1
|
Malik AA, Shariq M, Sheikh JA, Fayaz H, Srivastava G, Thakuri D, Ahuja Y, Ali S, Alam A, Ehtesham NZ, Hasnain SE. Regulation of Type I Interferon and Autophagy in Immunity against Mycobacterium Tuberculosis: Role of CGAS and STING1. Adv Biol (Weinh) 2024:e2400174. [PMID: 38977406 DOI: 10.1002/adbi.202400174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/22/2024] [Indexed: 07/10/2024]
Abstract
Mycobacterium tuberculosis (M. tb) is a significant intracellular pathogen responsible for numerous infectious disease-related deaths worldwide. It uses ESX-1 T7SS to damage phagosomes and to enter the cytosol of host cells after phagocytosis. During infection, M. tb and host mitochondria release dsDNA, which activates the CGAS-STING1 pathway. This pathway leads to the production of type I interferons and proinflammatory cytokines and activates autophagy, which targets and degrades bacteria within autophagosomes. However, the role of type I IFNs in immunity against M. tb is controversial. While previous research has suggested a protective role, recent findings from cgas-sting1 knockout mouse studies have contradicted this. Additionally, a study using knockout mice and non-human primate models uncovered a new mechanism by which neutrophils recruited to lung infections form neutrophil extracellular traps. Activating plasmacytoid dendritic cells causes them to produce type I IFNs, which interfere with the function of interstitial macrophages and increase the likelihood of tuberculosis. Notably, M. tb uses its virulence proteins to disrupt the CGAS-STING1 signaling pathway leading to enhanced pathogenesis. Investigating the CGAS-STING1 pathway can help develop new ways to fight tuberculosis.
Collapse
Affiliation(s)
- Asrar Ahmad Malik
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh, 201306, India
| | - Mohd Shariq
- ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi, 110029, India
| | - Javaid Ahmad Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Haleema Fayaz
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh, 201306, India
| | - Gauri Srivastava
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh, 201306, India
| | - Deeksha Thakuri
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh, 201306, India
| | - Yashika Ahuja
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh, 201306, India
| | - Saquib Ali
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh, 201306, India
| | - Anwar Alam
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh, 201306, India
| | - Nasreen Z Ehtesham
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh, 201306, India
| | - Seyed E Hasnain
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh, 201306, India
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi, 110 016, India
| |
Collapse
|
2
|
Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [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: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| |
Collapse
|
3
|
Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [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: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| |
Collapse
|
4
|
Kosmachevskaya OV, Novikova NN, Yakunin SN, Topunov AF. Formation of Supplementary Metal-Binding Centers in Proteins under Stress Conditions. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S180-S204. [PMID: 38621750 DOI: 10.1134/s0006297924140104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/21/2023] [Accepted: 10/29/2023] [Indexed: 04/17/2024]
Abstract
In many proteins, supplementary metal-binding centers appear under stress conditions. They are known as aberrant or atypical sites. Physico-chemical properties of proteins are significantly changed after such metal binding, and very stable protein aggregates are formed, in which metals act as "cross-linking" agents. Supplementary metal-binding centers in proteins often arise as a result of posttranslational modifications caused by reactive oxygen and nitrogen species and reactive carbonyl compounds. New chemical groups formed as a result of these modifications can act as ligands for binding metal ions. Special attention is paid to the role of cysteine SH-groups in the formation of supplementary metal-binding centers, since these groups are the main target for the action of reactive species. Supplementary metal binding centers may also appear due to unmasking of amino acid residues when protein conformation changing. Appearance of such centers is usually considered as a pathological process. Such unilateral approach does not allow to obtain an integral view of the phenomenon, ignoring cases when formation of metal complexes with altered proteins is a way to adjust protein properties, activity, and stability under the changed redox conditions. The role of metals in protein aggregation is being studied actively, since it leads to formation of non-membranous organelles, liquid condensates, and solid conglomerates. Some proteins found in such aggregates are typical for various diseases, such as Alzheimer's and Huntington's diseases, amyotrophic lateral sclerosis, and some types of cancer.
Collapse
Affiliation(s)
- Olga V Kosmachevskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | | | - Sergey N Yakunin
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Alexey F Topunov
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| |
Collapse
|
5
|
Rastogi N, Zarin S, Alam A, Konduru GV, Manjunath P, Mishra A, Kumar S, Nagarajaram HA, Hasnain SE, Ehtesham NZ. Structural and Biophysical properties of therapeutically important proteins Rv1509 and Rv2231A of Mycobacterium tuberculosis. Int J Biol Macromol 2023; 245:125455. [PMID: 37331537 DOI: 10.1016/j.ijbiomac.2023.125455] [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: 04/14/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
Through comparative analyses using BLASTp and BLASTn of the 25 target sequences, our research identified two unique post-transcriptional modifiers, Rv1509 and Rv2231A, which serve as distinctive and characteristic proteins of M.tb - the Signature Proteins. Here, we have characterized these two signature proteins associated with pathophysiology of M.tb which may prove to be therapeutically important targets. Dynamic Light Scattering and Analytical Gel Filtration Chromatography exhibited that Rv1509 exists as a monomer while Rv2231A as a dimer in solution. Secondary structures were determined using Circular Dichroism and further validated through Fourier Transform Infrared spectroscopy. Both the proteins are capable of withstanding a wide range of temperature and pH variations. Fluorescence spectroscopy based binding affinity experiments showed that Rv1509 binds to iron and may promote organism growth by chelating iron. In the case of Rv2231A, a high affinity for its substrate RNA was observed, which is facilitated in presence of Mg2+ suggesting it might have RNAse activity, supporting the prediction through in-silico studies. This is the first study on biophysical characterization of these two therapeutically important proteins, Rv1509 and Rv2231A, providing important insights into their structure -function correlations which are crucial for development of new drugs/ early diagnostics tools targeting these proteins.
Collapse
Affiliation(s)
- Nilisha Rastogi
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi 110029, India
| | - Sheeba Zarin
- Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India; Department of Life Science, School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India
| | - Anwar Alam
- Department of Biotechnology, School of Engineering Sciences and Technology, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India
| | - Guruprasad Varma Konduru
- Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, India; Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - P Manjunath
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi 110029, India
| | - Abhay Mishra
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Saroj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Hampapathalu Adimurthy Nagarajaram
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Prof C.R. Rao Road, Hyderabad 500007, India
| | - Seyed Ehtesham Hasnain
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India.
| | - Nasreen Zafar Ehtesham
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India.
| |
Collapse
|
6
|
Padmanabhan S, Manjithaya R. Leaderless secretory proteins of the neurodegenerative diseases via TNTs: a structure-function perspective. Front Mol Neurosci 2023; 16:983108. [PMID: 37396786 PMCID: PMC10308029 DOI: 10.3389/fnmol.2023.983108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Neurodegenerative disease-causing proteins such as alpha-synuclein, tau, and huntingtin are known to traverse across cells via exosomes, extracellular vesicles and tunneling nanotubes (TNTs). There seems to be good synergy between exosomes and TNTs in intercellular communication. Interestingly, many of the known major neurodegenerative proteins/proteolytic products are leaderless and are also reported to be secreted out of the cell via unconventional protein secretion. Such classes contain intrinsically disordered proteins and regions (IDRs) within them. The dynamic behavior of these proteins is due to their heterogenic conformations that is exhibited owing to various factors that occur inside the cells. The amino acid sequence along with the chemical modifications has implications on the functional roles of IDRs inside the cells. Proteins that form aggregates resulting in neurodegeneration become resistant to degradation by the processes of autophagy and proteasome system thus leading to Tunneling nanotubes, TNT formation. The proteins that traverse across TNTs may or may not be dependent on the autophagy machinery. It is not yet clear whether the conformation of the protein plays a crucial role in its transport from one cell to another without getting degraded. Although there is some experimental data, there are many grey areas which need to be revisited. This review provides a different perspective on the structural and functional aspects of these leaderless proteins that get secreted outside the cell. In this review, attention has been focused on the characteristic features that lead to aggregation of leaderless secretory proteins (from structural-functional aspect) with special emphasis on TNTs.
Collapse
|
7
|
Basu S, Gsponer J, Kurgan L. DEPICTER2: a comprehensive webserver for intrinsic disorder and disorder function prediction. Nucleic Acids Res 2023:7151337. [PMID: 37140058 DOI: 10.1093/nar/gkad330] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Intrinsic disorder in proteins is relatively abundant in nature and essential for a broad spectrum of cellular functions. While disorder can be accurately predicted from protein sequences, as it was empirically demonstrated in recent community-organized assessments, it is rather challenging to collect and compile a comprehensive prediction that covers multiple disorder functions. To this end, we introduce the DEPICTER2 (DisorderEd PredictIon CenTER) webserver that offers convenient access to a curated collection of fast and accurate disorder and disorder function predictors. This server includes a state-of-the-art disorder predictor, flDPnn, and five modern methods that cover all currently predictable disorder functions: disordered linkers and protein, peptide, DNA, RNA and lipid binding. DEPICTER2 allows selection of any combination of the six methods, batch predictions of up to 25 proteins per request and provides interactive visualization of the resulting predictions. The webserver is freely available at http://biomine.cs.vcu.edu/servers/DEPICTER2/.
Collapse
Affiliation(s)
- Sushmita Basu
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| |
Collapse
|
8
|
Kovács D, Bodor A. The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs. RSC Adv 2023; 13:10182-10203. [PMID: 37006359 PMCID: PMC10065145 DOI: 10.1039/d3ra00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
In studying secondary structural propensities of proteins by nuclear magnetic resonance (NMR) spectroscopy, secondary chemical shifts (SCSs) serve as the primary atomic scale observables. For SCS calculation, the selection of an appropriate random coil chemical shift (RCCS) dataset is a crucial step, especially when investigating intrinsically disordered proteins (IDPs). The scientific literature is abundant in such datasets, however, the effect of choosing one over all the others in a concrete application has not yet been studied thoroughly and systematically. Hereby, we review the available RCCS prediction methods and to compare them, we conduct statistical inference by means of the nonparametric sum of ranking differences and comparison of ranks to random numbers (SRD-CRRN) method. We try to find the RCCS predictors best representing the general consensus regarding secondary structural propensities. The existence and the magnitude of resulting differences on secondary structure determination under varying sample conditions (temperature, pH) are demonstrated and discussed for globular proteins and especially IDPs.
Collapse
Affiliation(s)
- Dániel Kovács
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
- Eötvös Loránd University, Hevesy György PhD School of Chemistry Pázmány Péter sétány 1/A Budapest 1117 Hungary
| | - Andrea Bodor
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
| |
Collapse
|
9
|
Krishnamurthy K, Oh KS, Alghamdi S, Sriganeshan V, Poppiti R. A study of somatic BRCA variants and their putative effect on protein properties in malignant mesothelioma. Pleura Peritoneum 2023; 8:19-25. [PMID: 37020472 PMCID: PMC10067552 DOI: 10.1515/pp-2023-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 02/23/2023] [Indexed: 04/04/2023] Open
Abstract
Abstract
Objectives
The aim of this study is to analyze the prevalence of somatic mutations in BRCA1 and BRCA2 in malignant mesothelioma and their putative impact on protein properties.
Methods
Eighteen cases of malignant mesothelioma were retrieved from the archives and for next generation sequencing analysis of BRCA1 and BRCA2 genes. Variants were analyzed using Ensembl VEP17, Polyphen 2.0 software, SIFT software, MutpredV2, and SWISS-MODEL homology-modeling pipeline server.
Results
BRCA2 variants were found in significantly higher percentage (22%) of cases (p=0.02). Five missense variants were identified. These were p.A2351P, p.T2250A, p.A895V, pG1771D, and p.R2034C. The SIFT scores of all except one were ≥ 0.03. The Polyphen scores of these four alterations were ≤0.899. In case of p.A2315, the SIFT score was 0.01, while the Polyphen 2 score was 0.921. MutPred2 scores were ≤0.180 for all. Loss of intrinsic disorder was predicted (Pr=0.32, p=0.07) for p.R2034C, while gain of intrinsic disorder was predicted for p.A2351P (Pr=0.36, p=0.01) and p.G1771D (Pr=0.34, p=0.02).
Conclusions
BRCA2 somatic variants were identified in 22% cases of malignant mesotheliomas in this study. The variants localize more frequently to the disordered regions of the protein and are predicted to affect the level of disorder.
Collapse
Affiliation(s)
- Kritika Krishnamurthy
- Department of Pathology , Montefiore Medical Center, Albert Einstein College of Medicine , Bronx , NY , USA
| | - Kei Shing Oh
- AM Rywlin Department of Pathology , Mount Sinai Medical Center , Miami Beach , FL , USA
| | - Sarah Alghamdi
- AM Rywlin Department of Pathology , Mount Sinai Medical Center , Miami Beach , FL , USA
- Pathology , FIU/Herbert Werthein College of Medicine , Miami , FL , USA
| | - Vathany Sriganeshan
- AM Rywlin Department of Pathology , Mount Sinai Medical Center , Miami Beach , FL , USA
- Pathology , FIU/Herbert Werthein College of Medicine , Miami , FL , USA
| | - Robert Poppiti
- AM Rywlin Department of Pathology , Mount Sinai Medical Center , Miami Beach , FL , USA
- Pathology , FIU/Herbert Werthein College of Medicine , Miami , FL , USA
| |
Collapse
|
10
|
Gupta MN, Uversky VN. Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins. Int J Mol Sci 2023; 24:ijms24032424. [PMID: 36768742 PMCID: PMC9916686 DOI: 10.3390/ijms24032424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-494-5816
| |
Collapse
|
11
|
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
|
12
|
Sicilia C, Corral-Lugo A, Smialowski P, McConnell MJ, Martín-Galiano AJ. Unsupervised Machine Learning Organization of the Functional Dark Proteome of Gram-Negative "Superbugs": Six Protein Clusters Amenable for Distinct Scientific Applications. ACS OMEGA 2022; 7:46131-46145. [PMID: 36570227 PMCID: PMC9774411 DOI: 10.1021/acsomega.2c04076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/06/2022] [Indexed: 06/17/2023]
Abstract
Uncharacterized proteins have been underutilized as targets for the development of novel therapeutics for difficult-to-treat bacterial infections. To facilitate the exploration of these proteins, 2819 predicted, uncharacterized proteins (19.1% of the total) from reference strains of multidrug Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa species were organized using an unsupervised k-means machine learning algorithm. Classification using normalized values for protein length, pI, hydrophobicity, degree of conservation, structural disorder, and %AT of the coding gene rendered six natural clusters. Cluster proteins showed different trends regarding operon membership, expression, presence of unknown function domains, and interactomic relevance. Clusters 2, 4, and 5 were enriched with highly disordered proteins, nonworkable membrane proteins, and likely spurious proteins, respectively. Clusters 1, 3, and 6 showed closer distances to known antigens, antibiotic targets, and virulence factors. Up to 21.8% of proteins in these clusters were structurally covered by modeling, which allowed assessment of druggability and discontinuous B-cell epitopes. Five proteins (4 in Cluster 1) were potential druggable targets for antibiotherapy. Eighteen proteins (11 in Cluster 6) were strong B-cell and T-cell immunogen candidates for vaccine development. Conclusively, we provide a feature-based schema to fractionate the functional dark proteome of critical pathogens for fundamental and biomedical purposes.
Collapse
Affiliation(s)
- Carlos Sicilia
- Intrahospital
Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
| | - Andrés Corral-Lugo
- Intrahospital
Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
| | - Pawel Smialowski
- Core
Facility Bioinformatics, Biomedical Center Munich, Faculty of Medicine, Ludwig Maximilians Universität München, Munich 80539, Germany
- Institute
of Stem Cell Research, Helmholtz Center Munich, Planegg-Martinsried 82152, Germany
| | - Michael J. McConnell
- Intrahospital
Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
| | - Antonio J. Martín-Galiano
- Intrahospital
Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
| |
Collapse
|
13
|
Dean D. Virtual article collection on infectious diseases. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 171:2-3. [PMID: 35247374 PMCID: PMC8889788 DOI: 10.1016/j.pbiomolbio.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
14
|
Metabotropic Glutamate Receptors at Ribbon Synapses in the Retina and Cochlea. Cells 2022; 11:cells11071097. [PMID: 35406660 PMCID: PMC8998116 DOI: 10.3390/cells11071097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Our senses define our view of the world. They allow us to adapt to environmental stimuli and are essential for communication and social behaviour. For most humans, seeing and hearing are central senses for their daily life. Our eyes and ears respond to an extraordinary broad range of stimuli covering about 12 log units of light intensity or acoustic power, respectively. The cellular basis is represented by sensory cells (photoreceptors in the retina and inner hair cells in the cochlea) that convert sensory inputs into electrical signals. Photoreceptors and inner hair cells have developed a specific pre-synaptic structure, termed synaptic ribbon, that is decorated with numerous vesicles filled with the excitatory neurotransmitter glutamate. At these ribbon synapses, glutamatergic signal transduction is guided by distinct sets of metabotropic glutamate receptors (mGluRs). MGluRs belong to group II and III of the receptor classification can inhibit neuronal activity, thus protecting neurons from overstimulation and subsequent degeneration. Consequently, dysfunction of mGluRs is associated with vision and hearing disorders. In this review, we introduce the principle characteristics of ribbon synapses and describe group II and III mGluRs in these fascinating structures in the retina and cochlea.
Collapse
|
15
|
The Mycobacterium tuberculosis PE_PGRS Protein Family Acts as an Immunological Decoy to Subvert Host Immune Response. Int J Mol Sci 2022; 23:ijms23010525. [PMID: 35008950 PMCID: PMC8745494 DOI: 10.3390/ijms23010525] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/03/2021] [Accepted: 12/15/2021] [Indexed: 02/04/2023] Open
Abstract
Mycobacterium tuberculosis (M.tb) is a successful pathogen that can reside within the alveolar macrophages of the host and can survive in a latent stage. The pathogen has evolved and developed multiple strategies to resist the host immune responses. M.tb escapes from host macrophage through evasion or subversion of immune effector functions. M.tb genome codes for PE/PPE/PE_PGRS proteins, which are intrinsically disordered, redundant and antigenic in nature. These proteins perform multiple functions that intensify the virulence competence of M.tb majorly by modulating immune responses, thereby affecting immune mediated clearance of the pathogen. The highly repetitive, redundant and antigenic nature of PE/PPE/PE_PGRS proteins provide a critical edge over other M.tb proteins in terms of imparting a higher level of virulence and also as a decoy molecule that masks the effect of effector molecules, thereby modulating immuno-surveillance. An understanding of how these proteins subvert the host immunological machinery may add to the current knowledge about M.tb virulence and pathogenesis. This can help in redirecting our strategies for tackling M.tb infections.
Collapse
|
16
|
Nehvi IB, Quadir N, Khubaib M, Sheikh JA, Shariq M, Mohareer K, Banerjee S, Rahman SA, Ehtesham NZ, Hasnain SE. ArgD of Mycobacterium tuberculosis is a functional N-acetylornithine aminotransferase with moonlighting function as an effective immune modulator. Int J Med Microbiol 2022; 312:151544. [DOI: 10.1016/j.ijmm.2021.151544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/02/2021] [Accepted: 12/05/2021] [Indexed: 12/18/2022] Open
|
17
|
PGRS Domain of Rv0297 of Mycobacterium tuberculosis Functions in A Calcium Dependent Manner. Int J Mol Sci 2021; 22:ijms22179390. [PMID: 34502303 PMCID: PMC8430768 DOI: 10.3390/ijms22179390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/24/2021] [Indexed: 01/04/2023] Open
Abstract
Mycobacterium tuberculosis (M.tb), the pathogen causing tuberculosis, is a major threat to human health worldwide. Nearly 10% of M.tb genome encodes for a unique family of PE/PPE/PGRS proteins present exclusively in the genus Mycobacterium. The functions of most of these proteins are yet unexplored. The PGRS domains of these proteins have been hypothesized to consist of Ca2+ binding motifs that help these intrinsically disordered proteins to modulate the host cellular responses. Ca2+ is an important secondary messenger that is involved in the pathogenesis of tuberculosis in diverse ways. This study presents the calcium-dependent function of the PGRS domain of Rv0297 (PE_PGRS5) in M.tb virulence and pathogenesis. Tandem repeat search revealed the presence of repetitive Ca2+ binding motifs in the PGRS domain of the Rv0297 protein (Rv0297PGRS). Molecular Dynamics simulations and fluorescence spectroscopy revealed Ca2+ dependent stabilization of the Rv0297PGRS protein. Calcium stabilized Rv0297PGRS enhances the interaction of Rv0297PGRS with surface localized Toll like receptor 4 (TLR4) of macrophages. The Ca2+ stabilized binding of Rv0297PGRS with the surface receptor of macrophages enhances its downstream consequences in terms of Nitric Oxide (NO) production and cytokine release. Thus, this study points to hitherto unidentified roles of calcium-modulated PE_PGRS proteins in the virulence of M.tb. Understanding the pathogenic potential of Ca2+ dependent PE_PGRS proteins can aid in targeting these proteins for therapeutic interventions.
Collapse
|
18
|
P M, Ahmad J, Samal J, Sheikh JA, Arora SK, Khubaib M, Aggarwal H, Kumari I, Luthra K, Rahman SA, Hasnain SE, Ehtesham NZ. Mycobacterium tuberculosis Specific Protein Rv1509 Evokes Efficient Innate and Adaptive Immune Response Indicative of Protective Th1 Immune Signature. Front Immunol 2021; 12:706081. [PMID: 34386011 PMCID: PMC8354026 DOI: 10.3389/fimmu.2021.706081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/09/2021] [Indexed: 11/13/2022] Open
Abstract
Dissecting the function(s) of proteins present exclusively in Mycobacterium tuberculosis (M.tb) will provide important clues regarding the role of these proteins in mycobacterial pathogenesis. Using extensive computational approaches, we shortlisted ORFs/proteins unique to M.tb among 13 different species of mycobacteria and identified a hypothetical protein Rv1509 as a ‘signature protein’ of M.tb. This unique protein was found to be present only in M.tb and absent in all other mycobacterial species, including BCG. In silico analysis identified numerous putative T cell and B cell epitopes in Rv1509. Initial in vitro experiments using innate immune cells demonstrated Rv1509 to be immunogenic with potential to modulate innate immune responses. Macrophages treated with Rv1509 exhibited higher activation status along with substantial release of pro-inflammatory cytokines. Besides, Rv1509 protein boosts dendritic cell maturation by increasing the expression of activation markers such as CD80, HLA-DR and decreasing DC-SIGN expression and this interaction was mediated by innate immune receptor TLR2. Further, in vivo experiments in mice demonstrated that Rv1509 protein promotes the expansion of multifunctional CD4+ and CD8+T cells and induces effector memory response along with evoking a canonical Th1 type of immune response. Rv1509 also induces substantial B cell response as revealed by increased IgG reactivity in sera of immunized animals. This allowed us to demonstrate the diagnostic efficacy of this protein in sera of human TB patients compared to the healthy controls. Taken together, our results reveal that Rv1509 signature protein has immunomodulatory functions evoking immunological memory response with possible implications in serodiagnosis and TB vaccine development.
Collapse
Affiliation(s)
- Manjunath P
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India.,Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Javeed Ahmad
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Jasmine Samal
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India
| | | | - Simran Kaur Arora
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India.,Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Mohd Khubaib
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India.,Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Heena Aggarwal
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Seyed E Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India.,Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India
| | - Nasreen Z Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India
| |
Collapse
|
19
|
Sharma N, Shariq M, Quadir N, Singh J, Sheikh JA, Hasnain SE, Ehtesham NZ. Mycobacterium tuberculosis Protein PE6 (Rv0335c), a Novel TLR4 Agonist, Evokes an Inflammatory Response and Modulates the Cell Death Pathways in Macrophages to Enhance Intracellular Survival. Front Immunol 2021; 12:696491. [PMID: 34322125 PMCID: PMC8311496 DOI: 10.3389/fimmu.2021.696491] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/21/2021] [Indexed: 01/14/2023] Open
Abstract
Mycobacterium tuberculosis (M. tb) is an intracellular pathogen that exploits moonlighting functions of its proteins to interfere with host cell functions. PE/PPE proteins utilize host inflammatory signaling and cell death pathways to promote pathogenesis. We report that M. tb PE6 protein (Rv0335c) is a secretory protein effector that interacts with innate immune toll-like receptor TLR4 on the macrophage cell surface and promotes activation of the canonical NFĸB signaling pathway to stimulate secretion of proinflammatory cytokines TNF-α, IL-12, and IL-6. Using mouse macrophage TLRs knockout cell lines, we demonstrate that PE6 induced secretion of proinflammatory cytokines dependent on TLR4 and adaptor Myd88. PE6 possesses nuclear and mitochondrial targeting sequences and displayed time-dependent differential localization into nucleus/nucleolus and mitochondria, and exhibited strong Nucleolin activation. PE6 strongly induces apoptosis via increased production of pro-apoptotic molecules Bax, Cytochrome C, and pcMyc. Mechanistic details revealed that PE6 activates Caspases 3 and 9 and induces endoplasmic reticulum-associated unfolded protein response pathways to induce apoptosis through increased production of ATF6, Chop, BIP, eIF2α, IRE1α, and Calnexin. Despite being a potent inducer of apoptosis, PE6 suppresses innate immune defense strategy autophagy by inducing inhibitory phosphorylation of autophagy initiating kinase ULK1. Inversely, PE6 induces activatory phosphorylation of autophagy master regulator MtorC1, which is reflected by lower conversion of autophagy markers LC3BI to LC3BII and increased accumulation of autophagy substrate p62 which is also dependent on innate immune receptor TLR4. The use of pharmacological agents, rapamycin and bafilomycin A1, confirms the inhibitory effect of PE6 on autophagy, evidenced by the reduced conversion of LC3BI to LC3BII and increased accumulation of p62 in the presence of rapamycin and bafilomycin A1. We also observed that PE6 binds DNA, which could have significant implications in virulence. Furthermore, our analyses reveal that PE6 efficiently binds iron to likely aid in intracellular survival. Recombinant Mycobacterium smegmatis (M. smegmatis) containing pe6 displayed robust growth in iron chelated media compared to vector alone transformed cells, which suggests a role of PE6 in iron acquisition. These findings unravel novel mechanisms exploited by PE6 protein to subdue host immunity, thereby providing insights relevant to a better understanding of host–pathogen interaction during M. tb infection.
Collapse
Affiliation(s)
- Neha Sharma
- Indian Council of Medical Research-National Institute of Pathology, New Delhi, India.,Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Mohd Shariq
- Indian Council of Medical Research-National Institute of Pathology, New Delhi, India
| | - Neha Quadir
- Indian Council of Medical Research-National Institute of Pathology, New Delhi, India.,Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Jasdeep Singh
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Javaid A Sheikh
- Department of Biotechnology, School of Chemical and Life Science, Jamia Hamdard, New Delhi, India
| | - Seyed E Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, India.,Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India
| | - Nasreen Z Ehtesham
- Indian Council of Medical Research-National Institute of Pathology, New Delhi, India
| |
Collapse
|
20
|
Ehtram A, Shariq M, Ali S, Quadir N, Sheikh JA, Ahmad F, Sharma T, Ehtesham NZ, Hasnain SE. Teleological cooption of Mycobacterium tuberculosis PE/PPE proteins as porins: Role in molecular immigration and emigration. Int J Med Microbiol 2021; 311:151495. [PMID: 33730677 DOI: 10.1016/j.ijmm.2021.151495] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/01/2021] [Accepted: 03/05/2021] [Indexed: 01/09/2023] Open
Abstract
Permeation through bacterial cells for exchange or uptake of biomolecules and ions invariably depend upon the existence of pore-forming proteins (porins) in their outer membrane. Mycobacterium tuberculosis (M. tb) harbours one of the most rigid cell envelopes across bacterial genera and is devoid of the classical porins for solute transport across the cell membrane. Though canonical porins are incompatible with the evolution of permeability barrier, porin like activity has been reported from membrane preparations of pathogenic mycobacteria. This suggests a sophisticated transport mechanism that has been elusive until now, along with the protein family responsible for it. Recent evidence suggests that these slow-growing mycobacteria have co-opted some of PE/PPE family proteins as molecular transport channels, in place of porins, to facilitate uptake of nutrients required to thrive in the restrictive host environment. These reports advocate that PE/PPE proteins, due to their structural ability, have a potential role in importing small molecules to the cell's interior. This mechanism unveils how a successful pathogen overcomes its restrictive membrane's transport limitations for selective uptake of nutrients. If extrapolated to have a role in drug transport, these channels could help understand the emergence of drug resistance. Further, as these proteins are associated with the export of virulence factors, they can be exploited as novel drug targets. There remains, however, an interesting question that as the PE/PPE proteins can allow the 'import' of molecules from outside the cell, is the reverse transport also possible across the M. tb membrane. In this review, we have discussed recent evidence supporting PE/PPE's role as a specific transport channel for selective uptake of small molecule nutrients and, as possible molecular export machinery of M. tb. This newly discovered role as transmembrane channels demands further research on this enigmatic family of proteins to comprehend the pathomechanism of this very smart pathogen.
Collapse
Affiliation(s)
- Aquib Ehtram
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Mohd Shariq
- ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi, India
| | - Sabeeha Ali
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Neha Quadir
- ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi, India; Jamia Hamdard- Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - Javaid A Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Faraz Ahmad
- ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi, India
| | - Tarina Sharma
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India; ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi, India
| | - Nasreen Z Ehtesham
- ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi, India.
| | - Seyed E Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India.
| |
Collapse
|
21
|
Shariq M, Quadir N, Sharma N, Singh J, Sheikh JA, Khubaib M, Hasnain SE, Ehtesham NZ. Mycobacterium tuberculosis RipA Dampens TLR4-Mediated Host Protective Response Using a Multi-Pronged Approach Involving Autophagy, Apoptosis, Metabolic Repurposing, and Immune Modulation. Front Immunol 2021; 12:636644. [PMID: 33746976 PMCID: PMC7969667 DOI: 10.3389/fimmu.2021.636644] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/03/2021] [Indexed: 12/26/2022] Open
Abstract
Reductive evolution has endowed Mycobacterium tuberculosis (M. tb) with moonlighting in protein functions. We demonstrate that RipA (Rv1477), a peptidoglycan hydrolase, activates the NFκB signaling pathway and elicits the production of pro-inflammatory cytokines, TNF-α, IL-6, and IL-12, through the activation of an innate immune-receptor, toll-like receptor (TLR)4. RipA also induces an enhanced expression of macrophage activation markers MHC-II, CD80, and CD86, suggestive of M1 polarization. RipA harbors LC3 (Microtubule-associated protein 1A/1B-light chain 3) motifs known to be involved in autophagy regulation and indeed alters the levels of autophagy markers LC3BII and P62/SQSTM1 (Sequestosome-1), along with an increase in the ratio of P62/Beclin1, a hallmark of autophagy inhibition. The use of pharmacological agents, rapamycin and bafilomycin A1, reveals that RipA activates PI3K-AKT-mTORC1 signaling cascade that ultimately culminates in the inhibition of autophagy initiating kinase ULK1 (Unc-51 like autophagy activating kinase). This inhibition of autophagy translates into efficient intracellular survival, within macrophages, of recombinant Mycobacterium smegmatis expressing M. tb RipA. RipA, which also localizes into mitochondria, inhibits the production of oxidative phosphorylation enzymes to promote a Warburg-like phenotype in macrophages that favors bacterial replication. Furthermore, RipA also inhibited caspase-dependent programed cell death in macrophages, thus hindering an efficient innate antibacterial response. Collectively, our results highlight the role of an endopeptidase to create a permissive replication niche in host cells by inducing the repression of autophagy and apoptosis, along with metabolic reprogramming, and pointing to the role of RipA in disease pathogenesis.
Collapse
Affiliation(s)
- Mohd Shariq
- Indian Council of Medical Research-National Institute of Pathology, New Delhi, India
| | - Neha Quadir
- Indian Council of Medical Research-National Institute of Pathology, New Delhi, India.,Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Neha Sharma
- Indian Council of Medical Research-National Institute of Pathology, New Delhi, India.,Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Jasdeep Singh
- 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
| | - Mohd Khubaib
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Seyed E Hasnain
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India.,Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D) Hauz Khas, New Delhi, India
| | - Nasreen Z Ehtesham
- Indian Council of Medical Research-National Institute of Pathology, New Delhi, India
| |
Collapse
|
22
|
Blundell TL. Interdisciplinary research in physics, chemistry and biology is central to understanding biological processes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 156:1-2. [PMID: 32980033 DOI: 10.1016/j.pbiomolbio.2020.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
| |
Collapse
|
23
|
de Brevern AG. Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet. Biomolecules 2020; 10:biom10071080. [PMID: 32698546 PMCID: PMC7408373 DOI: 10.3390/biom10071080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 07/18/2020] [Indexed: 12/30/2022] Open
Abstract
Intrinsically-disordered protein (IDP) characterization was an amazing change of paradigm in our classical sequence-structure-function theory. Moreover, IDPs are over-represented in major disease pathways and are now often targeted using small molecules for therapeutic purposes. This has had created a complex continuum from order-that encompasses rigid and flexible regions-to disorder regions; the latter being not accessible through classical crystallographic methodologies. In X-ray structures, the notion of order is dictated by access to resolved atom positions, providing rigidity and flexibility information with low and high experimental B-factors, while disorder is associated with the missing (non-resolved) residues. Nonetheless, some rigid regions can be found in disorder regions. Using ensembles of IDPs, their local conformations were analyzed in the light of a structural alphabet. An entropy index derived from this structural alphabet allowed us to propose a continuum of states from rigidity to flexibility and finally disorder. In this study, the analysis was extended to comparing these results to disorder predictions, underlying a limited correlation, and so opening new ideas to characterize and predict disorder.
Collapse
Affiliation(s)
- Alexandre G de Brevern
- INSERM, UMR_S 1134, DSIMB, Univ Paris, INTS, Laboratoire d'Excellence GR-Ex, 75015 Paris, France
| |
Collapse
|