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Pal, J.

Publications and source records attributed to Pal, J..

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The SET1 protein of Leishmania donovani moderates the parasite's response to a hostile oxidative environment

SET domain proteins mediate their effects through the methylation of specific lysine residues on target substrates, resulting in either the stimulation or repression of downstream processes. Initially identified as histone lysine methyltransferases, they are now known to target a wide-ranging conglomeration of non-histone subtrates as well. Twenty-nine SET domain proteins have been identified in Leishmania donovani through genome sequence annotations. This study initiates the first investigation into these proteins. We find LdSET1 is predominantly cytosolic and constitutively expressed. The set1 gene is not essential, although its deletion slows promastigote growth and hypersensitizes the parasite to hydroxyurea-induced G1/S arrest. Intriguingly, set1-nulls proliferate more proficiently than set1+/+ parasites within host macrophages, suggesting that LdSET1 moderates the parasites response to the inhospitable intracellular oxidative environment. set1-null parasites are highly tolerant to H2O2-induced oxidative stress in in vitro promastigote cultures as well, reflected in their growth pattern as well as almost complete absence of DNA damage at the H2O2 concentrations tested. This is linked to ROS levels remaining virtually unperturbed in response to H2O2 treatment in set1-nulls, contrasting to increased ROS in set1+/+ cells under similar conditions. In analyzing the cells ability to scavenge hydroperoxides we find that peroxidase activity is not upregulated in response to H2O2 exposure in set1-nulls. Rather, the constitutive basal levels of peroxidase activity are significantly higher in these cells, implicating this to be a factor contributing to the parasites apparent resistance to H2O2. The higher levels of peroxidase activity in set1-nulls are coupled to upregulation of tryparedoxin peroxidase transcripts in these cells. Thus, LdSET1 tunes the parasites behavior within host cells, enabling establishment and persistence of infection, and maintaining the balance with host without eradicating the host cell population it needs for survival. These findings uncover a new dimension to the mechanisms controlling the interplay of Leishmania-host interactions. Author SummaryLeishmaniases are a group of diseases afflicting people across 88 countries. Manifested in three forms: cutaneous, subcutaneous and visceral, different species cause the different forms of the disease. Leishmania donovani is one of the species causing Visceral Leishmaniasis, and its cellular processes are an area of intensive investigations. These protozoan parasites display an unusual pattern of transcription, and gene regulation occurs primarily through epigenetic mechanisms and post-transcriptional processes. SET proteins control gene expression by methylating histones as well as non-histone proteins. In this study we have examined the role of the LdSET1 protein. We find that while the set1 gene is not essential to cell survival, deletion of the set1 gene makes the parasite highly tolerant to the effects of an oxidizing environment, signifying that the LdSET1 protein plays a role in regulating the cells response to oxidative stress. LdSET1 appears to moderate the parasites survival in the oxidative intracellular milieu of host macrophages, controlling it such that infection is firmly established, and persistent, without wiping out the population of host cells it needs for survival.

cell biology↗

Apurinic/apyrimidinic nuclease 1 drives genomic evolution contributing to chemoresistance and tumorigenesis in solid tumor

Genomic instability fuels genomic alterations that befit cancer cells with necessary adaptations to keep proliferating and overcome the impact of host anti-tumor immunity and cytotoxic therapy. Since DNA breaks are required for genomic rearrangements to take place, we hypothesized that dysregulated nuclease activity mediates genomic instability in cancer. Using an integrated genomics protocol, we identified a four gene deoxyribonuclease signature correlating with genomic instability in six human cancers which included adenocarcinomas of esophagus (EAC), lung, prostate, stomach, pancreas and triple negative breast cancer. Functional screens confirmed the role of these nucleases in genomic instability and growth of cancer cells. Apurinic/apyrimidinic nuclease 1 (APE1), identified as top nuclease in functional screen, was further investigated in five cell lines representing four solid tumors (EAC, lung, prostate and breast cancer). We demonstrate that chemical as well as transgenic suppression of APE1 impaired growth/colony formation and increased cytotoxicity of chemotherapeutic agent, whereas inhibited spontaneous as well as chemotherapy-induced DNA breaks, homologous recombination (HR) activity and genomic instability in all cancer cell types tested. Treatment with APE1 inhibitor also impaired tumor growth and significantly increased efficacy of a chemotherapeutic agent in a subcutaneous mouse model of EAC. Overexpression of APE1 in normal esophageal epithelial cells increased DNA breaks and HR activity, leading to massive mutational, copy number as well as karyotypic instability. Evaluation of by whole genome sequencing identified HR as the top mutational process activated by APE1. Normal cells overexpressing APE1 grew as tumors in mice and tumors removed from mice displayed additional karyotypic changes, providing evidence of genomic instability in vivo. Overall, our data demonstrate that elevated APE1 dysregulates HR activity, G2/M checkpoint and genome stability thus contributing to tumorigenesis and chemoresistance in cancer. Therefore, inhibitors of APE1 have potential to inhibit growth and increase cytotoxicity of chemotherapeutic agents while minimizing spontaneous as well as chemotherapy-induced genomic damage and instability in EAC and other solid tumors.

cancer biology↗

DNA replication protein Cdc45 directly interacts with PCNA via its PIP box in Leishmania donovani and the Cdc45 PIP box is essential for cell survival

DNA replication protein Cdc45 is an integral part of the eukaryotic replicative helicase whose other components are the Mcm2-7 core, and GINS. We identified a PIP box motif in Leishmania donovani Cdc45. This motif is typically linked to interaction with the eukaryotic clamp proliferating cell nuclear antigen (PCNA). The homotrimeric PCNA can potentially bind upto three different proteins simultaneously via a loop region present in each monomer. Multiple binding partners have been identified from among the replication machinery in other eukaryotes, and the concerted /sequential binding of these partners are central to the fidelity of the replication process. Though conserved in Cdc45 across Leishmania species and Trypanosoma cruzi, the PIP box is absent in Trypanosoma brucei Cdc45. Here we investigate the possibility of Cdc45-PCNA interaction and the role of such an interaction in the in vivo context. Having confirmed the importance of Cdc45 in Leishmania DNA replication we establish that Cdc45 and PCNA interact stably in whole cell extracts, interacting with each other directly in vitro also. The interaction is mediated via the Cdc45 PIP box. This PIP box is essential for Leishmania survival. The importance of the Cdc45 PIP box is also examined in Schizosaccharomyces pombe, and it is found to be essential for cell survival in this organism also. Our results implicate a role for the Leishmania Cdc45 PIP box in recruiting or stabilizing PCNA on chromatin. The Cdc45-PCNA interaction might help tether PCNA and associated replicative DNA polymerase to the DNA template, thus facilitating replication fork elongation. Though multiple replication proteins have been identified to associate with PCNA in other eukaryotes, this is the first report demonstrating a direct interaction between Cdc45 and PCNA, and while our analysis suggests the interaction may not occur in human cells, it indicates that it is not confined to trypanosomatids.\n\nAuthor SummaryLeishmaniases are manifested in three forms: cutaneous, sub-cutaneous and visceral. The prevalent form in the Indian subcontinent is visceral Leishmaniasis (VL), which is fatal if not treated on time. While there are drugs for treatment, the hunt for additional drugs continues due to emerging drug resistance patterns. The parasite is transmitted by the bite of the sandfly, whereupon it establishes itself within cells of the host immune system (macrophages) and reproduces by binary fission. The replication of its genome is essential for parasite survival. Eukaryotic DNA replication is generally conserved across species. This study targets Cdc45, a protein that helps unwind the DNA double helix to enable copying of the two strands into two daughter strands. The new chains of DNA are synthesized by DNA polymerases, and a trimeric protein, proliferating cell nuclear antigen (PCNA), helps clamp the polymerases onto the template. In this study we find Cdc45 to interact with PCNA, and have identified the motif in Cdc45 via which it does so. Our results suggest this interaction is seen in some other eukaryotes as well. Based on the results of our experiments we propose that Cdc45 may help moor PCNA-polymerase complexes to template DNA.

molecular biology↗

Isolation of phosphate solubilizing Pseudomonas strains from apple rhizosphere in the Trans Himalayan region of Himachal Pradesh, India

Total fifteen phosphate solubilizing bacteria were isolated from rhizosphere soil of apple tree on Kings B medium belonging to genus Pseudomonas spp. They were characterized on the basis of morphological and biochemical characteristics. Preliminary selection as phosphate solubilizing bacteria were done on the basis of formation of transparent zone around the colony on Pikovskayas agar medium containing 0.5% triclcium phosphate (TCP). Maximum in vitro phosphate solubilization on Pikovskayas agar plates after 72h incubation at 28{degrees}C was shown by An-15-Mg (46 mm), whereas in case of broth, again this strain showed maximum tricalcium phosphate (TCP) solubilization (76 g/ml). The pH of each inoculated broth was recorded daily and dropped significantly (pH 7.0-3.99). All the Pseudomonas isolates were further evaluated for overall plant growth promoting traits. Greatest siderophore activity was exhibited by An-14-Mg (71.23 %SU) followed by An-15-Mg (70.12 %SU) which were statiscally at par with each other. Whereas, maximum IAA production was observed again in An-15-Mg (95 g/ml). This isolate also showed the maximum production of HCN and ammonia. 16S rDNA and phylogenetic analysis showed that strain An-15-Mg exhibits 99% level of similarity with Pseudomonas aeruginosa. Therefore, it was designated as Pseudomonas aeruginosa strain An-15-Mg. HPLC analysis showed that the Pseudomonas aeruginosa strain An-15-Mg produced maximum concentration of succinic acid, malonic, citric and malic acid with small amounts of schimic, quinic, tartaric, fumaric and lactic acids. The strain An-15-Mg possessed phosphate solubilization as major PGP trait along with different PGP traits. The potential phosphate solubilizing strain of Pseudomonas aeruginosa was reported first time as PGPR which lives in close association with apple tree without harming the plant, therefore could be used as a promising phosphate solubilizer and biofertilizer in apple crop grown in high hills of Himachal Pradesh.\n\nAuthors contributionAll authors made significant efforts towards the completion of this research work and preparation of manuscript timely. Author Ranjna Sharma has done collection of soil samples of apple tree from two districts, isolation and characterization of phosphate solubilizing Pseudomonas isolates and their screening for different PGPTs, phenotypic characteriazation, 16S rRNA analysis and statistical analysis. Author S P Singh has done HPLC analysis at their institute. Author Ankita has done sequence analysis and phylogenetic tree preparation. Author Mohinder Kaur is my mentor and generated idea regarding this work. She guided me in completing this work successfully as well as manuscript writing.

microbiology↗