B. Roja’s research while affiliated with Bharathidasan University and other places

Objective: Clostridium botulinum type A is a neurotoxin-producing, spore-forming anaerobic bacterium that causes botulism in humans. The evolutionary genomic context of this organism is not yet known to understand its molecular virulence mechanisms in the human intestinal tract. Hence, this study aimed to investigate the mechanisms underlying virulence and pathogenesis by comparing the genomic contexts across species, serotypes, and subtypes. Methods: A comparative genomic approach was used to analyze evolutionary genomic relationships, intergenomic distances, syntenic blocks, replication origins, and gene abundance with phylogenomic neighbors. Results: Type A strains have shown genomic proximity to group I strains with distinct accessory genes and vary even within subtypes. Phylogenomic data showed that type C and D strains were distantly related to a group I and group II strains. Synthetic plots indicated that orthologous genes might have evolved from Clostridial ancestry to subtype A3 strains, whereas syntonic out-paralogs might have emerged between subtypes A3 and A1 through α-events. Gene abundance analysis revealed the key roles of genes involved in biofilm formation, cell-cell communication, human diseases, and drug resistance compared to the pathogenic Clostridia. Moreover, we identified 43 unique genes in the type A3 genome, of which 29 were involved in the pathophysiological processes and other genes contributed to amino acid metabolism. The C. botulinum type A3 genome contains 14 new virulence proteins that can provide the ability to confer antibiotic resistance, virulence exertion and adherence to host cells, the host immune system, and mobility of extrachromosomal genetic elements. Conclusion: The results of our study provide insight into the understanding of new virulence mechanisms to discover new therapeutics for the treatment of human diseases caused by type A3 strains.

Clostridium botulinum type A3 str. Loch Maree is a clinically important strain that produces botulinum neurotoxin type A3 and causes foodborne, infant, and wound botulism worldwide. Studying the mechanism underlying the virulence of this organism is imperative to understand its antibacterial resistance and discovering new drugs or inhibitors. The biochemical and molecular characteristics of this organism have been intensively studied, but their gene regulatory mechanisms are unclear. Hence, we reconstructed the transcriptional regulatory network from the complete genome of this organism and analyzed interactive genes from the identified hub module using a knowledge-based bottom-up approach. The biological reliability, topological properties, and robustness of the regulatory network model were validated with network parameters, followed by gene ontology terms and literature support. The reconstructed regulatory network consisted of 12 transcriptional regulators associated with 2369 coding genes. ResD, SpoOA, ComK, CcpC, DinR, DegU, CitT, CodY, GerE, GltC, GltR, IolR, and LevR were identified as transcriptional regulators from this organism homologous to Bacillus subtilis 168. These regulators have been shown to control beta-lactamase, methyl-accepting chemotaxis protein, DNA replication protein DnaD, sensor histidine kinase, and putative membrane proteins of this organism. This study also predicted all possible promoter sites in regulated genes and their associated molecular functions. We conclude that a global regulatory network model of this organism provides insights into its growth physiology and virulence elicitation in the human intestinal environment.

Coronavirus disease (COVID-19) has rapidly expanded into a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Genetic drift in global SARS-CoV-2 isolates and protein evolution have an impact on their ability to escape from current antiviral therapeutics. Hence, our study aimed to reveal how mutations in the folding kinetics of assembly and maturation proteins drive the hijack ability to emerge SARS-CoV-2 variants in humans. In this study, we predicted the folding rate of these proteins using multiple regression analysis and validated the prediction accuracy using machine learning algorithms. Hybrid machine learning using linear regression, random forest, and decision tree was used to evaluate the predicted folding rates compared with other machine learning models. In SARS-CoV-2 variants, the sequence-structure-function-folding rate link stabilizes or retains the mutated residues, making stable near-native protein structures. The folding rates of these protein mutants were increased in their structural classes, particularly β-sheets, which accommodated the hijacking ability of new variants in human host cells. E484A and L432R were identified as potent mutations that resulted in drastic changes in the folding pattern of the spike protein. We conclude that receptor-binding specificity, infectivity, multiplication rate, and hijacking ability are directly associated with an increase in the folding rate of their protein mutants.

In the present work, we addressed the impact of a human–food web–animal interface on the prevalence of food-borne pathogens in mixed farms of Tamil Nadu, India. We have isolated and identified six strains of Clostridium sp. and five strains of Enterococcus sp. from food and animal sources disposed near to the veterinary and poultry farms. Phylogenetic relationships of these strains were inferred from their homologies in 16S rDNA sequences and rRNA secondary structures. The strain PCP07 was taxonomically equivalent to C. botulinum confirmed by neurotoxin-specific PCR primers, followed by mouse bioassay. Other Clostridial and Enterococcal isolates have shown a phylogenetic similarity to the C. bifermentans and E. durans isolated from veterinary farms, respectively. Results of our study revealed that a human–food web–animal interface has influenced the disease incidence and prevalence of these isolates in the poultry to veterinary farms, where human food acted as a likely transmittance vehicle for their infections.