Dr. Abhishek Dey

RESEARCH INTERESTS

RNA structure and function in gene Regulation and Diseases, RNA-Protein interactions, RNA modifications and Gene Expression, RNA Therapeutics.

Scopus Publications

High-throughput sequencing: a breakthrough in molecular diagnosis for precision medicine
Dipali Barku Dongare, Shaik Shireen Nishad, Sakshi Y. Mastoli, Shubhini A. Saraf, Nidhi Srivastava, and Abhishek Dey
Springer Science and Business Media LLC



A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements
Samuel Lee, Shuting Yan, Abhishek Dey, Alain Laederach, and Tamar Schlick
American Chemical Society (ACS)
Targeting ribosomal frameshifting has emerged as a potential therapeutic intervention strategy against COVID-19. In this process, a −1 shift in the ribosomal reading frame encodes alternative viral proteins. Any interference with this process profoundly affects viral replication and propagation. For SARS-CoV-2, two RNA sites associated with ribosomal frameshifting are positioned on the 5′ and 3′ of the frameshifting residues. Although much attention has been focused on the 3′ frameshift element (FSE), the 5′ stem-loop (attenuator hairpin, AH) can play a role. Yet the relationship between the two regions is unknown. In addition, multiple folds of the FSE and FSE-containing RNA regions have been discovered. To gain more insight into these RNA folds in the larger sequence context that includes AH, we apply our graph-theory-based modeling tools to represent RNA secondary structures, “RAG” (RNA-As-Graphs), to generate conformational landscapes that suggest length-dependent conformational distributions. We show that the AH region can coexist as a stem-loop with main and alternative 3-stem pseudoknots of the FSE (dual graphs 3_6 and 3_3 in our notation) but that an alternative stem 1 (AS1) can disrupt the FSE pseudoknots and trigger other folds. A critical length for AS1 of 10-bp regulates key folding transitions. Together with designed mutants and available experimental data, we present a sequential view of length-dependent folds during frameshifting and suggest their mechanistic roles. These structural and mutational insights into both ends of the FSE advance our understanding of the SARS-CoV-2 frameshifting mechanism by suggesting how alternative folds play a role in frameshifting and defining potential therapeutic intervention techniques that target specific folds.


Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses
Abhishek Dey, Shuting Yan, Tamar Schlick, and Alain Laederach
Cold Spring Harbor Laboratory
The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases, including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, as verified by multiple experimental and computational approaches. However, the role these alternative conformations play in the frameshifting mechanism and how to quantify this structural abundance has been an ongoing challenge. Here, we show by DMS and dual-luciferase functional assays that previously predicted FSE mutants (using the RAG graph theory approach) suppress structural transitions and abolish frameshifting. Furthermore, correlated mutation analysis of DMS data by three programs (DREEM, DRACO, and DANCE-MaP) reveals important differences in their estimation of specific RNA conformations, suggesting caution in the interpretation of such complex conformational landscapes. Overall, the abolished frameshifting in three different mutants confirms that all alternative conformations play a role in the pathways of ribosomal transition.


Structural Modifications and Novel Protein-Binding Sites in Pre-miR-675—Explaining Its Regulatory Mechanism in Carcinogenesis
Abhishek Dey
MDPI AG
Pre-miR-675 is a microRNA expressed from the exon 1 of H19 long noncoding RNA, and the atypical expression of pre-miR-675 has been linked with several diseases and disorders including cancer. To execute its function inside the cell, pre-miR-675 is folded into a particular conformation, which aids in its interaction with several other biological molecules. However, the exact folding dynamics of pre-miR-675 and its protein-binding motifs are currently unknown. Moreover, how H19 lncRNA and pre-miR-675 crosstalk and modulate each other’s activities is also unclear. The detailed structural analysis of pre-miR-675 in this study determines its earlier unknown conformation and identifies novel protein-binding sites on pre-miR-675, thus making it an excellent therapeutic target against cancer. Co-folding analysis between H19 lncRNA and pre-miR-675 determine structural transformations in pre-miR-675, thus describing the earlier unknown mechanism of interaction between these two molecules. Comprehensively, this study details the conformation of pre-miR-675 and its protein-binding sites and explains its relationship with H19 lncRNA, which can be interpreted to understand the role of pre-miR-675 in the development and progression of tumorigenesis and designing new therapeutics against cancers.


Sequence and tissue targeting specificity of ZFP36L2 reveals Elavl2 as a novel target with co-regulation potential
Ian C Redmon, Matthew Ardizzone, Hilal Hekimoğlu, Breanne M Hatfield, Justin M Waldern, Abhishek Dey, Stephanie A Montgomery, Alain Laederach, and Silvia B V Ramos
Oxford University Press (OUP)
Abstract Zinc finger protein 36 like 2 (ZFP36L2) is an RNA-binding protein that destabilizes transcripts containing adenine-uridine rich elements (AREs). The overlap between ZFP36L2 targets in different tissues is minimal, suggesting that ZFP36L2-targeting is highly tissue specific. We developed a novel Zfp36l2-lacking mouse model (L2-fKO) to identify factors governing this tissue specificity. We found 549 upregulated genes in the L2-fKO spleen by RNA-seq. These upregulated genes were enriched in ARE motifs in the 3′UTRs, which suggests that they are ZFP36L2 targets, however the precise sequence requirement for targeting was not evident from motif analysis alone. We therefore used gel-shift mobility assays on 12 novel putative targets and established that ZFP36L2 requires a 7-mer (UAUUUAU) motif to bind. We observed a statistically significant enrichment of 7-mer ARE motifs in upregulated genes and determined that ZFP36L2 targets are enriched for multiple 7-mer motifs. Elavl2 mRNA, which has three 7-mer (UAUUUAU) motifs, was also upregulated in L2-fKO spleens. Overexpression of ZFP36L2, but not a ZFP36L2(C176S) mutant, reduced Elavl2 mRNA expression, suggesting a direct negative effect. Additionally, a reporter assay demonstrated that the ZFP36L2 effect on Elavl2 decay is dependent on the Elavl2-3′UTR and requires the 7-mer AREs. Our data indicate that Elavl2 mRNA is a novel target of ZFP36L2, specific to the spleen. Likely, ZFP36L2 combined with other RNA binding proteins, such as ELAVL2, governs tissue specificity.


Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing
Jayashree Kumar, Lela Lackey, Justin M Waldern, Abhishek Dey, Anthony M Mustoe, Kevin M Weeks, David H Mathews, and Alain Laederach
eLife Sciences Publications, Ltd
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.


In vivo architecture of the telomerase RNA catalytic core in Trypanosoma brucei
Abhishek Dey, Anais Monroy-Eklund, Kaitlin Klotz, Arpita Saha, Justin Davis, Bibo Li, Alain Laederach, and Kausik Chakrabarti
Oxford University Press (OUP)
Abstract Telomerase is a unique ribonucleoprotein (RNP) reverse transcriptase that utilizes its cognate RNA molecule as a template for telomere DNA repeat synthesis. Telomerase contains the reverse transcriptase protein, TERT and the template RNA, TR, as its core components. The 5’-half of TR forms a highly conserved catalytic core comprising of the template region and adjacent domains necessary for telomere synthesis. However, how telomerase RNA folding takes place in vivo has not been fully understood due to low abundance of the native RNP. Here, using unicellular pathogen Trypanosoma brucei as a model, we reveal important regional folding information of the native telomerase RNA core domains, i.e. TR template, template boundary element, template proximal helix and Helix IV (eCR4-CR5) domain. For this purpose, we uniquely combined in-cell probing with targeted high-throughput RNA sequencing and mutational mapping under three conditions: in vivo (in WT and TERT−/− cells), in an immunopurified catalytically active telomerase RNP complex and ex vivo (deproteinized). We discover that TR forms at least two different conformers with distinct folding topologies in the insect and mammalian developmental stages of T. brucei. Also, TERT does not significantly affect the RNA folding in vivo, suggesting that the telomerase RNA in T. brucei exists in a conformationally preorganized stable structure. Our observed differences in RNA (TR) folding at two distinct developmental stages of T. brucei suggest that important conformational changes are a key component of T. brucei development.


To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element
Tamar Schlick, Qiyao Zhu, Abhishek Dey, Swati Jain, Shuting Yan, and Alain Laederach
American Chemical Society (ACS)
The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has a profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, “RAG” (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.


The RNA structurome in the asexual blood stages of malaria pathogen plasmodium falciparum
Diana Renteria Alvarez, Alejandra Ospina, Tiffany Barwell, Bo Zheng, Abhishek Dey, Chong Li, Shrabani Basu, Xinghua Shi, Sabah Kadri, and Kausik Chakrabarti
Informa UK Limited
Plasmodium falciparum is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and noncoding transcripts from the asexual developmental cycle in P. falciparum in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite's asexual RBC cycle. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, approximately 71% of the genes with secondary structures are found to be protein coding mRNAs. The mapping pattern of these base-paired RNAs corresponded to all regions of mRNAs, including the 5' UTR, CDS and 3' UTR as well as the start and stop codons. Histone family genes which are known to form secondary structures in their mRNAs and transcripts from genes which are important for transcriptional and post-transcriptional control, such as the unique plant-like transcription factor family, ApiAP2, DNA/RNA binding protein, Alba3 and proteins important for RBC invasion and malaria cytoadherence also showed strong accumulation of duplex RNA reads in various asexual stages in P. falciparum. Intriguingly, our study determined stage-specific, dynamic relationships between mRNA structural contents and translation efficiency in P. falciparum asexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs.


The non-coding rna journal club: Highlights on recent papers-7
Hua Xiao, Patrick Shiu, Marta Gabryleska, Simon Conn, Abhishek Dey, Kausik Chakrabarti, Manuel Regouc, Martin Pichler, Ulf Ørom, Gaetano Santulli,et al.
MDPI AG
We are delighted to share with you our seventh Journal Club and highlight some of the most interesting papers published recently [...]


Innately Water-Soluble Isatoic Anhydrides with Modulated Reactivities for RNA SHAPE Analysis
Adam B. Fessler, Abhishek Dey, Dominic S. Finis, Anthony J. Fowler, Kausik Chakrabarti, and Craig A. Ogle
American Chemical Society (ACS)
1-methyl-7-nitroisatoic anhydride (1M7) and 2-methylnicotinic acid imidazolide (NAI) are two of the most com-monly applied RNA-SHAPE electrophiles; 1M7 due to its high reactivity and NAI for its solubility and cell permeability. While the addition of a nitro group yields desirable activation of the reagent, it also leads to poorer water solubility. This limited solubility has motivated the development of water-soluble reagents. We present alternative, isatoic anhydride-based reagents possessing variable reactivities that are simultaneously water soluble. Solubility is gained by using a quaternary ammonium while modulation of the reactivity is obtained by functionalization of the aryl ring. The syn-theses of the reagents are discussed, and the electrophiles are demonstrated to be suitable for use for an in vitro RNA SHAPE experiment when directly compared to 1M7.


Water-soluble isatoic anhydrides: A platform for RNA-SHAPE analysis and protein bioconjugation
Adam B. Fessler, Abhishek Dey, Corey B. Garmon, Dominic S. Finis, Nemah-Allah Saleh, Anthony J. Fowler, Daniel S. Jones, Kausik Chakrabarti, and Craig A. Ogle
American Chemical Society (ACS)
N-(3-Iodopropyl)isatoic anhydride (IPIA) has been demonstrated to serve as an efficient substrate for the development of an extended bioconjugation platform. Derivatives of IPIA are water-soluble and adaptable and share a common chromophore, rendering them easily quantifiable. We demonstrate the preparation of the readily diversified bioconjugation platform technology and application of the reagents in RNA-SHAPE analysis.


Sequence variation of rare outer membrane protein β-barrel domains in clinical strains provides insights into the evolution of treponema pallidum subsp. Pallidum, the syphilis spirochete
Sanjiv Kumar, Melissa J. Caimano, Arvind Anand, Abhishek Dey, Kelly L. Hawley, Morgan E. LeDoyt, Carson J. La Vake, Adriana R. Cruz, Lady G. Ramirez, Lenka Paštěková,et al.
American Society for Microbiology
ABSTRACT In recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) of Treponema pallidum subspecies pallidum , the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions of tprC , tprD , and bamA in 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database. To establish a phylogenetic framework, we used T. pallidum 0548 ( tp0548 ) genotyping and tp0558 sequences to assign strains to the Nichols or SS14 clades. We found that (i) β-barrels in clinical strains could be grouped according to allelic variants in T. pallidum subsp. pallidum reference genomes; (ii) for all three OMP loci, clinical strains within the Nichols or SS14 clades often harbored β-barrel variants that differed from the Nichols and SS14 reference strains; and (iii) OMP variable regions often reside in predicted extracellular loops containing B-cell epitopes. On the basis of structural models, nonconservative amino acid substitutions in predicted transmembrane β-strands of T. pallidum repeat C (TprC) and TprD2 could give rise to functional differences in their porin channels. OMP profiles of some clinical strains were mosaics of different reference strains and did not correlate with results from enhanced molecular typing. Our observations suggest that human host selection pressures drive T. pallidum subsp. pallidum OMP diversity and that genetic exchange contributes to the evolutionary biology of T. pallidum subsp. pallidum . They also set the stage for topology-based analysis of antibody responses to OMPs and help frame strategies for syphilis vaccine development. IMPORTANCE Despite recent progress characterizing outer membrane proteins (OMPs) of Treponema pallidum , little is known about how their surface-exposed, β-barrel-forming domains vary among strains circulating within high-risk populations. In this study, sequences for the β-barrel-encoding regions of three OMP loci, tprC , tprD , and bamA , in T. pallidum subsp. pallidum isolates from a large number of patient specimens from geographically disparate sites were examined. Structural models predict that sequence variation within β-barrel domains occurs predominantly within predicted extracellular loops. Amino acid substitutions in predicted transmembrane strands that could potentially affect porin channel function were also noted. Our findings suggest that selection pressures exerted within human populations drive T. pallidum subsp. pallidum OMP diversity and that recombination at OMP loci contributes to the evolutionary biology of syphilis spirochetes. These results also set the stage for topology-based analysis of antibody responses that promote clearance of T. pallidum subsp. pallidum and frame strategies for vaccine development based upon conserved OMP extracellular loops.


Current perspectives of telomerase structure and function in eukaryotes with emerging views on telomerase in human parasites
Abhishek Dey and Kausik Chakrabarti
MDPI AG
Replicative capacity of a cell is strongly correlated with telomere length regulation. Aberrant lengthening or reduction in the length of telomeres can lead to health anomalies, such as cancer or premature aging. Telomerase is a master regulator for maintaining replicative potential in most eukaryotic cells. It does so by controlling telomere length at chromosome ends. Akin to cancer cells, most single-cell eukaryotic pathogens are highly proliferative and require persistent telomerase activity to maintain constant length of telomere and propagation within their host. Although telomerase is key to unlimited cellular proliferation in both cases, not much was known about the role of telomerase in human parasites (malaria, Trypanosoma, etc.) until recently. Since telomerase regulation is mediated via its own structural components, interactions with catalytic reverse transcriptase and several factors that can recruit and assemble telomerase to telomeres in a cell cycle-dependent manner, we compare and discuss here recent findings in telomerase biology in cancer, aging and parasitic diseases to give a broader perspective of telomerase function in human diseases.


The major outer sheath protein forms distinct conformers and multimeric complexes in the outer membrane and periplasm of Treponema denticola
Robbins Puthenveetil, Sanjiv Kumar, Melissa J. Caimano, Abhishek Dey, Arvind Anand, Olga Vinogradova, and Justin D. Radolf
Springer Science and Business Media LLC
AbstractThe major outer sheath protein (MOSP) is a prominent constituent of the cell envelope of Treponema denticola (TDE) and one of its principal virulence determinants. Bioinformatics predicts that MOSP consists of N- and C-terminal domains, MOSPN and MOSPC. Biophysical analysis of constructs refolded in vitro demonstrated that MOSPC, previously shown to possess porin activity, forms amphiphilic trimers, while MOSPN forms an extended hydrophilic monomer. In TDE and E. coli expressing MOSP with a PelB signal sequence (PelB-MOSP), MOSPC is OM-embedded and surface-exposed, while MOSPN resides in the periplasm. Immunofluorescence assay, surface proteolysis, and novel cell fractionation schemes revealed that MOSP in TDE exists as outer membrane (OM) and periplasmic trimeric conformers; PelB-MOSP, in contrast, formed only OM-MOSP trimers. Although both conformers form hetero-oligomeric complexes in TDE, only OM-MOSP associates with dentilisin. Mass spectrometry (MS) indicated that OM-MOSP interacts with proteins in addition to dentilisin, most notably, oligopeptide-binding proteins (OBPs) and the β-barrel of BamA. MS also identified candidate partners for periplasmic MOSP, including TDE1658, a spirochete-specific SurA/PrsA ortholog. Collectively, our data suggest that MOSP destined for the TDE OM follows the canonical BAM pathway, while formation of a stable periplasmic conformer involves an export-related, folding pathway not present in E. coli.


Peptide uptake is essential for borrelia burgdorferi viability and involves structural and regulatory complexity of its oligopeptide transporter
Ashley M. Groshong, Abhishek Dey, Irina Bezsonova, Melissa J. Caimano, and Justin D. Radolf
American Society for Microbiology
ABSTRACT Borrelia burgdorferi is an extreme amino acid (AA) auxotroph whose genome encodes few free AA transporters and an elaborate oligopeptide transport system ( B. burgdorferi Opp [ Bb Opp]). Bb Opp consists of five oligopeptide-binding proteins (OBPs), two heterodimeric permeases, and a heterodimeric nucleotide-binding domain (NBD). Homology modeling based on the crystal structure of liganded Bb OppA4 revealed that each OBP likely binds a distinct range of peptides. Transcriptional analyses demonstrated that the OBPs are differentially and independently regulated whereas the permeases and NBDs are constitutively expressed. A conditional NBD mutant failed to divide in the absence of inducer and replicated in an IPTG (isopropyl-β- d -thiogalactopyranoside) concentration-dependent manner. NBD mutants grown without IPTG exhibited an elongated morphotype lacking division septa, often with flattening at the cell center due to the absence of flagellar filaments. Following cultivation in dialysis membrane chambers, NBD mutants recovered from rats not receiving IPTG also displayed an elongated morphotype. The NBD mutant was avirulent by needle inoculation, but infectivity was partially restored by oral administration of IPTG to infected mice. We conclude that peptides are a major source of AAs for B. burgdorferi both in vitro and in vivo and that peptide uptake is essential for regulation of morphogenesis, cell division, and virulence. IMPORTANCE Borrelia burgdorferi , the causative agent of Lyme disease, is an extreme amino acid (AA) auxotroph with a limited repertoire of annotated single-AA transporters. A major issue is how the spirochete meets its AA requirements as it transits between its arthropod vector and mammalian reservoir. While previous studies have confirmed that the B. burgdorferi oligopeptide transport ( opp ) system is capable of importing peptides, the importance of the system for viability and pathogenesis has not been established. Here, we evaluated the opp system structurally and transcriptionally to elucidate its ability to import a wide range of peptides during the spirochete’s enzootic cycle. Additionally, using a novel mutagenesis strategy to abrogate opp transporter function, we demonstrated that peptide uptake is essential for bacterial viability, morphogenesis, and infectivity. Our studies revealed a novel link between borrelial physiology and virulence and suggest that peptide uptake serves an intracellular signaling function regulating morphogenesis and division.


Crystal structure of mycobacterium tuberculosis H37Rv AldR (Rv2779c), a regulator of the ald gene : DNA bindig and identification of small molecule inhibitors
Abhishek Dey, Sonal Shree, Sarvesh Kumar Pandey, Rama Pati Tripathi, and Ravishankar Ramachandran
Elsevier BV
Here we report the crystal structure of M. tuberculosis AldR (Rv2779c) showing that the N-terminal DNA-binding domains are swapped, forming a dimer, and four dimers are assembled into an octamer through crystal symmetry. The C-terminal domain is involved in oligomeric interactions that stabilize the oligomer, and it contains the effector-binding sites. The latter sites are 30–60% larger compared with homologs like MtbFFRP (Rv3291c) and can consequently accommodate larger molecules. MtbAldR binds to the region upstream to the ald gene that is highly up-regulated in nutrient-starved tuberculosis models and codes for l-alanine dehydrogenase (MtbAld; Rv2780). Further, the MtbAldR-DNA complex is inhibited upon binding of Ala, Tyr, Trp and Asp to the protein. Studies involving a ligand-binding site G131T mutant show that the mutant forms a DNA complex that cannot be inhibited by adding the amino acids. Comparative studies suggest that binding of the amino acids changes the relative spatial disposition of the DNA-binding domains and thereby disrupt the protein-DNA complex. Finally, we identified small molecules, including a tetrahydroquinoline carbonitrile derivative (S010-0261), that inhibit the MtbAldR-DNA complex. The latter molecules represent the very first inhibitors of a feast/famine regulatory protein from any source and set the stage for exploring MtbAldR as a potential anti-tuberculosis target.


Cloning, overexpression, purification and preliminary X-ray analysis of a feast/famine regulatory protein (Rv2779c) from Mycobacterium tuberculosis H37Rv
Abhishek Dey and Ravishankar Ramachandran
International Union of Crystallography (IUCr)
Rv2779c from Mycobacterium tuberculosis is a feast/famine regulatory protein. This class of proteins are also known as the leucine-responsive regulatory protein/asparagine synthase C family (Lrp/AsnC) of transcriptional regulators and are known to be involved in various metabolic processes in bacteria and fungi. They contain a RAM (regulator of amino-acid metabolism) domain that is rarely found in humans and acts as the oligomerization domain. Since the oligomeric status is often linked to the particular functional role in these proteins, binding of ligands to the domain can elicit specific functional responses. Full-length Rv2779c corresponding to a molecular mass of 19.8 kDa and 179 residues was cloned and purified to homogeneity following transformation into Escherichia coli C41 (DE3) cells. Crystals were grown by vapour diffusion using the hanging-drop method. Diffraction data extending to 2.8 Å resolution were collected from a single crystal that belonged to space group P2(1)2(1)2, with unit-cell parameters a = 99.6, b = 146.0, c = 49.9 Å. Matthews coefficient (VM) calculations suggest that four molecules are present in the asymmetric unit, corresponding to a solvent content of ∼46%. Molecular-replacement calculations using the crystal structure of a homologue, Rv3291c, as the search model gave an unambiguous solution corresponding to four subunits in the asymmetric unit.


Ligand-Induced Structural Transitions, Mutational Analysis, and 'Open' Quaternary Structure of the M. tuberculosis Feast/Famine Regulatory Protein (Rv3291c)
Tripti Shrivastava, Abhishek Dey, and Ravishankar Ramachandran
Elsevier BV

RECENT SCHOLAR PUBLICATIONS

A Cascade of Conformational Switches in SARS-CoV‑2 Frameshifting: Coregulation by Upstream and Downstream Elements
TS Samuel Lee, Shuting Yan, Abhishek Dey, Alain Laederach
Biochemistry 2025



High-throughput sequencing: a breakthrough in molecular diagnosis for precision medicine
NSAD Dipali Barku Dongare, Shaik Shireen Nishad, Sakshi Y. Mastoli, Shubhini ...
Functional & Integrative Genomics 25 2025



An intricate balancing act: Upstream and downstream frameshift co-regulatory elements
TS Samuel Lee, Shuting Yan, Abhishek Dey, Alain Laederach
Biorxiv 2024



Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses
TS Abhishek Dey, Alain Laederach, Shuting Yan
BiorXiv 2024



Neuroprotective Effects of Carotenoid Rich Verbesina encelioides Flower Extract in Scopolamine Induced Memory Impaired Rats Mimicking Alzheimer’s Disease
KKP Abhishek Dey * , Nidhi Srivastava * , Swapnil Sharma * , Vartika Verma ...
Preprints 2024 2024



Structural Modifications and Novel Protein-Binding Sites in Pre-miR-675—Explaining Its Regulatory Mechanism in Carcinogenesis
D Abhishek
Non-Coding RNA 9 (4) 2023



Comprehensive structural and interactome analysis reveals novel interactions and protein binding sites in miR-675: a non-coding RNA critically involved in multiple diseases
A Dey
BioRXIV 2023



Acknowledgment to the Reviewers of Non‐Coding RNA in 2022
NCRNAE Office
Non‐Coding RNA 2023



Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing
J Kumar, L Lackey, JM Waldern, A Dey, AM Mustoe, KM Weeks, ...
elife 11, e73888 2022



Sequence and tissue targeting specificity of ZFP36L2 reveals Elavl2 as a novel target with co-regulation potential
SBVR Ian C Redmon, Matthew Ardizzone, Hilal Hekimoğlu, Breanne M Hatfield ...
Nucleic Acid Research 50 (7) 2022



Acknowledgment to Reviewers of IJMS in 2021
IJMS office
International Journal of Molecular Sciences 2022



Acknowledgment to Reviewers of Pharmaceutics in 2021
PE Office
Pharmaceutics 2022



In vivo architecture of the telomerase RNA catalytic core in Trypanosoma brucei
CK Abhishek Dey, Monroy-Eklund Anais, Klotz Kaitlin, Saha Arpita, Davis ...
Nucleic Acids Research 49 (21), 12445–12466 2021



To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element
LA Schlick Tamar, Zhu Qiyao, Dey Abhishek, Jain Swati, Yan Shuting
Journal of American Chemical Society 2021



The RNA Structurome in the Asexual Blood Stages of Malaria Pathogen Plasmodium falciparum
SKKC Diana Renteria Alvarez , Alejandra Ospina, Tiffany Barwell, Bo Zheng ...
RNA Biology 2021



Innately Water-Soluble Isatoic Anhydrides with Modulated Reactivities for RNA SHAPE Analysis.
OCA Fessler AB, Abhishek Dey, Finis DS, Fowler AJ, Chakrabarti K
Bioconjugate Chemistry 31 (3), 884-888 2020



The Non-Coding RNA Journal Club: Highlights on Recent Papers-7.
JH Xiao H, Shiu PKT, Gabryleska M, Conn SJ, Dey A, Chakrabarti K, Regouc M ...
Noncoding RNA 5 (2), E40 2019



Water-Soluble Isatoic Anhydrides: A Platform for RNA-SHAPE Analysis and Protein Bioconjugation
OCA Fessler AB, Dey A, Garmon CB, Finis DS, Saleh NA, Fowler AJ, Jones DS ...
Bioconjugate chemistry 29 (9), 3196-3202 2018



Sequence variation of rare outer membrane protein β-barrel domains in clinical strains provides insights into the evolution of Treponema pallidum subsp. pallidum, the syphilis
S Kumar, MJ Caimano, A Anand, A Dey, KL Hawley, ME LeDoyt, ...
MBio 9 (3), 10.1128/mbio. 01006-18 2018



Current Perspectives of Telomerase Structure and Function in Eukaryotes with Emerging Views on Telomerase in Human Parasites
D Abhishek, C Kausik
International Journal of Molecular Sciences 19 (333), 1-28 2018

MOST CITED SCHOLAR PUBLICATIONS

To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element
LA Schlick Tamar, Zhu Qiyao, Dey Abhishek, Jain Swati, Yan Shuting
Journal of American Chemical Society 2021
Citations: 62



Current Perspectives of Telomerase Structure and Function in Eukaryotes with Emerging Views on Telomerase in Human Parasites
D Abhishek, C Kausik
International Journal of Molecular Sciences 19 (333), 1-28 2018
Citations: 55



Sequence variation of rare outer membrane protein β-barrel domains in clinical strains provides insights into the evolution of Treponema pallidum subsp. pallidum, the syphilis
S Kumar, MJ Caimano, A Anand, A Dey, KL Hawley, ME LeDoyt, ...
MBio 9 (3), 10.1128/mbio. 01006-18 2018
Citations: 42



Peptide Uptake Is Essential for Borrelia burgdorferi Viability and Involves Structural and Regulatory Complexity of its Oligopeptide Transporter
AM Groshong, A Dey, I Bezsonova, MJ Caimano, JD Radolf
MBio 8 (6), 10.1128/mbio. 02047-17 2017
Citations: 38



Crystal structure of Mycobacterium tuberculosis H37Rv AldR (Rv2779c), a regulator of the ald gene: DNA binding and identification of small molecule inhibitors
A Dey, S Shree, SK Pandey, RP Tripathi, R Ramachandran
Journal of Biological Chemistry 291 (23), 11967-11980 2016
Citations: 20



Ligand-Induced Structural Transitions, Mutational Analysis, and ‘Open’ Quaternary Structure of the M. tuberculosis Feast/Famine Regulatory Protein (Rv3291c)
ADRR Tripti Shrivastava
JOURNAL OF MOLECULAR BIOLOGY 392, 1007-1019 2009
Citations: 19



The major outer sheath protein forms distinct conformers and multimeric complexes in the outer membrane and periplasm of Treponema denticola.
JDR Robbins Puthenveetil, Sanjiv Kumar, Melissa J. Caimano, Abhishek Dey ...
Scientific Reports: NPG 7, 13260-13278 2017
Citations: 14



Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing
J Kumar, L Lackey, JM Waldern, A Dey, AM Mustoe, KM Weeks, ...
elife 11, e73888 2022
Citations: 13



In vivo architecture of the telomerase RNA catalytic core in Trypanosoma brucei
CK Abhishek Dey, Monroy-Eklund Anais, Klotz Kaitlin, Saha Arpita, Davis ...
Nucleic Acids Research 49 (21), 12445–12466 2021
Citations: 12



The RNA Structurome in the Asexual Blood Stages of Malaria Pathogen Plasmodium falciparum
SKKC Diana Renteria Alvarez , Alejandra Ospina, Tiffany Barwell, Bo Zheng ...
RNA Biology 2021
Citations: 9



Water-Soluble Isatoic Anhydrides: A Platform for RNA-SHAPE Analysis and Protein Bioconjugation
OCA Fessler AB, Dey A, Garmon CB, Finis DS, Saleh NA, Fowler AJ, Jones DS ...
Bioconjugate chemistry 29 (9), 3196-3202 2018
Citations: 9



Cloning, overexpression, purification and preliminary X-ray analysis of a feast/famine regulatory protein (Rv2779c) from Mycobacterium tuberculosis H37Rv
A Dey, R Ramachandran
Acta Crystallographica Section F 70, 97-100 2014
Citations: 9



Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses
TS Abhishek Dey, Alain Laederach, Shuting Yan
BiorXiv 2024
Citations: 8



Sequence and tissue targeting specificity of ZFP36L2 reveals Elavl2 as a novel target with co-regulation potential
SBVR Ian C Redmon, Matthew Ardizzone, Hilal Hekimoğlu, Breanne M Hatfield ...
Nucleic Acid Research 50 (7) 2022
Citations: 7



Structural Modifications and Novel Protein-Binding Sites in Pre-miR-675—Explaining Its Regulatory Mechanism in Carcinogenesis
D Abhishek
Non-Coding RNA 9 (4) 2023
Citations: 6



Innately Water-Soluble Isatoic Anhydrides with Modulated Reactivities for RNA SHAPE Analysis.
OCA Fessler AB, Abhishek Dey, Finis DS, Fowler AJ, Chakrabarti K
Bioconjugate Chemistry 31 (3), 884-888 2020
Citations: 5



An intricate balancing act: Upstream and downstream frameshift co-regulatory elements
TS Samuel Lee, Shuting Yan, Abhishek Dey, Alain Laederach
Biorxiv 2024
Citations: 2



The Non-Coding RNA Journal Club: Highlights on Recent Papers-7.
JH Xiao H, Shiu PKT, Gabryleska M, Conn SJ, Dey A, Chakrabarti K, Regouc M ...
Noncoding RNA 5 (2), E40 2019
Citations: 1