Our Technophile
Suresha G P
Past PhD student
Suresha G. Prabhu (2019-2024): Defended his PhD thesis entitled, “Mouse mammary tumor virus (MMTV) genomic RNA (gRNA) packaging: selective gRNA encapsidation is facilitated by long-range interactions (LRIs) that facilitate specific Gag binding”. Briefly, Suresha thesis project was directed towards validating the existence and the biological significance of U5-Gag LRIs and the architectural role these LRIs may play in stabilizing the overall RNA secondary structure of MMTV packaging signal RNA employing a combination of in vitro and in vivo approaches. Part of his thesis work was published in the top 1% journal (Prabhu et al., PLoS Biology, 2024). In addition, he contributed significantly to other projects in the laboratory to be a co-author on other manuscripts from the laboratory (Pillai et al., J. Mol. Biol., 2021; Pillai et al., Heliyon, 2023; Krishnan et al., RNA, 2024; Jehad et al., FEMS Microbiology Reviews, 2025). He also presented his thesis work at the prestigious annual Retrovirus meeting of the Cold Spring Harbor Laboratory, New York, 2024. Currently, Suresha is working as a postdoctoral fellow at Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Dubai. Link to the thesis defense
Publications
2026
Jehad, Mohammad Abdullah; Ali, Lizna M; Pillai, Vineeta N; Prabhu, Suresha G; Mustafa, Farah; Rizvi, Tahir A
Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication Journal Article
In: FEMS Microbiology Reviews, vol. 50, 2026, ISSN: 1574-6976.
@article{Jehad2025b,
title = {Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication},
author = {Mohammad Abdullah Jehad and Lizna M Ali and Vineeta N Pillai and Suresha G Prabhu and Farah Mustafa and Tahir A Rizvi},
editor = {Christian Münz},
doi = {10.1093/femsre/fuaf066},
issn = {1574-6976},
year = {2026},
date = {2026-01-10},
urldate = {2026-01-10},
journal = {FEMS Microbiology Reviews},
volume = {50},
publisher = {Oxford University Press (OUP)},
abstract = {Retroviruses are exclusive group of positive-sense RNA viruses defined by their ability to reverse transcribe their RNA genome and integrate it into the host’s chromosomal DNA. This distinctive replication strategy enables persistent infection and has profoundly shaped our understanding of molecular biology, gene regulation, and evolution. Retroviruses have contributed to landmark discoveries, including the identification of oncogenes, mechanisms of transcriptional control, and the development of gene therapy vectors. This review provides an updated overview of retroviral molecular biology, emphasizing the coordinated steps of the viral life cycle and emerging insights that are reshaping classical models. It explores virion structure, genome organization, and the interplay of cis-acting sequences and trans-acting factors that govern replication. Special focus is given to recent advances in understanding nuclear trafficking of capsids, spatial dynamics of reverse transcription and integration leading to provirus formation, RNA nuclear export, and selective genome packaging. The structural and functional roles of viral proteins, particularly Gag, are discussed in the context of assembly and maturation. By integrating foundational concepts with new discoveries, this review highlights the molecular sophistication of retroviral replication and identifies outstanding questions that guide future research, with implications extending to antiviral strategies, gene therapy, cancer biology, and evolution.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Retroviruses are exclusive group of positive-sense RNA viruses defined by their ability to reverse transcribe their RNA genome and integrate it into the host’s chromosomal DNA. This distinctive replication strategy enables persistent infection and has profoundly shaped our understanding of molecular biology, gene regulation, and evolution. Retroviruses have contributed to landmark discoveries, including the identification of oncogenes, mechanisms of transcriptional control, and the development of gene therapy vectors. This review provides an updated overview of retroviral molecular biology, emphasizing the coordinated steps of the viral life cycle and emerging insights that are reshaping classical models. It explores virion structure, genome organization, and the interplay of cis-acting sequences and trans-acting factors that govern replication. Special focus is given to recent advances in understanding nuclear trafficking of capsids, spatial dynamics of reverse transcription and integration leading to provirus formation, RNA nuclear export, and selective genome packaging. The structural and functional roles of viral proteins, particularly Gag, are discussed in the context of assembly and maturation. By integrating foundational concepts with new discoveries, this review highlights the molecular sophistication of retroviral replication and identifies outstanding questions that guide future research, with implications extending to antiviral strategies, gene therapy, cancer biology, and evolution.
2024
Prabhu, Suresha G.; Pillai, Vineeta N.; Ali, Lizna Mohamed; Vivet-Boudou, Valérie; Chameettachal, Akhil; Bernacchi, Serena; Mustafa, Farah; Marquet, Roland; Rizvi, T. A.
MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals Journal Article
In: PLOS Biology, vol. 22, no. 10, pp. 1-34, 2024.
@article{10.1371/journal.pbio.3002827,
title = {MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals},
author = {Suresha G. Prabhu and Vineeta N. Pillai and Lizna Mohamed Ali and Valérie Vivet-Boudou and Akhil Chameettachal and Serena Bernacchi and Farah Mustafa and Roland Marquet and T. A. Rizvi},
url = {https://doi.org/10.1371/journal.pbio.3002827},
doi = {10.1371/journal.pbio.3002827},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {PLOS Biology},
volume = {22},
number = {10},
pages = {1-34},
publisher = {Public Library of Science},
abstract = {The packaging of genomic RNA (gRNA) into retroviral particles relies on the specific recognition by the Gag precursor of packaging signals (Psi), which maintain a complex secondary structure through long-range interactions (LRIs). However, it remains unclear whether the binding of Gag to Psi alone is enough to promote RNA packaging and what role LRIs play in this process. Using mouse mammary tumor virus (MMTV), we investigated the effects of mutations in 4 proposed LRIs on gRNA structure and function. Our findings revealed the presence of an unsuspected extended LRI, and hSHAPE revealed that maintaining a wild-type–like Psi structure is crucial for efficient packaging. Surprisingly, filter-binding assays demonstrated that most mutants, regardless of their packaging capability, exhibited significant binding to Pr77Gag, suggesting that Gag binding to Psi is insufficient for efficient packaging. Footprinting experiments indicated that efficient RNA packaging is promoted when Pr77Gag binds to 2 specific sites within Psi, whereas binding elsewhere in Psi does not lead to efficient packaging. Taken together, our results suggest that the 3D structure of the Psi/Pr77Gag complex regulates the assembly of viral particles around gRNA, enabling effective discrimination against other viral and cellular RNAs that may also bind Gag efficiently.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The packaging of genomic RNA (gRNA) into retroviral particles relies on the specific recognition by the Gag precursor of packaging signals (Psi), which maintain a complex secondary structure through long-range interactions (LRIs). However, it remains unclear whether the binding of Gag to Psi alone is enough to promote RNA packaging and what role LRIs play in this process. Using mouse mammary tumor virus (MMTV), we investigated the effects of mutations in 4 proposed LRIs on gRNA structure and function. Our findings revealed the presence of an unsuspected extended LRI, and hSHAPE revealed that maintaining a wild-type–like Psi structure is crucial for efficient packaging. Surprisingly, filter-binding assays demonstrated that most mutants, regardless of their packaging capability, exhibited significant binding to Pr77Gag, suggesting that Gag binding to Psi is insufficient for efficient packaging. Footprinting experiments indicated that efficient RNA packaging is promoted when Pr77Gag binds to 2 specific sites within Psi, whereas binding elsewhere in Psi does not lead to efficient packaging. Taken together, our results suggest that the 3D structure of the Psi/Pr77Gag complex regulates the assembly of viral particles around gRNA, enabling effective discrimination against other viral and cellular RNAs that may also bind Gag efficiently.
Krishnan, A.; Ali, L. M.; Prabhu, Suresha G; Pillai, V. N.; Chameettachal, A.; Vivet-Boudou, Valérie; Bernacchi, Serena; Mustafa, F.; Marquet, Roland; Rizvi, T. A.
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging Journal Article
In: RNA, vol. 30, no. 1, pp. 68–88, 2024, ISSN: 1469-9001.
@article{Krishnan2023,
title = {Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging},
author = {A. Krishnan and L. M. Ali and Suresha G Prabhu and V. N. Pillai and A. Chameettachal and Valérie Vivet-Boudou and Serena Bernacchi and F. Mustafa and Roland Marquet and T. A. Rizvi},
doi = {10.1261/rna.079840.123},
issn = {1469-9001},
year = {2024},
date = {2024-01-00},
urldate = {2024-01-00},
journal = {RNA},
volume = {30},
number = {1},
pages = {68--88},
publisher = {Cold Spring Harbor Laboratory},
abstract = {The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5′ end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ sequences using genetic, biochemical, and structure–function relationship approaches. Our mutational analysis revealed that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput selective 2′ hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences, with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained nucleotides 80–92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA–Pr50Gag interactions. Delineating sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of FIV-based vectors for human gene therapy.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5′ end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ sequences using genetic, biochemical, and structure–function relationship approaches. Our mutational analysis revealed that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput selective 2′ hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences, with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained nucleotides 80–92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA–Pr50Gag interactions. Delineating sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of FIV-based vectors for human gene therapy.
2023
Pillai, V. N.; Ali, L. M.; Prabhu, S. G.; Krishnan, A.; Tariq, S.; Mustafa, F.; Rizvi, T. A.
Expression, purification, and functional characterization of soluble recombinant full-length simian immunodeficiency virus (SIV) Pr55(Gag) Journal Article
In: Heliyon, vol. 9, no. 1, pp. e12892, 2023, ISSN: 2405-8440 (Print) 2405-8440.
@article{RN115,
title = {Expression, purification, and functional characterization of soluble recombinant full-length simian immunodeficiency virus (SIV) Pr55(Gag)},
author = {V. N. Pillai and L. M. Ali and S. G. Prabhu and A. Krishnan and S. Tariq and F. Mustafa and T. A. Rizvi},
doi = {10.1016/j.heliyon.2023.e12892},
issn = {2405-8440 (Print) 2405-8440},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Heliyon},
volume = {9},
number = {1},
pages = {e12892},
abstract = {The simian immunodeficiency virus (SIV) precursor polypeptide Pr55(Gag) drives viral assembly and facilitates specific recognition and packaging of the SIV genomic RNA (gRNA) into viral particles. While several studies have tried to elucidate the role of SIV Pr55(Gag) by expressing its different components independently, studies using full-length SIV Pr55(Gag) have not been conducted, primarily due to the unavailability of purified and biologically active full-length SIV Pr55(Gag). We successfully expressed soluble, full-length SIV Pr55(Gag) with His(6)-tag in bacteria and purified it using affinity and gel filtration chromatography. In the process, we identified within Gag, a second in-frame start codon downstream of a putative Shine-Dalgarno-like sequence resulting in an additional truncated form of Gag. Synonymously mutating this sequence allowed expression of full-length Gag in its native form. The purified Gag assembled into virus-like particles (VLPs) in vitro in the presence of nucleic acids, revealing its biological functionality. In vivo experiments also confirmed formation of functional VLPs, and quantitative reverse transcriptase PCR demonstrated efficient packaging of SIV gRNA by these VLPs. The methodology we employed ensured the availability of >95% pure, biologically active, full-length SIV Pr55(Gag) which should facilitate future studies to understand protein structure and RNA-protein interactions involved during SIV gRNA packaging.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The simian immunodeficiency virus (SIV) precursor polypeptide Pr55(Gag) drives viral assembly and facilitates specific recognition and packaging of the SIV genomic RNA (gRNA) into viral particles. While several studies have tried to elucidate the role of SIV Pr55(Gag) by expressing its different components independently, studies using full-length SIV Pr55(Gag) have not been conducted, primarily due to the unavailability of purified and biologically active full-length SIV Pr55(Gag). We successfully expressed soluble, full-length SIV Pr55(Gag) with His(6)-tag in bacteria and purified it using affinity and gel filtration chromatography. In the process, we identified within Gag, a second in-frame start codon downstream of a putative Shine-Dalgarno-like sequence resulting in an additional truncated form of Gag. Synonymously mutating this sequence allowed expression of full-length Gag in its native form. The purified Gag assembled into virus-like particles (VLPs) in vitro in the presence of nucleic acids, revealing its biological functionality. In vivo experiments also confirmed formation of functional VLPs, and quantitative reverse transcriptase PCR demonstrated efficient packaging of SIV gRNA by these VLPs. The methodology we employed ensured the availability of >95% pure, biologically active, full-length SIV Pr55(Gag) which should facilitate future studies to understand protein structure and RNA-protein interactions involved during SIV gRNA packaging.
2021
Pillai, V. N.; Ali, L. M.; Prabhu, S. G.; Krishnan, A.; Chameettachal, A.; Pitchai, F. N. N.; Mustafa, F.; Rizvi, T. A.
A Stretch of Unpaired Purines in the Leader Region of Simian Immunodeficiency Virus (SIV) Genomic RNA is Critical for its Packaging into Virions Journal Article
In: J Mol Biol, vol. 433, no. 23, pp. 167293, 2021, ISSN: 0022-2836.
@article{RN38,
title = {A Stretch of Unpaired Purines in the Leader Region of Simian Immunodeficiency Virus (SIV) Genomic RNA is Critical for its Packaging into Virions},
author = {V. N. Pillai and L. M. Ali and S. G. Prabhu and A. Krishnan and A. Chameettachal and F. N. N. Pitchai and F. Mustafa and T. A. Rizvi},
doi = {10.1016/j.jmb.2021.167293},
issn = {0022-2836},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {J Mol Biol},
volume = {433},
number = {23},
pages = {167293},
abstract = {Simian immunodeficiency virus (SIV) is an important lentivirus used as a non-human primate model to study HIV replication, and pathogenesis of human AIDS, as well as a potential vector for human gene therapy. This study investigated the role of single-stranded purines (ssPurines) as potential genomic RNA (gRNA) packaging determinants in SIV replication. Similar ssPurines have been implicated as important motifs for gRNA packaging in many retroviruses like, HIV-1, MPMV, and MMTV by serving as Gag binding sites during virion assembly. In examining the secondary structure of the SIV 5' leader region, as recently deduced using SHAPE methodology, we identified four specific stretches of ssPurines (I-IV) in the region that harbors major packaging determinants of SIV. The significance of these ssPurine motifs were investigated by mutational analysis coupled with a biologically relevant single round of replication assay. These analyses revealed that while ssPurine II was essential, the others (ssPurines I, III, & IV) did not significantly contribute to SIV gRNA packaging. Any mutation in the ssPurine II, such as its deletion or substitution, or other mutations that caused base pairing of ssPurine II loop resulted in near abrogation of RNA packaging, further substantiating the crucial role of ssPurine II and its looped conformation in SIV gRNA packaging. Structure prediction analysis of these mutants further corroborated the biological results and further revealed that the unpaired nature of ssPurine II is critical for its function during SIV RNA packaging perhaps by enabling it to function as a specific binding site for SIV Gag.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Simian immunodeficiency virus (SIV) is an important lentivirus used as a non-human primate model to study HIV replication, and pathogenesis of human AIDS, as well as a potential vector for human gene therapy. This study investigated the role of single-stranded purines (ssPurines) as potential genomic RNA (gRNA) packaging determinants in SIV replication. Similar ssPurines have been implicated as important motifs for gRNA packaging in many retroviruses like, HIV-1, MPMV, and MMTV by serving as Gag binding sites during virion assembly. In examining the secondary structure of the SIV 5' leader region, as recently deduced using SHAPE methodology, we identified four specific stretches of ssPurines (I-IV) in the region that harbors major packaging determinants of SIV. The significance of these ssPurine motifs were investigated by mutational analysis coupled with a biologically relevant single round of replication assay. These analyses revealed that while ssPurine II was essential, the others (ssPurines I, III, & IV) did not significantly contribute to SIV gRNA packaging. Any mutation in the ssPurine II, such as its deletion or substitution, or other mutations that caused base pairing of ssPurine II loop resulted in near abrogation of RNA packaging, further substantiating the crucial role of ssPurine II and its looped conformation in SIV gRNA packaging. Structure prediction analysis of these mutants further corroborated the biological results and further revealed that the unpaired nature of ssPurine II is critical for its function during SIV RNA packaging perhaps by enabling it to function as a specific binding site for SIV Gag.