Biology subjects

Gopal, K.

Publications and source records attributed to Gopal, K..

5 recordsLinked to original sources

bioRxiv2026

Investigating the dynamics of proviral silencing in polyclonal HIV-1 infected Jurkat cell populations

Previous work demonstrated that individual HIV-1 provirus-containing Jurkat cell clones maintain stable bimodal expression patterns throughout 8 to 9 days of culture. However, within polyclonal infected cell pools, the overall proportion of cells displaying HIV-1 expression declines with time. Here, we examined the processes underlying population silencing in polyclonal pools comprised of hundreds of individual barcoded proviral clones throughout culturing periods of 22 and 90 days. Monitoring HIV-1 LTR activity via a GFP reporter confirmed that initially most clones exhibited bimodal expression, with mixtures of transcriptionally active and inactive cells. Over time, however, the overall fraction of LTR-active cells declined substantially. High-throughput clonal tracking showed that this decline was not driven by uniform transcriptional silencing. Instead, population silencing resulted from a combination of mechanisms: selective expansion of clones with low LTR activity, reductions in expression within certain clones, and long-term maintenance of stable bimodal expression in others. Notably, over half of clones retained stable bimodal expression patterns after 22 days, and approximately 17% of the clones retained stable bimodal expression even after 90 days in an independent second experiment, despite ongoing phenotypic switching at the single-cell level. These findings demonstrate that population-level HIV-1 silencing emerges from heterogeneous, clone-specific behaviors rather than uniform transcriptional repression. These observations confirm stability for a large subset of clones and provide insight into how integrants with diverse replication and expression properties can act together during HIV-1 polyclonal population silencing.

microbiology↗

bioRxiv2025

Efficient packaging of HIV-1 genomes via recognition of its adenosine-rich content by a heterologous RNA-binding domain

The HIV-1 genome (gRNA) has an unusually biased nucleotide content and is rich in adenosines. Selective packaging of the gRNA is thought to be driven by specific binding of the nucleocapsid (NC) domain of the viral Gag protein to the packaging signal ({Psi}) in the host cell cytosol. However, deletion of regions within {Psi} reduces--but does not completely abolish--genome packaging. To probe whether another feature of the gRNA may contribute to the selective gRNA packaging process, we replaced NC with heterologous RNA-binding domains (RBDs) with distinct RNA-binding properties. Surprisingly, despite disparate RNA binding specificities, all Gag-RBD chimeras successfully recruited the gRNA to the plasma membrane, suggesting that the initial gRNA recognition in the cytosol is not rate limiting. Notwithstanding, many chimeras exhibiting G/C binding specificity were arrested at the assembly stage. Only the Gag-SRSF5 chimera, which multimerized efficiently on adenosine-rich sequences on the gRNA, assembled efficiently and packaged gRNA at near wild-type levels. Importantly, rationally designed mutations that altered the A/G-rich binding specificity of Gag-SRSF5 decreased genome encapsidation efficiency. Furthermore, many Gag chimeras displayed potent dominant negative activities, highlighting NC functions as a targetable step in virus replication. Together, our findings reveal an unexpected aspect of the HIV-1 gRNA, its biased nucleotide content, as a key driver of selective genome packaging. SIGNIFICANCEHow HIV-1 selectively packages its genome (gRNA) into virions is poorly understood. To probe this, we replaced the viral nucleocapsid (NC) protein with heterologous RNA-binding domains (RBDs) from cellular hnRNP and SR protein families. Remarkably, despite their distinct RNA-binding specificities, all Gag-RBD chimeras successfully recruited the gRNA to the plasma membrane, suggesting that the initial gRNA recognition is not rate limiting. Only the Gag-SRSF5 chimera packaged gRNA efficiently which correlated with its capacity to multimerize on adenosine-rich sequences on the gRNA. Notably, several Gag chimeras exhibited strong dominant negative effects, underscoring NC functions as a targetable step in virus replication. Together, these findings uncover that the biased nucleotide content of the HIV-1 gRNA facilitates its selective packaging into virus particles.

microbiology↗

bioRxiv2024

HIV-1 single transcription start site mutants display complementary replication functions that are restored by reversion

HIV-1 transcription initiates at two positions, generating RNAs with either cap1G or cap3G 5' ends. The replication fates of these RNAs differ, with viral particles encapsidating almost exclusively cap1G RNAs and cap3G RNAs retained in cells where they are enriched on polysomes and among spliced viral RNAs. Here, we studied replication properties of virus promoter mutants that produced only one RNA 5' isoform or the other: separately, in combination, and during spreading infection. Results showed that either single start RNA could serve as both mRNA and genomic RNA when present as the only form in cells, although cap3G RNA was more efficiently translated and spliced while cap1G RNA was packaged into nascent virions slightly better than RNAs from the parental virus. When co-expressed from separate vectors, cap1G RNA was preferentially packaged into virions. During spreading infection cap1G-only virus displayed only minor defects but cap3G-only virus showed severe replication delays in both the highly permissive MT-4 cell line and in primary human CD4+ T cells. Passage of cap3G-only virus yielded revertants that replicated as well as the twinned (cap1G+ cap3G) transcription start site parent. These revertants displayed restored packaging and splicing levels and had regained multiple transcription start site use. ImportanceHIV-1 generates two RNAs during its replication that differ by only two nucleotides in length. Despite this very minor difference, the RNAs perform different and complementary replication functions. When mutants that expressed only one RNA were forced to revert, they regained functions associated with the second RNA.

microbiology↗

bioRxiv2023

Loss of Skeletal Muscle Pyruvate Dehydrogenase Induces Lactic Acidosis and Adaptive Anaplerotic Compensation via Pyruvate-Alanine Cycling and Glutaminolysis

Pyruvate dehydrogenase (PDH) is the rate-limiting enzyme for glucose oxidation that links glycolysis-derived pyruvate with the TCA cycle. Although skeletal muscle is a significant site for glucose oxidation and is closely linked with metabolic flexibility, the importance of muscle PDH during rest and exercise has yet to be fully elucidated. Here, we demonstrate that mice with muscle-specific deletion of PDH exhibit rapid weight loss and suffer from severe lactic acidosis, ultimately leading to early mortality under low-fat diet provision. Furthermore, loss of muscle PDH induces adaptive anaplerotic compensation by increasing pyruvate-alanine cycling and glutaminolysis. Interestingly, high-fat diet supplementation effectively abolishes the early mortality and rescues the overt metabolic phenotype induced by muscle PDH deficiency. Despite increased reliance on fatty acid oxidation during high-fat diet provision, loss of muscle PDH worsens exercise performance and induces lactic acidosis. These observations illustrate the importance of muscle PDH in maintaining metabolic flexibility and preventing the development of metabolic disorders. HighlightsO_LISkeletal Muscle PDH is essential for survival C_LIO_LILoss of muscle PDH induces lactic acidosis and premature death C_LIO_LILoss of muscle PDH enhances pyruvate transformations and glutaminolysis C_LIO_LIHigh-fat diet supplementation abolishes early mortality and overt phenotype induced by muscle PDH loss C_LI

cell biology↗

bioRxiv2018

Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response

The RecA protein orchestrates the cellular response to DNA damage via its multiple roles in the bacterial SOS response. Lack of tools that provide unambiguous access to the various RecA states within the cell have prevented understanding of the spatial and temporal changes in RecA structure/function that underlie control of the damage response. Here, we develop a monomeric C-terminal fragment of the {lambda} repressor as a novel fluorescent probe that specifically interacts with RecA filaments on single-stranded DNA (RecA*). Single-molecule imaging techniques in live cells demonstrate that RecA is largely sequestered in storage structures during normal metabolism. Upon DNA damage, the storage structures dissolve and the cytosolic pool of RecA rapidly nucleates to form early SOS-signaling complexes, maturing into DNA-bound RecA bundles at later time points. Both before and after SOS induction, RecA* largely appears at locations distal from replisomes. Upon completion of repair, RecA storage structures reform.

biophysics↗