1
|
Aftab H, Donegan RK. Regulation of heme biosynthesis via the coproporphyrin dependent pathway in bacteria. Front Microbiol 2024; 15:1345389. [PMID: 38577681 PMCID: PMC10991733 DOI: 10.3389/fmicb.2024.1345389] [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: 11/27/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
Heme biosynthesis in the Gram-positive bacteria occurs mostly via a pathway that is distinct from that of eukaryotes and Gram-negative bacteria in the three terminal heme synthesis steps. In many of these bacteria heme is a necessary cofactor that fulfills roles in respiration, gas sensing, and detoxification of reactive oxygen species. These varying roles for heme, the requirement of iron and glutamate, as glutamyl tRNA, for synthesis, and the sharing of intermediates with the synthesis of other porphyrin derivatives necessitates the need for many points of regulation in response to nutrient availability and metabolic state. In this review we examine the regulation of heme biosynthesis in these bacteria via heme, iron, and oxygen species. We also discuss our perspective on emerging roles of protein-protein interactions and post-translational modifications in regulating heme biosynthesis.
Collapse
|
2
|
von Rosen T, Pepelnjak M, Quast JP, Picotti P, Weber-Ban E. ATP-independent substrate recruitment to proteasomal degradation in mycobacteria. Life Sci Alliance 2023; 6:e202301923. [PMID: 37562848 PMCID: PMC10415612 DOI: 10.26508/lsa.202301923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Mycobacteria and other actinobacteria possess proteasomal degradation pathways in addition to the common bacterial compartmentalizing protease systems. Proteasomal degradation plays a crucial role in the survival of these bacteria in adverse environments. The mycobacterial proteasome interacts with several ring-shaped activators, including the bacterial proteasome activator (Bpa), which enables energy-independent degradation of heat shock repressor HspR. However, the mechanism of substrate selection and processing by the Bpa-proteasome complex remains unclear. In this study, we present evidence that disorder in substrates is required but not sufficient for recruitment to Bpa-mediated proteasomal degradation. We demonstrate that Bpa binds to the folded N-terminal helix-turn-helix domain of HspR, whereas the unstructured C-terminal tail of the substrate acts as a sequence-specific threading handle to promote efficient proteasomal degradation. In addition, we establish that the heat shock chaperone DnaK, which interacts with and co-regulates HspR, stabilizes HspR against Bpa-mediated proteasomal degradation. By phenotypical characterization of Mycobacterium smegmatis parent and bpa deletion mutant strains, we show that Bpa-dependent proteasomal degradation supports the survival of the bacterium under stress conditions by degrading HspR that regulates vital chaperones.
Collapse
Affiliation(s)
- Tatjana von Rosen
- ETH Zurich, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Monika Pepelnjak
- ETH Zurich, Institute of Molecular Systems Biology, Zurich Switzerland
| | - Jan-Philipp Quast
- ETH Zurich, Institute of Molecular Systems Biology, Zurich Switzerland
| | - Paola Picotti
- ETH Zurich, Institute of Molecular Systems Biology, Zurich Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| |
Collapse
|
3
|
Zhu H, Jiang S, Zhou W, Chi H, Sun J, Shi J, Zhang Z, Chang L, Yu L, Zhang L, Lyu Z, Xu P, Zhang Y. Ac-LysargiNase efficiently helps genome reannotation of Mycolicibacterium smegmatis MC2 155. J Proteomics 2022; 264:104622. [DOI: 10.1016/j.jprot.2022.104622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
|
4
|
Kavalchuk M, Jomaa A, Müller AU, Weber-Ban E. Structural basis of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa-proteasome complex. Nat Commun 2022; 13:276. [PMID: 35022401 PMCID: PMC8755798 DOI: 10.1038/s41467-021-27787-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/13/2021] [Indexed: 12/19/2022] Open
Abstract
Proteasomes are present in eukaryotes, archaea and Actinobacteria, including the human pathogen Mycobacterium tuberculosis, where proteasomal degradation supports persistence inside the host. In mycobacteria and other members of Actinobacteria, prokaryotic ubiquitin-like protein (Pup) serves as a degradation tag post-translationally conjugated to target proteins for their recruitment to the mycobacterial proteasome ATPase (Mpa). Here, we use single-particle cryo-electron microscopy to determine the structure of Mpa in complex with the 20S core particle at an early stage of pupylated substrate recruitment, shedding light on the mechanism of substrate translocation. Two conformational states of Mpa show how substrate is translocated stepwise towards the degradation chamber of the proteasome core particle. We also demonstrate, in vitro and in vivo, the importance of a structural feature in Mpa that allows formation of alternating charge-complementary interactions with the proteasome resulting in radial, rail-guided movements during the ATPase conformational cycle. Pup is the bacterial analog of ubiquitin for targeting proteins to the proteasome. Here, the authors use cryoEM to visualize structures of the Mycobacterium tuberculosis proteasome translocating a Pup-tagged substrate.
Collapse
Affiliation(s)
- Mikhail Kavalchuk
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland
| | - Ahmad Jomaa
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland.
| | - Andreas U Müller
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland.
| |
Collapse
|
5
|
von Rosen T, Keller LM, Weber-Ban E. Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways. Front Mol Biosci 2021; 8:685757. [PMID: 34179091 PMCID: PMC8223512 DOI: 10.3389/fmolb.2021.685757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.
Collapse
Affiliation(s)
- Tatjana von Rosen
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Lena Ml Keller
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
6
|
Auliah FN, Nilamyani AN, Shoombuatong W, Alam MA, Hasan MM, Kurata H. PUP-Fuse: Prediction of Protein Pupylation Sites by Integrating Multiple Sequence Representations. Int J Mol Sci 2021; 22:ijms22042120. [PMID: 33672741 PMCID: PMC7924619 DOI: 10.3390/ijms22042120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 12/30/2022] Open
Abstract
Pupylation is a type of reversible post-translational modification of proteins, which plays a key role in the cellular function of microbial organisms. Several proteomics methods have been developed for the prediction and analysis of pupylated proteins and pupylation sites. However, the traditional experimental methods are laborious and time-consuming. Hence, computational algorithms are highly needed that can predict potential pupylation sites using sequence features. In this research, a new prediction model, PUP-Fuse, has been developed for pupylation site prediction by integrating multiple sequence representations. Meanwhile, we explored the five types of feature encoding approaches and three machine learning (ML) algorithms. In the final model, we integrated the successive ML scores using a linear regression model. The PUP-Fuse achieved a Mathew correlation value of 0.768 by a 10-fold cross-validation test. It also outperformed existing predictors in an independent test. The web server of the PUP-Fuse with curated datasets is freely available.
Collapse
Affiliation(s)
- Firda Nurul Auliah
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; (F.N.A.); (A.N.N.); (M.M.H.)
| | - Andi Nur Nilamyani
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; (F.N.A.); (A.N.N.); (M.M.H.)
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand;
| | - Md Ashad Alam
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; (F.N.A.); (A.N.N.); (M.M.H.)
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; (F.N.A.); (A.N.N.); (M.M.H.)
- Correspondence:
| |
Collapse
|
7
|
Nicholson KR, Mousseau CB, Champion MM, Champion PA. The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens. PLoS Pathog 2021; 17:e1009124. [PMID: 33411813 PMCID: PMC7790235 DOI: 10.1371/journal.ppat.1009124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mycobacterial pathogens pose a sustained threat to human health. There is a critical need for new diagnostics, therapeutics, and vaccines targeting both tuberculous and nontuberculous mycobacterial species. Understanding the basic mechanisms used by diverse mycobacterial species to cause disease will facilitate efforts to design new approaches toward detection, treatment, and prevention of mycobacterial disease. Molecular, genetic, and biochemical approaches have been widely employed to define fundamental aspects of mycobacterial physiology and virulence. The recent expansion of genetic tools in mycobacteria has further increased the accessibility of forward genetic approaches. Proteomics has also emerged as a powerful approach to further our understanding of diverse mycobacterial species. Detection of large numbers of proteins and their modifications from complex mixtures of mycobacterial proteins is now routine, with efforts of quantification of these datasets becoming more robust. In this review, we discuss the “genetic proteome,” how the power of genetics, molecular biology, and biochemistry informs and amplifies the quality of subsequent analytical approaches and maximizes the potential of hypothesis-driven mycobacterial research. Published proteomics datasets can be used for hypothesis generation and effective post hoc supplementation to experimental data. Overall, we highlight how the integration of proteomics, genetic, molecular, and biochemical approaches can be employed successfully to define fundamental aspects of mycobacterial pathobiology.
Collapse
Affiliation(s)
- Kathleen R. Nicholson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - C. Bruce Mousseau
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
| |
Collapse
|
8
|
Müller AU, Imkamp F, Weber-Ban E. The Mycobacterial LexA/RecA-Independent DNA Damage Response Is Controlled by PafBC and the Pup-Proteasome System. Cell Rep 2019; 23:3551-3564. [PMID: 29924998 DOI: 10.1016/j.celrep.2018.05.073] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/16/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
Mycobacteria exhibit two DNA damage response pathways: the LexA/RecA-dependent SOS response and a LexA/RecA-independent pathway. Using a combination of transcriptomics and genome-wide binding site analysis, we demonstrate that PafBC (proteasome accessory factor B and C), encoded in the Pup-proteasome system (PPS) gene locus, is the transcriptional regulator of the predominant LexA/RecA-independent pathway. Comparison of the resulting PafBC regulon with the DNA damage response of Mycobacterium smegmatis reveals that the majority of induced DNA repair genes are upregulated by PafBC. We further demonstrate that RecA, a member of the PafBC regulon and principal regulator of the SOS response, is degraded by the PPS when DNA damage stress has been overcome. Our results suggest a model for the regulation of the mycobacterial DNA damage response that employs the concerted action of PafBC as master transcriptional activator and the PPS for removal of DNA repair proteins to maintain a temporally controlled stress response.
Collapse
Affiliation(s)
- Andreas U Müller
- ETH Zurich, Institute of Molecular Biology and Biophysics, 8093 Zurich, Switzerland
| | - Frank Imkamp
- University of Zurich, Institute of Medical Microbiology, 8006 Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology and Biophysics, 8093 Zurich, Switzerland.
| |
Collapse
|
9
|
Abstract
Over the past decade the number and variety of protein post-translational modifications that have been detected and characterized in bacteria have rapidly increased. Most post-translational protein modifications occur in a relatively low number of bacterial proteins in comparison with eukaryotic proteins, and most of the modified proteins carry low, substoichiometric levels of modification; therefore, their structural and functional analysis is particularly challenging. The number of modifying enzymes differs greatly among bacterial species, and the extent of the modified proteome strongly depends on environmental conditions. Nevertheless, evidence is rapidly accumulating that protein post-translational modifications have vital roles in various cellular processes such as protein synthesis and turnover, nitrogen metabolism, the cell cycle, dormancy, sporulation, spore germination, persistence and virulence. Further research of protein post-translational modifications will fill current gaps in the understanding of bacterial physiology and open new avenues for treatment of infectious diseases.
Collapse
|
10
|
Pupylated proteins are subject to broad proteasomal degradation specificity and differential depupylation. PLoS One 2019; 14:e0215439. [PMID: 31009487 PMCID: PMC6476560 DOI: 10.1371/journal.pone.0215439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 04/02/2019] [Indexed: 11/19/2022] Open
Abstract
In actinobacteria, post-translational modification of proteins with prokaryotic ubiquitin-like protein Pup targets them for degradation by a bacterial proteasome assembly consisting of the 20S core particle (CP) and the mycobacterial proteasomal ATPase (Mpa). Modification of hundreds of cellular proteins with Pup at specific surface lysines is carried out by a single Pup-ligase (PafA, proteasome accessory factor A). Pupylated substrates are recruited to the degradative pathway by binding of Pup to the N-terminal coiled-coil domains of Mpa. Alternatively, pupylation can be reversed by the enzyme Dop (deamidase of Pup). Although pupylated substrates outcompete free Pup in proteasomal degradation, potential discrimination of the degradation complex between the various pupylated substrates has not been investigated. Here we show that Mpa binds stably to an open-gate variant of the proteasome (oCP) and associates with bona fide substrates with highly similar affinities. The proteasomal degradation of substrates differing in size, structure and assembly state was recorded in real-time, showing that the pupylated substrates are processed by the Mpa-oCP complex with comparable kinetic parameters. Furthermore, the members of a complex, pupylated proteome (pupylome) purified from Mycobacterium smegmatis are degraded evenly as followed by western blotting. In contrast, analysis of the depupylation behavior of several pupylome members suggests substrate-specific differences in enzymatic turnover, leading to the conclusion that largely indiscriminate degradation competes with differentiated depupylation to control the ultimate fate of pupylated substrates.
Collapse
|
11
|
Müller AU, Weber-Ban E. The Bacterial Proteasome at the Core of Diverse Degradation Pathways. Front Mol Biosci 2019; 6:23. [PMID: 31024929 PMCID: PMC6466877 DOI: 10.3389/fmolb.2019.00023] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/18/2019] [Indexed: 12/02/2022] Open
Abstract
Proteasomal protein degradation exists in mycobacteria and other actinobacteria, and expands their repertoire of compartmentalizing protein degradation pathways beyond the usual bacterial types. A product of horizontal gene transfer, bacterial proteasomes have evolved to support the organism's survival under challenging environmental conditions like nutrient starvation and physical or chemical stresses. Like the eukaryotic 20S proteasome, the bacterial core particle is gated and must associate with a regulator complex to form a fully active protease capable of recruiting and internalizing substrate proteins. By association with diverse regulator complexes that employ different recruitment strategies, the bacterial 20S core particle is able to act in different cellular degradation pathways. In association with the mycobacterial proteasomal ATPase Mpa, the proteasome degrades substrates post-translationally modified with prokaryotic, ubiquitin-like protein Pup in a process called pupylation. Upon interaction with the ATP-independent bacterial proteasome activator Bpa, poorly structured substrates are recruited for proteasomal degradation. A potential third degradation route might employ a Cdc48-like protein of actinobacteria (Cpa), for which interaction with the 20S core was recently demonstrated but no degradation substrates have been identified yet. The alternative interaction partners and wide range of substrate proteins suggest that the bacterial proteasome is a modular, functionally flexible and conditionally regulated degradation machine in bacteria that encounter rapidly changing and challenging conditions.
Collapse
Affiliation(s)
- Andreas U Müller
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
12
|
The Mycobacterium tuberculosis Pup-proteasome system regulates nitrate metabolism through an essential protein quality control pathway. Proc Natl Acad Sci U S A 2019; 116:3202-3210. [PMID: 30723150 DOI: 10.1073/pnas.1819468116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis encodes a proteasome that carries out regulated degradation of bacterial proteins. It has been proposed that the proteasome contributes to nitrogen metabolism in M. tuberculosis, although this hypothesis had not been tested. Upon assessing M. tuberculosis growth in several nitrogen sources, we found that a mutant strain lacking the Mycobacterium proteasomal activator Mpa was unable to use nitrate as a sole nitrogen source due to a specific failure in the pathway of nitrate reduction to ammonium. We found that the robust activity of the nitrite reductase complex NirBD depended on expression of the groEL/groES chaperonin genes, which are regulated by the repressor HrcA. We identified HrcA as a likely proteasome substrate, and propose that the degradation of HrcA is required for the full expression of chaperonin genes. Furthermore, our data suggest that degradation of HrcA, along with numerous other proteasome substrates, is enhanced during growth in nitrate to facilitate the derepression of the chaperonin genes. Importantly, growth in nitrate is an example of a specific condition that reduces the steady-state levels of numerous proteasome substrates in M. tuberculosis.
Collapse
|
13
|
Yao Z, Guo Z, Wang Y, Li W, Fu Y, Lin Y, Lin W, Lin X. Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophila. Mol Cell Proteomics 2019; 18:200-215. [PMID: 30352804 PMCID: PMC6356075 DOI: 10.1074/mcp.ra118.001035] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/27/2018] [Indexed: 01/21/2023] Open
Abstract
Protein modification by lysine succinylation is a newly identified post-translational modification (PTM) of lysine residues and plays an important role in diverse physiological functions, although their associated biological characteristics are still largely unknown. Here, we investigated the effects of lysine succinylation on the physiological regulation within a well-known fish pathogen, Aeromonas hydrophila A high affinity purification method was used to enrich peptides with lysine succinylation in A. hydrophila ATCC 7966, and a total of 2,174 lysine succinylation sites were identified on 666 proteins using LC-MS/MS. Gene ontology analysis indicated that these succinylated proteins are involved in diverse metabolic pathways and biological processes, including translation, protein export, and central metabolic pathways. The modifications of several selected candidates were further validated by Western blotting. Using site-directed mutagenesis, we observed that the succinylation of lysines on S-ribosylhomocysteine lyase (LuxS) at the K23 and K30 sites positively regulate the production of the quorum sensing autoinducer AI-2, and that these PTMs ultimately alter its competitiveness with another pathogen, Vibrio alginolyticus Moreover, subsequent metabolomic analyses indicated that K30 succinylation on LuxS may suppress the activated methyl cycle (AMC) and that both the K23 and K30 sites are involved in amino acid metabolism. Taken together, the results from this study provide significant insights into the functions of lysine succinylation and its critical roles on LuxS in regulating the cellular physiology of A. hydrophila.
Collapse
Affiliation(s)
- Zujie Yao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China;; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, PR China
| | - Zhuang Guo
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Yuqian Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Wanxin Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Yuying Fu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Yuexu Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China;.
| |
Collapse
|
14
|
Abstract
Proteasomes are a class of protease that carry out the degradation of a specific set of cellular proteins. While essential for eukaryotic life, proteasomes are found only in a small subset of bacterial species. In this chapter, we present the current knowledge of bacterial proteasomes, detailing the structural features and catalytic activities required to achieve proteasomal proteolysis. We describe the known mechanisms by which substrates are doomed for degradation, and highlight potential non-degradative roles for components of bacterial proteasome systems. Additionally, we highlight several pathways of microbial physiology that rely on proteasome activity. Lastly, we explain the various gaps in our understanding of bacterial proteasome function and emphasize several opportunities for further study.
Collapse
Affiliation(s)
- Samuel H Becker
- Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, Room 312, New York, NY, 10016, USA
| | - Huilin Li
- Van Andel Research Institute, Cryo-EM Structural Biology Laboratory, 333 Bostwick Ave, NE, Grand Rapids, MI, 4950, USA
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, Room 312, New York, NY, 10016, USA.
| |
Collapse
|
15
|
Muthu M, Deenadayalan A, Ramachandran D, Paul D, Gopal J, Chun S. A state-of-art review on the agility of quantitative proteomics in tuberculosis research. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
16
|
Lupoli TJ, Vaubourgeix J, Burns-Huang K, Gold B. Targeting the Proteostasis Network for Mycobacterial Drug Discovery. ACS Infect Dis 2018; 4:478-498. [PMID: 29465983 PMCID: PMC5902792 DOI: 10.1021/acsinfecdis.7b00231] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the world's deadliest infectious diseases and urgently requires new antibiotics to treat drug-resistant strains and to decrease the duration of therapy. During infection, Mtb encounters numerous stresses associated with host immunity, including hypoxia, reactive oxygen and nitrogen species, mild acidity, nutrient starvation, and metal sequestration and intoxication. The Mtb proteostasis network, composed of chaperones, proteases, and a eukaryotic-like proteasome, provides protection from stresses and chemistries of host immunity by maintaining the integrity of the mycobacterial proteome. In this Review, we explore the proteostasis network as a noncanonical target for antibacterial drug discovery.
Collapse
Affiliation(s)
- Tania J. Lupoli
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Kristin Burns-Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| |
Collapse
|
17
|
Jiang HW, Czajkowsky DM, Wang T, Wang XD, Wang JB, Zhang HN, Liu CX, Wu FL, He X, Xu ZW, Chen H, Guo SJ, Li Y, Bi LJ, Deng JY, Xie J, Pei JF, Zhang XE, Tao SC. Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis. EBioMedicine 2018; 30:225-236. [PMID: 29622495 PMCID: PMC5952411 DOI: 10.1016/j.ebiom.2018.03.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 12/26/2022] Open
Abstract
Owing to the spread of multidrug resistance (MDR) and extensive drug resistance (XDR), there is a pressing need to identify potential targets for the development of more-effective anti-M. tuberculosis (Mtb) drugs. PafA, as the sole Prokaryotic Ubiquitin-like Protein ligase in the Pup-proteasome System (PPS) of Mtb, is an attractive drug target. Here, we show that the activity of purified Mtb PafA is significantly inhibited upon the association of AEBSF (4-(2-aminoethyl) benzenesulfonyl fluoride) to PafA residue Serine 119 (S119). Mutation of S119 to amino acids that resemble AEBSF has similar inhibitory effects on the activity of purified Mtb PafA. Structural analysis reveals that although S119 is distant from the PafA catalytic site, it is located at a critical position in the groove where PafA binds the C-terminal region of Pup. Phenotypic studies demonstrate that S119 plays critical roles in the function of Mtb PafA when tested in M. smegmatis. Our study suggests that targeting S119 is a promising direction for developing an inhibitor of M. tuberculosis PafA. The pupylation activity of purified M. tuberculosis PafA is almost completely inhibited upon the association of AEBSF. The AEBSF binding site, Ser 119 plays critical roles in both the pupylation and depupylation activity of purified M. tuberculosis PafA. Disruption of purified M. tuberculosis PafA Ser 119 causes a dramatic reduction in Pup binding.
Drug-resistant tuberculosis is a major challenge worldwide, there is an urgent need to identify potential drug targets for developing more effective anti-tubercular drugs. M. tuberculosis ubiquitin-like protein ligase PafA is an attractive drug target, however, effective PafA inhibitors have not yet been identified. Here, we show that interruption of a single amino acid, S119, causes dramatic loss of PafA activity. S119 could thus serve as a promising precise target for developing M. tuberculosis PafA inhibitors.
Collapse
Affiliation(s)
- He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai 200240, China; School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China; SZCDC-SUSTech Joint Key Laboratory for Tropical Diseases, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xu-De Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jia-Bin Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng-Xi Liu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan-Lin Wu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiang He
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhao-Wei Xu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li-Jun Bi
- National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; TB Healthcare Biotechnology Co., Ltd., Foshan, Guangdong 528000, China; School of Stomatology and Medicine, Foshan University, Foshan 528000, Guangdong Province, China
| | - Jiao-Yu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jin Xie
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jian-Feng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
18
|
Akhter Y, Thakur S. Targets of ubiquitin like system in mycobacteria and related actinobacterial species. Microbiol Res 2017; 204:9-29. [PMID: 28870295 DOI: 10.1016/j.micres.2017.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 06/22/2017] [Accepted: 07/05/2017] [Indexed: 12/22/2022]
Abstract
Protein turnover and recycling is a prerequisite in all living organisms to maintain normal cellular physiology. Many bacteria are proteasome deficient but they possess typical protease enzymes for carrying out protein turnover. However, several groups of actinobacteria such as mycobacteria harbor both proteasome and proteases. In these bacteria, for cellular protein turnover the target proteins undergo post-translational modification referred as pupylation in which a small protein Pup (prokaryotic ubiquitin-like protein) is tagged to the specific lysine residues of the target proteins and after that those target proteins undergo proteasomal degradation. Thus, Pup serves as a degradation signal, helps in directing proteins toward the bacterial proteasome for a turnover. Although the Pup-proteasome system has a multifaceted role in environmental stresses, pathogenicity and regulation of cellular signaling, but the fate of all types of pupylation such as mono and polypupylation on the proteins is still not completely understood. In this review, we present the mechanisms involved in the activation and conjugation of Pup to the target proteins, describing the structural sketch of pupylation and fundamental differences between the eukaryotic ubiquitin-proteasome and bacterial Pup-proteasome systems. We are also presenting a concise classification and cataloging of the complete battery of experimentally identified Pup-substrates from various species of actinobacteria.
Collapse
Affiliation(s)
- Yusuf Akhter
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh, 176206, India.
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh, 176206, India
| |
Collapse
|
19
|
Delley CL, Müller AU, Ziemski M, Weber-Ban E. Prokaryotic Ubiquitin-Like Protein and Its Ligase/Deligase Enyzmes. J Mol Biol 2017; 429:3486-3499. [PMID: 28478282 DOI: 10.1016/j.jmb.2017.04.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/11/2017] [Accepted: 04/28/2017] [Indexed: 11/30/2022]
Abstract
Prokaryotic ubiquitin-like protein (Pup) and the modification enzymes involved in attaching Pup to or removing it from target proteins present a fascinating example of convergent evolution with respect to eukaryotic ubiquitination. Like ubiquitin (Ub), Pup is a small protein that can be covalently attached to lysine side chains of cellular proteins, and like Ub, it can serve to recruit tagged proteins for proteasomal degradation. However, unlike Ub, Pup is conformationally highly dynamic, exhibits a different linkage connectivity to its target lysines, and its ligase belongs to a different class of enzymes than the E1/E2/E3 cascade of ubiquitination. A specific feature of actinobacteria (aside from sporadic cases in a few other lineages), pupylation appears to have evolved to provide an advantage to the bacteria under certain environmental stresses rather than act as a constitutive modification. For Mycobacterium tuberculosis, pupylation and the recruitment of pupylated substrates to the proteasome support persistence inside host macrophages during pathogenesis, rendering the Pup-proteasome system an attractive drug target. In this review, we consider the dynamic nature of Pup in relation to its function, discuss the reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, and put them in context of the evolutionary history of this post-translational modification.
Collapse
Affiliation(s)
- Cyrille L Delley
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Andreas U Müller
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Michal Ziemski
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| |
Collapse
|
20
|
A Method for Microalgae Proteomics Analysis Based on Modified Filter-Aided Sample Preparation. Appl Biochem Biotechnol 2017; 183:923-930. [DOI: 10.1007/s12010-017-2473-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
|
21
|
Cantù C, Pagella P, Shajiei TD, Zimmerli D, Valenta T, Hausmann G, Basler K, Mitsiadis TA. A cytoplasmic role of Wnt/β-catenin transcriptional cofactors Bcl9, Bcl9l, and Pygopus in tooth enamel formation. Sci Signal 2017; 10:10/465/eaah4598. [PMID: 28174279 DOI: 10.1126/scisignal.aah4598] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Wnt-stimulated β-catenin transcriptional regulation is necessary for the development of most organs, including teeth. Bcl9 and Bcl9l are tissue-specific transcriptional cofactors that cooperate with β-catenin. In the nucleus, Bcl9 and Bcl9l simultaneously bind β-catenin and the transcriptional activator Pygo2 to promote the transcription of a subset of Wnt target genes. We showed that Bcl9 and Bcl9l function in the cytoplasm during tooth enamel formation in a manner that is independent of Wnt-stimulated β-catenin-dependent transcription. Bcl9, Bcl9l, and Pygo2 localized mainly to the cytoplasm of the epithelial-derived ameloblasts, the cells responsible for enamel production. In ameloblasts, Bcl9 interacted with proteins involved in enamel formation and proteins involved in exocytosis and vesicular trafficking. Conditional deletion of both Bcl9 and Bcl9l or both Pygo1 and Pygo2 in mice produced teeth with defective enamel that was bright white and deficient in iron, which is reminiscent of human tooth enamel pathologies. Overall, our data revealed that these proteins, originally defined through their function as β-catenin transcriptional cofactors, function in odontogenesis through a previously uncharacterized cytoplasmic mechanism, revealing that they have roles beyond that of transcriptional cofactors.
Collapse
Affiliation(s)
- Claudio Cantù
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Pierfrancesco Pagella
- Orofacial Development and Regeneration, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, 8032 Zurich, Switzerland
| | - Tania D Shajiei
- Orofacial Development and Regeneration, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, 8032 Zurich, Switzerland
| | - Dario Zimmerli
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Tomas Valenta
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - George Hausmann
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.
| | - Thimios A Mitsiadis
- Orofacial Development and Regeneration, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, 8032 Zurich, Switzerland.
| |
Collapse
|