barrios S, Valenzuela C, Marcoleta AE, Berríos-Pastén C, Santiviago CA, Chávez FP. Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium discoideum. Front Cell Infect Microbiol 2018; 8:8. [PMID: 29441327 PMCID: PMC5797601 DOI: 10.3389/fcimb.2018.00008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/09/2018] [Indexed: 01/26/2023] Open
Abstract
Inorganic polyphosphate (polyP) deficiency in enteric bacterial pathogens reduces their ability to invade and establish systemic infections in different hosts. For instance, inactivation of the polyP kinase gene (ppk) encoding the enzyme responsible for polyP biosynthesis reduces invasiveness and intracellular survival of Salmonella enterica serovar Typhimurium (S. Typhimurium) in epithelial cells and macrophages in vitro. In addition, the virulence in vivo of a S. Typhimurium Δppk mutant is significantly reduced in a murine infection model. In spite of these observations, the role played by polyP during the Salmonella-host interaction is not well understood. The social amoeba Dictyostelium discoideum has proven to be a useful model for studying relevant aspects of the host-pathogen interaction. In fact, many intracellular pathogens can survive within D. discoideum cells using molecular mechanisms also required to survive within macrophages. Recently, we established that S. Typhimurium is able to survive intracellularly in D. discoideum and identified relevant genes linked to virulence that are crucial for this process. The aim of this study was to determine the effect of a polyP deficiency in S. Typhimurium during its interaction with D. discoideum. To do this, we evaluated the intracellular survival of wild-type and Δppk strains of S. Typhimurium in D. discoideum and the ability of these strains to delay the social development of the amoeba. In contrast to the wild-type strain, the Δppk mutant was unable to survive intracellularly in D. discoideum and enabled the social development of the amoeba. Both phenotypes were complemented using a plasmid carrying a copy of the ppk gene. Next, we simultaneously evaluated the proteomic response of both S. Typhimurium and D. discoideum during host-pathogen interaction via global proteomic profiling. The analysis of our results allowed the identification of novel molecular signatures that give insight into Salmonella-Dictyostelium interaction. Altogether, our results indicate that inorganic polyP is essential for S. Typhimurium virulence and survival in D. discoideum. In addition, we have validated the use of global proteomic analyses to simultaneously evaluate the host-pathogen interaction of S. Typhimurium and D. discoideum. Furthermore, our infection assays using these organisms can be exploited to screen for novel anti-virulence molecules targeting inorganic polyP biosynthesis.
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Affiliation(s)
- Macarena A Varas
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sebastián Riquelme-Barrios
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Camila Valenzuela
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Andrés E Marcoleta
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Carlos A Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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24
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LaVoie SP, Summers AO. Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure. BMC Genomics 2018; 19:52. [PMID: 29338696 PMCID: PMC5769350 DOI: 10.1186/s12864-017-4413-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022] Open
Abstract
Background The protean chemical properties of mercury have long made it attractive for diverse applications, but its toxicity requires great care in its use, disposal, and recycling. Mercury occurs in multiple chemical forms, and the molecular basis for the distinct toxicity of its various forms is only partly understood. Global transcriptomics applied over time can reveal how a cell recognizes a toxicant and what cellular subsystems it marshals to repair and recover from the damage. The longitudinal effects on the transcriptome of exponential phase E. coli were compared during sub-acute exposure to mercuric chloride (HgCl2) or to phenylmercuric acetate (PMA) using RNA-Seq. Results Differential gene expression revealed common and distinct responses to the mercurials throughout recovery. Cultures exhibited growth stasis immediately after each mercurial exposure but returned to normal growth more quickly after PMA exposure than after HgCl2 exposure. Correspondingly, PMA rapidly elicited up-regulation of a large number of genes which continued for 30 min, whereas fewer genes were up-regulated early after HgCl2 exposure only some of which overlapped with PMA up-regulated genes. By 60 min gene expression in PMA-exposed cells was almost indistinguishable from unexposed cells, but HgCl2 exposed cells still had many differentially expressed genes. Relative expression of energy production and most metabolite uptake pathways declined with both compounds, but nearly all stress response systems were up-regulated by one or the other mercurial during recovery. Conclusions Sub-acute exposure influenced expression of ~45% of all genes with many distinct responses for each compound, reflecting differential biochemical damage by each mercurial and the corresponding resources available for repair. This study is the first global, high-resolution view of the transcriptional responses to any common toxicant in a prokaryotic model system from exposure to recovery of active growth. The responses provoked by these two mercurials in this model bacterium also provide insights about how higher organisms may respond to these ubiquitous metal toxicants. Electronic supplementary material The online version of this article (10.1186/s12864-017-4413-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephen P LaVoie
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
| | - Anne O Summers
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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25
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Bhattacharjee S, Dasgupta R, Bagchi A. Elucidation of the molecular mechanism of heat shock proteins and its correlation with K722Q mutations in Lon protease. Biosystems 2017; 159:12-22. [PMID: 28676239 DOI: 10.1016/j.biosystems.2017.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/22/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
Cells withstand the effects of temperature change with the help of small heat shock proteins IbpA and IbpB. The IbpAB protein complex interacts with Lon protease in their free form and gets degraded at physiological temperature when there is no temperature stress. However, the proteolytic degradation of IbpAB is diminished when Lon is mutated. The mutation K722Q in Lon brings about some structural changes so that the proteolytic interactions between the heat shock proteins with that of the mutated Lon protease are lost. However, the detailed molecular aspects of the interactions are not yet fully understood. In the present, we made an attempt to analyze the biochemical aspects of the interactions between the small heat shock proteins IbpAB with wild type and mutant Lon protease. We for the first time deciphered the molecular details of the mechanism of interaction of small heat shock proteins with Lon protease bearing K722Q mutation i.e. the interaction pattern of heat shock proteins with mutant Lon protease at physiological temperature in absence of proteolytic machinery. Our study may therefore be useful to elucidate the mechanistic details of the correlation with IbpA, IbpB and Lon protease.
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Affiliation(s)
- Sanchari Bhattacharjee
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India.
| | - Rakhi Dasgupta
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India.
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India.
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Karlowicz A, Wegrzyn K, Gross M, Kaczynska D, Ropelewska M, Siemiątkowska M, Bujnicki JM, Konieczny I. Defining the crucial domain and amino acid residues in bacterial Lon protease for DNA binding and processing of DNA-interacting substrates. J Biol Chem 2017; 292:7507-7518. [PMID: 28292931 DOI: 10.1074/jbc.m116.766709] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/14/2017] [Indexed: 12/19/2022] Open
Abstract
Lon protease previously has been shown to interact with DNA, but the role of this interaction for Lon proteolytic activity has not been characterized. In this study, we used truncated Escherichia coli Lon constructs, bioinformatics analysis, and site-directed mutagenesis to identify Lon domains and residues crucial for Lon binding with DNA and effects on Lon proteolytic activity. We found that deletion of Lon's ATPase domain abrogated interactions with DNA. Substitution of positively charged amino acids in this domain in full-length Lon with residues conferring a net negative charge disrupted binding of Lon to DNA. These changes also affected the degradation of nucleic acid-binding protein substrates of Lon, intracellular localization of Lon, and cell morphology. In vivo tests revealed that Lon-DNA interactions are essential for Lon activity in cell division control. In summary, we demonstrate that the ability of Lon to bind DNA is determined by its ATPase domain, that this binding is required for processing protein substrates in nucleoprotein complexes, and that Lon may help regulate DNA replication in response to growth conditions.
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Affiliation(s)
- Anna Karlowicz
- From the Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Katarzyna Wegrzyn
- From the Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Marta Gross
- From the Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Dagmara Kaczynska
- From the Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Malgorzata Ropelewska
- From the Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Małgorzata Siemiątkowska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland, and
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland, and.,Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Igor Konieczny
- From the Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland,
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Bittner LM, Kraus A, Schäkermann S, Narberhaus F. The Copper Efflux Regulator CueR Is Subject to ATP-Dependent Proteolysis in Escherichia coli. Front Mol Biosci 2017; 4:9. [PMID: 28293558 PMCID: PMC5329002 DOI: 10.3389/fmolb.2017.00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/13/2017] [Indexed: 11/13/2022] Open
Abstract
The trace element copper serves as cofactor for many enzymes but is toxic at elevated concentrations. In bacteria, the intracellular copper level is maintained by copper efflux systems including the Cue system controlled by the transcription factor CueR. CueR, a member of the MerR family, forms homodimers, and binds monovalent copper ions with high affinity. It activates transcription of the copper tolerance genes copA and cueO via a conserved DNA-distortion mechanism. The mechanism how CueR-induced transcription is turned off is not fully understood. Here, we report that Escherichia coli CueR is prone to proteolysis by the AAA+ proteases Lon, ClpXP, and ClpAP. Using a set of CueR variants, we show that CueR degradation is not altered by mutations affecting copper binding, dimerization or DNA binding of CueR, but requires an accessible C terminus. Except for a twofold stabilization shortly after a copper pulse, proteolysis of CueR is largely copper-independent. Our results suggest that ATP-dependent proteolysis contributes to copper homeostasis in E. coli by turnover of CueR, probably to allow steady monitoring of changes of the intracellular copper level and shut-off of CueR-dependent transcription.
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Bittner LM, Arends J, Narberhaus F. Mini review: ATP-dependent proteases in bacteria. Biopolymers 2017; 105:505-17. [PMID: 26971705 DOI: 10.1002/bip.22831] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/11/2016] [Accepted: 03/07/2016] [Indexed: 01/22/2023]
Abstract
AAA(+) proteases are universal barrel-like and ATP-fueled machines preventing the accumulation of aberrant proteins and regulating the proteome according to the cellular demand. They are characterized by two separate operating units, the ATPase and peptidase domains. ATP-dependent unfolding and translocation of a substrate into the proteolytic chamber is followed by ATP-independent degradation. This review addresses the structure and function of bacterial AAA(+) proteases with a focus on the ATP-driven mechanisms and the coordinated movements in the complex mainly based on the knowledge of ClpXP. We conclude by discussing strategies how novel protease substrates can be trapped by mutated AAA(+) protease variants. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 505-517, 2016.
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Affiliation(s)
| | - Jan Arends
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
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Arends J, Thomanek N, Kuhlmann K, Marcus K, Narberhaus F. In vivo trapping of FtsH substrates by label-free quantitative proteomics. Proteomics 2016; 16:3161-3172. [DOI: 10.1002/pmic.201600316] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/09/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Jan Arends
- Ruhr-Universität Bochum; Lehrstuhl Biologie der Mikroorganismen; Bochum Germany
| | - Nikolas Thomanek
- Ruhr-Universität Bochum; Medizinisches Proteom-Center; Bochum Germany
| | - Katja Kuhlmann
- Ruhr-Universität Bochum; Medizinisches Proteom-Center; Bochum Germany
| | - Katrin Marcus
- Ruhr-Universität Bochum; Medizinisches Proteom-Center; Bochum Germany
| | - Franz Narberhaus
- Ruhr-Universität Bochum; Lehrstuhl Biologie der Mikroorganismen; Bochum Germany
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The Protease Locus of Francisella tularensis LVS Is Required for Stress Tolerance and Infection in the Mammalian Host. Infect Immun 2016; 84:1387-1402. [PMID: 26902724 DOI: 10.1128/iai.00076-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 02/12/2016] [Indexed: 02/05/2023] Open
Abstract
Francisella tularensis is the causative agent of tularemia and a category A potential agent of bioterrorism, but the pathogenic mechanisms of F. tularensis are largely unknown. Our previous transposon mutagenesis screen identified 95 lung infectivity-associated F. tularensis genes, including those encoding the Lon and ClpP proteases. The present study validates the importance of Lon and ClpP in intramacrophage growth and infection of the mammalian host by using unmarked deletion mutants of the F. tularensis live vaccine strain (LVS). Further experiments revealed that lon and clpP are also required for F. tularensis tolerance to stressful conditions. A quantitative proteomic comparison between heat-stressed LVS and the isogenic Lon-deficient mutant identified 29 putative Lon substrate proteins. The follow-up protein degradation experiments identified five substrates of the F. tularensis Lon protease (FTL578, FTL663, FTL1217, FTL1228, and FTL1957). FTL578 (ornithine cyclodeaminase), FTL663 (heat shock protein), and FTL1228 (iron-sulfur activator complex subunit SufD) have been previously described as virulence-associated factors in F. tularensis Identification of these Lon substrates has thus provided important clues for further understanding of the F. tularensis stress response and pathogenesis. The high-throughput approach developed in this study can be used for systematic identification of the Lon substrates in other prokaryotic and eukaryotic organisms.
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Goto-Yamada S, Mano S, Yamada K, Oikawa K, Hosokawa Y, Hara-Nishimura I, Nishimura M. Dynamics of the Light-Dependent Transition of Plant Peroxisomes. PLANT & CELL PHYSIOLOGY 2015; 56:1264-71. [PMID: 26063394 DOI: 10.1093/pcp/pcv081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/29/2015] [Indexed: 05/21/2023]
Abstract
Peroxisomes are present in almost all plant cells. These organelles are involved in various metabolic processes, such as lipid catabolism and photorespiration. A notable feature of plant peroxisomes is their flexible adaptive responses to environmental conditions such as light. When plants shift from heterotrophic to autotrophic growth during the post-germinative stage, peroxisomes undergo a dynamic response, i.e. enzymes involved in lipid catabolism are replaced with photorespiratory enzymes. Although the detailed molecular mechanisms underlying the functional transition of peroxisomes have previously been unclear, recent analyses at the cellular level have enabled this detailed machinery to be characterized. During the functional transition, obsolete enzymes are degraded inside peroxisomes by Lon protease, while newly synthesized enzymes are transported into peroxisomes. In parallel, mature and oxidized peroxisomes are eliminated via autophagy; this functional transition occurs in an efficient manner. Moreover, it has become clear that quality control mechanisms are important for the peroxisomal response to environmental stimuli. In this review, we highlight recent advances in elucidating the molecular mechanisms required for the regulation of peroxisomal roles in response to changes in environmental conditions.
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Affiliation(s)
| | - Shoji Mano
- Laboratory of Biological Diversity, Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology, Okazaki, 444-8585 Japan Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585 Japan
| | - Kenji Yamada
- Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
| | - Kazusato Oikawa
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181 Japan
| | - Yoichiroh Hosokawa
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | | | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan Present address: Research Enhancement Strategy Office, National Institute for Basic Biology, Okazaki, 444-8585 Japan.
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Goeser L, Fan TJ, Tchaptchet S, Stasulli N, Goldman WE, Sartor RB, Hansen JJ. Small heat-shock proteins, IbpAB, protect non-pathogenic Escherichia coli from killing by macrophage-derived reactive oxygen species. PLoS One 2015; 10:e0120249. [PMID: 25798870 PMCID: PMC4370416 DOI: 10.1371/journal.pone.0120249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/28/2015] [Indexed: 01/29/2023] Open
Abstract
Many intracellular bacterial pathogens possess virulence factors that prevent detection and killing by macrophages. However, similar virulence factors in non-pathogenic bacteria are less well-characterized and may contribute to the pathogenesis of chronic inflammatory conditions such as Crohn’s disease. We hypothesize that the small heat shock proteins IbpAB, which have previously been shown to reduce oxidative damage to proteins in vitro and be upregulated in luminal non-pathogenic Escherichia strain NC101 during experimental colitis in vivo, protect commensal E. coli from killing by macrophage-derived reactive oxygen species (ROS). Using real-time PCR, we measured ibpAB expression in commensal E. coli NC101 within wild-type (wt) and ROS-deficient (gp91phox-/-) macrophages and in NC101 treated with the ROS generator paraquat. We also quantified survival of NC101 and isogenic mutants in wt and gp91phox-/- macrophages using gentamicin protection assays. Similar assays were performed using a pathogenic E. coli strain O157:H7. We show that non-pathogenic E. coli NC101inside macrophages upregulate ibpAB within 2 hrs of phagocytosis in a ROS-dependent manner and that ibpAB protect E. coli from killing by macrophage-derived ROS. Moreover, we demonstrate that ROS-induced ibpAB expression is mediated by the small E. coli regulatory RNA, oxyS. IbpAB are not upregulated in pathogenic E. coli O157:H7 and do not affect its survival within macrophages. Together, these findings indicate that ibpAB may be novel virulence factors for certain non-pathogenic E. coli strains.
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Affiliation(s)
- Laura Goeser
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ting-Jia Fan
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sandrine Tchaptchet
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Nikolas Stasulli
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - William E. Goldman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - R. Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jonathan J. Hansen
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Morrow G, Tanguay RM. Drosophila melanogaster Hsp22: a mitochondrial small heat shock protein influencing the aging process. Front Genet 2015; 6:1026. [PMID: 25852752 PMCID: PMC4360758 DOI: 10.3389/fgene.2015.00103] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/27/2015] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are involved in many key cellular processes and therefore need to rely on good protein quality control (PQC). Three types of mechanisms are in place to insure mitochondrial protein integrity: reactive oxygen species scavenging by anti-oxidant enzymes, protein folding/degradation by molecular chaperones and proteases and clearance of defective mitochondria by mitophagy. Drosophila melanogaster Hsp22 is part of the molecular chaperone axis of the PQC and is characterized by its intra-mitochondrial localization and preferential expression during aging. As a stress biomarker, the level of its expression during aging has been shown to partially predict the remaining lifespan of flies. Since over-expression of this small heat shock protein increases lifespan and resistance to stress, Hsp22 most likely has a positive effect on mitochondrial integrity. Accordingly, Hsp22 has recently been implicated in the mitochondrial unfolding protein response of flies. This review will summarize the key findings on D. melanogaster Hsp22 and emphasis on its links with the aging process.
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Affiliation(s)
- Geneviève Morrow
- Laboratoire de Génétique Cellulaire et Développementale, Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Institut de Biologie Intégrative et des Systémes and PROTEO, Université Laval Québec, QC, Canada
| | - Robert M Tanguay
- Laboratoire de Génétique Cellulaire et Développementale, Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Institut de Biologie Intégrative et des Systémes and PROTEO, Université Laval Québec, QC, Canada
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Shi X, Yan L, Zhang H, Sun K, Chang Z, Fu X. Differential degradation for small heat shock proteins IbpA and IbpB is synchronized in Escherichia coli: Implications for their functional cooperation in substrate refolding. Biochem Biophys Res Commun 2014; 452:402-7. [DOI: 10.1016/j.bbrc.2014.08.084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 11/30/2022]
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Krajewski SS, Narberhaus F. Temperature-driven differential gene expression by RNA thermosensors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:978-988. [PMID: 24657524 DOI: 10.1016/j.bbagrm.2014.03.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/28/2014] [Accepted: 03/14/2014] [Indexed: 12/20/2022]
Abstract
Many prokaryotic genes are organized in operons. Genes organized in such transcription units are co-transcribed into a polycistronic mRNA. Despite being clustered in a single mRNA, individual genes can be subjected to differential regulation, which is mainly achieved at the level of translation depending on initiation and elongation. Efficiency of translation initiation is primarily determined by the structural accessibility of the ribosome binding site (RBS). Structured cis-regulatory elements like RNA thermometers (RNATs) can contribute to differential regulation of individual genes within a polycistronic mRNA. RNATs are riboregulators that mediate temperature-responsive regulation of a downstream gene by modulating the accessibility of its RBS. At low temperature, the RBS is trapped by intra-molecular base pairing prohibiting translation initiation. The secondary structure melts with increasing temperature thus liberating the RBS. Here, we present an overview of different RNAT types and specifically highlight recently discovered RNATs. The main focus of this review is on RNAT-based differential control of polycistronic operons. Finally, we discuss the influence of temperature on other riboregulators and the potential of RNATs in synthetic RNA biology. This article is part of a Special Issue entitled: Riboswitches.
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Goto-Yamada S, Mano S, Nakamori C, Kondo M, Yamawaki R, Kato A, Nishimura M. Chaperone and Protease Functions of LON Protease 2 Modulate the Peroxisomal Transition and Degradation with Autophagy. ACTA ACUST UNITED AC 2014; 55:482-96. [DOI: 10.1093/pcp/pcu017] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Nafissi N, Sum CH, Wettig S, Slavcev RA. Optimization of a one-step heat-inducible in vivo mini DNA vector production system. PLoS One 2014; 9:e89345. [PMID: 24586704 PMCID: PMC3930727 DOI: 10.1371/journal.pone.0089345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/18/2014] [Indexed: 11/18/2022] Open
Abstract
While safer than their viral counterparts, conventional circular covalently closed (CCC) plasmid DNA vectors offer a limited safety profile. They often result in the transfer of unwanted prokaryotic sequences, antibiotic resistance genes, and bacterial origins of replication that may lead to unwanted immunostimulatory responses. Furthermore, such vectors may impart the potential for chromosomal integration, thus potentiating oncogenesis. Linear covalently closed (LCC), bacterial sequence free DNA vectors have shown promising clinical improvements in vitro and in vivo. However, the generation of such minivectors has been limited by in vitro enzymatic reactions hindering their downstream application in clinical trials. We previously characterized an in vivo temperature-inducible expression system, governed by the phage λ pL promoter and regulated by the thermolabile λ CI[Ts]857 repressor to produce recombinant protelomerase enzymes in E. coli. In this expression system, induction of recombinant protelomerase was achieved by increasing culture temperature above the 37°C threshold temperature. Overexpression of protelomerase led to enzymatic reactions, acting on genetically engineered multi-target sites called "Super Sequences" that serve to convert conventional CCC plasmid DNA into LCC DNA minivectors. Temperature up-shift, however, can result in intracellular stress responses and may alter plasmid replication rates; both of which may be detrimental to LCC minivector production. We sought to optimize our one-step in vivo DNA minivector production system under various induction schedules in combination with genetic modifications influencing plasmid replication, processing rates, and cellular heat stress responses. We assessed different culture growth techniques, growth media compositions, heat induction scheduling and temperature, induction duration, post-induction temperature, and E. coli genetic background to improve the productivity and scalability of our system, achieving an overall LCC DNA minivector production efficiency of ∼ 90%.We optimized a robust technology conferring rapid, scalable, one-step in vivo production of LCC DNA minivectors with potential application to gene transfer-mediated therapeutics.
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Affiliation(s)
- Nafiseh Nafissi
- School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada
| | - Chi Hong Sum
- School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada
| | - Shawn Wettig
- School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada
| | - Roderick A. Slavcev
- School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada
- * E-mail:
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Trudeau K, Vu KD, Déziel É, Shareck F, Lacroix M. Effect of γ-irradiation on gene expression of heat shock proteins in the foodborne pathogen Escherichia coli O157:H7. Int J Radiat Biol 2014; 90:268-73. [PMID: 24168176 DOI: 10.3109/09553002.2014.859766] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE The expression levels of seven genes (clpB, dnaK, groES, grpE, htpG, htpX and ibpB) encoding heat shock proteins (HSP) in Escherichia coli O157:H7 (E. coli) gamma irradiated was investigated. Timing impact of post-irradiated RNA extraction on the expression levels of these seven genes was also studied at a dose damaging the bacterial cells (0.4 kGy). METHODS Bacterial samples were γ-irradiated at 0.4 kGy and at a lethal dose of 1.3 kGy. RNA was extracted at 0 min post irradiation for both irradiation doses and at 15, 30, 60, 90 or 120 min post-irradiation at the dose damaging the cells. Quantification of the gene expression was performed using quantitative real-time polymerase chain reaction (q-RT-PCR). RESULTS The expression of genes encoding HSP was a very dynamic process evolving rapidly when E. coli cells were irradiated at 0.4 kGy. Notably, groES, grpE and ibpB were more up- regulated at 1.3 kGy than those at 0.4 kGy. CONCLUSIONS For the seven genes studied there were more damaged proteins during irradiation at the lethal dose and this dose causes increased expression in HSP which contributes to damage reparation. Expression patterns of genes encoding HSP in E. coli treated by γ-irradiation are different from those treated by heat shock.
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Affiliation(s)
- Karine Trudeau
- Research Laboratory in Sciences Applied to Food, Canadian Irradiation Center, INRS-Institut Armand-Frappier , Laval, Quebec
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Goto-Yamada S, Mano S, Oikawa K, Shibata M, Nishimura M. Interaction between chaperone and protease functions of LON2, and autophagy during the functional transition of peroxisomes. PLANT SIGNALING & BEHAVIOR 2014; 9:e28838. [PMID: 24739336 PMCID: PMC4091321 DOI: 10.4161/psb.28838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Functional transition of glyoxysomes to leaf peroxisomes is observed in greening cotyledons. Glyoxysomal proteins are rapidly degraded and leaf-peroxisomal proteins are transported into peroxisomes after cotyledons are exposed to light, but the molecular mechanisms underlying these processes remain unclear. We recently discovered that two degradation pathways are involved in the functional transition of peroxisomes using Arabidopsis thaliana. Lon protease 2 (LON2) is responsible for the degradation of glyoxysomal proteins inside peroxisomes, and, in parallel, autophagy eliminates damaged or obsolete peroxisomes. A double mutant defective in both the LON2- and autophagy-dependent degradation pathways accumulated glyoxysomal proteins after the cotyledons became green. Our study also demonstrated that the LON2- and autophagy-dependent pathways are interdependent, with the chaperone function of LON2 suppressing autophagic peroxisome degradation. Moreover, the peptidase domain of LON2 interferes with the suppression of autophagy, indicating that autophagy is regulated by intramolecular modulation between the proteolysis and chaperone functions of LON2.
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Affiliation(s)
- Shino Goto-Yamada
- Department of Cell Biology; National Institute for Basic Biology; Okazaki, Japan
| | - Shoji Mano
- Department of Cell Biology; National Institute for Basic Biology; Okazaki, Japan
- Department of Basic Biology; School of Life Science; The Graduate University for Advanced Studies; Okazaki, Japan
| | - Kazusato Oikawa
- Department of Applied Biological Chemistry; Niigata University; Niigata, Japan
| | - Michitaro Shibata
- Department of Cell Biology; National Institute for Basic Biology; Okazaki, Japan
- Department of Basic Biology; School of Life Science; The Graduate University for Advanced Studies; Okazaki, Japan
| | - Mikio Nishimura
- Department of Cell Biology; National Institute for Basic Biology; Okazaki, Japan
- Department of Basic Biology; School of Life Science; The Graduate University for Advanced Studies; Okazaki, Japan
- Correspondence to: Mikio Nishimura,
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Redelberger D, Genest O, Arabet D, Méjean V, Ilbert M, Iobbi-Nivol C. Quality control of a molybdoenzyme by the Lon protease. FEBS Lett 2013; 587:3935-42. [PMID: 24211448 DOI: 10.1016/j.febslet.2013.10.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 01/20/2023]
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Cimdins A, Roßmanith J, Langklotz S, Bandow JE, Narberhaus F. Differential control of Salmonella heat shock operons by structured mRNAs. Mol Microbiol 2013; 89:715-31. [PMID: 23802546 DOI: 10.1111/mmi.12308] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2013] [Indexed: 12/29/2022]
Abstract
DnaK-DnaJ-GrpE and GroES-GroEL are the major chaperone machineries in bacteria. In many species, dnaKJ and groESL are encoded in bicistronic operons. Quantitative proteomics revealed that DnaK and GroEL amounts in Salmonella dominate over DnaJ and GroES respectively. An imperfect transcriptional terminator in the intergenic region of dnaKJ is known to result in higher transcript levels of the first gene. Here, we examined the groESL operon and asked how the second gene in a heat shock operon can be preferentially expressed and found that an RNA structure in the 5'untranslated region of groES is responsible. The secondary structure masks the Shine-Dalgarno (SD) sequence and AUG start codon and thereby modulates translation of groES mRNA. Reporter gene assays combined with structure probing and toeprinting analysis revealed a dynamic temperature-sensitive RNA structure. Following an increase in temperature, only the second of two RNA hairpins melts and partially liberates the SD sequence, thus facilitating translation. Translation of groEL is not temperature-regulated leading to an excess of the chaperonin in the cell at low temperature. Discussion in a broader context shows how structured RNA segments can differentially control expression of temperature-affected operons in various ways.
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Affiliation(s)
- Annika Cimdins
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780 Bochum, Germany
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Distinct quaternary structures of the AAA+ Lon protease control substrate degradation. Proc Natl Acad Sci U S A 2013; 110:E2002-8. [PMID: 23674680 DOI: 10.1073/pnas.1307066110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Lon is an ATPase associated with cellular activities (AAA+) protease that controls cell division in response to stress and also degrades misfolded and damaged proteins. Subunits of Lon are known to assemble into ring-shaped homohexamers that enclose an internal degradation chamber. Here, we demonstrate that hexamers of Escherichia coli Lon also interact to form a dodecamer at physiological protein concentrations. Electron microscopy of this dodecamer reveals a prolate structure with the protease chambers at the distal ends and a matrix of N domains forming an equatorial hexamer-hexamer interface, with portals of ∼45 Å providing access to the enzyme lumen. Compared with hexamers, Lon dodecamers are much less active in degrading large substrates but equally active in degrading small substrates. Our results support a unique gating mechanism that allows the repertoire of Lon substrates to be tuned by its assembly state.
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43
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Bhat NH, Vass RH, Stoddard PR, Shin DK, Chien P. Identification of ClpP substrates in Caulobacter crescentus reveals a role for regulated proteolysis in bacterial development. Mol Microbiol 2013; 88:1083-92. [PMID: 23647068 DOI: 10.1111/mmi.12241] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2013] [Indexed: 12/01/2022]
Abstract
Energy-dependent proteases ensure the timely removal of unwanted proteins in a highly selective fashion. In Caulobacter crescentus, protein degradation by the ClpXP protease is critical for cell cycle progression; however, only a handful of substrates are currently known. Here, we use a trapping approach to identify putative substrates of the ClpP associated proteases in C. crescentus. Biochemical validation of several of these targets reveals specific protease recognition motifs and suggests a need for ClpXP-specific degradation beyond degradation of known cell cycle regulators. We focus on a particular instance of regulated proteolysis in Caulobacter by exploring the role of ClpXP in degrading the stalk synthesis transcription factor TacA. We show that TacA degradation is controlled during the cell cycle dependent on the ClpXP regulator CpdR and that stabilization of TacA increases degradation of another ClpXP substrate, CtrA, while restoring deficiencies associated with prolific CpdR activity. Together, our work reveals a number of new validated ClpXP substrates, clarifies rules of protease substrate selection, and demonstrates how regulated protein degradation is critical for Caulobacter development and cell cycle progression.
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Affiliation(s)
- Nowsheen H Bhat
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
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44
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Micevski D, Dougan DA. Proteolytic regulation of stress response pathways in Escherichia coli. Subcell Biochem 2013; 66:105-28. [PMID: 23479439 DOI: 10.1007/978-94-007-5940-4_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Maintaining correct cellular function is a fundamental biological process for all forms of life. A critical aspect of this process is the maintenance of protein homeostasis (proteostasis) in the cell, which is largely performed by a group of proteins, referred to as the protein quality control (PQC) network. This network of proteins, comprised of chaperones and proteases, is critical for maintaining proteostasis not only during favourable growth conditions, but also in response to stress. Indeed proteases play a crucial role in the clearance of unwanted proteins that accumulate during stress, but more importantly, in the activation of various different stress response pathways. In bacteria, the cells response to stress is usually orchestrated by a specific transcription factor (sigma factor). In Escherichia coli there are seven different sigma factors, each of which responds to a particular stress, resulting in the rapid expression of a specific set of genes. The cellular concentration of each transcription factor is tightly controlled, at the level of transcription, translation and protein stability. Here we will focus on the proteolytic regulation of two sigma factors (σ(32) and σ(S)), which control the heat and general stress response pathways, respectively. This review will also briefly discuss the role proteolytic systems play in the clearance of unwanted proteins that accumulate during stress.
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Affiliation(s)
- Dimce Micevski
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, 3086, Australia
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46
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Hilton GR, Lioe H, Stengel F, Baldwin AJ, Benesch JLP. Small heat-shock proteins: paramedics of the cell. Top Curr Chem (Cham) 2012; 328:69-98. [PMID: 22576357 DOI: 10.1007/128_2012_324] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The small heat-shock proteins (sHSPs) comprise a family of molecular chaperones which are widespread but poorly understood. Despite considerable effort, comparatively few high-resolution structures have been determined for the sHSPs, a likely consequence of their tendency to populate ensembles of inter-converting conformational and oligomeric states at equilibrium. This dynamic structure appears to underpin the sHSPs' ability to bind and sequester target proteins rapidly, and renders them the first line of defence against protein aggregation during disease and cellular stress. Here we describe recent studies on the sHSPs, with a particular focus on those which have provided insight into the structure and dynamics of these proteins. The combined literature reveals a picture of a remarkable family of molecular chaperones whose thermodynamic and kinetic properties are exquisitely balanced to allow functional regulation by subtle changes in cellular conditions.
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47
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Gur E, Biran D, Ron EZ. Regulated proteolysis in Gram-negative bacteria--how and when? Nat Rev Microbiol 2011; 9:839-48. [PMID: 22020261 DOI: 10.1038/nrmicro2669] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Most bacteria live in a dynamic environment where temperature, availability of nutrients and the presence of various chemicals vary, which requires rapid adaptation. Many of the adaptive changes are determined by changes in the transcription of global regulatory networks, but this response is slow because most bacterial proteins are stable and their concentration remains high even after transcription slows down. To respond rapidly, an additional level of regulation has evolved: the degradation of key proteins. However, as proteolysis is an irreversible process, it is subject to tight regulation of substrate binding and degradation. Here we review the roles of the proteolytic enzymes in Gram-negative bacteria and how these enzymes can be regulated to target only a subset of proteins.
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Affiliation(s)
- Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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48
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Global transcriptome analysis of the E. coli O157 response to Agrimonia pilosa extract. Mol Cell Toxicol 2011. [DOI: 10.1007/s13273-011-0036-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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49
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Langklotz S, Narberhaus F. The Escherichia coli replication inhibitor CspD is subject to growth-regulated degradation by the Lon protease. Mol Microbiol 2011; 80:1313-25. [DOI: 10.1111/j.1365-2958.2011.07646.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Involvement of an ATP-dependent protease, PA0779/AsrA, in inducing heat shock in response to tobramycin in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2011; 55:1874-82. [PMID: 21357290 DOI: 10.1128/aac.00935-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The adaptive resistance of Pseudomonas aeruginosa to aminoglycosides is known to occur during chronic lung infections in cystic fibrosis patients in response to nonlethal concentrations of aminoglycosides. Not only is it difficult to achieve high levels of drug throughout the dehydrated mucus in the lung, but also steep oxygen gradients exist across the mucus layer, further reducing the bactericidal activity of aminoglycosides. In this study, microarray analysis was utilized to examine the gene responses of P. aeruginosa to lethal, inhibitory, and subinhibitory concentrations of tobramycin under aerobic and anaerobic conditions. While prolonged exposure to subinhibitory concentrations of tobramycin caused increased levels of expression predominantly of the efflux pump genes mexXY, the greatest increases in gene expression levels in response to lethal concentrations of tobramycin involved a number of heat shock genes and the PA0779 gene (renamed here asrA), encoding an alternate Lon protease. Microarray analysis of an asrA::luxCDABE transposon mutant revealed that the induction of heat shock genes in response to tobramycin in this mutant was significantly decreased compared to that in the parent strain. The level of expression of asrA was induced from an arabinose-inducible promoter to 35-fold greater than wild-type expression levels in the absence of tobramycin, and this overexpression alone caused an increased expression of the heat shock genes, as determined by quantitative PCR (qPCR). This overexpression of asrA conferred short-term protection against lethal levels (4 μg/ml) of tobramycin but did not affect the tobramycin MIC. The RpoH heat shock sigma factor was found to be involved in the regulation of asrA in response to both heat shock and tobramycin at the posttranscriptional level. The results of this work suggest that the tobramycin concentration has a significant impact on the gene expression of P. aeruginosa, with lethal concentrations resulting in immediate adaptations conferring short-term protection, such as the induction of the heat shock response, and with subinhibitory concentrations leading to more sustainable long-term protection mechanisms, such as increased efflux.
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