Subramaniyam Ravichandran

All Publications

• G-quadruplex as an essential structural element in cytomegalovirus replication origin. Nature communications Park, D., Chung, W. C., Gong, S., Ravichandran, S., Lee, G. M., Han, M., Kim, K. K., Ahn, J. H. 2024; 15 (1): 7353

  Abstract

  G-quadruplex (G4) structures are found in eukaryotic cell replication origins, but their role in origin function remains unclear. In this study G4 motifs are found in the lytic DNA replication origin (oriLyt) of human cytomegalovirus (HCMV) and recombinant viruses show that a G4 motif in oriLyt essential region I (ER-I) is necessary for viral growth. Replication assays of oriLyt-containing plasmids and biochemical/biophysical analyses show that G4 formation in ER-I is crucial for viral DNA replication. G4 pull-down analysis identifies viral DNA replication factors, such as IE2, UL84, and UL44, as G4-binding proteins. In enzyme-linked immunosorbent assays, specific G4-binding ligands inhibit G4 binding by the viral proteins. The Epstein-Barr virus oriLyt core element also forms a stable G4 that could substitute for the oriLyt ER-I G4 in HCMV. These results demonstrate that viral G4s in replication origins represent an essential structural element in recruiting replication factors and might be a therapeutic target against viral infections.

  View details for DOI 10.1038/s41467-024-51797-6

  View details for PubMedID 39191758

  View details for PubMedCentralID 7115845

• Stabilization of RNA G-quadruplexes in the SARS-CoV-2 genome inhibits viral infection via translational suppression. Archives of pharmacal research Razzaq, M., Han, J. H., Ravichandran, S., Kim, J., Bae, J., Park, M., Kannappan, S., Chung, W., Ahn, J., Song, M. J., Kim, K. K. 2023

  Abstract

  The G-quadruplex (G4) formed in single-stranded DNAs or RNAs plays a key role in diverse biological processes and is considered as a potential antiviral target. In the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 25 putative G4-forming sequences are predicted; however, the effects of G4-binding ligands on SARS-CoV-2 replication have not been studied in the context of viral infection. In this study, we investigated whether G4-ligands suppressed SARS-CoV-2 replication and whether their antiviral activity involved stabilization of viral RNA G4s and suppression of viral gene expression. We found that pyridostatin (PDS) suppressed viral gene expression and genome replication as effectively as the RNA polymerase inhibitor remdesivir. Biophysical analyses revealed that the 25 predicted G4s in the SARS-CoV-2 genome formed a parallel G4 structure. In particular, G4-644 and G4-3467 located in the 5' region of ORF1a, formed a G4 structure that could be effectively stabilized by PDS. We also showed that PDS significantly suppressed translation of the reporter genes containing these G4s. Taken together, our results demonstrate that stabilization of RNA G4s by PDS in the SARS-CoV-2 genome inhibits viral infection via translational suppression, highlighting the therapeutic potential of G4-ligands in SARS-CoV-2 infection.

  View details for DOI 10.1007/s12272-023-01458-x

  View details for PubMedID 37563335

• G-quadruplexes formed by Varicella-Zoster virus reiteration sequences suppress expression of glycoprotein C and regulate viral cell-to-cell spread. PLoS pathogens Chung, W. C., Ravichandran, S., Park, D., Lee, G. M., Kim, Y. E., Choi, Y., Song, M. J., Kim, K. K., Ahn, J. H. 2023; 19 (1): e1011095

  Abstract

  G-quadruplex (G4) formed by repetitive guanosine-rich sequences plays important roles in diverse cellular processes; however, its roles in viral infection are not fully understood. In this study, we investigated the genome-wide distribution of G4-forming sequences (G4 motifs) in Varicella-Zoster virus (VZV) and found that G4 motifs are enriched in the internal repeat short and the terminal repeat short regions flanking the unique short region and also in some reiteration (R) sequence regions. A high density of G4 motifs in the R2 region was found on the template strand of ORF14, which encodes glycoprotein C (gC), a virulent factor for viral growth in skin. Analyses such as circular dichroism spectroscopy, thermal difference spectra, and native polyacrylamide gel electrophoresis with oligodeoxynucleotides demonstrated that several G4 motifs in ORF14 form stable G4 structures. In transfection assays, gC expression from the G4-disrupted ORF14 gene was increased at the transcriptional level and became more resistant to suppression by G4-ligand treatment. The recombinant virus containing the G4-disrupted ORF14 gene expressed a higher level of gC mRNA, while it showed a slightly reduced growth. This G4-disrupted ORF14 virus produced smaller plaques than the wild-type virus. Our results demonstrate that G4 formation via reiteration sequences suppresses gC expression during VZV infection and regulates viral cell-to-cell spread.

  View details for DOI 10.1371/journal.ppat.1011095

  View details for PubMedID 36630443

• The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex (vol 49, pg 10689, 2021) NUCLEIC ACIDS RESEARCH Ravichandran, S., Razzaq, M., Parveen, N., Ghosh, A., Kim, K. 2021; 49 (20): 12004

  View details for DOI 10.1093/nar/gkab1140

  View details for Web of Science ID 000836401700042

• The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex NUCLEIC ACIDS RESEARCH Ravichandran, S., Razzaq, M., Parveen, N., Ghosh, A., Kim, K. 2021; 49 (18): 10689-10706

  Abstract

  G-quadruplex (G4), a four-stranded DNA or RNA structure containing stacks of guanine tetrads, plays regulatory roles in many cellular functions. So far, conventional G4s containing loops of 1-7 nucleotides have been widely studied. Increasing experimental evidence suggests that unconventional G4s, such as G4s containing long loops (long-loop G4s), play a regulatory role in the genome by forming a stable structure. Other secondary structures such as hairpins in the loop might thus contribute to the stability of long-loop G4s. Therefore, investigation of the effect of the hairpin-loops on the structure and function of G4s is required. In this study, we performed a systematic biochemical investigation of model G4s containing long loops with various sizes and structures. We found that the long-loop G4s are less stable than conventional G4s, but their stability increased when the loop forms a hairpin (hairpin-G4). We also verified the biological significance of hairpin-G4s by showing that hairpin-G4s present in the genome also form stable G4s and regulate gene expression as confirmed by in cellulo reporter assays. This study contributes to expanding the scope and diversity of G4s, thus facilitating future studies on the role of G4s in the human genome.

  View details for DOI 10.1093/nar/gkab739

  View details for Web of Science ID 000715870700038

  View details for PubMedID 34450640

  View details for PubMedCentralID PMC8501965

• Unraveling the Regulatory G-Quadruplex Puzzle: Lessons From Genome and Transcriptome-Wide Studies FRONTIERS IN GENETICS Ravichandran, S., Ahn, J., Kim, K. 2019; 10: 1002

  Abstract

  G-quadruplexes (G4s) are among the best-characterized DNA secondary structures and are enriched in regulatory regions, especially promoters, of several prokaryote and eukaryote genomes, indicating a possible role in cis regulation of genes. Many studies have focused on evaluating the impact of specific G4-forming sequences in the promoter regions of genes. However, the lack of correlation between the presence of G4s and the functional impact on cis gene regulation, evidenced by the variable expression fold change in the presence of G4 stabilizers, shows that not all G4s affect transcription in the same manner. This indicates that the regulatory effect of the G4 is significantly influenced by its position, the surrounding DNA topology, and other environmental factors within the cell. In this review, we compare individual gene studies with high-throughput differential expression studies to highlight the importance of formulating a combined approach that can be applied in humans, bacteria, and viruses to better understand the effect of G4-mediated gene regulation.

  View details for DOI 10.3389/fgene.2019.01002

  View details for Web of Science ID 000494338000001

  View details for PubMedID 31681431

  View details for PubMedCentralID PMC6813735

• Pneumococcal VncR Strain-Specifically Regulates Capsule Polysaccharide Synthesis FRONTIERS IN MICROBIOLOGY Ghosh, P., Shah, M., Ravichandran, S., Park, S., Iqbal, H., Choi, S., Kim, K., Rhee, D. 2019; 10: 2279

  Abstract

  Capsular polysaccharides (CPS), a major virulence factor in Streptococcus pneumoniae, become thicker during blood invasion while not during asymptomatic nasopharyngeal colonization. However, the underlying mechanism controlling this differential pneumococcal CPS regulation remain unclear. Here, we show how VncR, the response regulator of the vancomycin resistance locus (vncRS operon), regulates CPS expression in vncR mutants in three serotype (type 2, 3, and 6B) backgrounds upon exposure to serum lactoferrin (LF). Comparative analysis of CPS levels in the wild type (WT) of three strains and their isogenic vncR mutants after LF exposure revealed a strain-specific alteration in CPS production. Consistently, VncR-mediated strain-specific CPS production is correlated with pneumococcal virulence, in vivo. Electrophoretic mobility-shift assay and co-immunoprecipitation revealed an interaction between VncR and the cps promoter (cpsp) in the presence of serum. In addition, in silico analysis uncovered this protein-DNA interaction, suggesting that VncR binds with the cpsp, and recognizes the strain-specific significance of the tandem repeats in cpsp. Taken together, the interaction of VncR and cpsp after serum exposure plays an essential role in regulating differential strain-specific CPS production, which subsequently determines strain-specific systemic virulence. This study highlights how host protein LF contributes to pneumococcal VncR-mediated CPS production. As CPS plays a significant role in immune evasion, these findings suggest that drugs designed to interrupt the VncR-mediated CPS production could help to combat pneumococcal infections.

  View details for DOI 10.3389/fmicb.2019.02279

  View details for Web of Science ID 000491276300001

  View details for PubMedID 31632380

  View details for PubMedCentralID PMC6781885

• Z-DNA in the genome: from structure to disease. Biophysical reviews Ravichandran, S., Subramani, V. K., Kim, K. K. 2019; 11 (3): 383-387

  Abstract

  The scope of studies investigating the architecture of genomic DNA has progressed steadily since the elucidation of the structure of B-DNA. In recent years, several non-canonical DNA structures including Z-DNA, G-quadruplexes, H-DNA, cruciform DNA, and i-motifs have been reported to form in genomic DNA and are closely related to the evolution and development of disease. The ability of these structures to form in genomic DNA indicates that they might have important cellular roles and are therefore retained during evolution. Understanding the impact of the formation of these secondary structures on cellular processes can enable identification of new targets for therapeutics. In this review, we report the state of understanding of Z-DNA structure and formation and their implication in disease. Finally, we state our perspective on the potential of Z-DNA as a therapeutic target.

  View details for DOI 10.1007/s12551-019-00534-1

  View details for PubMedID 31119604

• Chemical-induced formation of BZ-junction with base extrusion BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS Subramani, V., Ravichandran, S., Bansal, V., Kim, K. 2019; 508 (4): 1215-1220

  Abstract

  The crystal structure of BZ-junction reveals that left-handed Z-DNA stabilized by Z-DNA binding domain (Zα) is continuously stacked to right-handed B-DNA with AT bases' extrusion in the junction site. However, this structure might not fully represent the BZ-junction in solution due to the possibility of the junction formation either by crystal packing or Zα interaction. Therefore, we investigated BZ-junction in solution with chemical Z-DNA inducers using CD and 2-aminopurine base-extrusion assay. We confirmed the formation of Z-DNA and BZ-junction with base-extrusion by chemical Z-DNA inducers. However, neither typical Z-DNA nor base-extrusion could be detected with some inducers such as spermine, suggesting that the energy barrier for the formation of the BZ junction might vary depending on the Z-DNA induction conditions.

  View details for DOI 10.1016/j.bbrc.2018.12.045

  View details for Web of Science ID 000456491900036

  View details for PubMedID 30558789

• Genome-wide analysis of regulatory G-quadruplexes affecting gene expression in human cytomegalovirus PLOS PATHOGENS Ravichandran, S., Kim, Y., Bansal, V., Ghosh, A., Hur, J., Subramani, V., Pradhan, S., Lee, M., Kim, K., Ahn, J. 2018; 14 (9): e1007334

  Abstract

  G-quadruplex (G4), formed by repetitive guanosine-rich sequences, is known to play various key regulatory roles in cells. Herpesviruses containing a large double-stranded DNA genome show relatively higher density of G4-forming sequences in their genomes compared to human and mouse. However, it remains poorly understood whether all of these sequences form G4 and how they play a role in the virus life cycle. In this study, we performed genome-wide analyses of G4s present in the putative promoter or gene regulatory regions of a 235-kb human cytomegalovirus (HCMV) genome and investigated their roles in viral gene expression. We evaluated 36 putative G4-forming sequences associated with 20 genes for their ability to form G4 and for the stability of G4s in the presence or absence of G4-stabilizing ligands, by circular dichroism and melting temperature analyses. Most identified sequences formed a stable G4; 28 sequences formed parallel G4s, one formed an antiparallel G4, and four showed mixed conformations. However, when we assessed the effect of G4 on viral promoters by cloning the 20 putative viral promoter regions containing 36 G4-forming sequences into the luciferase reporter and monitoring the expression of luciferase reporter gene in the presence of G4-stabilizing chemicals, we found that only 9 genes were affected by G4 formation. These results revealed promoter context-dependent gene suppression by G4 formation. Mutational analysis of two potential regulatory G4s also demonstrated gene suppression by the sequence-specific G4 formation. Furthermore, the analysis of a mutant virus incapable of G4 formation in the UL35 promoter confirmed promoter regulation by G4 in the context of virus infection. Our analyses provide a platform for assessing G4 functions at the genomic level and demonstrate the properties of the HCMV G4s and their regulatory roles in viral gene expression.

  View details for DOI 10.1371/journal.ppat.1007334

  View details for Web of Science ID 000448975900039

  View details for PubMedID 30265731

  View details for PubMedCentralID PMC6179306

• Bioinorganic Nanohybrid Catalyst for Multistep Synthesis of Acetaminophen, an Analgesic ACS APPLIED MATERIALS & INTERFACES San, B., Ravichandran, S., Park, K., Subramani, V., Kim, K. 2016; 8 (44): 30058-30065

  Abstract

  A bioinorganic nanohybrid catalyst was synthesized by combining esterase with a platinum nanoparticle (PtNP). The combination of two catalysts resulted in enhanced catalytic activities, esterase hydrolysis, and hydrogenation in PtNPs, as compared to each catalyst alone. This hybrid catalyst can be successfully used in the multistep synthesis of acetaminophen (paracetamol), an analgesic and antipyretic drug, in a one-pot reaction with high yield and efficacy within a short time, demonstrating that the nanobiohybrid catalyst offers advantages in the synthesis of fine chemicals in industrial applications.

  View details for DOI 10.1021/acsami.6b12875

  View details for Web of Science ID 000387737200025

  View details for PubMedID 27797174

• A novel approach for the biosynthesis of silver oxide nanoparticles using aqueous leaf extract of Callistemon lanceolatus (Myrtaceae) and their therapeutic potential JOURNAL OF EXPERIMENTAL NANOSCIENCE Ravichandran, S., Paluri, V., Kumar, G., Loganathan, K., Venkata, B. 2016; 11 (6): 445-458

  View details for DOI 10.1080/17458080.2015.1077534

  View details for Web of Science ID 000371343400004