51
|
Martín JF, Liras P, Sánchez S. Modulation of Gene Expression in Actinobacteria by Translational Modification of Transcriptional Factors and Secondary Metabolite Biosynthetic Enzymes. Front Microbiol 2021; 12:630694. [PMID: 33796086 PMCID: PMC8007912 DOI: 10.3389/fmicb.2021.630694] [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: 11/18/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. There are two types of phosphorylations involved in the control of transcriptional factors: (1) phosphorylation of sensor kinases and transfer of the phosphate group to the receiver domain of response regulators, which alters the expression of regulator target genes. (2) Phosphorylation systems involving promiscuous serine/threonine/tyrosine kinases that modify proteins at several amino acid residues, e.g., the phosphorylation of the global nitrogen regulator GlnR. Another post-translational modification is the acetylation at the epsilon amino group of lysine residues. The protein acetylation/deacetylation controls the activity of many short and long-chain acyl-CoA synthetases, transcriptional factors, key proteins of bacterial metabolism, and enzymes for the biosynthesis of non-ribosomal peptides, desferrioxamine, streptomycin, or phosphinic acid-derived antibiotics. Acetyltransferases catalyze acetylation reactions showing different specificity for the acyl-CoA donor. Although it functions as acetyltransferase, there are examples of malonylation, crotonylation, succinylation, or in a few cases acylation activities using bulky acyl-CoA derivatives. Substrates activation by nucleoside triphosphates is one of the central reactions inhibited by lysine acetyltransferases. Phosphorylation/dephosphorylation or acylation/deacylation reactions on global regulators like PhoP, GlnR, AfsR, and the carbon catabolite regulator glucokinase strongly affects the expression of genes controlled by these regulators. Finally, a different type of post-translational protein modification is the phosphopantetheinylation, catalized by phosphopantetheinyl transferases (PPTases). This reaction is essential to modify those enzymes requiring phosphopantetheine groups like non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. Up to five PPTases are present in S. tsukubaensis and S. avermitilis. Different PPTases modify substrate proteins in the PCP or ACP domains of tacrolimus biosynthetic enzymes. Directed mutations of genes encoding enzymes involved in the post-translational modification is a promising tool to enhance the production of bioactive metabolites.
Collapse
Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Paloma Liras
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, Mexico
| |
Collapse
|
52
|
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
|
53
|
Narain A, Dubey RK, Verma AK, Srivastava A, Kant S. Potential Role of Proteasome Accessory Factor-C in Resistance against Second Line Drugs in Mycobacteria. J Lab Physicians 2021; 12:250-262. [PMID: 33390674 PMCID: PMC7773444 DOI: 10.1055/s-0040-1722552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Objectives Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), can survive inside the host granuloma courtesy the various extrinsic and intrinsic factors involved. Continuous use or misuse of the anti TB drugs over the years has led to the development of resistance in MTB against antibiotics. Drug-resistant TB in particular has been a menace since treating it requires exposing the patient to drugs for a prolonged period of time. Multidrug-resistant (MDR) and extensively drug resistant TB cases have increased over the years mostly due to the exposure of MTB to suboptimal levels of drug. Proteasomes provide MTB its pathogenicity and hence helps it to survive inside the host even in the presence of drugs. Materials and Methods The recombinantly expressed proteasome accessory factor-C (PafC) protein was purified via Ni-NTA affinity chromatography and overexpressed in the nonpathogenic strain of mycobacteria (Mycobacterium smegmatis) for the comparative analysis of minimum inhibitory concentrations of antimycobacterial drugs. The bacteria were subjected to various stress conditions. Secretory nature of PafC was analyzed by probing the purified protein against patient sera. Quantitative mRNA analysis of paf C, lex A, and rec A was performed to check for their level under fluoroquinolone (FQ) presence. The data were validated in clinical samples of pulmonary TB patients. Results pafC , that forms one part of paf operon, is involved in providing MTB its resistance against FQs. Through a series of experiments, we established the fact that PafC is upregulated in mycobacteria upon exposure to FQs and it leads to the increased intracellular survival of mycobacteria under the stresses generated by FQs. The study also refers to the correlation of pafC to deoxyribonucleic acid (DNA) damage repair enzymes lexA and recA at transcriptional level. The results obtained in vitro corroborated when the pulmonary TB patients' samples were subjected to the same molecular analysis. Statistical Analysis All experiments were conducted at least in triplicate. p -Value of <0.05 was considered to be statistically significant Conclusion PafC plays a significant role in providing resistance to mycobacteria against FQ class of drugs by increasing its intracellular survival through increased drug efflux and getting involved with DNA damage repair machinery.
Collapse
Affiliation(s)
- Apoorva Narain
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Rikesh K Dubey
- Department of Microbiology, Central Drug Research Institute (CSIR), Lucknow, Uttar Pradesh, India
| | - Ajay Kumar Verma
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Anand Srivastava
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Surya Kant
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| |
Collapse
|
54
|
PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids. Genes (Basel) 2020; 11:genes11121431. [PMID: 33260770 PMCID: PMC7761138 DOI: 10.3390/genes11121431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/23/2022] Open
Abstract
Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant role in regulating biological processes. The traditional experimental practice to detect pupylation sites proved to be expensive and requires a lot of time and resources. Thus, there have been many computational predictors developed to challenge this issue. However, performance is still limited. In this study, we propose another computational method, named PupStruct, which uses the structural information of amino acids with a radial basis kernel function Support Vector Machine (SVM) to predict pupylated lysine residues. We compared PupStruct with three state-of-the-art predictors from the literature where PupStruct has validated a significant improvement in performance over them with statistical metrics such as sensitivity (0.9234), specificity (0.9359), accuracy (0.9296), precision (0.9349), and Mathew’s correlation coefficient (0.8616) on a benchmark dataset.
Collapse
|
55
|
Scholz N, Kurian KM, Siebzehnrubl FA, Licchesi JDF. Targeting the Ubiquitin System in Glioblastoma. Front Oncol 2020; 10:574011. [PMID: 33324551 PMCID: PMC7724090 DOI: 10.3389/fonc.2020.574011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma is the most common primary brain tumor in adults with poor overall outcome and 5-year survival of less than 5%. Treatment has not changed much in the last decade or so, with surgical resection and radio/chemotherapy being the main options. Glioblastoma is highly heterogeneous and frequently becomes treatment-resistant due to the ability of glioblastoma cells to adopt stem cell states facilitating tumor recurrence. Therefore, there is an urgent need for novel therapeutic strategies. The ubiquitin system, in particular E3 ubiquitin ligases and deubiquitinating enzymes, have emerged as a promising source of novel drug targets. In addition to conventional small molecule drug discovery approaches aimed at modulating enzyme activity, several new and exciting strategies are also being explored. Among these, PROteolysis TArgeting Chimeras (PROTACs) aim to harness the endogenous protein turnover machinery to direct therapeutically relevant targets, including previously considered "undruggable" ones, for proteasomal degradation. PROTAC and other strategies targeting the ubiquitin proteasome system offer new therapeutic avenues which will expand the drug development toolboxes for glioblastoma. This review will provide a comprehensive overview of E3 ubiquitin ligases and deubiquitinating enzymes in the context of glioblastoma and their involvement in core signaling pathways including EGFR, TGF-β, p53 and stemness-related pathways. Finally, we offer new insights into how these ubiquitin-dependent mechanisms could be exploited therapeutically for glioblastoma.
Collapse
Affiliation(s)
- Nico Scholz
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Kathreena M. Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, United Kingdom
| | - Florian A. Siebzehnrubl
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
| | | |
Collapse
|
56
|
Tyagi R, Srivastava M, Jain P, Pandey RP, Asthana S, Kumar D, Raj VS. Development of potential proteasome inhibitors against Mycobacterium tuberculosis. J Biomol Struct Dyn 2020; 40:2189-2203. [PMID: 33074049 DOI: 10.1080/07391102.2020.1835722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) has been recently declared as a health emergency because of sporadic increase in Multidrug-resistant Tuberculosis (MDR-TB) problem throughout the world. TB causing bacteria, Mycobacterium tuberculosis has become resistant to the first line of treatment along with second line of treatment and drugs, which are accessible to us. Thus, there is an urgent need of identification of key targets and development of potential therapeutic approach(s), which can overcome the Mycobacterium tuberculosis complications. In the present study, Mycobacterium tuberculosis proteasome has been taken as a potential target as it is one of the key regulatory proteins in Mycobacterium tuberculosis propagation. Further, a library of 400 compounds (small molecule) from Medicines for Malaria Venture (MMV) were screened against the target (proteasome) using molecular docking and simulation approach, and selected lead compounds were validated in in vitro model. In this study, we have identified two potent small molecules from the MMV Pathogen Box library, MMV019838 and MMV687146 with -9.8 kcal/mol and -8.7 kcal/mol binding energy respectively, which actively interact with the catalytic domain/active domain of Mycobacterium tuberculosis proteasome and inhibit the Mycobacterium tuberculosis growth in in vitro culture. Furthermore, the molecular docking and simulation study of MMV019838 and MMV687146 with proteasome show strong and stable interaction with Mycobacterium tuberculosis compared to human proteasome and show no cytotoxicity effect. A better understanding of proteasome inhibition in Mycobacterium tuberculosis in in vitro and in vivo model would eventually allow us to understand the molecular mechanism(s) and discover a novel and potent therapeutic agent against Tuberculosis. Active efflux of drugs mediated by efflux pumps that confer drug resistance is one of the mechanisms developed by bacteria to counter the adverse effects of antibiotics and chemicals. Efflux pump activity was tested for a specific compound MMV019838 which was showing good in silico results than MIC values.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rashmi Tyagi
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Preeti Jain
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida, India
| | - V Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
| |
Collapse
|
57
|
Abstract
Acetylation was initially discovered as a post-translational modification (PTM) on the unstructured, highly basic N-terminal tails of eukaryotic histones in the 1960s. Histone acetylation constitutes part of the "histone code", which regulates chromosome compaction and various DNA processes such as gene expression, recombination, and DNA replication. In bacteria, nucleoid-associated proteins (NAPs) are responsible these functions in that they organize and compact the chromosome and regulate some DNA processes. The highly conserved DNABII family of proteins are considered functional homologues of eukaryotic histones despite having no sequence or structural conservation. Within the past decade, a growing interest in Nε-lysine acetylation led to the discovery that hundreds of bacterial proteins are acetylated with diverse cellular functions, in direct contrast to the original thought that this was a rare phenomenon. Similarly, other previously undiscovered bacterial PTMs, like serine, threonine, and tyrosine phosphorylation, have also been characterized. In this review, the various PTMs that were discovered among DNABII family proteins, specifically histone-like protein (HU) orthologues, from large-scale proteomic studies are discussed. The functional significance of these modifications and the enzymes involved are also addressed. The discovery of novel PTMs on these proteins begs this question: is there a histone-like code in bacteria?
Collapse
Affiliation(s)
- Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| |
Collapse
|
58
|
Prathiviraj R, Chellapandi P. Deciphering Molecular Virulence Mechanism of Mycobacterium tuberculosis Dop isopeptidase Based on Its Sequence-Structure-Function Linkage. Protein J 2020; 39:33-45. [PMID: 31760575 DOI: 10.1007/s10930-019-09876-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The pupylation pathway marks proteins for prokaryotic ubiquitin-like protein (Pup)-proteasomal degradation and survival strategy of mycobacteria inside of the host macrophages. Deamidase of Pup (Dop) plays a central role in the pupylation pathway. It is still a matter of investigation to know the function of Dop in virulence of mycobacterial lineage. Hence, the present study was intended to describe the sequence-structure-function-virulence link of Dop for understanding the molecular virulence mechanism of Mycobacterium tuberculosis H37Rv (Mtb). Phylogenetic analysis of this study indicated that Dop has extensively diverged across the proteasome-harboring bacteria. The functional part of Dop was converged across the pathogenic mycobacterial lineage. The genome-wide analysis pointed out that the pupylation gene locus was identical to each other, but its genome neighborhood differed from species to species. Molecular modeling and dynamic studies proved that the predicted structure of Mtb Dop was energetically stable and low conformational freedom. Moreover, evolutionary constraints in Mtb Dop were intensively analyzed for inferring its sequence-structure-function relationships for the full virulence of Mtb. It indicated that evolutionary optimization was extensively required to stabilize its local structural environment at the side chains of mutable residues. The sequence-structure-function-virulence link of Dop might have retained in Mtb by reordering hydrophobic and hydrogen bonding patterns in the local structural environment. Thus, the results of our study provide a quest to understand the molecular virulence and pathogenesis mechanisms of Mtb during the infection process.
Collapse
Affiliation(s)
- R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
| |
Collapse
|
59
|
Majumder P, Baumeister W. Proteasomes: unfoldase-assisted protein degradation machines. Biol Chem 2020; 401:183-199. [PMID: 31665105 DOI: 10.1515/hsz-2019-0344] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/02/2019] [Indexed: 01/05/2023]
Abstract
Proteasomes are the principal molecular machines for the regulated degradation of intracellular proteins. These self-compartmentalized macromolecular assemblies selectively degrade misfolded, mistranslated, damaged or otherwise unwanted proteins, and play a pivotal role in the maintenance of cellular proteostasis, in stress response, and numerous other processes of vital importance. Whereas the molecular architecture of the proteasome core particle (CP) is universally conserved, the unfoldase modules vary in overall structure, subunit complexity, and regulatory principles. Proteasomal unfoldases are AAA+ ATPases (ATPases associated with a variety of cellular activities) that unfold protein substrates, and translocate them into the CP for degradation. In this review, we summarize the current state of knowledge about proteasome - unfoldase systems in bacteria, archaea, and eukaryotes, the three domains of life.
Collapse
Affiliation(s)
- Parijat Majumder
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| |
Collapse
|
60
|
Regulation of Protein Post-Translational Modifications on Metabolism of Actinomycetes. Biomolecules 2020; 10:biom10081122. [PMID: 32751230 PMCID: PMC7464533 DOI: 10.3390/biom10081122] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
Protein post-translational modification (PTM) is a reversible process, which can dynamically regulate the metabolic state of cells through regulation of protein structure, activity, localization or protein–protein interactions. Actinomycetes are present in the soil, air and water, and their life cycle is strongly determined by environmental conditions. The complexity of variable environments urges Actinomycetes to respond quickly to external stimuli. In recent years, advances in identification and quantification of PTMs have led researchers to deepen their understanding of the functions of PTMs in physiology and metabolism, including vegetative growth, sporulation, metabolite synthesis and infectivity. On the other hand, most donor groups for PTMs come from various metabolites, suggesting a complex association network between metabolic states, PTMs and signaling pathways. Here, we review the mechanisms and functions of PTMs identified in Actinomycetes, focusing on phosphorylation, acylation and protein degradation in an attempt to summarize the recent progress of research on PTMs and their important role in bacterial cellular processes.
Collapse
|
61
|
Evolutionary genetic analysis of unassigned peptidase clan-associated microbial virulence and pathogenesis. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00529-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
62
|
The Iron Deficiency Response of Corynebacterium glutamicum and a Link to Thiamine Biosynthesis. Appl Environ Microbiol 2020; 86:AEM.00065-20. [PMID: 32144105 DOI: 10.1128/aem.00065-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 02/28/2020] [Indexed: 12/20/2022] Open
Abstract
The response to iron limitation of the Gram-positive soil bacterium Corynebacterium glutamicum was analyzed with respect to secreted metabolites, the transcriptome, and the proteome. During growth in glucose minimal medium, iron limitation caused a shift from lactate to pyruvate as the major secreted organic acid complemented by l-alanine and 2-oxoglutarate. Transcriptome and proteome analyses revealed that a pronounced iron starvation response governed by the transcriptional regulators DtxR and RipA was detectable in the late, but not in the early, exponential-growth phase. A link between iron starvation and thiamine pyrophosphate (TPP) biosynthesis was uncovered by the strong upregulation of thiC As phosphomethylpyrimidine synthase (ThiC) contains an iron-sulfur cluster, limiting activities of the TPP-dependent pyruvate-2-oxoglutarate dehydrogenase supercomplex probably cause the excretion of pyruvate and 2-oxoglutarate. In line with this explanation, thiamine supplementation could strongly diminish the secretion of these acids. The upregulation of thiC and other genes involved in thiamine biosynthesis and transport is presumably due to TPP riboswitches present at the 5' end of the corresponding operons. The results obtained in this study provide new insights into iron homeostasis in C. glutamicum and demonstrate that the metabolic consequences of iron limitation can be due to the iron dependency of coenzyme biosynthesis.IMPORTANCE Iron is an essential element for most organisms but causes problems due to poor solubility under oxic conditions and due to toxicity by catalyzing the formation of reactive oxygen species (ROS). Therefore, bacteria have evolved complex regulatory networks for iron homeostasis aiming at a sufficient iron supply while minimizing ROS formation. In our study, the responses of the actinobacterium Corynebacterium glutamicum to iron limitation were analyzed, resulting in a detailed view on the processes involved in iron homeostasis in this model organism. In particular, we provide evidence that iron limitation causes TPP deficiency, presumably due to insufficient activity of the iron-dependent phosphomethylpyrimidine synthase (ThiC). TPP deficiency was deduced from the upregulation of genes controlled by a TPP riboswitch and secretion of metabolites caused by insufficient activity of the TPP-dependent enzymes pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase. To our knowledge, the link between iron starvation and thiamine synthesis has not been elaborated previously.
Collapse
|
63
|
Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
Collapse
Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| |
Collapse
|
64
|
Berglund J, Gjondrekaj R, Verney E, Maupin-Furlow JA, Edelmann MJ. Modification of the host ubiquitome by bacterial enzymes. Microbiol Res 2020; 235:126429. [PMID: 32109687 PMCID: PMC7369425 DOI: 10.1016/j.micres.2020.126429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 12/14/2022]
Abstract
Attachment of ubiquitin molecules to protein substrates is a reversible post-translational modification (PTM), which occurs ubiquitously in eukaryotic cells and controls most cellular processes. As a consequence, ubiquitination is an attractive target of pathogen-encoded virulence factors. Pathogenic bacteria have evolved multiple mechanisms to hijack the host's ubiquitin system to their advantage. In this review, we discuss the bacteria-encoded E3 ligases and deubiquitinases translocated to the host for an addition or removal of eukaryotic ubiquitin modification, effectively hijacking the host's ubiquitination processes. We review bacterial enzymes homologous to host proteins in sequence and functions, as well as enzymes with novel mechanisms in ubiquitination, which have significant structural differences in comparison to the mammalian E3 ligases. Finally, we will also discuss examples of molecular "counter-weapons" - eukaryotic proteins, which counteract pathogen-encoded E3 ligases. The many examples of the pathogen effector molecules that catalyze eukaryotic ubiquitin modification bring to light the intricate pathways involved in the pathogenesis of some of the most virulent bacterial infections with human pathogens. The role of these effector molecules remains an essential determinant of bacterial virulence in terms of infection, invasion, and replication. A comprehensive understanding of the mechanisms dictating the mimicry employed by bacterial pathogens is of vital importance in developing new strategies for therapeutic approaches.
Collapse
Affiliation(s)
- Jennifer Berglund
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Rafaela Gjondrekaj
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Ellen Verney
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Mariola J Edelmann
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA.
| |
Collapse
|
65
|
Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
Collapse
Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| |
Collapse
|
66
|
Uchikura H, Ninomiya K, Takahashi K, Tsuge Y. Requirement of de novo synthesis of pyruvate carboxylase in long-term succinic acid production in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2020; 104:4313-4320. [PMID: 32232530 DOI: 10.1007/s00253-020-10556-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/11/2020] [Accepted: 03/16/2020] [Indexed: 11/28/2022]
Abstract
Protein turnover through de novo synthesis is critical for sustainable cellular functions. We previously found that glucose consumption rate in Corynebacterium glutamicum under anaerobic conditions increased at temperature higher than the upper limit of growth temperature. Here, we showed that production of lactic and succinic acids increased at higher temperature for long-term (48 h) anaerobic reaction in metabolically engineered strains. At 42 °C, beyond the upper limit of growth temperature range, biomass-specific lactic acid production rate was 8% higher than that at 30 °C, the optimal growth temperature. In contrast, biomass-specific succinic acid production rate was highest at 36 °C, 28% higher than that at 30 °C, although the production at 42 °C was still 23% higher than that at 30 °C. As enzymes are usually unstable at high temperatures, we investigated whether protein turnover of metabolic enzymes is required for the production of lactic and succinic acids under these conditions. Interestingly, when de novo protein synthesis was inhibited by addition of chloramphenicol, after 6 h, only succinic acid production was inhibited. Because glycolytic enzymes are involved in both lactic and succinic acids synthesis, enzymes in the anaplerotic pathway and the tricarboxylic acid (TCA) cycle leading to succinic acid synthesis were likely to be responsible for its decreased production. Among the five enzymes examined, the specific activity of only pyruvate carboxylase was drastically decreased after 48 h at 42 °C. Thus, the de novo synthesis of pyruvate carboxylase is required for long-term production of succinic acid. Graphical abstract KEY POINTS: • Long-term reaction for organic acids can be improved at temperature beyond ideal growth conditions. • De novo synthesis of pyruvate carboxylase is required for long-term succinic acid production.
Collapse
Affiliation(s)
- Hiroto Uchikura
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Kazuaki Ninomiya
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.,Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Kenji Takahashi
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Yota Tsuge
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan. .,Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.
| |
Collapse
|
67
|
Hecht N, Becher M, Korman M, Vishkautzan M, Gur E. Inter- and intramolecular regulation of protein depupylation in Mycobacterium smegmatis. FEBS J 2020; 287:4389-4400. [PMID: 32037686 DOI: 10.1111/febs.15245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/30/2019] [Accepted: 01/28/2020] [Indexed: 12/24/2022]
Abstract
Whereas intracellular proteolysis is essential for proper cellular function, it is a destructive process, which must be tightly regulated. In some bacteria, a Pup-proteasome system tags target proteins for degradation by a bacterial proteasome. Pup, a small modifier protein, is attached to target proteins by PafA, the sole Pup ligase, in a process termed pupylation. In mycobacteria, including Mycobacterium smegmatis and Mycobacterium tuberculosis, Pup undergoes a deamidation step by the enzyme Dop prior to its PafA-mediated attachment to a target. The catalytic mechanism of Pup deamidation is also used by Dop to perform depupylation, namely the removal of Pup from already tagged proteins. Hence, Dop appears to play contradictory roles: On the one hand, deamidation of Pup promotes pupylation, while on the other hand, depupylation reduces tagged protein levels. To avoid futile pupylation-depupylation cycles, Dop activity must be regulated. An intramolecular regulatory mechanism directs Dop to catalyze deamidation more effectively than depupylation. A complementary intermolecular mechanism results in Dop depletion under conditions where protein pupylation and degradation are favorable. In this work, we studied these regulatory mechanisms and identified a flexible loop in Dop, previously termed the Dop-loop, that acts as an intramolecular regulatory element that allosterically controls substrate preference. To investigate regulation at the intermolecular level, we used the CRISPR interference system to knock down the expression of M. smegmatis ATP-dependent intracellular proteases and found that the ClpCP protease is responsible for Dop depletion under starvation conditions. These findings clarify previous observations and introduce a new level for the regulation of Dop activity. DATABASE: Structural data are available in the PDB database under the accession numbers 4BJR and 4B0S.
Collapse
Affiliation(s)
- Nir Hecht
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mika Becher
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maayan Korman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Marina Vishkautzan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| |
Collapse
|
68
|
Bhattacharya S, Ghosh P, Banerjee D, Banerjee A, Ray S. In Silico Drug Target Discovery Through Proteome Mining from M. tuberculosis: An Insight into Antivirulent Therapy. Comb Chem High Throughput Screen 2020; 23:253-268. [PMID: 32072892 DOI: 10.2174/1386207323666200219120903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/23/2020] [Accepted: 02/01/2020] [Indexed: 11/22/2022]
Abstract
AIM AND OBJECTIVE One of the challenges to conventional therapies against Mycobacterium tuberculosis is the development of multi-drug resistant pathogenic strains. This study was undertaken to explore new therapeutic targets for the revolutionary antivirulence therapy utilizing the pathogen's essential hypothetical proteins, serving as virulence factors, which is the essential first step in novel drug designing. METHODS Functional annotations of essential hypothetical proteins from Mycobacterium tuberculosis (H37Rv strain) were performed through domain annotation, Gene Ontology analysis, physicochemical characterization and prediction of subcellular localization. Virulence factors among the essential hypothetical proteins were predicted, among which pathogen-specific drug target candidates, non-homologous to human and gut microbiota, were identified. This was followed by druggability and spectrum analysis of the identified targets. RESULTS AND CONCLUSION The study successfully assigned functions of 83 essential hypothetical proteins of Mycobacterium tuberculosis, among which 25 were identified as virulence factors. Out of 25, 12 virulence factors were observed as potential pathogen-specific drug target candidates. Nine potential targets had druggable properties and rest three were considered as novel targets. Exploration of these targets will provide new insights into future drug development. Characterization of subcellular localizations revealed that most of the predicted targets were cytoplasmic which could be ideal for intracellular drugs, while two drug targets were membranebound, ideal for vaccines. Spectrum analysis identified one broad-spectrum and 11 narrowspectrum targets. This study would, therefore, instigate designing novel therapeutics for antivirulence therapy, which have the potential to serve as revolutionary treatment instead of conventional antibiotic therapies to overcome the lethality of antibiotic-resistant strains.
Collapse
Affiliation(s)
| | - Puja Ghosh
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | | | - Arundhati Banerjee
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| |
Collapse
|
69
|
Gan N, Guan H, Huang Y, Yu T, Fu J, Nakayasu ES, Puvar K, Das C, Wang D, Ouyang S, Luo Z. Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination. EMBO J 2020; 39:e102806. [PMID: 31825121 PMCID: PMC7024838 DOI: 10.15252/embj.2019102806] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 12/21/2022] Open
Abstract
The Legionella pneumophila effector MavC induces ubiquitination of the E2 ubiquitin-conjugating enzyme UBE2N by transglutamination, thereby abolishing its function in the synthesis of K63 -type polyubiquitin chains. The inhibition of UBE2N activity creates a conundrum because this E2 enzyme is important in multiple signaling pathways, including some that are important for intracellular L. pneumophila replication. Here, we show that prolonged inhibition of UBE2N activity by MavC restricts intracellular bacterial replication and that the activity of UBE2N is restored by MvcA, an ortholog of MavC (50% identity) with ubiquitin deamidase activity. MvcA functions to deubiquitinate UBE2N-Ub using the same catalytic triad required for its deamidase activity. Structural analysis of the MvcA-UBE2N-Ub complex reveals a crucial role of the insertion domain in MvcA in substrate recognition. Our study establishes a deubiquitination mechanism catalyzed by a deamidase, which, together with MavC, imposes temporal regulation of the activity of UBE2N during L. pneumophila infection.
Collapse
Affiliation(s)
- Ninghai Gan
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Hongxin Guan
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Yini Huang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Ting Yu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Jiaqi Fu
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Ernesto S Nakayasu
- Biological Science DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Kedar Puvar
- Department of ChemistryPurdue UniversityWest LafayetteINUSA
| | | | - Dongmei Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Songying Ouyang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Zhao‐Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| |
Collapse
|
70
|
Victor TW, O'Toole KH, Easthon LM, Ge M, Smith RJ, Huang X, Yan H, Chu YS, Chen S, Gursoy D, Ralle M, Imperiali B, Allen KN, Miller LM. Lanthanide-Binding Tags for 3D X-ray Imaging of Proteins in Cells at Nanoscale Resolution. J Am Chem Soc 2020; 142:2145-2149. [PMID: 31923358 DOI: 10.1021/jacs.9b11571] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the application of lanthanide-binding tags (LBTs) for two- and three-dimensional X-ray imaging of individual proteins in cells with a sub-15 nm beam. The method combines encoded LBTs, which are tags of minimal size (ca. 15-20 amino acids) affording high-affinity lanthanide ion binding, and X-ray fluorescence microscopy (XFM). This approach enables visualization of LBT-tagged proteins while simultaneously measuring the elemental distribution in cells at a spatial resolution necessary for visualizing cell membranes and eukaryotic subcellular organelles.
Collapse
Affiliation(s)
- Tiffany W Victor
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Katherine H O'Toole
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Lindsey M Easthon
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Mingyuan Ge
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Randy J Smith
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Xiaojing Huang
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Hanfei Yan
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Yong S Chu
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Si Chen
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Doga Gursoy
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States.,Department of Electrical Engineering and Computer Science , Northwestern University , Evanston , Illinois 60298 , United States
| | - Martina Ralle
- Department of Molecular and Medical Genetics , Oregon Health Science University , Portland , Oregon 97239 , United States
| | - Barbara Imperiali
- Department of Biology , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Karen N Allen
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Lisa M Miller
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| |
Collapse
|
71
|
Dynamic Characterization of Protein and Posttranslational Modification Levels in Mycobacterial Cholesterol Catabolism. mSystems 2020; 5:5/1/e00424-19. [PMID: 31911463 PMCID: PMC6946793 DOI: 10.1128/msystems.00424-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cholesterol assimilation is a critical step in mycobacterial chronic infection. However, knowledge from the dynamic characterization of cholesterol metabolism in mycobacteria at the protein expression and PTM levels remains limited. Our study uncovered the landscape of protein expression, lysine acetylation, lysine propionylation, and S/T/Y phosphorylation during the metabolic changes from glucose to cholesterol in mycobacteria. The data showed that cholesterol-induced carbon shift resulted in the elevation of protein expression and lysine acylation in diverse metabolic enzymes involved in cholesterol degradation and that the presence of cholesterol also promoted the perturbations at the phosphorylation level in the kinase system in mycobacteria. This study systematically characterized the regulation of cholesterol catabolism at several different levels, which provided the detailed references in mycobacterial proteome and potential antimycobacterial strategies. Cholesterol of the host macrophage membrane is vital for mycobacterial infection, replication, and persistence. During chronic infection within host lung tissues, cholesterol facilitates the phagocytosis of mycobacteria into macrophages. Cholesterol degradation leads to increased flux of acetyl-coenzyme A (CoA) and propionyl-CoA, providing energy and building blocks for virulence macromolecules as well as donors for global protein acylation. Potential functions of lysine acylation are gradually revealed in bacterial survival and pathogenesis. However, the mycobacterial proteome and posttranslational modification (PTM) changes involved in the cholesterol catabolism bioprocess remain unclear. Here, we used nonpathogenic Mycobacterium smegmatis as a model and simultaneously monitored mycobacterial proteome and acetylome changes in the presence of glucose and cholesterol. We discovered that cholesterol metabolic enzymes were upregulated with respect to both protein expression levels and lysine acylation levels during the metabolic shift from glucose to cholesterol. After that, adenylating enzymes related to cholesterol metabolism were proven to be precisely regulated at the propionylation level by mycobacterial acyltransferase M. smegmatis Kat (MsKat) in response to cellular propionyl-CoA accumulation. Furthermore, the kinase expression and phosphorylation levels were also changed along with fluctuations in cholesterol levels. Our results expanded current knowledge of acylation regulation in the cholesterol catabolism of mycobacteria and provided references for possible antimycobacterium strategy. IMPORTANCE Cholesterol assimilation is a critical step in mycobacterial chronic infection. However, knowledge from the dynamic characterization of cholesterol metabolism in mycobacteria at the protein expression and PTM levels remains limited. Our study uncovered the landscape of protein expression, lysine acetylation, lysine propionylation, and S/T/Y phosphorylation during the metabolic changes from glucose to cholesterol in mycobacteria. The data showed that cholesterol-induced carbon shift resulted in the elevation of protein expression and lysine acylation in diverse metabolic enzymes involved in cholesterol degradation and that the presence of cholesterol also promoted the perturbations at the phosphorylation level in the kinase system in mycobacteria. This study systematically characterized the regulation of cholesterol catabolism at several different levels, which provided the detailed references in mycobacterial proteome and potential antimycobacterial strategies.
Collapse
|
72
|
Mendes ML, Fougeras MR, Dittmar G. Analysis of ubiquitin signaling and chain topology cross-talk. J Proteomics 2020; 215:103634. [PMID: 31918034 DOI: 10.1016/j.jprot.2020.103634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/13/2019] [Accepted: 01/05/2020] [Indexed: 12/12/2022]
Abstract
Protein ubiquitination is a powerful post-translational modification implicated in many cellular processes. Although ubiquitination is associated with protein degradation, depending on the topology of polyubiquitin chains, protein ubiquitination is connected to non-degradative events in DNA damage response, cell cycle control, immune response, trafficking, intracellular localization, and vesicle fusion events. It has been shown that a ubiquitin chain can contain two or more topologies at the same time. These branched chains add another level of complexity to ubiquitin signaling, increasing its versatility and specificity. Mass spectrometry-based proteomics has been playing an important role in the identification of all types of ubiquitin chains and linkages. This review aims to provide an overview of ubiquitin chain topology and associated signaling pathways and discusses the MS-based proteomic methodologies used to determine such topologies. SIGNIFICANCE: Ubiquitination plays important roles in many cellular processes. Proteins can be monoubiquitinated or polyubiquitinated forming non-branched or branched chains in a high number of possible combinations, each associated with different cellular processes. The detection and the topology of ubiquitin chains is thus of extreme importance in order to explain such processes. Advances in mass spectrometry based proteomics allowed for the discovery and topology mapping of many ubiquitin chains. This review revisits the state of the art in ubiquitin chain identification by mass spectrometry and gives an insight on the implication of such chains in many cellular processes.
Collapse
Affiliation(s)
- Marta L Mendes
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Miriam R Fougeras
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg.
| |
Collapse
|
73
|
Shin D, Mukherjee R, Liu Y, Gonzalez A, Bonn F, Liu Y, Rogov VV, Heinz M, Stolz A, Hummer G, Dötsch V, Luo ZQ, Bhogaraju S, Dikic I. Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Mol Cell 2020; 77:164-179.e6. [PMID: 31732457 PMCID: PMC6941232 DOI: 10.1016/j.molcel.2019.10.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/07/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022]
Abstract
The family of bacterial SidE enzymes catalyzes non-canonical phosphoribosyl-linked (PR) serine ubiquitination and promotes infectivity of Legionella pneumophila. Here, we describe identification of two bacterial effectors that reverse PR ubiquitination and are thus named deubiquitinases for PR ubiquitination (DUPs; DupA and DupB). Structural analyses revealed that DupA and SidE ubiquitin ligases harbor a highly homologous catalytic phosphodiesterase (PDE) domain. However, unlike SidE ubiquitin ligases, DupA displays increased affinity to PR-ubiquitinated substrates, which allows DupA to cleave PR ubiquitin from substrates. Interfering with DupA-ubiquitin binding switches its activity toward SidE-type ligase. Given the high affinity of DupA to PR-ubiquitinated substrates, we exploited a catalytically inactive DupA mutant to trap and identify more than 180 PR-ubiquitinated host proteins in Legionella-infected cells. Proteins involved in endoplasmic reticulum (ER) fragmentation and membrane recruitment to Legionella-containing vacuoles (LCV) emerged as major SidE targets. The global map of PR-ubiquitinated substrates provides critical insights into host-pathogen interactions during Legionella infection.
Collapse
Affiliation(s)
- Donghyuk Shin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Rukmini Mukherjee
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Yaobin Liu
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Alexis Gonzalez
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Yan Liu
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University, Frankfurt, Germany
| | - Marcel Heinz
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Alexandra Stolz
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University, Frankfurt, Germany
| | - Zhao-Qing Luo
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Sagar Bhogaraju
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
74
|
Abstract
Alzheimer's disease (AD) is the most common form of dementia, most prevalent in the elderly population and has a significant impact on individuals and their family as well as the health care system and the economy. While the number of patients affected by various forms of dementia including AD is on the increase, there is currently no cure. Although genome-wide association studies have identified genetic markers for familial AD, the molecular mechanisms underlying the initiation and development of both familial and sporadic AD remain poorly understood. Most neurodegenerative diseases and in particular those associated with dementia have been defined as proteinopathies due to the presence of intra- and/or extracellular protein aggregates in the brain of affected individuals. Although loss of proteostasis in AD has been known for decades, it is only in recent years that we have come to appreciate the role of ubiquitin-dependent mechanisms in brain homeostasis and in brain diseases. Ubiquitin is a highly versatile post-translational modification which regulates many aspects of protein fate and function, including protein degradation by the Ubiquitin-Proteasome System (UPS), autophagy-mediated removal of damaged organelles and proteins, lysosomal turnover of membrane proteins and of extracellular molecules brought inside the cell through endocytosis. Amyloid-β (Aβ) fragments as well as hyperphosphorylation of Tau are hallmarks of AD, and these are found in extracellular plaques and intracellular fibrils in the brain of individuals with AD, respectively. Yet, whether it is the oligomeric or the soluble species of Aβ and Tau that mediate toxicity is still unclear. These proteins impact on mitochondrial energy metabolism, inflammation, as well as a number of housekeeping processes including protein degradation through the UPS and autophagy. In this chapter, we will discuss the role of ubiquitin in neuronal homeostasis as well as in AD; summarise crosstalks between the enzymes that regulate protein ubiquitination and the toxic proteins Tau and Aβ; highlight emerging molecular mechanisms in AD as well as future strategies which aim to exploit the ubiquitin system as a source for next-generation therapeutics.
Collapse
|
75
|
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
|
76
|
Xu X, Wang T, Niu Y, Liang K, Yang Y. The ubiquitin-like modification by ThiS and ThiF in Escherichia coli. Int J Biol Macromol 2019; 141:351-357. [PMID: 31442507 DOI: 10.1016/j.ijbiomac.2019.08.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/22/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
Abstract
Escherichia coli, one of the most well-studied gram-negative bacterial species, encodes two ubiquitin-like proteins (UBLs), ThiS and MoaD. The studies on prokaryotic UBLs such as Pup, and small archaeal modifier protein have revealed the function of UBLs. However, in gram-negative bacteria, the functions of UBLs in protein modification are still poorly understood to date. Here, we report that ThiS, which has a β-grasp fold and carboxy-terminal diglycine motif similar to ubiquitin, is able to form protein conjugates in vivo and in vitro. We also constructed in vitro ThiS conjugation (thisylation) system and identified the modified lysine sites by MS/MS, this provides an essential platform for studying the UBLs thisylation system in E. coli. The modification system is dependent on lysine 83 (ATPase activity site) and cysteine 169 (zinc binding site) in ThiF and three important substrates, GroEL, PriC, FtsA, were found to be covalently modified by this system in vitro. Taken together, this study provided evidence that the protein conjugation function of β-grasp fold UBLs is conserved in the three major evolutionary lineages of life.
Collapse
Affiliation(s)
- Xibing Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; Medical College, Henan University of Science and Technology, Luoyang 471000, China
| | - Tao Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yulong Niu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Ke Liang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China.
| |
Collapse
|
77
|
Lopez‐Barbosa N, Ludwicki MB, DeLisa MP. Proteome editing using engineered proteins that hijack cellular quality control machinery. AIChE J 2019. [DOI: 10.1002/aic.16854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Natalia Lopez‐Barbosa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Morgan B. Ludwicki
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Matthew P. DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
- Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University Ithaca New York
- Biochemistry, Molecular and Cell Biology Cornell University Ithaca New York
| |
Collapse
|
78
|
Regev O, Linder H, Gur E. Pup-Click-A New Chemoenzymatic Method for the Generation of Singly Pupylated Targets. Bioconjug Chem 2019; 30:2909-2916. [PMID: 31663726 DOI: 10.1021/acs.bioconjchem.9b00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conjugation of the prokaryotic ubiquitin-like protein (Pup) to cellular proteins tags these proteins for degradation by a proteasome in actinobacteria. To study the Pup-proteasome system in in vitro biochemical assays, Pup-tagged (i.e., pupylated) proteins are often used. However, the purification of a homogeneous preparation of pupylated proteins often suffers from poor yields and limitations in terms of selecting the target protein and its site of pupylation. Here, we report on the development of a biochemical methodology we term Pup-Click for the generation of pupylated protein mimics in vitro. Pup-Click relies on a natural pupylation reaction combined with the use of a synthetic peptide and genetic code expansion via the use of unnatural amino acids and Click chemistry. In principle, this approach allows for conjugation of Pup to any selected target at potentially any desired position. Importantly, pupylated protein mimics generated by Pup-Click are recognized and processed by enzymes of the Pup-proteasome system. As such, Pup-Click can serve as a powerful tool for studying this protein degradation pathway.
Collapse
|
79
|
Santin YG. Uncovering the In Vivo Proxisome Using Proximity‐Tagging Methods. Bioessays 2019; 41:e1900131. [DOI: 10.1002/bies.201900131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/04/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Yoann G. Santin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université – CNRS UMR7255 31 Chemin Joseph Aiguier, CS70071, 13402 Marseille Cedex 09 France
| |
Collapse
|
80
|
Zhan W, Hsu HC, Morgan T, Ouellette T, Burns-Huang K, Hara R, Wright AG, Imaeda T, Okamoto R, Sato K, Michino M, Ramjee M, Aso K, Meinke PT, Foley M, Nathan CF, Li H, Lin G. Selective Phenylimidazole-Based Inhibitors of the Mycobacterium tuberculosis Proteasome. J Med Chem 2019; 62:9246-9253. [PMID: 31560200 DOI: 10.1021/acs.jmedchem.9b01187] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteasomes of pathogenic microbes have become attractive targets for anti-infectives. Coevolving with its human host, Mycobacterium tuberculosis (Mtb) has developed mechanisms to resist host-imposed nitrosative and oxidative stresses. Genetic deletion or pharmacological inhibition of the Mtb proteasome (Mtb20S) renders nonreplicating Mtb susceptible to reactive nitrogen species in vitro and unable to survive in the lungs of mice, validating the Mtb proteasome as a promising target for anti-Mtb agents. Using a structure-guided and flow chemistry-enabled study of structure-activity relationships, we developed phenylimidazole-based peptidomimetics that are highly potent for Mtb20S. X-ray structures of selected compounds with Mtb20S shed light on their selectivity for mycobacterial over human proteasomes.
Collapse
Affiliation(s)
- Wenhu Zhan
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Hao-Chi Hsu
- Structural Biology Program , Van Andel Institute , 333 Bostwick Avenue Northeast , Grand Rapids , Michigan 49503 , United States
| | - Trevor Morgan
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Tierra Ouellette
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Kristin Burns-Huang
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Ryoma Hara
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Adrian G Wright
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Toshihiro Imaeda
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Rei Okamoto
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Kenjiro Sato
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Manoj Ramjee
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Kazuyoshi Aso
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Peter T Meinke
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Michael Foley
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Carl F Nathan
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Huilin Li
- Structural Biology Program , Van Andel Institute , 333 Bostwick Avenue Northeast , Grand Rapids , Michigan 49503 , United States
| | - Gang Lin
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| |
Collapse
|
81
|
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
|
82
|
Szafran MJ, Strzałka A, Jakimowicz D. A highly processive actinobacterial topoisomerase I - thoughts on Streptomyces' demand for an enzyme with a unique C-terminal domain. MICROBIOLOGY-SGM 2019; 166:120-128. [PMID: 31390324 PMCID: PMC7398561 DOI: 10.1099/mic.0.000841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Topoisomerase I (TopA) is an essential enzyme that is required to remove excess negative supercoils from chromosomal DNA. Actinobacteria encode unusual TopA homologues with a unique C-terminal domain that contains lysine repeats and confers high enzyme processivity. Interestingly, the longest stretch of lysine repeats was identified in TopA from Streptomyces, environmental bacteria that undergo complex differentiation and produce a plethora of secondary metabolites. In this review, we aim to discuss potential advantages of the lysine repeats in Streptomyces TopA. We speculate that the chromosome organization, transcriptional regulation and lifestyle of these species demand a highly processive but also fine-tuneable relaxase. We hypothesize that the unique TopA provides flexible control of chromosomal topology and globally regulates gene expression.
Collapse
Affiliation(s)
- Marcin J Szafran
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Agnieszka Strzałka
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Dagmara Jakimowicz
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| |
Collapse
|
83
|
Korman M, Schlussel S, Vishkautzan M, Gur E. Multiple layers of regulation determine the cellular levels of the Pup ligase PafA inMycobacterium smegmatis. Mol Microbiol 2019; 112:620-631. [DOI: 10.1111/mmi.14278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Maayan Korman
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
| | - Shai Schlussel
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
| | - Marina Vishkautzan
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
- The National Institute for Biotechnology in the Negev Ben‐Gurion University of the Negev Beer‐Sheva84105Israel
| | - Eyal Gur
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
- The National Institute for Biotechnology in the Negev Ben‐Gurion University of the Negev Beer‐Sheva84105Israel
| |
Collapse
|
84
|
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
|
85
|
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
|
86
|
Long MJC, Liu X, Aye Y. Chemical Biology Gateways to Mapping Location, Association, and Pathway Responsivity. Front Chem 2019; 7:125. [PMID: 30949469 PMCID: PMC6437114 DOI: 10.3389/fchem.2019.00125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/18/2019] [Indexed: 12/14/2022] Open
Abstract
Here we discuss, how by applying chemical concepts to biological problems, methods have been developed to map spatiotemporal regulation of proteins and small-molecule modulation of proteome signaling responses. We outline why chemical-biology platforms are ideal for such purposes. We further discuss strengths and weaknesses of chemical-biology protocols, contrasting them against classical genetic and biochemical approaches. We make these evaluations based on three parameters: occupancy; functional information; and spatial restriction. We demonstrate how the specific choice of chemical reagent and experimental set-up unite to resolve biological problems. Potential improvements/extensions as well as specific controls that in our opinion are often overlooked or employed incorrectly are also considered. Finally, we discuss some of the latest emerging methods to illuminate how chemical-biology innovations provide a gateway toward information hitherto inaccessible by conventional genetic/biochemical means. Finally, we also caution against solely relying on chemical-biology strategies and urge the field to undertake orthogonal validations to ensure robustness of results.
Collapse
Affiliation(s)
| | - Xuyu Liu
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne, Switzerland
| | - Yimon Aye
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne, Switzerland
| |
Collapse
|
87
|
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
|
88
|
van Wijk SJ, Fulda S, Dikic I, Heilemann M. Visualizing ubiquitination in mammalian cells. EMBO Rep 2019; 20:embr.201846520. [PMID: 30665942 DOI: 10.15252/embr.201846520] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/17/2018] [Accepted: 12/21/2018] [Indexed: 12/19/2022] Open
Abstract
Covalent modification of proteins with ubiquitin is essential for the majority of biological processes in mammalian cells. Numerous proteins are conjugated with single or multiple ubiquitin molecules or chains in a dynamic fashion, often determining protein half-lives, localization or function. Experimental approaches to study ubiquitination have been dominated by genetic and biochemical analysis of enzyme structure-function relationships, reaction mechanisms and physiological relevance. Here, we provide an overview of recent developments in microscopy-based imaging of ubiquitination, available reagents and technologies. We discuss the progress in direct and indirect imaging of differentially linked ubiquitin chains in fixed and living cells using confocal fluorescence microscopy and super-resolution microscopy, illustrated by the role of ubiquitin in antibacterial autophagy and pro-inflammatory signalling. Finally, we speculate on future developments and forecast a transition from qualitative to quantitative super-resolution approaches to understand fundamental aspects of ubiquitination and the formation and distribution of functional E3 ligase protein complexes in their native environment.
Collapse
Affiliation(s)
- Sjoerd Jl van Wijk
- Institute for Experimental Cancer Research in Paediatrics, Goethe University, Frankfurt am Main, Germany
| | - Simone Fulda
- Institute for Experimental Cancer Research in Paediatrics, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University - Medical Faculty, University Hospital Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| |
Collapse
|
89
|
Sciolino N, Burz DS, Shekhtman A. In-Cell NMR Spectroscopy of Intrinsically Disordered Proteins. Proteomics 2019; 19:e1800055. [PMID: 30489014 DOI: 10.1002/pmic.201800055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/29/2018] [Indexed: 01/14/2023]
Abstract
This review summarizes the results of in-cell Nuclear Magnetic Resonance, NMR, spectroscopic investigations of the eukaryotic and prokaryotic intrinsically disordered proteins, IDPs: α-synuclein, prokaryotic ubiquitin-like protein, Pup, tubulin-related neuronal protein, Tau, phenylalanyl-glycyl-repeat-rich nucleoporins, FG Nups, and the negative regulator of flagellin synthesis, FlgM. The results show that the cellular behavior of IDPs may differ significantly from that observed in the test tube.
Collapse
Affiliation(s)
- Nicholas Sciolino
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| |
Collapse
|
90
|
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
|
91
|
Korman M, Elharar Y, Fishov I, Gur E. The transcription of pafA, encoding the prokaryotic ubiquitin-like protein ligase, is regulated by PafBC. Future Microbiol 2018; 14:11-21. [PMID: 30547686 DOI: 10.2217/fmb-2018-0278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Mycobacterium tuberculosis possesses an intracellular tagging and degradation system, which has emerged as a target for development of anti-tuberculosis agents. In this system, PafA is the ligase that marks proteins for degradation by their covalent modification with a protein modifier. Here, we studied pafA transcriptional regulation, which remained elusive despite its importance for M. tuberculosis virulence. MATERIALS & METHODS Working with Mycobacterium smegmatis, a mycobacterial model organism, we examined the involvement of the global regulators PafB and PafC in pafA regulation. RESULTS PafBC activated pafA transcription following DNA damage, resulting in efficient cellular recovery. CONCLUSION The results unraveled the involvement of PafBC in pafA transcription, and revealed the importance of proper PafA regulation in mycobacterial physiology.
Collapse
Affiliation(s)
- Maayan Korman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yifat Elharar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Itzhak Fishov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| |
Collapse
|
92
|
Li T, Chen Y, Li T, Jia C. Recognition of Protein Pupylation Sites by Adopting Resampling Approach. Molecules 2018; 23:molecules23123097. [PMID: 30486421 PMCID: PMC6321382 DOI: 10.3390/molecules23123097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 12/28/2022] Open
Abstract
With the in-depth study of posttranslational modification sites, protein ubiquitination has become the key problem to study the molecular mechanism of posttranslational modification. Pupylation is a widely used process in which a prokaryotic ubiquitin-like protein (Pup) is attached to a substrate through a series of biochemical reactions. However, the experimental methods of identifying pupylation sites is often time-consuming and laborious. This study aims to propose an improved approach for predicting pupylation sites. Firstly, the Pearson correlation coefficient was used to reflect the correlation among different amino acid pairs calculated by the frequency of each amino acid. Then according to a descending ranked order, the multiple types of features were filtered separately by values of Pearson correlation coefficient. Thirdly, to get a qualified balanced dataset, the K-means principal component analysis (KPCA) oversampling technique was employed to synthesize new positive samples and Fuzzy undersampling method was employed to reduce the number of negative samples. Finally, the performance of our method was verified by means of jackknife and a 10-fold cross-validation test. The average results of 10-fold cross-validation showed that the sensitivity (Sn) was 90.53%, specificity (Sp) was 99.8%, accuracy (Acc) was 95.09%, and Matthews Correlation Coefficient (MCC) was 0.91. Moreover, an independent test dataset was used to further measure its performance, and the prediction results achieved the Acc of 83.75%, MCC of 0.49, which was superior to previous predictors. The better performance and stability of our proposed method showed it is an effective way to predict pupylation sites.
Collapse
Affiliation(s)
- Tao Li
- School of Transportation Management, Dalian Maritime University, Dalian 116026, China.
- China Waterborne Transport Research Institute, Beijing 100088, China.
| | - Yan Chen
- School of Transportation Management, Dalian Maritime University, Dalian 116026, China.
| | - Taoying Li
- School of Transportation Management, Dalian Maritime University, Dalian 116026, China.
| | - Cangzhi Jia
- College of Science, Dalian Maritime University, Dalian 116026, China.
| |
Collapse
|
93
|
Chi X, Chang Y, Li M, Lin J, Liu Y, Li C, Tang S, Zhang J. Biochemical characterization of mt‐Pem
IK
, a novel toxin‐antitoxin system in
Mycobacterium tuberculosis. FEBS Lett 2018; 592:4039-4050. [DOI: 10.1002/1873-3468.13280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/14/2018] [Accepted: 10/15/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Xiaodong Chi
- The Key Laboratory of Cell Proliferation and Regulation Biology Ministry of Education Institute of Cell Biology College of Life Sciences Beijing Normal University China
| | - Yunqing Chang
- Department of Bacteriology and Immunology Beijing Key Laboratory on Drug‐Resistant Tuberculosis Research Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital Capital Medical University Beijing China
- Multidisciplinary Diagnosis and Treatment Center of Tuberculosis Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital Capital Medical University Beijing China
| | - Mengmiao Li
- The Key Laboratory of Cell Proliferation and Regulation Biology Ministry of Education Institute of Cell Biology College of Life Sciences Beijing Normal University China
| | - Jin Lin
- The Key Laboratory of Cell Proliferation and Regulation Biology Ministry of Education Institute of Cell Biology College of Life Sciences Beijing Normal University China
| | - Yi Liu
- Department of Bacteriology and Immunology Beijing Key Laboratory on Drug‐Resistant Tuberculosis Research Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital Capital Medical University Beijing China
| | - Chuanyou Li
- Department of Bacteriology and Immunology Beijing Key Laboratory on Drug‐Resistant Tuberculosis Research Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital Capital Medical University Beijing China
| | - Shenjie Tang
- Multidisciplinary Diagnosis and Treatment Center of Tuberculosis Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital Capital Medical University Beijing China
| | - Junjie Zhang
- The Key Laboratory of Cell Proliferation and Regulation Biology Ministry of Education Institute of Cell Biology College of Life Sciences Beijing Normal University China
| |
Collapse
|
94
|
BoseDasgupta S, Pieters J. Macrophage-microbe interaction: lessons learned from the pathogen Mycobacterium tuberculosis. Semin Immunopathol 2018; 40:577-591. [PMID: 30306257 DOI: 10.1007/s00281-018-0710-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/17/2018] [Indexed: 02/07/2023]
Abstract
Macrophages, being the cornerstone of the immune system, have adapted the ancient nutrient acquisition mechanism of phagocytosis to engulf various infectious organisms thereby helping to orchestrate an appropriate host response. Phagocytosis refers to the process of internalization and degradation of particulate material, damaged and senescent cells and microorganisms by specialized cells, after which the vesicle containing the ingested particle, the phagosome, matures into acidic phagolysosomes upon fusion with hydrolytic enzyme-containing lysosomes. The destructive power of the macrophage is further exacerbated through the induction of macrophage activation upon a variety of inflammatory stimuli. Despite being the end-point for many phagocytosed microbes, the macrophage can also serve as an intracellular survival niche for a number of intracellular microorganisms. One microbe that is particularly successful at surviving within macrophages is the pathogen Mycobacterium tuberculosis, which can efficiently manipulate the macrophage at several levels, including modulation of the phagocytic pathway as well as interfering with a number of immune activation pathways that normally would lead to eradication of the internalized bacilli. M. tuberculosis excels at circumventing destruction within macrophages, thus establishing itself successfully for prolonged times within the macrophage. In this contribution, we describe a number of general features of macrophages in the context of their function to clear an infection, and highlight the strategies employed by M. tuberculosis to counter macrophage attack. Interestingly, research on the evasion tactics employed by M. tuberculosis within macrophages not only helps to design strategies to curb tuberculosis, but also allows a better understanding of host cell biology.
Collapse
Affiliation(s)
- Somdeb BoseDasgupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
| | - Jean Pieters
- Department of Biochemistry, Biozentrum, University of Basel, 50-70 Klingelbergstrasse, 4056, Basel, Switzerland.
| |
Collapse
|
95
|
A proximity-tagging system to identify membrane protein-protein interactions. Nat Methods 2018; 15:715-722. [PMID: 30104635 DOI: 10.1038/s41592-018-0100-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 05/29/2018] [Indexed: 11/08/2022]
Abstract
The communication between cells and between cellular organelles is often controlled by the interaction of membrane proteins. Although many methods for the detection of protein-protein interactions (PPIs) exist, membrane PPIs remain difficult to detect. Here we developed a proximity-based tagging system, PUP-IT (pupylation-based interaction tagging), to identify membrane protein interactions. In this approach, a small protein tag, Pup, is applied to proteins that interact with a PafA-fused bait, enabling transient and weak interactions to be enriched and detected by mass spectrometry. Pup does not diffuse from the enzyme, which allows high-specificity labeling. We applied this approach to CD28, a critical costimulatory receptor for T lymphocyte activation, and identified known CD28 binding partners and multiple potential interacting proteins. In addition, we demonstrated that this method can identify the interaction between a cell surface receptor and its ligand.
Collapse
|
96
|
Avila-Jaime B, Kawas J, Garcia-Mazcorro J. Prediction of functional metagenomic composition using archived 16S rDNA sequence data from the gut microbiota of livestock. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
97
|
Ziemski M, Jomaa A, Mayer D, Rutz S, Giese C, Veprintsev D, Weber-Ban E. Cdc48-like protein of actinobacteria (Cpa) is a novel proteasome interactor in mycobacteria and related organisms. eLife 2018; 7:34055. [PMID: 29809155 PMCID: PMC6017811 DOI: 10.7554/elife.34055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 05/21/2018] [Indexed: 01/18/2023] Open
Abstract
Cdc48 is a AAA+ ATPase that plays an essential role for many cellular processes in eukaryotic cells. An archaeal homologue of this highly conserved enzyme was shown to directly interact with the 20S proteasome. Here, we analyze the occurrence and phylogeny of a Cdc48 homologue in Actinobacteria and assess its cellular function and possible interaction with the bacterial proteasome. Our data demonstrate that Cdc48-like protein of actinobacteria (Cpa) forms hexameric rings and that the oligomeric state correlates directly with the ATPase activity. Furthermore, we show that the assembled Cpa rings can physically interact with the 20S core particle. Comparison of the Mycobacterium smegmatis wild-type with a cpa knockout strain under carbon starvation uncovers significant changes in the levels of around 500 proteins. Pathway mapping of the observed pattern of changes identifies ribosomal proteins as a particular hotspot, pointing amongst others toward a role of Cpa in ribosome adaptation during starvation. Cells use proteins to carry out the biological processes necessary for life. If a protein becomes damaged or is no longer needed, cells must dispose of it, just as we might take out the trash. The cell’s main ‘garbage disposal unit’ is the proteasome, a barrel-shaped molecular machine that breaks down unwanted proteins. The proteasome binds to other molecules called regulators, which select the proteins to be dismantled. The proteasomes of mycobacteria – a group that includes the bacteria that cause tuberculosis – help them to survive hostile or rapidly changing environments. Mycobacteria contain a molecule called Cpa whose structure is like a regulator that is found in many non-bacterial cells. Ziemski et al. therefore set out to investigate whether Cpa performs a similar role in bacteria. The results of biochemical experiments performed in test tubes revealed that Cpa forms rings made up of six copies of itself. These rings can bind to proteasomes. Ziemski et al. also created genetically modified mycobacteria that could not produce Cpa and studied how they coped with starvation. These modified bacteria stopped growing sooner than their similarly starved genetically normal counterparts. The two groups of bacteria also produced different amounts of some proteins. Ziemski et al. used a technique that pulled Cpa out of the starving genetically normal cells to analyse the proteins that Cpa physically interacts with. These proteins included building blocks of the ribosome, the cellular machinery that produces new proteins. It therefore appears that Cpa helps mycobacteria to cope with starvation by reducing the amount of protein made by the cell. Cpa may also help mycobacteria to survive in other stressful conditions, such as those that the bacteria experience when they infect the human body. Developing drugs that prevent Cpa from working could therefore potentially lead to new treatments for a number of diseases caused by mycobacteria, such as tuberculosis.
Collapse
Affiliation(s)
- Michal Ziemski
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Ahmad Jomaa
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Daniel Mayer
- Laboratory of Biomolecular Research, Paul Scherrer Institute, ETH Zurich, Villigen, Switzerland
| | - Sonja Rutz
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Dmitry Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institute, ETH Zurich, Villigen, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
98
|
Inobe T, Tsukamoto M, Nozaki M. Proteasome-mediated protein degradation is enhanced by fusion ubiquitin with unstructured degron. Biochem Biophys Res Commun 2018; 501:948-954. [PMID: 29777695 DOI: 10.1016/j.bbrc.2018.05.088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 11/28/2022]
Abstract
Methods to induce proteasomal degradation of unwanted proteins are valuable in biomedical studies and thus receive increasing attention. For efficient degradation, the proteasome requires both a ubiquitin tag, which delivers substrates to the proteasome, and an unstructured region, where the proteasome engages the substrate for unfolding and degradation. We fused two degron components into a single molecule to create a fusion protein comprising ubiquitin and Rpn4-derived unstructured region. We demonstrated that the fusion protein retained its function to polyubiquitinate target proteins, thereby inducing more efficient proteasomal target degradation than wild-type ubiquitin in vitro and in cells. These results provide novel strategies for robust degradation enhancement of polyubiquitinated proteins.
Collapse
Affiliation(s)
- Tomonao Inobe
- Department of Life Sciences and Bioengineering, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan; Graduate School of Innovative Life Sciences, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan.
| | - Masayuki Tsukamoto
- Department of Life Sciences and Bioengineering, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan
| | - Miyuki Nozaki
- Department of Life Sciences and Bioengineering, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan
| |
Collapse
|
99
|
Xu HD, Wang LN, Wen PP, Shi SP, Qiu JD. Site-Specific Systematic Analysis of Lysine Modification Crosstalk. Proteomics 2018. [DOI: 10.1002/pmic.201700292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hao-Dong Xu
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
| | - Li-Na Wang
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
| | - Ping-Ping Wen
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
| | - Shao-Ping Shi
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
| | - Jian-Ding Qiu
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
- Department of Materials and Chemical Engineering; Pingxiang University; Pingxiang P. R. China
| |
Collapse
|
100
|
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
|