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Lyngdoh DL, Nag N, Uversky VN, Tripathi T. Prevalence and functionality of intrinsic disorder in human FG-nucleoporins. Int J Biol Macromol 2021; 175:156-170. [PMID: 33548309 DOI: 10.1016/j.ijbiomac.2021.01.218] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/19/2021] [Accepted: 01/31/2021] [Indexed: 11/27/2022]
Abstract
The nuclear-cytoplasmic transport of biomolecules is assisted by the nuclear pores composed of evolutionarily conserved proteins termed nucleoporins (Nups). The central Nups, characterized by multiple FG-repeats, are highly dynamic and contain a high level of intrinsically disordered regions (IDPRs). FG-Nups bind several protein partners and play critical roles in molecular interactions and the regulation of cellular functions through their IDPRs. In the present study, we performed a multiparametric bioinformatics analysis to characterize the prevalence and functionality of IDPRs in human FG-Nups. These analyses revealed that the sequence of all FG-Nups contained >50% IDPRs (except Nup54 and Nup358). Nup98, Nup153, and POM121 were extremely disordered with ~80% IDPRs. The functional disorder-based binding regions in the FG-Nups were identified. The phase separation behavior of FG-Nups indicated that all FG-Nups have the potential to undergo liquid-to-liquid phase separation that could stabilize their liquid state. The inherent structural flexibility in FG-Nups is mechanistically and functionally advantageous. Since certain FG-Nups interact with disease-relevant protein aggregates, their complexes can be exploited for drug design. Furthermore, consideration of the FG-Nups from the intrinsic disorder perspective provides critical information that can guide future experimental studies to uncover novel pathways associated with diseases linked with protein misfolding and aggregation.
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Affiliation(s)
- Denzelle Lee Lyngdoh
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
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Pandey T, Ghosh A, Todur VN, Rajendran V, Kalita P, Kalita J, Shukla R, Chetri PB, Shukla H, Sonkar A, Lyngdoh DL, Singh R, Khan H, Nongkhlaw J, Das KC, Tripathi T. Draft Genome of the Liver Fluke Fasciola gigantica. ACS Omega 2020; 5:11084-11091. [PMID: 32455229 PMCID: PMC7241025 DOI: 10.1021/acsomega.0c00980] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/23/2020] [Indexed: 05/22/2023]
Abstract
Fascioliasis, a neglected foodborne disease caused by liver flukes (genus Fasciola), affects more than 200 million people worldwide. Despite technological advances, little is known about the molecular biology and biochemistry of these flukes. We present the draft genome of Fasciola gigantica for the first time. The assembled draft genome has a size of ∼1.04 Gb with an N50 and N90 of 129 and 149 kb, respectively. A total of 20 858 genes were predicted. The de novo repeats identified in the draft genome were 46.85%. The pathway included all of the genes of glycolysis, Krebs cycle, and fatty acid metabolism but lacked the key genes of the fatty acid biosynthesis pathway. This indicates that the fatty acid required for survival of the fluke may be acquired from the host bile. It may be hypothesized that the relatively larger F. gigantica genome did not evolve through genome duplications but rather is interspersed with many repetitive elements. The genomic information will provide a comprehensive resource to facilitate the development of novel interventions for fascioliasis control.
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Affiliation(s)
- Tripti Pandey
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Arpita Ghosh
- Eurofins
Genomics India Pvt. Ltd., Doddanekkundi, Bengaluru 560048, India
| | - Vivek N. Todur
- Eurofins
Genomics India Pvt. Ltd., Doddanekkundi, Bengaluru 560048, India
| | - Vijayakumar Rajendran
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Parismita Kalita
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Jupitara Kalita
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Rohit Shukla
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Purna B. Chetri
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Amit Sonkar
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Denzelle Lee Lyngdoh
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Radhika Singh
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Heena Khan
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Joplin Nongkhlaw
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Kanhu Charan Das
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
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Namdev P, Lyngdoh DL, Dar HY, Chaurasiya SK, Srivastava R, Tripathi T, Anupam R. Intrinsically Disordered Human T Lymphotropic Virus Type 1 p30 Protein: Experimental and Computational Evidence. AIDS Res Hum Retroviruses 2019; 35:477-487. [PMID: 30618266 DOI: 10.1089/aid.2018.0196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Human T lymphotropic virus type 1 (HTLV-1) causes adult T cell leukemia and lymphoma and other neuroinflammatory diseases. The pX region of HTLV-1 genome encodes an accessory protein p30 that is required for viral persistence and spread in the host. p30 regulates viral gene expression at the transcription level by competing with Tax for p300 binding and at posttranscriptional level by nuclear retention of tax/rex messenger RNA (mRNA). In addition, p30 modulates the host cellular environment by binding to various host proteins such as ATM, REGγ, and PRMT5. However, the low expression levels of p30 has been a major hurdle in studying its structure-function relationship in the context of HTLV-1 pathobiology, which is most likely due to its intrinsically disordered nature. To investigate the unstable nature of p30, flow cytometric analysis of p30-GFP fusion protein expressed in Escherichia coli was conducted and bioinformatics analysis of p30 was performed. The bacterial cells were green fluorescent protein (GFP) positive, indicating that p30-GFP was in the soluble fraction. Induction, particularly at higher temperature, reduced the expression of p30-GFP. Moreover, p30-GFP was detected exclusively in insoluble fraction upon cell lysis, suggesting its unstable and disordered nature. The bioinformatics analysis of p30 protein sequence and amino acid content revealed that p30 has highly disordered regions from amino acids 75-155 and 197-241. Furthermore, p30 has regions for macromolecular interactions that could stabilize it and these regions coincide with the unstable regions. Collectively, the study indicates that HTLV-1 p30 is an intrinsically disordered protein.
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Affiliation(s)
- Priyanka Namdev
- Department of Biotechnology, Dr. Harisingh Gour University, Sagar, India
| | - Denzelle Lee Lyngdoh
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Hamid Y. Dar
- Department of Zoology, Dr. Harisingh Gour University, Sagar, India
| | - Shivendra K. Chaurasiya
- Host-Pathogen Interaction and Signal Transduction Laboratory, Department of Microbiology, Dr. Harisingh Gour University, Sagar, India
| | | | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Rajaneesh Anupam
- Department of Biotechnology, Dr. Harisingh Gour University, Sagar, India
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Sonkar A, Lyngdoh DL, Shukla R, Shukla H, Tripathi T, Ahmed S. Point mutation A394E in the central intrinsic disordered region of Rna14 leads to chromosomal instability in fission yeast. Int J Biol Macromol 2018; 119:785-791. [PMID: 30076928 DOI: 10.1016/j.ijbiomac.2018.07.193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/31/2018] [Accepted: 07/31/2018] [Indexed: 12/01/2022]
Abstract
Accurate chromosomal segregation is crucial for the maintenance of genomic integrity. Rna14 is a major component of the yeast pre-mRNA 3'-end processing factor, the cleavage factor IA complex, and is involved in cleavage and polyadenylation of mRNA in the nucleus. Rna14 is also essential for the maintenance of genomic integrity in fission yeast Schizosaccharomyces pombe. In the present study, we report that a non-homologous mutation, A394E that is present in the central intrinsic disordered region of Rna14 leads to chromosomal instability in fission yeast. This mutation was shown to disrupt chromosome segregation and 3'-end maturation, and also affects the pre-mRNA splicing in vivo at non-permissive temperatures. We observed that a significant part of Rna14 is intrinsically disordered, that includes the N- and C-terminal of Rna14, as well as the central region containing the HAT repeats and the mutation within amino acid residues 372-435. These regions are crucial for the function of Rna14 as they are involved in the interaction of Rna14 with other proteins.
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Affiliation(s)
- Amit Sonkar
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Denzelle Lee Lyngdoh
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
| | - Shakil Ahmed
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow 226031, India.
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