1
|
Purić E, Nilsson UJ, Anderluh M. Galectin-8 inhibition and functions in immune response and tumor biology. Med Res Rev 2024; 44:2236-2265. [PMID: 38613488 DOI: 10.1002/med.22041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 03/03/2024] [Accepted: 03/29/2024] [Indexed: 04/15/2024]
Abstract
Galectins are among organisms' most abundantly expressed lectins (carbohydrate-binding proteins) that specifically bind β-galactosides. They act not only outside the cell, where they bind to extracellular matrix glycans, but also inside the cell, where they have a significant impact on signaling pathways. Galectin-8 is a galectin family protein encoded by the LGALS8 gene. Its role is evident in both T- and B-cell immunity and in the innate immune response, where it acts directly on dendritic cells and induces some pro-inflammatory cytokines. Galectin-8 also plays an important role in the defense against bacterial and viral infections. It is known to promote antibacterial autophagy by recognizing and binding glycans present on the vacuolar membrane, thus acting as a danger receptor. The most important role of galectin-8 is the regulation of cancer growth, metastasis, tumor progression, and tumor cell survival. Importantly, the expression of galectins is typically higher in tumor tissues than in noncancerous tissues. In this review article, we focus on galectin-8 and its function in immune response, microbial infections, and cancer. Given all of these functions of galectin-8, we emphasize the importance of developing new and selective galectin-8 inhibitors and report the current status of their development.
Collapse
Affiliation(s)
- Edvin Purić
- Department of Pharmaceutical Chemistry, University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Ulf J Nilsson
- Department of Chemistry, Lund University, Lund, Sweden
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| |
Collapse
|
2
|
Farrell LA, O'Rourke MB, Padula MP, Souza-Fonseca-Guimaraes F, Caramori G, Wark PAB, Dharmage SC, Hansbro PM. The Current Molecular and Cellular Landscape of Chronic Obstructive Pulmonary Disease (COPD): A Review of Therapies and Efforts towards Personalized Treatment. Proteomes 2024; 12:23. [PMID: 39189263 DOI: 10.3390/proteomes12030023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) ranks as the third leading cause of global illness and mortality. It is commonly triggered by exposure to respiratory irritants like cigarette smoke or biofuel pollutants. This multifaceted condition manifests through an array of symptoms and lung irregularities, characterized by chronic inflammation and reduced lung function. Present therapies primarily rely on maintenance medications to alleviate symptoms, but fall short in impeding disease advancement. COPD's diverse nature, influenced by various phenotypes, complicates diagnosis, necessitating precise molecular characterization. Omics-driven methodologies, including biomarker identification and therapeutic target exploration, offer a promising avenue for addressing COPD's complexity. This analysis underscores the critical necessity of improving molecular profiling to deepen our comprehension of COPD and identify potential therapeutic targets. Moreover, it advocates for tailoring treatment strategies to individual phenotypes. Through comprehensive exploration-based molecular characterization and the adoption of personalized methodologies, innovative treatments may emerge that are capable of altering the trajectory of COPD, instilling optimism for efficacious disease-modifying interventions.
Collapse
Affiliation(s)
- Luke A Farrell
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Centre for Inflammation, Ultimo, NSW 2007, Australia
| | - Matthew B O'Rourke
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Centre for Inflammation, Ultimo, NSW 2007, Australia
| | - Matthew P Padula
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | | | - Gaetano Caramori
- Pulmonology, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Peter A B Wark
- School of Translational Medicine, Monash University, Melbourne, VIC 3000, Australia
| | - Shymali C Dharmage
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Phillip M Hansbro
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Centre for Inflammation, Ultimo, NSW 2007, Australia
| |
Collapse
|
3
|
Zhu C, Duan Y, Dong J, Jia H, Zhang L, Xing A, Li Z, Du B, Sun Q, Huang Y, Zhang Z, Pan L. Quantitative analysis of the lysine acetylome reveals the role of SIRT3-mediated HSP60 deacetylation in suppressing intracellular Mycobacterium tuberculosis survival. Microbiol Spectr 2024; 12:e0074924. [PMID: 38916288 PMCID: PMC11302147 DOI: 10.1128/spectrum.00749-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/13/2024] [Indexed: 06/26/2024] Open
Abstract
Protein acetylation and deacetylation are key epigenetic modifications that regulate the initiation and development of several diseases. In the context of infection with Mycobacterium tuberculosis (M. tb), these processes are essential for host-pathogen interactions and immune responses. However, the specific effects of acetylation and deacetylation on cellular functions during M. tb infection are not fully understood. This study employed Tandem Mass Tag (TMT) labeling for quantitative proteomic profiling to examine the acetylproteome (acetylome) profiles of noninfected and M. tb-infected macrophages. We identified 715 acetylated peptides from 1,072 proteins and quantified 544 lysine acetylation sites (Kac) in 402 proteins in noninfected and M. tb-infected macrophages. Our research revealed a link between acetylation events and metabolic changes during M. tb infection. Notably, the deacetylation of heat shock protein 60 (HSP60), a key chaperone protein, was significantly associated with this process. Specifically, the deacetylation of HSP60 at K96 by sirtuin3 (SIRT3) enhances macrophage apoptosis, leading to the elimination of intracellular M. tb. These findings underscore the pivotal role of the SIRT3-HSP60 axis in the host immune response to M. tb. This study offers a new perspective on host protein acetylation and suggests that targeting host-directed therapies could be a promising approach for tuberculosis immunotherapy. IMPORTANCE Protein acetylation is crucial for the onset, development, and outcome of tuberculosis (TB). Our study comprehensively investigated the dynamics of lysine acetylation during M. tb infection, shedding light on the intricate host-pathogen interactions that underlie the pathogenesis of tuberculosis. Using an advanced quantitative lysine proteomics approach, different profiles of acetylation sites and proteins in macrophages infected with M. tb were identified. Functional enrichment and protein-protein network analyses revealed significant associations between acetylated proteins and key cellular pathways, highlighting their critical role in the host response to M. tb infection. Furthermore, the deacetylation of HSP60 and its influence on macrophage-mediated clearance of M. tb underscore the functional significance of acetylation in tuberculosis pathogenesis. In conclusion, this study provides valuable insights into the regulatory mechanisms governing host immune responses to M. tb infection and offers promising avenues for developing novel therapeutic interventions against TB.
Collapse
Affiliation(s)
- Chuanzhi Zhu
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yuheng Duan
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jing Dong
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongyan Jia
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Lanyue Zhang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Aiying Xing
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zihui Li
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Boping Du
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Qi Sun
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yinxia Huang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zongde Zhang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liping Pan
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
4
|
Wen Z, Wang L, Ma H, Li L, Wan L, Shi L, Li H, Chen H, Hao W, Song S, Xue Q, Wei Y, Li F, Xu J, Zhang S, Wong KW, Song Y. Integrated single-cell transcriptome and T cell receptor profiling reveals defects of T cell exhaustion in pulmonary tuberculosis. J Infect 2024; 88:106158. [PMID: 38642678 DOI: 10.1016/j.jinf.2024.106158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/07/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
Tuberculosis-affected lungs with chronic inflammation harbor abundant immunosuppressive immune cells but the nature of such inflammation is unclear. Dysfunction in T cell exhaustion, while implicated in chronic inflammatory diseases, remains unexplored in tuberculosis. Given that immunotherapy targeting exhaustion checkpoints exacerbates tuberculosis, we speculate that T cell exhaustion is dysfunctional in tuberculosis. Using integrated single-cell RNA sequencing and T cell receptor profiling we reported defects in exhaustion responses within inflamed tuberculosis-affected lungs. Tuberculosis lungs demonstrated significantly reduced levels of exhausted CD8+ T cells and exhibited diminished expression of exhaustion-related transcripts among clonally expanded CD4+ and CD8+ T cells. Additionally, clonal expansion of CD4+ and CD8+ T cells bearing T cell receptors specific for CMV was observed. Expanded CD8+ T cells expressed the cytolytic marker GZMK. Hence, inflamed tuberculosis-affected lungs displayed dysfunction in T cell exhaustion. Our findings likely hold implications for understanding the reactivation of tuberculosis observed in patients undergoing immunotherapy targeting the exhaustion checkpoint.
Collapse
Affiliation(s)
- Zilu Wen
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lin Wang
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hui Ma
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Leilei Li
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Laiyi Wan
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lei Shi
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hongwei Li
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hui Chen
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wentao Hao
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shu Song
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qinghua Xue
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yutong Wei
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Feng Li
- Department of Respiratory Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jianqing Xu
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shulin Zhang
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Ka-Wing Wong
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Yanzheng Song
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| |
Collapse
|
5
|
Truong T, Martin K, Salemi M, Ray A, Phinney BS, Penn BH. The balance between antiviral and antibacterial responses during M. tuberculosis infection is regulated by the ubiquitin ligase CBL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594178. [PMID: 38798543 PMCID: PMC11118416 DOI: 10.1101/2024.05.15.594178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
As a first line of host defense, macrophages must be able to effectively sense and respond to diverse types of pathogens, and while a particular type of immune response may be beneficial in some circumstances, it can be detrimental in others. Upon infecting a macrophage, M. tuberculosis (Mtb) induces proinflammatory cytokines that activate antibacterial responses. Surprisingly, Mtb also triggers antiviral responses that actually hinder the ability of macrophages to control Mtb infection. The ubiquitin ligase CBL suppresses these antiviral responses and shifts macrophages toward a more antibacterial state during Mtb infection, however, the mechanisms by which CBL regulates immune signaling are unknown. We found that CBL controls responses to multiple stimuli and broadly suppresses the expression of antiviral effector genes. We then used mass-spectrometry to investigate potential CBL substrates and identified over 46,000 ubiquitylated peptides in Mtb-infected macrophages, as well as roughly 400 peptides with CBL-dependent ubiquitylation. We then performed genetic interaction analysis of CBL and its putative substrates, and identified the Fas associated factor 2 (FAF2) adapter protein as a key signaling molecule protein downstream of CBL. Together, these analyses identify thousands of new ubiquitin-mediated signaling events during the innate immune response and reveal an important new regulatory hub in this response.
Collapse
Affiliation(s)
- Tina Truong
- Department of Internal Medicine, University of California, Davis, Davis, California, United States of America
- Graduate Group in Immunology, University of California, Davis, Davis, California, United States of America
| | - Kelsey Martin
- Department of Internal Medicine, University of California, Davis, Davis, California, United States of America
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, Davis, California, United States of America
| | - Abigail Ray
- Department of Internal Medicine, University of California, Davis, Davis, California, United States of America
- Microbiology Graduate Group, University of California, Davis, Davis, California, United States of America
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Davis, Davis, California, United States of America
| | - Bennett H. Penn
- Department of Internal Medicine, University of California, Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, United States of America
| |
Collapse
|
6
|
Lee FFY, Harris C, Alper S. RNA Binding Proteins that Mediate LPS-induced Alternative Splicing of the MyD88 Innate Immune Regulator. J Mol Biol 2024; 436:168497. [PMID: 38369277 PMCID: PMC11001520 DOI: 10.1016/j.jmb.2024.168497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Inflammation driven by Toll-like receptor (TLR) signaling pathways is required to combat infection. However, inflammation can damage host tissues; thus it is essential that TLR signaling ultimately is terminated to prevent chronic inflammatory disorders. One mechanism that terminates persistent TLR signaling is alternative splicing of the MyD88 signaling adaptor, which functions in multiple TLR signaling pathways. While the canonical long isoform of MyD88 (MyD88-L) mediates TLR signaling and promotes inflammation, an alternatively-spliced shorter isoform of MyD88 (MyD88-S) produces a dominant negative inhibitor of TLR signaling. MyD88-S production is induced by inflammatory agonists including lipopolysaccharide (LPS), and thus MyD88-S induction is thought to act as a negative feedback loop that prevents chronic inflammation. Despite the potential role that MyD88-S production plays in inflammatory disorders, the mechanisms controlling MyD88 alternative splicing remain unclear. Here, we identify two RNA binding proteins, SRSF1 and HNRNPU, that regulate LPS-induced alternative splicing of MyD88.
Collapse
Affiliation(s)
- Frank Fang Yao Lee
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA
| | - Chelsea Harris
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA
| | - Scott Alper
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA.
| |
Collapse
|
7
|
Scott HM, Smith MH, Coleman AK, Armijo KS, Chapman MJ, Apostalo SL, Wagner AR, Watson RO, Patrick KL. Serine/arginine-rich splicing factor 7 promotes the type I interferon response by activating Irf7 transcription. Cell Rep 2024; 43:113816. [PMID: 38393946 PMCID: PMC11056844 DOI: 10.1016/j.celrep.2024.113816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Tight regulation of macrophage immune gene expression is required to fight infection without risking harmful inflammation. The contribution of RNA-binding proteins (RBPs) to shaping the macrophage response to pathogens remains poorly understood. Transcriptomic analysis reveals that a member of the serine/arginine-rich (SR) family of mRNA processing factors, SRSF7, is required for optimal expression of a cohort of interferon-stimulated genes in macrophages. Using genetic and biochemical assays, we discover that in addition to its canonical role in regulating alternative splicing, SRSF7 drives transcription of interferon regulatory transcription factor 7 (IRF7) to promote antiviral immunity. At the Irf7 promoter, SRSF7 maximizes STAT1 transcription factor binding and RNA polymerase II elongation via cooperation with the H4K20me1 histone methyltransferase KMT5a (SET8). These studies define a role for an SR protein in activating transcription and reveal an RBP-chromatin network that orchestrates macrophage antiviral gene expression.
Collapse
Affiliation(s)
- Haley M Scott
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Mackenzie H Smith
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Aja K Coleman
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Kaitlyn S Armijo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Morgan J Chapman
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Summer L Apostalo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Allison R Wagner
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Robert O Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Kristin L Patrick
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA.
| |
Collapse
|
8
|
Steinbach A, Bhadkamkar V, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila. Mol Biol Cell 2024; 35:ar27. [PMID: 38117589 PMCID: PMC10916871 DOI: 10.1091/mbc.e23-06-0260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 12/22/2023] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila (L.p.) manipulates eukaryotic host ubiquitination machinery to form its replicative vacuole. While nearly 10% of L.p.'s ∼330 secreted effector proteins are ubiquitin ligases or deubiquitinases, a comprehensive measure of temporally resolved changes in the endogenous host ubiquitinome during infection has not been undertaken. To elucidate how L.p. hijacks host cell ubiquitin signaling, we generated a proteome-wide analysis of changes in protein ubiquitination during infection. We discover that L.p. infection increases ubiquitination of host regulators of subcellular trafficking and membrane dynamics, most notably ∼40% of mammalian Ras superfamily small GTPases. We determine that these small GTPases undergo nondegradative ubiquitination at the Legionella-containing vacuole (LCV) membrane. Finally, we find that the bacterial effectors SidC/SdcA play a central role in cross-family small GTPase ubiquitination, and that these effectors function upstream of SidE family ligases in the polyubiquitination and retention of GTPases in the LCV membrane. This work highlights the extensive reconfiguration of host ubiquitin signaling by bacterial effectors during infection and establishes simultaneous ubiquitination of small GTPases across the Ras superfamily as a novel consequence of L.p. infection. Our findings position L.p. as a tool to better understand how small GTPases can be regulated by ubiquitination in uninfected contexts.
Collapse
Affiliation(s)
- Adriana Steinbach
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
- George Williams Hooper Foundation, University of California, San Francisco, CA 94143
| | - Varun Bhadkamkar
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
- George Williams Hooper Foundation, University of California, San Francisco, CA 94143
| | - David Jimenez-Morales
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, CA 94309
| | - Erica Stevenson
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Gwendolyn M. Jang
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Nevan J. Krogan
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Danielle L. Swaney
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Shaeri Mukherjee
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
- George Williams Hooper Foundation, University of California, San Francisco, CA 94143
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| |
Collapse
|
9
|
Bullen CK, Singh AK, Krug S, Lun S, Thakur P, Srikrishna G, Bishai WR. MDA5 RNA-sensing pathway activation by Mycobacterium tuberculosis promotes innate immune subversion and pathogen survival. JCI Insight 2023; 8:e166242. [PMID: 37725440 PMCID: PMC10619499 DOI: 10.1172/jci.insight.166242] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 09/13/2023] [Indexed: 09/21/2023] Open
Abstract
Host cytosolic sensing of Mycobacterium tuberculosis (M. tuberculosis) RNA by the RIG-I-like receptor (RLR) family perturbs innate immune control within macrophages; however, a distinct role of MDA5, a member of the RLR family, in M. tuberculosis pathogenesis has yet to be fully elucidated. To further define the role of MDA5 in M. tuberculosis pathogenesis, we evaluated M. tuberculosis intracellular growth and innate immune responses in WT and Mda5-/- macrophages. Transfection of M. tuberculosis RNA strongly induced proinflammatory cytokine production in WT macrophages, which was abrogated in Mda5-/- macrophages. M. tuberculosis infection in macrophages induced MDA5 protein expression, accompanied by an increase in MDA5 activation as assessed by multimer formation. IFN-γ-primed Mda5-/- macrophages effectively contained intracellular M. tuberculosis proliferation to a markedly greater degree than WT macrophages. Further comparisons of WT versus Mda5-/- macrophages revealed that during M. tuberculosis infection MDA5 contributed to IL-1β production and inflammasome activation and that loss of MDA5 led to a substantial increase in autophagy. In the mouse TB model, loss of MDA5 conferred host survival benefits with a concomitant reduction in M. tuberculosis bacillary burden. These data reveal that loss of MDA5 is host protective during M. tuberculosis infection in vitro and in vivo, suggesting that M. tuberculosis exploits MDA5 to subvert immune containment.
Collapse
|
10
|
Steinbach AM, Bhadkamkar VL, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551750. [PMID: 37577546 PMCID: PMC10418220 DOI: 10.1101/2023.08.03.551750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The intracellular bacterial pathogen Legionella pneumophila (L.p.) manipulates eukaryotic host ubiquitination machinery to form its replicative vacuole. While nearly 10% of L.p.'s arsenal of ~330 secreted effector proteins have been biochemically characterized as ubiquitin ligases or deubiquitinases, a comprehensive measure of temporally resolved changes in the endogenous host ubiquitinome during infection has not been undertaken. To elucidate how L.p hijacks ubiquitin signaling within the host cell, we undertook a proteome-wide analysis of changes in protein ubiquitination during infection. We discover that L.p. infection results in increased ubiquitination of host proteins regulating subcellular trafficking and membrane dynamics, most notably 63 of ~160 mammalian Ras superfamily small GTPases. We determine that these small GTPases predominantly undergo non-degradative monoubiquitination, and link ubiquitination to recruitment to the Legionella-containing vacuole membrane. Finally, we find that the bacterial effectors SidC/SdcA play a central, but likely indirect, role in cross-family small GTPase ubiquitination. This work highlights the extensive reconfiguration of host ubiquitin signaling by bacterial effectors during infection and establishes simultaneous ubiquitination of small GTPases across the Ras superfamily as a novel consequence of L.p. infection. This work positions L.p. as a tool to better understand how small GTPases can be regulated by ubiquitination in uninfected contexts.
Collapse
Affiliation(s)
- Adriana M. Steinbach
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- George Williams Hooper Foundation, University of California, San Francisco, San Francisco, California, United States of America
| | - Varun L. Bhadkamkar
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- George Williams Hooper Foundation, University of California, San Francisco, San Francisco, California, United States of America
| | - David Jimenez-Morales
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, California, United States of America
| | - Erica Stevenson
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Gwendolyn M. Jang
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Nevan J. Krogan
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Danielle L. Swaney
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Shaeri Mukherjee
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- George Williams Hooper Foundation, University of California, San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
11
|
Huang Y, Zhu C, Pan L, Zhang Z. The role of Mycobacterium tuberculosis acetyltransferase and protein acetylation modifications in tuberculosis. Front Cell Infect Microbiol 2023; 13:1218583. [PMID: 37560320 PMCID: PMC10407107 DOI: 10.3389/fcimb.2023.1218583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023] Open
Abstract
Tuberculosis (TB) is a widespread infectious disease caused by Mycobacterium tuberculosis (M. tb), which has been a significant burden for a long time. Post-translational modifications (PTMs) are essential for protein function in both eukaryotic and prokaryotic cells. This review focuses on the contribution of protein acetylation to the function of M. tb and its infected macrophages. The acetylation of M. tb proteins plays a critical role in virulence, drug resistance, regulation of metabolism, and host anti-TB immune response. Similarly, the PTMs of host proteins induced by M. tb are crucial for the development, treatment, and prevention of diseases. Host protein acetylation induced by M. tb is significant in regulating host immunity against TB, which substantially affects the disease's development. The review summarizes the functions and mechanisms of M. tb acetyltransferase in virulence and drug resistance. It also discusses the role and mechanism of M. tb in regulating host protein acetylation and immune response regulation. Furthermore, the current scenario of isoniazid usage in M. tb therapy treatment is examined. Overall, this review provides valuable information that can serve as a preliminary basis for studying pathogenic research, developing new drugs, exploring in-depth drug resistance mechanisms, and providing precise treatment for TB.
Collapse
Affiliation(s)
| | | | - Liping Pan
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing TB and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zongde Zhang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing TB and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
12
|
Scott HM, Smith MH, Coleman AK, Apostalo SL, Wagner AR, Watson RO, Patrick KL. Serine arginine-rich splicing factor (SRSF7) cooperates with the histone methyltransferase KMT5a to promote the type I interferon response via transcriptional activation of IRF7. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540055. [PMID: 37503164 PMCID: PMC10369877 DOI: 10.1101/2023.05.09.540055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tight regulation of macrophage immune gene expression is required to fight infection without risking harmful inflammation. The contribution of RNA binding proteins (RBPs) to shaping the macrophage response to pathogens remains poorly understood. Transcriptomic analysis revealed that a member of the serine/arginine-rich (SR) family of mRNA processing factors, SRSF7, is required for optimal expression of a cohort of interferon stimulated genes (ISGs) in macrophages. Using genetic and biochemical assays, we discovered that in addition to its canonical role in regulating alternative splicing, SRSF7 drives transcription of interferon regulatory transcription factor 7 (IRF7) to promote antiviral immunity. At the Irf7 promoter, SRSF7 maximizes STAT1 transcription factor binding and RNA polymerase II elongation via cooperation with the H4K20me1 histone methyltransferase KMT5a (SET8). These studies define an unorthodox role for an SR protein in activating transcription and reveal an unappreciated RNA binding protein-chromatin network that orchestrates macrophage antiviral gene expression.
Collapse
|
13
|
Sadee W, Cheeseman IH, Papp A, Pietrzak M, Seweryn M, Zhou X, Lin S, Williams AM, Wewers MD, Curry HM, Zhang H, Cai H, Kunsevi-Kilola C, Tshivhula H, Walzl G, Restrepo BI, Kleynhans L, Ronacher K, Wang Y, Arnett E, Azad AK, Schlesinger LS. Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability. RESEARCH SQUARE 2023:rs.3.rs-2986649. [PMID: 37333188 PMCID: PMC10275041 DOI: 10.21203/rs.3.rs-2986649/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Mycobacterium tuberculosis (M.tb), the causative bacterium of tuberculosis (TB), establishes residence and grows in human alveolar macrophages (AMs). Inter-individual variation in M.tb-human AM interactions can indicate TB risk and the efficacy of therapies and vaccines; however, we currently lack an understanding of the gene and protein expression programs that dictate this variation in the lungs. Results Herein, we systematically analyze interactions of a virulent M.tb strain H37Rv with freshly isolated human AMs from 28 healthy adult donors, measuring host RNA expression and secreted candidate proteins associated with TB pathogenesis over 72h. A large set of genes possessing highly variable inter-individual expression levels are differentially expressed in response to M.tb infection. Eigengene modules link M.tb growth rate with host transcriptional and protein profiles at 24 and 72h. Systems analysis of differential RNA and protein expression identifies a robust network with IL1B, STAT1, and IDO1 as hub genes associated with M.tb growth. RNA time profiles document stimulation towards an M1-type macrophage gene expression followed by emergence of an M2-type profile. Finally, we replicate these results in a cohort from a TB-endemic region, finding a substantial portion of significant differentially expressed genes overlapping between studies. Conclusions We observe large inter-individual differences in bacterial uptake and growth, with tenfold variation in M.tb load by 72h.The fine-scale resolution of this work enables the identification of genes and gene networks associated with early M.tb growth dynamics in defined donor clusters, an important step in developing potential biological indicators of individual susceptibility to M.tb infection and response to therapies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Hong Cai
- University of Texas at San Antonio
| | | | | | | | - Blanca I Restrepo
- University of Texas Rio Grande Valley, South Texas Diabetes and Obesity Institute
| | | | | | | | | | | | | |
Collapse
|
14
|
Morrison HM, Craft J, Rivera-Lugo R, Johnson JR, Golovkine GR, Bell SL, Dodd CE, Van Dis E, Beatty WL, Margolis SR, Repasy T, Shaker I, Lee AY, Vance RE, Stanley SA, Watson RO, Krogan NJ, Portnoy DA, Penn BH, Cox JS. Deficiency in Galectin-3, -8, and -9 impairs immunity to chronic Mycobacterium tuberculosis infection but not acute infection with multiple intracellular pathogens. PLoS Pathog 2023; 19:e1011088. [PMID: 37352334 PMCID: PMC10325092 DOI: 10.1371/journal.ppat.1011088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 07/06/2023] [Accepted: 05/01/2023] [Indexed: 06/25/2023] Open
Abstract
Macrophages employ an array of pattern recognition receptors to detect and eliminate intracellular pathogens that access the cytosol. The cytosolic carbohydrate sensors Galectin-3, -8, and -9 (Gal-3, Gal-8, and Gal-9) recognize damaged pathogen-containing phagosomes, and Gal-3 and Gal-8 are reported to restrict bacterial growth via autophagy in cultured cells. However, the contribution of these galectins to host resistance during bacterial infection in vivo remains unclear. We found that Gal-9 binds directly to Mycobacterium tuberculosis (Mtb) and Salmonella enterica serovar Typhimurium (Stm) and localizes to Mtb in macrophages. To determine the combined contribution of membrane damage-sensing galectins to immunity, we generated Gal-3, -8, and -9 triple knockout (TKO) mice. Mtb infection of primary macrophages from TKO mice resulted in defective autophagic flux but normal bacterial replication. Surprisingly, these mice had no discernable defect in resistance to acute infection with Mtb, Stm or Listeria monocytogenes, and had only modest impairments in bacterial growth restriction and CD4 T cell activation during chronic Mtb infection. Collectively, these findings indicate that while Gal-3, -8, and -9 respond to an array of intracellular pathogens, together these membrane damage-sensing galectins play a limited role in host resistance to bacterial infection.
Collapse
Affiliation(s)
- Huntly M. Morrison
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Julia Craft
- Department of Internal Medicine, Division of Infectious Diseases, University of California, Davis, Davis, California, United States of America
| | - Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Jeffery R. Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco; Quantitative Biosciences Institute (QBI), University of California, San Francisco; Gladstone Institutes, San Francisco, California, United States of America
| | - Guillaume R. Golovkine
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Samantha L. Bell
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of Medicine, Bryan, Texas, United States of America
| | - Claire E. Dodd
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Wandy L. Beatty
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shally R. Margolis
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Teresa Repasy
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Isaac Shaker
- Department of Internal Medicine, Division of Infectious Diseases, University of California, Davis, Davis, California, United States of America
| | - Angus Y. Lee
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, California, United States of America
| | - Russell E. Vance
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
| | - Sarah A. Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, Berkeley, California, United States of America
| | - Robert O. Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of Medicine, Bryan, Texas, United States of America
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco; Quantitative Biosciences Institute (QBI), University of California, San Francisco; Gladstone Institutes, San Francisco, California, United States of America
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Bennett H. Penn
- Department of Internal Medicine, Division of Infectious Diseases, University of California, Davis, Davis, California, United States of America
| | - Jeffery S. Cox
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| |
Collapse
|
15
|
Chan GKL, Maisel S, Hwang YC, Pascual BC, Wolber RRB, Vu P, Patra KC, Bouhaddou M, Kenerson HL, Lim HC, Long D, Yeung RS, Sethupathy P, Swaney DL, Krogan NJ, Turnham RE, Riehle KJ, Scott JD, Bardeesy N, Gordan JD. Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms. eLife 2023; 12:e69521. [PMID: 36692000 PMCID: PMC9925115 DOI: 10.7554/elife.69521] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 01/22/2023] [Indexed: 01/25/2023] Open
Abstract
Genetic alterations that activate protein kinase A (PKA) are found in many tumor types. Yet, their downstream oncogenic signaling mechanisms are poorly understood. We used global phosphoproteomics and kinase activity profiling to map conserved signaling outputs driven by a range of genetic changes that activate PKA in human cancer. Two signaling networks were identified downstream of PKA: RAS/MAPK components and an Aurora Kinase A (AURKA)/glycogen synthase kinase (GSK3) sub-network with activity toward MYC oncoproteins. Findings were validated in two PKA-dependent cancer models: a novel, patient-derived fibrolamellar carcinoma (FLC) line that expresses a DNAJ-PKAc fusion and a PKA-addicted melanoma model with a mutant type I PKA regulatory subunit. We identify PKA signals that can influence both de novo translation and stability of the proto-oncogene c-MYC. However, the primary mechanism of PKA effects on MYC in our cell models was translation and could be blocked with the eIF4A inhibitor zotatifin. This compound dramatically reduced c-MYC expression and inhibited FLC cell line growth in vitro. Thus, targeting PKA effects on translation is a potential treatment strategy for FLC and other PKA-driven cancers.
Collapse
Affiliation(s)
- Gary KL Chan
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Samantha Maisel
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Yeonjoo C Hwang
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Bryan C Pascual
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Rebecca RB Wolber
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Phuong Vu
- Department of Medicine, Harvard Medical SchoolBostonUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Krushna C Patra
- Department of Medicine, Harvard Medical SchoolBostonUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Mehdi Bouhaddou
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
- J. David Gladstone InstituteSan FranciscoUnited States
| | - Heidi L Kenerson
- Department of Surgery and Northwest Liver Research Program, University of WashingtonSeattleUnited States
| | - Huat C Lim
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Donald Long
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityNew YorkUnited States
| | - Raymond S Yeung
- Department of Surgery and Northwest Liver Research Program, University of WashingtonSeattleUnited States
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityNew YorkUnited States
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
- J. David Gladstone InstituteSan FranciscoUnited States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
| | - Rigney E Turnham
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Kimberly J Riehle
- Department of Surgery and Northwest Liver Research Program, University of WashingtonSeattleUnited States
| | - John D Scott
- Department of Pharmacology, University of Washington Medical CenterSeattleUnited States
| | - Nabeel Bardeesy
- Department of Medicine, Harvard Medical SchoolBostonUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - John D Gordan
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| |
Collapse
|
16
|
Shariq M, Quadir N, Alam A, Zarin S, Sheikh JA, Sharma N, Samal J, Ahmad U, Kumari I, Hasnain SE, Ehtesham NZ. The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection. Autophagy 2023; 19:3-23. [PMID: 35000542 PMCID: PMC9809970 DOI: 10.1080/15548627.2021.2021495] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Intracellular pathogens have evolved various efficient molecular armaments to subvert innate defenses. Cellular ubiquitination, a normal physiological process to maintain homeostasis, is emerging one such exploited mechanism. Ubiquitin (Ub), a small protein modifier, is conjugated to diverse protein substrates to regulate many functions. Structurally diverse linkages of poly-Ub to target proteins allow enormous functional diversity with specificity being governed by evolutionarily conserved enzymes (E3-Ub ligases). The Ub-binding domain (UBD) and LC3-interacting region (LIR) are critical features of macroautophagy/autophagy receptors that recognize Ub-conjugated on protein substrates. Emerging evidence suggests that E3-Ub ligases unexpectedly protect against intracellular pathogens by tagging poly-Ub on their surfaces and targeting them to phagophores. Two E3-Ub ligases, PRKN and SMURF1, provide immunity against Mycobacterium tuberculosis (M. tb). Both enzymes conjugate K63 and K48-linked poly-Ub to M. tb for successful delivery to phagophores. Intriguingly, M. tb exploits virulence factors to effectively dampen host-directed autophagy utilizing diverse mechanisms. Autophagy receptors contain LIR-motifs that interact with conserved Atg8-family proteins to modulate phagophore biogenesis and fusion to the lysosome. Intracellular pathogens have evolved a vast repertoire of virulence effectors to subdue host-immunity via hijacking the host ubiquitination process. This review highlights the xenophagy-mediated clearance of M. tb involving host E3-Ub ligases and counter-strategy of autophagy inhibition by M. tb using virulence factors. The role of Ub-binding receptors and their mode of autophagy regulation is also explained. We also discuss the co-opting and utilization of the host Ub system by M. tb for its survival and virulence.Abbreviations: APC: anaphase promoting complex/cyclosome; ATG5: autophagy related 5; BCG: bacille Calmette-Guerin; C2: Ca2+-binding motif; CALCOCO2: calcium binding and coiled-coil domain 2; CUE: coupling of ubiquitin conjugation to ER degradation domains; DUB: deubiquitinating enzyme; GABARAP: GABA type A receptor-associated protein; HECT: homologous to the E6-AP carboxyl terminus; IBR: in-between-ring fingers; IFN: interferon; IL1B: interleukin 1 beta; KEAP1: kelch like ECH associated protein 1; LAMP1: lysosomal associated membrane protein 1; LGALS: galectin; LIR: LC3-interacting region; MAPK11/p38: mitogen-activated protein kinase 11; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK8/JNK: mitogen-activated protein kinase 8; MHC-II: major histocompatibility complex-II; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB1/p50: nuclear factor kappa B subunit 1; OPTN: optineurin; PB1: phox and bem 1; PE/PPE: proline-glutamic acid/proline-proline-glutamic acid; PknG: serine/threonine-protein kinase PknG; PRKN: parkin RBR E3 ubiquitin protein ligase; RBR: RING-in between RING; RING: really interesting new gene; RNF166: RING finger protein 166; ROS: reactive oxygen species; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; Ub: ubiquitin; UBA: ubiquitin-associated; UBAN: ubiquitin-binding domain in ABIN proteins and NEMO; UBD: ubiquitin-binding domain; UBL: ubiquitin-like; ULK1: unc-51 like autophagy activating kinase 1.
Collapse
Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Neha Quadir
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Anwar Alam
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Sheeba Zarin
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Javaid A. Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Neha Sharma
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Jasmine Samal
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Uzair Ahmad
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Seyed E. Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), New Delhi, India,Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India,Seyed E. Hasnain ; ; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110 016, India
| | - Nasreen Z. Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,CONTACT Nasreen Z. Ehtesham ; ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi110029, India
| |
Collapse
|
17
|
White J, Suklabaidya S, Vo MT, Choi YB, Harhaj EW. Multifaceted roles of TAX1BP1 in autophagy. Autophagy 2023; 19:44-53. [PMID: 35470757 PMCID: PMC9809930 DOI: 10.1080/15548627.2022.2070331] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 01/09/2023] Open
Abstract
TAX1BP1 is a selective macroautophagy/autophagy receptor that plays a central role in host defense to pathogens and in regulating the innate immune system. TAX1BP1 facilitates the xenophagic clearance of pathogenic bacteria such as Salmonella typhimurium and Mycobacterium tuberculosis and regulates TLR3 (toll-like receptor 3)-TLR4 and DDX58/RIG-I-like receptor (RLR) signaling by targeting TICAM1 and MAVS for autophagic degradation respectively. In addition to these canonical autophagy receptor functions, TAX1BP1 can also exert multiple accessory functions that influence the biogenesis and maturation of autophagosomes. In this review, we will discuss and integrate recent findings related to the autophagy function of TAX1BP1 and highlight outstanding questions regarding its functions in autophagy and regulation of innate immunity and host defense.Abbreviations: ATG: autophagy related; CALCOCO: calcium binding and coiled-coil domain; CC: coiled-coil; CHUK/IKKα: conserved helix-loop-helix ubiquitous kinase; CLIR: noncanonical LC3-interacting region; GABARAP: gamma-aminobutyric acid receptor associated protein; HTLV-1: human T-lymphotropic virus 1; IFN: interferon; IL1B/IL1β: interleukin 1 beta; LIR: LC3-interacting region; LPS: lipopolysaccharide; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK/JNK: mitogen-activated protein kinase; mATG8: mammalian Atg8 homolog; MAVS: mitochondrial antiviral signaling protein; MEF: mouse embryonic fibroblast; MTB: Mycobacterium tuberculosis; MYD88: myeloid differentiation primary response gene 88; NBR1: NBR1, autophagy cargo receptor; NFKB/NF-κB: nuclear factor of kappa light polypeptide gene enhancer in B cells; OPTN: optineurin; Poly(I:C): polyinosinic:polycytidylic acid; PTM: post-translational modification; RB1CC1: RB1-inducible coiled-coil 1; RIPK: receptor (TNFRSF)-interacting serine-threonine kinase; RLR: DDX58/RIG-I-like receptor; RSV: respiratory syncytia virus; SKICH: SKIP carboxyl homology; SLR: SQSTM1 like receptor; SQSTM1: sequestosome 1; TAX1BP1: Tax1 (human T cell leukemia virus type I) binding protein 1; TBK1: TANK-binding kinase 1; TICAM1: toll-like receptor adaptor molecule 1; TLR: toll-like receptor; TNF: tumor necrosis factor; TNFAIP3: TNF alpha induced protein 3; TNFR: tumor necrosis factor receptor; TOM1: target of myb1 trafficking protein; TRAF: TNF receptor-associated factor; TRIM32: tripartite motif-containing 32; UBD: ubiquitin binding domain; ZF: zinc finger.
Collapse
Affiliation(s)
- Jesse White
- Department of Microbiology and Immunology, Penn State College School of Medicine, Hershey, Pennsylvania, USA
| | - Sujit Suklabaidya
- Department of Microbiology and Immunology, Penn State College School of Medicine, Hershey, Pennsylvania, USA
| | - Mai Tram Vo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Young Bong Choi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Edward W. Harhaj
- Department of Microbiology and Immunology, Penn State College School of Medicine, Hershey, Pennsylvania, USA
| |
Collapse
|
18
|
Wagner AR, Weindel CG, West KO, Scott HM, Watson RO, Patrick KL. SRSF6 balances mitochondrial-driven innate immune outcomes through alternative splicing of BAX. eLife 2022; 11:e82244. [PMID: 36409059 PMCID: PMC9718523 DOI: 10.7554/elife.82244] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022] Open
Abstract
To mount a protective response to infection while preventing hyperinflammation, gene expression in innate immune cells must be tightly regulated. Despite the importance of pre-mRNA splicing in shaping the proteome, its role in balancing immune outcomes remains understudied. Transcriptomic analysis of murine macrophage cell lines identified Serine/Arginine Rich Splicing factor 6 (SRSF6) as a gatekeeper of mitochondrial homeostasis. SRSF6-dependent orchestration of mitochondrial health is directed in large part by alternative splicing of the pro-apoptosis pore-forming protein BAX. Loss of SRSF6 promotes accumulation of BAX-κ, a variant that sensitizes macrophages to undergo cell death and triggers upregulation of interferon stimulated genes through cGAS sensing of cytosolic mitochondrial DNA. Upon pathogen sensing, macrophages regulate SRSF6 expression to control the liberation of immunogenic mtDNA and adjust the threshold for entry into programmed cell death. This work defines BAX alternative splicing by SRSF6 as a critical node not only in mitochondrial homeostasis but also in the macrophage's response to pathogens.
Collapse
Affiliation(s)
- Allison R Wagner
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Chi G Weindel
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Kelsi O West
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Haley M Scott
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Robert O Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Kristin L Patrick
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| |
Collapse
|
19
|
Deretic V, Lazarou M. A guide to membrane atg8ylation and autophagy with reflections on immunity. J Cell Biol 2022; 221:e202203083. [PMID: 35699692 PMCID: PMC9202678 DOI: 10.1083/jcb.202203083] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/16/2022] [Accepted: 05/26/2022] [Indexed: 12/11/2022] Open
Abstract
The process of membrane atg8ylation, defined herein as the conjugation of the ATG8 family of ubiquitin-like proteins to membrane lipids, is beginning to be appreciated in its broader manifestations, mechanisms, and functions. Classically, membrane atg8ylation with LC3B, one of six mammalian ATG8 family proteins, has been viewed as the hallmark of canonical autophagy, entailing the formation of characteristic double membranes in the cytoplasm. However, ATG8s are now well described as being conjugated to single membranes and, most recently, proteins. Here we propose that the atg8ylation is coopted by multiple downstream processes, one of which is canonical autophagy. We elaborate on these biological outputs, which impact metabolism, quality control, and immunity, emphasizing the context of inflammation and immunological effects. In conclusion, we propose that atg8ylation is a modification akin to ubiquitylation, and that it is utilized by different systems participating in membrane stress responses and membrane remodeling activities encompassing autophagy and beyond.
Collapse
Affiliation(s)
- Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
20
|
Expanding the search for small-molecule antibacterials by multidimensional profiling. Nat Chem Biol 2022; 18:584-595. [PMID: 35606559 DOI: 10.1038/s41589-022-01040-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 04/15/2022] [Indexed: 11/08/2022]
Abstract
New techniques for systematic profiling of small-molecule effects can enhance traditional growth inhibition screens for antibiotic discovery and change how we search for new antibacterial agents. Computational models that integrate physicochemical compound properties with their phenotypic and molecular downstream effects can not only predict efficacy of molecules yet to be tested, but also reveal unprecedented insights on compound modes of action (MoAs). The unbiased characterization of compounds that themselves are not growth inhibitory but exhibit diverse MoAs, can expand antibacterial strategies beyond direct inhibition of core essential functions. Early and systematic functional annotation of compound libraries thus paves the way to new models in the selection of lead antimicrobial compounds. In this Review, we discuss how multidimensional small-molecule profiling and the ever-increasing computing power are accelerating the discovery of unconventional antibacterials capable of bypassing resistance and exploiting synergies with established antibacterial treatments and with protective host mechanisms.
Collapse
|
21
|
Ubiquitination-Proteasome System (UPS) and Autophagy Two Main Protein Degradation Machineries in Response to Cell Stress. Cells 2022; 11:cells11050851. [PMID: 35269473 PMCID: PMC8909305 DOI: 10.3390/cells11050851] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023] Open
Abstract
In response to environmental stimuli, cells make a series of adaptive changes to combat the injury, repair the damage, and increase the tolerance to the stress. However, once the damage is too serious to repair, the cells will undergo apoptosis to protect the overall cells through suicidal behavior. Upon external stimulation, some intracellular proteins turn into unfolded or misfolded protein, exposing their hydrophobic regions to form protein aggregation, which may ultimately produce serious damage to the cells. Ubiquitin plays an important role in the degradation of these unnatural proteins by tagging with ubiquitin chains in the ubiquitin-proteasome or autophagy system. If the two processes fail to eliminate the abnormal protein aggregates, the cells will move to apoptosis and death. Dysregulation of ubiquitin-proteasome system (UPS) and autophagy may result in the development of numerous diseases. This review focuses on the molecular mechanisms of UPS and autophagy in clearance of intracellular protein aggregates, and the relationship between dysregulation of ubiquitin network and diseases.
Collapse
|
22
|
Abstract
Ceragenins are a family of synthetic amphipathic molecules designed to mimic the properties of naturally occurring cationic antimicrobial peptides (CAMPs). Although ceragenins have potent antimicrobial activity, whether their mode of action is similar to that of CAMPs has remained elusive. Here, we reported the results of a comparative study of the bacterial responses to two well-studied CAMPs, LL37 and colistin, and two ceragenins with related structures, CSA13 and CSA131. Using transcriptomic and proteomic analyses, we found that Escherichia coli responded similarly to both CAMPs and ceragenins by inducing a Cpx envelope stress response. However, whereas E. coli exposed to CAMPs increased expression of genes involved in colanic acid biosynthesis, bacteria exposed to ceragenins specifically modulated functions related to phosphate transport, indicating distinct mechanisms of action between these two classes of molecules. Although traditional genetic approaches failed to identify genes that confer high-level resistance to ceragenins, using a Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) approach we identified E. coli essential genes that when knocked down modify sensitivity to these molecules. Comparison of the essential gene-antibiotic interactions for each of the CAMPs and ceragenins identified both overlapping and distinct dependencies for their antimicrobial activities. Overall, this study indicated that, while some bacterial responses to ceragenins overlap those induced by naturally occurring CAMPs, these synthetic molecules target the bacterial envelope using a distinctive mode of action. IMPORTANCE The development of novel antibiotics is essential because the current arsenal of antimicrobials will soon be ineffective due to the widespread occurrence of antibiotic resistance. The development of naturally occurring cationic antimicrobial peptides (CAMPs) for therapeutics to combat antibiotic resistance has been hampered by high production costs and protease sensitivity, among other factors. The ceragenins are a family of synthetic CAMP mimics that kill a broad spectrum of bacterial species but are less expensive to produce, resistant to proteolytic degradation, and seemingly resistant to the development of high-level resistance. Determining how ceragenins function may identify new essential biological pathways of bacteria that are less prone to the development of resistance and will further our understanding of the design principles for maximizing the effects of synthetic CAMPs.
Collapse
|
23
|
Elkington P, Polak ME, Reichmann MT, Leslie A. Understanding the tuberculosis granuloma: the matrix revolutions. Trends Mol Med 2022; 28:143-154. [PMID: 34922835 PMCID: PMC8673590 DOI: 10.1016/j.molmed.2021.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023]
Abstract
Mycobacterium tuberculosis (Mtb) causes the human disease tuberculosis (TB) and remains the top global infectious pandemic after coronavirus disease 2019 (COVID-19). Furthermore, TB has killed many more humans than any other pathogen, after prolonged coevolution to optimise its pathogenic strategies. Full understanding of fundamental disease processes in humans is necessary to successfully combat this highly successful pathogen. While the importance of immunodeficiency has been long recognised, biologic therapies and unbiased approaches are providing unprecedented insights into the intricacy of the host-pathogen interaction. The nature of a protective response is more complex than previously hypothesised. Here, we integrate recent evidence from human studies and unbiased approaches to consider how Mtb causes human TB and highlight the recurring theme of extracellular matrix (ECM) turnover.
Collapse
Affiliation(s)
- Paul Elkington
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
| | - Marta E Polak
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Michaela T Reichmann
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Alasdair Leslie
- Department of Infection and Immunity, University College London, London, UK; Africa Health Research Institute, KwaZulu-Natal, South Africa
| |
Collapse
|
24
|
Maculins T, Dikic I. Gasdermin B in the host-pathogen tug-of-war. Cell Res 2021; 31:1043-1044. [PMID: 34341491 PMCID: PMC8486812 DOI: 10.1038/s41422-021-00544-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Timurs Maculins
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA.
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany.
| |
Collapse
|
25
|
Pamela BE, Vasudevan P, Thamizhmaran S, Moorthy RK, Oommen A, Manoj J, Thanigachalam A, Zhang M, Drevets DA, Carabin H, Rajshekhar V. Monocyte Gene Expression Distinguishes Enhancing Brain Parenchymal Cysticercal Granulomas From Tuberculomas. Open Forum Infect Dis 2021; 8:ofab427. [PMID: 34557561 PMCID: PMC8454506 DOI: 10.1093/ofid/ofab427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/11/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND In patients with enhancing brain parenchymal lesions, parenchymal neurocysticercosis (pNCC) is often difficult to distinguish from tuberculoma, necessitating biopsy or empirical therapy. METHODS In a prospective study, peripheral blood monocytes were isolated from patients with definitive pNCC (n = 39) and brain tuberculomas (n = 20). Patients with tuberculomas were diagnosed by the presence of concurrent systemic tuberculosis (n = 7), pathological or bacteriological confirmation (n = 5), and resolution of typical brain lesions following a therapeutic trial of antituberculous therapy (n = 8). Expressions of 14 NCC-associated monocyte genes were determined by quantitative polymerase chain reaction and analyzed for diagnostic usefulness between the 2 groups. RESULTS Expression of 7 genes (TAX1BP1, RAP1A, PLCG2, TOR3A, GBP1P1, LRRFIP2, and FEZ2) was significantly higher in pNCC patients than in tuberculoma patients, with TAX1BP1 and RAP1A expressions more than 22- and 5-fold higher in pNCC patients. TAX1BP1 had the highest sensitivity of 66.7% at a specificity of 100% in discriminating pNCC from tuberculoma. A combination of TAX1BP1 and RAP1A increased the sensitivity to 84.6%, and including GBP1P1 with TAX1BP1 and RAP1A further increased sensitivity to 87.2% while maintaining specificity of 100%. CONCLUSIONS Expression of a panel of genes in blood monocytes distinguishes pNCC from brain tuberculomas in patients with enhancing brain lesions.
Collapse
Affiliation(s)
| | - Prabhakaran Vasudevan
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamilnadu, India
| | - Subashini Thamizhmaran
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamilnadu, India
| | - Ranjith K Moorthy
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamilnadu, India
| | - Anna Oommen
- Gudalur Adivasi Hospital, Gudalur, Tamilnadu, India
| | - Josephin Manoj
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamilnadu, India
| | - Anupriya Thanigachalam
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamilnadu, India
| | - Miao Zhang
- Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Douglas A Drevets
- Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Medical Services, Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, USA
| | - Hélène Carabin
- Department of Pathology and Microbiology, University of Montreal, Montreal, Quebec, Canada
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Centre de Recherche en Santé Publique (CReSP) de l’Université de Montréal et du CIUSS du Centre Sud de Montréal, Montreal, Quebec, Canada
- Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique (GREZOSP), Montreal, Quebec, Canada
| | - Vedantam Rajshekhar
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamilnadu, India
| |
Collapse
|
26
|
Bell SL, Lopez KL, Cox JS, Patrick KL, Watson RO. Galectin-8 Senses Phagosomal Damage and Recruits Selective Autophagy Adapter TAX1BP1 To Control Mycobacterium tuberculosis Infection in Macrophages. mBio 2021; 12:e0187120. [PMID: 34225486 PMCID: PMC8406326 DOI: 10.1128/mbio.01871-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 06/03/2021] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) causes one of the deadliest infectious diseases worldwide. Upon infection, Mtb is phagocytosed by macrophages and uses its virulence-associated ESX-1 secretion system to modulate the host cell. We showed previously that the ESX-1 secretion system perturbs the Mtb-containing phagosome, and a population (∼30%) of intracellular Mtb is tagged with ubiquitin and targeted to selective autophagy. However, our understanding of how macrophages sense and respond to damaged Mtb-containing phagosomes remains incomplete. Here, we demonstrate that several cytosolic glycan-binding proteins called galectins recognize Mtb-containing phagosomes; in macrophage cell lines and in primary macrophages, galectin-3, -8, and -9 are all recruited to the same Mtb population that colocalizes with selective autophagy markers (ubiquitin, p62, and LC3). To test whether galectins are required for controlling Mtb replication in macrophages, we generated CRISPR/Cas9 knockouts and found that galectin-8-/- and galectin-3/8/9-/- macrophages were similarly defective in targeting Mtb to selective autophagy and controlling replication. This suggests galectin-8 plays a unique role in anti-Mtb autophagy. In investigating galectin-8's role, we identified a novel and specific interaction between galectin-8 and the selective autophagy adapter TAX1BP1 and found that this galectin-8/TAX1BP1 interaction was necessary for macrophages to efficiently target Mtb to selective autophagy. Remarkably, overexpressing galectin-8 increased targeting of Mtb to autophagy and limited Mtb replication. Taken together, these data demonstrate that while several galectins are capable of recognizing damaged Mtb-containing phagosomes, galectin-8 plays a privileged role in recruiting downstream autophagy machinery and may represent a promising target for host-directed tuberculosis therapies. IMPORTANCE Mycobacterium tuberculosis (Mtb) infects one-quarter of the global population and causes one of the deadliest infectious diseases worldwide. Macrophages are the first line of defense against Mtb infection and are typically incredibly efficient at destroying intracellular pathogens, but Mtb has evolved to survive and replicate in this harsh environment. Previous work has found that a portion of intracellular Mtb bacilli damage their phagosomes, leaving them vulnerable to detection by the host and delivery to an antibacterial pathway called selective autophagy. Here, we show that in macrophages, galectin-8 recognizes damaged Mtb-containing phagosomes and targets Mtb to selective autophagy; we found that galectin-8, unlike other highly similar and closely related galectins, is required for targeting and controlling Mtb in macrophages. The specific role for galectin-8 appears to stem from its interaction with TAX1BP1, a selective autophagy adapter protein. Interestingly, overexpressing galectin-8 helps macrophages target and control Mtb, highlighting the importance of galectin-8 in the innate immune response to Mtb.
Collapse
Affiliation(s)
- Samantha L. Bell
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Kayla L. Lopez
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Jeffery S. Cox
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kristin L. Patrick
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Robert O. Watson
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
| |
Collapse
|
27
|
Decoding post translational modification crosstalk with proteomics. Mol Cell Proteomics 2021; 20:100129. [PMID: 34339852 PMCID: PMC8430371 DOI: 10.1016/j.mcpro.2021.100129] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/06/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modification (PTM) of proteins allows cells to regulate protein functions, transduce signals and respond to perturbations. PTMs expand protein functionality and diversity, which leads to increased proteome complexity. PTM crosstalk describes the combinatorial action of multiple PTMs on the same or on different proteins for higher order regulation. Here we review how recent advances in proteomic technologies, mass spectrometry instrumentation, and bioinformatics spurred the proteome-wide identification of PTM crosstalk through measurements of PTM sites. We provide an overview of the basic modes of PTM crosstalk, the proteomic methods to elucidate PTM crosstalk, and approaches that can inform about the functional consequences of PTM crosstalk. Description of basic modules and different modes of PTM crosstalk. Overview of current proteomic methods to identify and infer PTM crosstalk. Discussion of large-scale approaches to characterize functional PTM crosstalk. Future directions and potential proteomic methods for elucidating PTM crosstalk.
Collapse
|
28
|
Li Z, Hu J, Liu P, Cui D, Di H, Wu S. Microarray-based selection of a serum biomarker panel that can discriminate between latent and active pulmonary TB. Sci Rep 2021; 11:14516. [PMID: 34267288 PMCID: PMC8282789 DOI: 10.1038/s41598-021-93893-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Bacterial culture of M. tuberculosis (MTB), the causative agent of tuberculosis (TB), from clinical specimens is the gold standard for laboratory diagnosis of TB, but is slow and culture-negative TB cases are common. Alternative immune-based and molecular approaches have been developed, but cannot discriminate between active TB (ATB) and latent TB (LTBI). Here, to identify biomarkers that can discriminate between ATB and LTBI/healthy individuals (HC), we profiled 116 serum samples (HC, LTBI and ATB) using a protein microarray containing 257 MTB secreted proteins, identifying 23 antibodies against MTB antigens that were present at significantly higher levels in patients with ATB than in those with LTBI and HC (Fold change > 1.2; p < 0.05). A 4-protein biomarker panel (Rv0934, Rv3881c, Rv1860 and Rv1827), optimized using SAM and ROC analysis, had a sensitivity of 67.3% and specificity of 91.2% for distinguishing ATB from LTBI, and 71.2% sensitivity and 96.3% specificity for distinguishing ATB from HC. Validation of the four candidate biomarkers in ELISA assays using 440 serum samples gave consistent results. The promising sensitivity and specificity of this biomarker panel suggest it merits further investigation for its potential as a diagnostic for discriminating between latent and active TB.
Collapse
Affiliation(s)
- Zhihui Li
- Hebei Chest Hospital, Shijiazhuang, 050041, China
| | - Jianjun Hu
- Hebei Chest Hospital, Shijiazhuang, 050041, China
| | | | - Dan Cui
- Hebei Chest Hospital, Shijiazhuang, 050041, China
| | - Hongqin Di
- Hebei Chest Hospital, Shijiazhuang, 050041, China
| | - Shucai Wu
- Hebei Chest Hospital, Shijiazhuang, 050041, China.
| |
Collapse
|
29
|
Wagner AR, Scott HM, West KO, Vail KJ, Fitzsimons TC, Coleman AK, Carter KE, Watson RO, Patrick KL. Global Transcriptomics Uncovers Distinct Contributions From Splicing Regulatory Proteins to the Macrophage Innate Immune Response. Front Immunol 2021; 12:656885. [PMID: 34305890 PMCID: PMC8299563 DOI: 10.3389/fimmu.2021.656885] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Pathogen sensing via pattern recognition receptors triggers massive reprogramming of macrophage gene expression. While the signaling cascades and transcription factors that activate these responses are well-known, the role of post-transcriptional RNA processing in modulating innate immune gene expression remains understudied. Given their crucial role in regulating pre-mRNA splicing and other RNA processing steps, we hypothesized that members of the SR/hnRNP protein families regulate innate immune gene expression in distinct ways. We analyzed steady state gene expression and alternatively spliced isoform production in ten SR/hnRNP knockdown RAW 264.7 macrophage-like cell lines following infection with the bacterial pathogen Salmonella enterica serovar Typhimurium (Salmonella). We identified thousands of transcripts whose abundance is increased or decreased by SR/hnRNP knockdown in macrophages. Notably, we observed that SR and hnRNP proteins influence expression of different genes in uninfected versus Salmonella-infected macrophages, suggesting functionalization of these proteins upon pathogen sensing. Likewise, we found that knockdown of SR/hnRNPs promoted differential isoform usage (DIU) for thousands of macrophage transcripts and that these alternative splicing changes were distinct in uninfected and Salmonella-infected macrophages. Finally, having observed a surprising degree of similarity between the differentially expressed genes (DEGs) and DIUs in hnRNP K and U knockdown macrophages, we found that hnRNP K and U knockdown macrophages are both more restrictive to Vesicular Stomatitis Virus (VSV), while hnRNP K knockdown macrophages are more permissive to Salmonella Typhimurium. Based on these findings, we conclude that many innate immune genes evolved to rely on one or more SR/hnRNPs to ensure the proper magnitude of their induction, supporting a model wherein pre-mRNA splicing is critical for regulating innate immune gene expression and controlling infection outcomes in macrophages ex vivo.
Collapse
Affiliation(s)
- Allison R Wagner
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Haley M Scott
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Kelsi O West
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Krystal J Vail
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States.,Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Timothy C Fitzsimons
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Aja K Coleman
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Kaitlyn E Carter
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Robert O Watson
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Kristin L Patrick
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| |
Collapse
|
30
|
Anand C, Santoshi M, Singh PR, Nagaraja V. Rv0802c is an acyltransferase that succinylates and acetylates Mycobacterium tuberculosis nucleoid-associated protein HU. MICROBIOLOGY-SGM 2021; 167. [PMID: 34224344 DOI: 10.1099/mic.0.001058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Among the nucleoid-associated proteins (NAPs), HU is the most conserved in eubacteria, engaged in overall chromosome organization and regulation of gene expression. Unlike other bacteria, HU from Mycobacterium tuberculosis (MtHU), has a long carboxyl terminal domain enriched in basic amino acids, resembling eukaryotic histone N-terminal tails. As with histones, MtHU undergoes post-translational modifications and we have previously identified interacting kinases, methyltransferases, an acetyltransferase and a deacetylase. Here we show that Rv0802c interacts and succinylates MtHU. Although categorized as a succinyltransferase, we show that this GNAT superfamily member can catalyse both succinylation and acetylation of MtHU with comparable kinetic parameters. Like acetylation of MtHU, succinylation of MtHU caused reduced interaction of the NAP with DNA, determined by electrophoretic mobility shift assay and surface plasmon resonance. However, in vivo expression of Rv0802c did not significantly alter the nucleoid architecture. Although such succinylation of NAPs is rare, these modifications of the archetypal NAP may provide avenues to the organism to compensate for the underrepresentation of NAPs in its genome to control the dynamics of nucleoid architecture and cellular functions.
Collapse
Affiliation(s)
- Chinmay Anand
- Department of Microbiology and Cell biology, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Meghna Santoshi
- Department of Microbiology and Cell biology, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Prakruti R Singh
- Department of Microbiology and Cell biology, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell biology, Indian Institute of Science, Bengaluru, Karnataka 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
| |
Collapse
|
31
|
Mishra R, Yadav V, Guha M, Singh A. Heterogeneous Host-Pathogen Encounters Coordinate Antibiotic Resilience in Mycobacterium tuberculosis. Trends Microbiol 2021; 29:606-620. [PMID: 33309526 PMCID: PMC7611257 DOI: 10.1016/j.tim.2020.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022]
Abstract
Successful treatment of tuberculosis (TB) depends on the eradication of its causative agent Mycobacterium tuberculosis (Mtb) in the host. However, the emergence of phenotypically drug-resistant Mtb in the host environment tempers the ability of antibiotics to cure disease. Host immunity produces diverse microenvironmental niches that are exploited by Mtb to mobilize adaptation programs. Such differential interactions amplify pre-existing heterogeneity in the host-pathogen milieu to influence disease pathology and therapy outcome. Therefore, comprehending the intricacies of phenotypic heterogeneity can be an empirical step forward in potentiating drug action. With this goal, we review the interconnectedness of the lesional, cellular, and bacterial heterogeneity underlying phenotypic drug resistance. Based on this information, we anticipate the development of new therapeutic strategies targeting host-pathogen heterogeneity to cure TB.
Collapse
Affiliation(s)
- Richa Mishra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru-560012, India; Centre for Infectious Disease and Research (CIDR), Indian Institute of Science, Bengaluru-560012, India
| | - Vikas Yadav
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru-560012, India; Centre for Infectious Disease and Research (CIDR), Indian Institute of Science, Bengaluru-560012, India
| | - Madhura Guha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru-560012, India; Centre for Infectious Disease and Research (CIDR), Indian Institute of Science, Bengaluru-560012, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru-560012, India; Centre for Infectious Disease and Research (CIDR), Indian Institute of Science, Bengaluru-560012, India.
| |
Collapse
|
32
|
Simeone R, Sayes F, Lawarée E, Brosch R. Breaching the phagosome, the case of the tuberculosis agent. Cell Microbiol 2021; 23:e13344. [PMID: 33860624 DOI: 10.1111/cmi.13344] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/14/2022]
Abstract
The interactions between microbes and their hosts are among the most complex biological phenomena known today. The interaction may reach from overall beneficial interaction, as observed for most microbiome/microbiota related interactions to interaction with virulent pathogens, against which host cells have evolved sophisticated defence strategies. Among the latter, the confinement of invading pathogens in a phagosome plays a key role, which often results in the destruction of the invader, whereas some pathogens may counteract phagosomal arrest and survive by gaining access to the cytosol of the host cell. In the current review, we will discuss recent insights into this dynamic process of host-pathogen interaction, using Mycobacterium tuberculosis and related pathogenic mycobacteria as main examples.
Collapse
Affiliation(s)
- Roxane Simeone
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Fadel Sayes
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Emeline Lawarée
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| |
Collapse
|
33
|
Kinsella RL, Zhu DX, Harrison GA, Mayer Bridwell AE, Prusa J, Chavez SM, Stallings CL. Perspectives and Advances in the Understanding of Tuberculosis. ANNUAL REVIEW OF PATHOLOGY 2021; 16:377-408. [PMID: 33497258 DOI: 10.1146/annurev-pathol-042120-032916] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), remains a leading cause of death due to infection in humans. To more effectively combat this pandemic, many aspects of TB control must be developed, including better point of care diagnostics, shorter and safer drug regimens, and a protective vaccine. To address all these areas of need, better understanding of the pathogen, host responses, and clinical manifestations of the disease is required. Recently, the application of cutting-edge technologies to the study of Mtb pathogenesis has resulted in significant advances in basic biology, vaccine development, and antibiotic discovery. This leaves us in an exciting era of Mtb research in which our understanding of this deadly infection is improving at a faster rate than ever, and renews hope in our fight to end TB. In this review, we reflect on what is known regarding Mtb pathogenesis, highlighting recent breakthroughs that will provide leverage for the next leaps forward in the field.
Collapse
Affiliation(s)
- Rachel L Kinsella
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Dennis X Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Gregory A Harrison
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Anne E Mayer Bridwell
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Jerome Prusa
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Sthefany M Chavez
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| |
Collapse
|
34
|
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
|
35
|
Shariq M, Quadir N, Sheikh JA, Singh AK, Bishai WR, Ehtesham NZ, Hasnain SE. Post translational modifications in tuberculosis: ubiquitination paradox. Autophagy 2020; 17:814-817. [PMID: 33190592 DOI: 10.1080/15548627.2020.1850009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Innate immune signaling and xenophagy are crucial innate defense strategies exploited by the host to counteract intracellular pathogens with ubiquitination as a critical regulator of these processes. These pathogens, including Mycobacterium tuberculosis (M. tb), co-opt the host ubiquitin machinery by utilizing secreted or cell surface effectors to dampen innate host defenses. Inversely, the host utilizes ubiquitin ligase-mediated ubiquitination of intracellular pathogens and recruits autophagy receptors to induce xenophagy. In the current article, we discuss the co-option of the ubiquitin pathway by the M. tb virulence effectors.Abbreviations: ANAPC2: anaphase promoting complex subunit 2; IL: interleukin; Lys: lysine (K); MAPK: mitogen-activated protein kinase; MAP3K7/TAK1; mitogen-activated protein kinase kinase kinase 7; M. tb: Mycobacterium tuberculosis; NFKB/NF-κB: nuclear factor kappa B subunit; PtpA: protein tyrosine phosphatase; SQSTM1/p62: sequestosome 1; V-ATPase: vacuolar-type H+-ATPase; UBA: a eukaryotic-like ubiquitin-associated domain.
Collapse
Affiliation(s)
- Mohd Shariq
- ICMR-National Institute of Pathology, New Delhi, India
| | - Neha Quadir
- ICMR-National Institute of Pathology, New Delhi, India.,JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Javaid Ahmad Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, New Delhi, India
| | - Alok Kumar Singh
- Johns Hopkins School of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - William R Bishai
- Johns Hopkins School of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | | | - Seyed E Hasnain
- JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| |
Collapse
|
36
|
Strong EJ, Jurcic Smith KL, Saini NK, Ng TW, Porcelli SA, Lee S. Identification of Autophagy-Inhibiting Factors of Mycobacterium tuberculosis by High-Throughput Loss-of-Function Screening. Infect Immun 2020; 88:e00269-20. [PMID: 32989037 PMCID: PMC7671894 DOI: 10.1128/iai.00269-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
The interaction of host cells with mycobacteria is complex and can lead to multiple outcomes ranging from bacterial clearance to progressive or latent infection. Autophagy is recognized as one component of host cell responses that has an essential role in innate and adaptive immunity to intracellular bacteria. Many microbes, including Mycobacterium tuberculosis, have evolved to evade or exploit autophagy, but the precise mechanisms and virulence factors are mostly unknown. Through a loss-of-function screening of an M. tuberculosis transposon mutant library, we identified 16 genes that contribute to autophagy inhibition, six of which encoded the PE/PPE protein family. Their expression in Mycobacterium smegmatis confirmed that these PE/PPE proteins inhibit autophagy and increase intracellular bacterial persistence or replication in infected cells. These effects were associated with increased mammalian target of rapamycin (mTOR) activity and also with decreased production of tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β). We also confirmed that the targeted deletion of the pe/ppe genes in M. tuberculosis resulted in enhanced autophagy and improved intracellular survival rates compared to those of wild-type bacteria in the infected macrophages. Differential expression of these PE/PPE proteins was observed in response to various stress conditions, suggesting that they may confer advantages to M. tuberculosis by modulating its interactions with host cells under various conditions. Our findings demonstrated that multiple M. tuberculosis PE/PPE proteins are involved in inhibiting autophagy during infection of host phagocytes and may provide strategic targets in developing therapeutics or vaccines against tuberculosis.
Collapse
Affiliation(s)
- Emily J Strong
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Neeraj K Saini
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tony W Ng
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Steven A Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sunhee Lee
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| |
Collapse
|
37
|
Sukumaran A, Woroszchuk E, Ross T, Geddes-McAlister J. Proteomics of host-bacterial interactions: new insights from dual perspectives. Can J Microbiol 2020; 67:213-225. [PMID: 33027598 DOI: 10.1139/cjm-2020-0324] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass-spectrometry (MS)-based proteomics is a powerful and robust platform for studying the interactions between biological systems during health and disease. Bacterial infections represent a significant threat to global health and drive the pursuit of novel therapeutic strategies to combat emerging and resistant pathogens. During infection, the interplay between a host and pathogen determines the ability of the microbe to survive in a hostile environment and promotes an immune response by the host as a protective measure. It is the protein-level changes from either biological system that define the outcome of infection, and MS-based proteomics provides a rapid and effective platform to identify such changes. In particular, proteomics detects alterations in protein abundance, quantifies protein secretion and (or) release, measures an array of post-translational modifications that influence signaling cascades, and profiles protein-protein interactions through protein complex and (or) network formation. Such information provides new insight into the role of known and novel bacterial effectors, as well as the outcome of host cell activation. In this Review, we highlight the diverse applications of MS-based proteomics in profiling the relationship between bacterial pathogens and the host. Our work identifies a plethora of strategies for exploring mechanisms of infection from dual perspectives (i.e., host and pathogen), and we suggest opportunities to extrapolate the current knowledgebase to other biological systems for applications in therapeutic discovery.
Collapse
Affiliation(s)
- Arjun Sukumaran
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Elizabeth Woroszchuk
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Taylor Ross
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jennifer Geddes-McAlister
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
38
|
Yu X, Liu C, Yang W, Stojkoska A, Cheng G, Yang H, Yue R, Wang J, Liao Y, Sun X, Zhou X, Xie J. Global quantitative phosphoproteome reveals phosphorylation network of bovine lung tissue altered by Mycobacterium bovis. Microb Pathog 2020; 147:104402. [PMID: 32712114 DOI: 10.1016/j.micpath.2020.104402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/08/2020] [Accepted: 07/15/2020] [Indexed: 10/23/2022]
Abstract
Bovine tuberculosis caused by Mycobacterium bovis remains a major cause of economic loss in cattle industries worldwide. However, the pathogenic mechanisms remain poorly understood. Post-translation modifications (PTM) such as phosphorylation play a crucial role in pathogenesis. While the change of transcriptome and proteome during the interaction between M. bovis and cattle were studied, there are no reports on the phosphoproteome change. We apply Tandem Mass Tag-based (TMT) quantitative proteomics coupled with immobilized metal-chelated affinity chromatography (IMAC) enrichment to obtain the quantified phosphorylation in vivo of M. bovis infected cattle lung tissue. The phosphorylated proteins are widespread in the nucleus, cytoplasm and plasma membrane. By using a change fold of 1.2, 165 phosphosites from 147 proteins were enriched, with 88 upregulated and 77 downregulated sites respectively. We further constructed the protein-protein interaction (PPI) networks of STAT3, SRRM2 and IRS-1 based on their number of differential phosphorylation sites and KEGG pathways. Similar patterns of gene expression dynamics of selected genes were observed in Mycobacterium tuberculosis infected human sample GEO dataset, implicating crucial roles of these genes in pathogenic Mycobacteria - host interaction. The first phosphorproteome reveals the relationship between bovine tuberculosis and glucose metabolism, and will help further refinement of target proteins for mechanistic study.
Collapse
Affiliation(s)
- Xi Yu
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, 400715, China
| | - Chunfa Liu
- Chinese Center for Disease Control and Prevention, National Tuberculosis Reference Laboratory, Changping, 102206, Beijing, China
| | - Wenmin Yang
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, 400715, China
| | - Andrea Stojkoska
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, 400715, China
| | - Guangyu Cheng
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Hongjun Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Ruichao Yue
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Jie Wang
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Yi Liao
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Xin Sun
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Xiangmei Zhou
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China.
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
39
|
Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. eLife 2020; 9:e51461. [PMID: 31951200 PMCID: PMC7030789 DOI: 10.7554/elife.51461] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/16/2020] [Indexed: 12/23/2022] Open
Abstract
Macrophages are highly plastic cells with critical roles in immunity, cancer, and tissue homeostasis, but how these distinct cellular fates are triggered by environmental cues is poorly understood. To uncover how primary murine macrophages respond to bacterial pathogens, we globally assessed changes in post-translational modifications of proteins during infection with Mycobacterium tuberculosis, a notorious intracellular pathogen. We identified hundreds of dynamically regulated phosphorylation and ubiquitylation sites, indicating that dramatic remodeling of multiple host pathways, both expected and unexpected, occurred during infection. Most of these cellular changes were not captured by mRNA profiling, and included activation of ubiquitin-mediated autophagy, an evolutionarily ancient cellular antimicrobial system. This analysis also revealed that a particular autophagy receptor, TAX1BP1, mediates clearance of ubiquitylated Mtb and targets bacteria to LC3-positive phagophores. These studies provide a new resource for understanding how macrophages shape their proteome to meet the challenge of infection.
Collapse
Affiliation(s)
- Jonathan M Budzik
- Department of MedicineUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Danielle L Swaney
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Gladstone InstitutesSan FranciscoUnited States
| | - David Jimenez-Morales
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Gladstone InstitutesSan FranciscoUnited States
- Department of Medicine, Division of Cardiovascular MedicineStanford UniversityStanfordUnited States
| | - Jeffrey R Johnson
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Gladstone InstitutesSan FranciscoUnited States
| | - Nicholas E Garelis
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Teresa Repasy
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Allison W Roberts
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Lauren M Popov
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Trevor J Parry
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Dexter Pratt
- Department of MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Trey Ideker
- Department of MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Nevan J Krogan
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Gladstone InstitutesSan FranciscoUnited States
| | - Jeffery S Cox
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| |
Collapse
|