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Kumar A, Pandey SC, Samant M. DNA-based microarray studies in visceral leishmaniasis: identification of biomarkers for diagnostic, prognostic and drug target for treatment. Acta Trop 2020; 208:105512. [PMID: 32389452 DOI: 10.1016/j.actatropica.2020.105512] [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] [Received: 10/07/2019] [Revised: 03/04/2020] [Accepted: 04/18/2020] [Indexed: 02/05/2023]
Abstract
Visceral leishmaniasis (VL) is one of the major infectious diseases affecting the poorest regions of the world. Current therapy is not very much satisfactory. The alarming rise of drug resistance and the unavailability of an effective vaccine against VL urges research towards identifying new targets or biomarkers for its effective treatment. New technology developments offer some fresh hope in its diagnosis, treatment, and control. DNA microarray approach is now broadly used in parasitology research to facilitate the thoughtful of mechanisms of disease and identification of drug targets and biomarkers for diagnostic and therapeutic development. An electronic search on "VL" and "Microarray" was conducted in Medline and Scopus and papers published in the English mentioning use of DNA microarray on VL were selected and read to write this paper review. Functional analysis and interpretation of microarray results remain very challenging due to the inherent nature of experimental workflows, access, cost, and complexity of data obtained. We have explained and emphasized the use of curate knowledge of microarray in the case of VL for the identification of therapeutic target and biomarker and their selection/implementation in clinical use.
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Affiliation(s)
- Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur (Chhattisgarh), INDIA
| | - Satish Chandra Pandey
- Cell and Molecular biology laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora (Uttarakhand), INDIA; Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Nainital (Uttarakhand), INDIA
| | - Mukesh Samant
- Cell and Molecular biology laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora (Uttarakhand), INDIA.
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Datta M, Kaushik S, Jyoti A, Mathur N, Kothari SL, Jain A. SIZ1-mediated SUMOylation during phosphate homeostasis in plants: Looking beyond the tip of the iceberg. Semin Cell Dev Biol 2017; 74:123-132. [PMID: 28903074 DOI: 10.1016/j.semcdb.2017.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 11/27/2022]
Abstract
Availability of phosphate (Pi) is often limited in rhizospheres in different agroclimatic zones and adversely affects growth and development of plants. To circumvent this impasse, there is an urgent need and global consensus to develop Pi use efficient crops. To achieve this goal, it is essential to identify the molecular entities that exert regulatory influences on the sensing and signaling cascade governing Pi homeostasis. SIZ1 encodes a small ubiquitin-like modifier (SUMO E3) ligase, and plays a pivotal role in the post-translational SUMOylation of proteins. In this review, we discuss the reverse genetics approach conventionally used for providing circumstantial evidence towards the regulatory influences of SIZ1 on several morphophysiological and molecular traits that govern Pi homeostasis in taxonomically diverse Arabidopsis thaliana (Arabidopsis) and Oryza sativa (rice) model species. However, the efforts have been rather modest in identifying SUMO protein targets that play key roles in the maintenance of Pi homeostasis in these model plants contrary to the plethora of them now known in lower organisms and animals. Therefore, to predict the SIZ1-mediated SUMOylome involved in Pi homeostasis, the state-of-the-art high-throughput technologies often used for animals thus provide an attractive paradigm towards achieving the long-term goal of developing Pi use efficient crops.
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Affiliation(s)
- Manali Datta
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Anupam Jyoti
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Nidhi Mathur
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Shanker L Kothari
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Ajay Jain
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India.
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Rapid identification of ubiquitination and SUMOylation target sites by microfluidic peptide array. Biochem Biophys Rep 2016; 5:430-438. [PMID: 27047992 PMCID: PMC4817105 DOI: 10.1016/j.bbrep.2016.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
SUMOylation and ubiquitination are two essential post translational modifications (PTMs) involved in the regulation of important biological processes in eukaryotic cells. Identification of ubiquitin (Ub) and small ubiquitin-related modifier (SUMO)-conjugated lysine residues in proteins is critical for understanding the role of ubiquitination and SUMOylation, but remains experimentally challenging. We have developed a powerful in vitro Ub/SUMO assay using a novel high density peptide array incorporated within a microfluidic device that allows rapid identification of ubiquitination and SUMOylation sites on target proteins. We performed the assay with a panel of human proteins and a microbial effector with known target sites for Ub or SUMO modifications, and determined that 80% of these proteins were modified by Ub or specific SUMO isoforms at the sites previously determined using conventional methods. Our results confirm the specificity for both SUMO isoform and individual target proteins at the peptide level. In summary, this microfluidic high density peptide array approach is a rapid screening assay to determine sites of Ub and SUMO modification of target substrates, which will provide new insights into the composition, selectivity and specificity of these PTM target sites.
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Preuss KD, Pfreundschuh M, Weigert M, Fadle N, Regitz E, Kubuschok B. Sumoylated HSP90 is a dominantly inherited plasma cell dyscrasias risk factor. J Clin Invest 2014; 125:316-23. [PMID: 25485683 DOI: 10.1172/jci76802] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/02/2014] [Indexed: 11/17/2022] Open
Abstract
Posttranslationally modified proteins serve as autoimmunogenic targets in a wide spectrum of autoimmune diseases. Here, we identified a posttranslationally modified paraprotein target (paratargs) in monoclonal gammopathies of undetermined significance (MGUS), multiple myelomas (MM), and Waldenstrom's macroglobulinemias (WM) using protein macroarrays that were sumoylated and screened for reactivity with paraproteins from MGUS, MM, and WM patients. We found that paraproteins from a proportion of European, African-American, and Japanese patients specifically reacted with the sumoylated heat-shock protein 90 β isoform-α (HSP90-SUMO1, where SUMO indicates small ubiquitin-like modifier), while no reactivity with HSP90-SUMO1 was detected in over 800 controls. HSP90-SUMO1 was present in blood cells from all patients with HSP90-SUMO1-binding paraproteins. We determined that the HSP90-SUMO1 carrier state is autosomal-dominantly inherited and caused by the inability of SUMO peptidase sentrin/SUMO-specific protease 2 (SENP2) to desumoylate HSP90-SUMO1. HSP90-SUMO1 was detected in a small percentage of healthy individuals from all backgrounds; however, only MGUS, MM, and WM patients who were HSP90-SUMO1 carriers produced HSP90-SUMO1-specific paraproteins, suggesting that sumoylated HSP90 promotes pathogenesis of these diseases through chronic antigenic stimulation. This study demonstrates that harboring HSP90-SUMO1 identifies healthy individuals at risk for plasma cell dyscrasias and that dominant inheritance of posttranslationally modified autoantigenic paratargs is one of the strongest molecular defined risk factors for MGUS, MM, and WM.
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Brandt M, Szewczuk LM, Zhang H, Hong X, McCormick PM, Lewis TS, Graham TI, Hung ST, Harper-Jones AD, Kerrigan JJ, Wang DY, Dul E, Hou W, Ho TF, Meek TD, Cheung MH, Johanson KO, Jones CS, Schwartz B, Kumar S, Oliff AI, Kirkpatrick RB. Development of a High-Throughput Screen to Detect Inhibitors of TRPS1 Sumoylation. Assay Drug Dev Technol 2013; 11:308-25. [DOI: 10.1089/adt.2012.501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Martin Brandt
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | | | - Hong Zhang
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Xuan Hong
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | | | - Tia S. Lewis
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Taylor I. Graham
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Sunny T. Hung
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | | | - John J. Kerrigan
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Da-Yuan Wang
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Edward Dul
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Wangfang Hou
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Thau F. Ho
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Thomas D. Meek
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Mui H. Cheung
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Kyung O. Johanson
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | | | - Benjamin Schwartz
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Sanjay Kumar
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Allen I. Oliff
- Molecular Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania
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Abstract
Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.
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Selective SUMO modification of cAMP-specific phosphodiesterase-4D5 (PDE4D5) regulates the functional consequences of phosphorylation by PKA and ERK. Biochem J 2010; 428:55-65. [DOI: 10.1042/bj20091672] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Enzymes from the PDE (phosphodiesterase) 4 cAMP-specific PDE family are crucial for the maintenance of compartmentalized cAMP responses in many cell types. Regulation of PDE activity can be achieved via post-translational modification such as phosphorylation by ERK (extracellular-signal-regulated kinase) MAPKs (mitogen-activated protein kinases) and PKA (protein kinase A). In the present paper, we report for the first time that PDE4 isoforms from the PDE4A and PDE4D subfamilies can be selectively modified by SUMO (small ubiquitin-related modifier). We have identified a single SUMO site within a consensus tetrapeptide motif, ΨKXE (where Ψ represents a hydrophobic residue), which lies in the catalytic unit of these enzymes. SUMO modification of PDE4 at this site was observed upon overexpression of the SUMO E3 ligase PIASy [protein inhibitor of activated STAT (signal transducer and activator of transcription) Y] in HEK (human embryonic kidney)-293 cells and we identify PIASy as a novel binding partner for long PDE4 isoforms. Site-directed mutagenesis of the acceptor lysine residue ablated conjugation of PDE4 with SUMO, suggesting the presence of a single SUMO site in the first subdomain of the conserved PDE4 catalytic unit. This observation was supported by both cell-free in vitro SUMOylation assays and analysis of SUMOylated spot-immobilized peptide arrays. SUMO modification of long PDE4 isoforms serves to augment their activation by PKA phosphorylation and repress their inhibition by ERK phosphorylation. Following ligation of β-adrenergic receptors, SUMOylation of PDE4 isoforms sufficiently amplified PKA-stimulated PDE4 activity to reduce markedly the PKA phosphorylation status of the β2-adrenergic receptor. These results highlight a new means whereby cells might achieve the selective regulation of the activity of cAMP-specific PDE4 enyzmes.
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Mi Z, Fu J, Xiong Y, Tang H. SUMOylation of RIG-I positively regulates the type I interferon signaling. Protein Cell 2010; 1:275-83. [PMID: 21203974 PMCID: PMC4875083 DOI: 10.1007/s13238-010-0030-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 01/21/2010] [Indexed: 12/25/2022] Open
Abstract
Retinoic acid-inducible gene-I (RIG-I) functions as an intracellular pattern recognition receptor (PRR) that recognizes the 5'-triphosphate moiety of single-stranded RNA viruses to initiate the innate immune response. Previous studies have shown that Lys63-linked ubiquitylation is required for RIG-I activation and the downstream anti-viral type I interferon (IFN-I) induction. Herein we reported that, RIG-I was also modified by small ubiquitin-like modifier-1 (SUMO-1). Functional analysis showed that RIG-I SUMOylation enhanced IFN-I production through increased ubiquitylation and the interaction with its downstream adaptor molecule Cardif. Our results therefore suggested that SUMOylation might serve as an additional regulatory tier for RIG-I activation and IFN-I signaling.
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Affiliation(s)
- Zhiqiang Mi
- Center for Molecular Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Key Laboratory of Infection and Immunity of Chinese Academy of Sciences, Institute of Biophysics, Beijing, 100101 China
| | - Jihuan Fu
- Key Laboratory of Infection and Immunity of Chinese Academy of Sciences, Institute of Biophysics, Beijing, 100101 China
| | - Yanbao Xiong
- Key Laboratory of Infection and Immunity of Chinese Academy of Sciences, Institute of Biophysics, Beijing, 100101 China
| | - Hong Tang
- Key Laboratory of Infection and Immunity of Chinese Academy of Sciences, Institute of Biophysics, Beijing, 100101 China
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Carlson CB, Horton RA, Vogel KW. A toolbox approach to high-throughput TR-FRET-based SUMOylation and DeSUMOylation assays. Assay Drug Dev Technol 2009; 7:348-55. [PMID: 19656081 DOI: 10.1089/adt.2008.0188] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The posttranslational modification of target substrates by the ubiquitin-like proteins, specifically the small ubiquitin-like modifier (SUMO), has emerged as an essential mechanism to regulate protein function and control intracellular trafficking. Traditional methods for monitoring either the attachment or removal of SUMO, such as gel electrophoresis or western blot, are effective but typically suffer from a lack of throughput. Here, we report the development and application of time-resolved Förster resonance energy transfer (TR-FRET)-based assays capable of detecting SUMOylation or deSUMOylation in a high-throughput screening (HTS) format. Using Ran GTPase-activating protein (RanGAP1) as a model target substrate, we have demonstrated that the SUMOylation of this protein can be detected using LanthaScreen (Invitrogen, Carlsbad, CA) TR-FRET technology. Additionally, we have generated reagents useful for assessing the deSUMOylation activity of a sentrin-specific protease. All assays are performed in 384-well format and display excellent statistical data (Z' > 0.7) with high signal-to-background levels. Together, this collection of tools can be utilized in a modular approach to develop HTS assays for inhibitors of SUMOylation or deSUMOylation.
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Affiliation(s)
- Coby B Carlson
- Invitrogen Discovery Assays and Services, Madison, Wisconsin 53719, USA.
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Abstract
Enzymes are key molecules in signal transduction pathways. However, only a small fraction of more than 500 predicted human kinases, 250 proteases and 250 phosphatases is characterized so far. Peptide microarray-based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. Additionally, patterns of enzymatic activities could be used to fingerprint the status of cells or organisms. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimization of enzyme substrates. A comprehensive overview regarding enzyme profiling using peptide microarrays is presented with special focus on assay principles.
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Affiliation(s)
- Alexandra Thiele
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
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