Biology subjects

Kumar, K. A.

Publications and source records attributed to Kumar, K. A..

4 recordsLinked to original sources

bioRxiv2026

Structural basis of substrate recognition and conformational gating in the bacteriophage M15 metalloendopeptidase LysPH

The rapid emergence of antimicrobial resistance has led to a surge in multidrug-resistant strains, jeopardising the efficacy of frontline and last-resort antibiotics and thereby aggravating the antimicrobial resistance crisis. Bacteriophage-derived endolysins represent a promising class of next-generation antimicrobials. Here, we report the isolation of a novel bacteriophage, PA_Ganga_001, targeting multidrug-resistant Pseudomonas aeruginosa. Genomic sequencing of this phage identified a previously uncharacterised endolysin LysPH, a zinc-dependent globular endolysin that exhibits antibacterial activity against multiple multidrug-resistant Gram-negative pathogens, including Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Site-directed mutagenesis of the endolysin LysPH suggests that His77, Asp84, His159, Arg41, and Asp156 are essential for catalysis and substrate accommodation. To understand the structural basis of substrate binding and catalysis, we determined the crystal structures of the apo-enzyme (1.8 [A]) and the catalytically attenuated D156A mutant in complex with a synthetic pentapeptide stem (PGX) of peptidoglycan (2.0 [A]). The pentapeptide-bound complex revealed a defined substrate-binding groove, and a pronounced displacement of the Thr42-Ser75 loop was observed. This led to an approximately six-fold volumetric expansion of the catalytic cleft, indicative of a substrate-induced transition to an open, catalytically competent conformation. Notably, a distinctive C-terminal helical element, which diverges sequentially from characterised M15 homologues, is predicted to interact with the NAG-NAM scaffold and may contribute to the positioning of the stem pentapeptide for Zn2+ dependent catalysis. These distinct structural features establish the molecular basis for L-Ala-D-Glu hydrolysis by M15 bacteriophage endolysins and provide a foundational framework for the rational design and engineering of the next generation of antimicrobial enzymes.

biochemistry↗

bioRxiv2024

Geographical distribution, disease association and diversity of Klebsiella pneumoniae KL and O antigens in India: roadmap for vaccine development

Klebsiella pneumoniae poses a significant healthcare challenge due to its multidrug resistance and diverse serotype landscape. This study aimed to explore the serotype diversity of 1072 K. pneumoniae and its association with geographical distribution, disease severity and antimicrobial/virulence patterns in India. Whole-genome sequencing was performed on the Illumina platform, and genomic analysis was carried out using the Kleborate tool. KL64 (n=264/1072, 26%), KL51 (249/1072, 24%), KL2 (n=88/1072, 8%), O1/O2v1 (n=471/1072, 44%), O1/O2v2 (n=353/1072, 33%), and OL101 (n=66/1072, 6%) were the most prevalent serotypes. The study identified 119 different sequence types (STs) with varying serotypes, with KL64 being the most predominant in ST231 (26%). O serotypes were strongly linked with STs, with O1/O2v1 predominantly associated with ST231 (44%). Simpsons diversity index and Fishers exact test revealed higher serotype diversity in the north and east regions, along with intriguing associations between specific serotypes and resistance profiles. No significant association between KL or O types and disease severity was observed. Furthermore, we found no specific association of virulence factors with KL types or O antigen types (P>0.05). Conventionally described hypervirulent clones (i.e., KL1 and KL2) in India lacked typical virulent markers (i.e., aerobactin), contrasting with other regional serotypes. The cumulative distribution of KL and O serotypes suggests that future vaccines may have to include either [~]20 KL types or 4 O types to cover >85% of the carbapenemase-producing Indian K. pneumoniae population. The findings underscore the need for a vaccine with broad coverage to address the diverse landscape of K. pneumoniae strains in different regions of India. Understanding regional serotype dynamics is pivotal for targeted surveillance, interventions, and tailored vaccine strategies to tackle the diverse landscape of K. pneumoniae infections across India. Data SummaryO_LIAll the sequenced data has been submitted to the European Nucleotide Archive (ENA) under the Bioproject numbers PRJEB29740 and PRJEB50614. Run Accessions and Biosample numbers are provided in Supplementary Table 1 with corresponding metadata for each sample used in the study. C_LIO_LIThe Microreact link for the genomic analysis is provided (https://microreact.org/project/oqKM84GBszEPW9Emt2FKnP-klebsiella-pneumoniae-indian-serotypes). C_LIO_LIThe pipelines used in the study are published in gitlab (https://gitlab.com/cgps/ghru/pipelines). C_LIO_LIThe tools details and the implementation of the pipelines are described in protocols.io (https://www.protocols.io/view/ghru-genomic-surveillance-of-antimicrobial-resista-bp2l6b11kgqe/v4). C_LIO_LIThe R scripts used with all the input files used for each script have been published in Fishare (https://doi.org/10.6084/m9.figshare.25414807.v1) C_LI Impact StatementKlebsiella pneumoniae produces polysaccharide capsules, which serve as both epidemiological markers and significant virulence factors. The increasing accessibility of whole genome sequencing has made it easier than ever to investigate this capsule diversity. This study is the first of its kind in India to comprehensively investigate the serotype diversity of K. pneumoniae strains and their association with disease severity, antimicrobial resistance/virulence patterns, and geographical distribution across various regions of the subcontinent. This multi-dimensional analysis not only provides valuable insights into the molecular epidemiology of K. pneumoniae in India but also offers crucial data for the development of targeted interventions, including vaccine formulations tailored to address the prevailing serotypes. These findings serve as a foundation for informed decision-making in the management and prevention of K. pneumoniae infections, ultimately contributing to improved public health outcomes in the region.

genomics↗

bioRxiv2023

Breeding and identification of promising Mauritius x Kew pineapple hybrids with high heterosis for fruit and plant traits

Leading cultivars of pineapple Mauritius and Kew were hybridized and 25 hybrids were evaluated under open field conditions, using randomized block design with two replications. Performance of the female parent cum check variety Mauritius, male parent Kew and check variety in Kerala state, India, Amritha, were also evaluated and compared. Based on the performance, heterobeltiosis, average heterosis and standard heterosis over two check varieties, in each hybrid, for 10 plant growth traits and 24 fruit traits, were calculated. For fruit weight, hybrid H35 had the highest heterobeltiosis and standard heterosis over Amritha whereas H62 had highest standard heterosis over Mauritius and average heterosis. For pulp weight, hybrid H17 had the highest values for all heterosis parameters. For TSS, hybrid H62 had the highest heterobeltiosis and other parameters were highest in H43. For days to attain physiological maturity, crown weight, peel weight and acidity, H27, H30, H77 and H43, respectively were lowest in all heterosis parameters. Based on the selection criterion [{sum}average heterosis (fruit weight, TSS, pulp weight) - {sum}average heterosis (crown weight, peel weight, eye profile, eye relative surface, time taken for physiological maturity, acidity)] developed using the average heterosis values for desirable and undesirable fruit traits, six hybrids H66, H17, H59, H43, H70 and H35 were identified for further evaluation. The identified hybrids also satisfied the requirements in fruit weight ([≥]1.0 kg), pulp weight ([≥]750.58 g), TSS ([≥]14.49 {circ}Brix), days to attain physiological maturity ([≤]185.70 days), crown weight ([≤]305.50 g), peel weight ([≤]159.27 g) and acidity ([≤]1.05).

plant biology↗

bioRxiv2022

Crystal structure and activity profiling of deubiquitinating inhibitors-bound to SARS-CoV-2 papain like protease revealed new allosteric sites for antiviral therapies

SARS-CoV-2 papain-like protease (PLpro) is a key antiviral target as it plays a dual role in viral replication and in modulation of innate immune responses by deubiquitinating or deISGylating host proteins. Thus, therapeutic targeting of PLpro serves as a two-pronged approach to abate SARS-CoV-2. Interestingly, PLpro shares structural and functional similarities with the cellular deubiquitinating enzymes (DUBs) and in this study this fact has been exploited to identify DUBs inhibitors that target the Ubiquitin/ISG15 binding site and the known catalytic substrate binding pocket of PLpro. Among these identified compounds, flupenthixol, lithocholic acid, teneligliptin, and linagliptin markedly inhibited the proteolytic activity of purified PLpro and demonstrated potent antiviral efficacies against SARS-CoV-2 infection in a dose dependent manner. Treatment with lithocholic acid and linagliptin suppressed the expression levels of inflammatory mediators, thereby, restoring immune responses. Crystal structures of SARS-CoV-2 PLpro in complex with linagliptin and with lithocholic acid determined in this study, revealed insights into the inhibition mechanism with unique interactions within the Ubiquitin/ISG15 binding site (S2 site; Phe69, His73, Asn128, His175) and the substrate binding cleft. Additionally, oral and intraperitoneal treatments with linagliptin increased survival, reduced lung viral load, and ameliorated histopathological damage in mouse-adapted model of SARS-CoV-2 infection. The study for the first time demonstrates a two-pronged strategy using DUB inhibitors that target the proteolytic activity of PLpro and simultaneously reinstates the hosts immune response against SARS-CoV-2.

molecular biology↗