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Jalandra R, Dalal N, Mohan A, Solanki PR, Kumar A. A novel method for enrichment of Morganella morganii in fecal samples using designed culture medium. Cell Biochem Funct 2024; 42:e4004. [PMID: 38583079 DOI: 10.1002/cbf.4004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
Morganella morganii is a gram negative, facultative anaerobic rod-shaped bacterium, commonly found in environment and in the intestine of human, mammals, and reptiles as a part of their gut microbiome. M. morganii can cause Gram-negative folliculitis, black nail infection, acute retiform purpura, fetal demise, and subdural empyema. The increasing frequency of M. morganii infections generate the need for efficient methods to enrich the presence of M. morganii in clinical samples to make its detection easier. Culturomics aims to grow and maximize the number of culturable bacteria. Different methods are followed to maximize the growth of minority population of bacteria by disrupting the growth of bacteria which are present in higher concentration. This article presents a method for selective enriching the M. morganii in human fecal samples. This method includes prior incubation of fecal microbiota in an anaerobic environment, adding supplement like fecal water to give dormant bacteria a break to become active to grow to threshold concentration, and an enrichment stage which provides the additional opportunity of growing to M. morganii on the selective medium. This method also provides an ingenuous way for augmenting the growth of fecal M. morganii species.
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Affiliation(s)
- Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
- Department of Zoology, Maharshi Dayanand University, Rohtak, India
| | - Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
- Azraeli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Anand Mohan
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | | | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
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Kaur E, Agrawal R, Arun R, Madhavan V, Srivastava V, Kumar D, Rath PP, Kumar N, Vedagopuram S, Pandey N, Priya S, Legembre P, Gourinath S, Bajaj A, Sengupta S. Small molecules that disrupt RAD54-BLM interaction hamper tumor proliferation in colon cancer chemoresistance models. J Clin Invest 2024; 134:e161941. [PMID: 38421735 PMCID: PMC11014671 DOI: 10.1172/jci161941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
RAD54 and BLM helicase play pivotal roles during homologous recombination repair (HRR) to ensure genome maintenance. BLM amino acids (aa 181-212) interact with RAD54 and enhance its chromatin remodeling activity. Functionally, this interaction heightens HRR, leading to a decrease in residual DNA damage in colon cancer cells. This contributes to chemoresistance in colon cancer cells against cisplatin, camptothecin, and oxaliplatin, eventually promoting tumorigenesis in preclinical colon cancer mouse models. ChIP-Seq analysis and validation revealed increased BLM and RAD54 corecruitment on the MRP2 promoter in camptothecin-resistant colon cancer cells, leading to BLM-dependent enhancement of RAD54-mediated chromatin remodeling. We screened the Prestwick small-molecule library, with the intent to revert camptothecin- and oxaliplatin-induced chemoresistance by disrupting the RAD54-BLM interaction. Three FDA/European Medicines Agency-approved candidates were identified that could disrupt this interaction. These drugs bound to RAD54, altered its conformation, and abrogated RAD54-BLM-dependent chromatin remodeling on G5E4 and MRP2 arrays. Notably, the small molecules also reduced HRR efficiency in resistant lines, diminished anchorage-independent growth, and hampered the proliferation of tumors generated using camptothecin- and oxaliplatin-resistant colon cancer cells in both xenograft and syngeneic mouse models in BLM-dependent manner. Therefore, the 3 identified small molecules can serve as possible viable candidates for adjunct therapy in colon cancer treatment.
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Affiliation(s)
- Ekjot Kaur
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Ritu Agrawal
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Rimpy Arun
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Vinoth Madhavan
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Vivek Srivastava
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Dilip Kumar
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Nitin Kumar
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Sreekanth Vedagopuram
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Nishant Pandey
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Swati Priya
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Patrick Legembre
- UMR CNRS 7276, INSERM U1262, CRIBL, Université Limoges, Limoges, France
| | | | - Avinash Bajaj
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sagar Sengupta
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
- Biotechnology Research Innovation Council—National Institute of Biomedical Genomics (BRIC-NIBMG), Kalyani, India
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Das A, Jawla N, Meena V, Gopinath SD, Arimbasseri GA. Lack of vitamin D signalling shifts skeletal muscles towards oxidative metabolism. J Cachexia Sarcopenia Muscle 2024; 15:67-80. [PMID: 38041597 PMCID: PMC10834326 DOI: 10.1002/jcsm.13378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/24/2023] [Accepted: 10/18/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Mice lacking vitamin D receptor (VDR) exhibit a glycogen storage disorder, disrupting carbohydrate utilization in muscle. Here, we asked if the defective carbohydrate metabolism alters the fat utilization by the skeletal muscles of vdr-/- mice. METHODS To check the effect of high-fat-containing diets on muscle mass and metabolism of vdr-/- mice, we subjected them to two different milk fat-based diets (milk fat diet with 60% of energy from milk fat and milk-based diet [MBD] with 37% of energy from milk fat) and lard-based high-fat diet (HFD) containing 60% of energy from lard fat. Skeletal muscles and pancreas from these mice were analysed using RNA sequencing, quantitative reverse transcription polymerase chain reaction and western blot to understand the changes in signalling and metabolic pathways. Microscopic analyses of cryosections stained with haematoxylin and eosin, BODIPY, succinate dehydrogenase and periodic acid-Schiff reagent were performed to understand changes in morphology and metabolism of muscle fibres and pancreatic islets. RESULTS Transcriptomic analyses showed that the skeletal muscles of vdr-/- mice exhibit upregulation of the fatty acid oxidation pathways, suggesting a shift towards increased lipid utilization even in a carbohydrate-enriched regular chow diet (chow). Two different milk fat-enriched diets restored body weight (12.01 ± 0.33 g in chow vs. 17.99 ± 0.62 g in MBD) and muscle weights (38.58 ± 3.84 mg in chow vs. 110.72 ± 1.96 mg in MBD for gastrocnemius [GAS]) of vdr-/- mice. Muscle ATP levels (0.56 ± 0.18 μmol in chow vs. 1.48 ± 0.08 μmol in MBD) and protein synthesis (0.25 ± 0.04 A.U. in chow vs. 2.02 ± 0.06 A.U. in MBD) were upregulated by MBD. However, despite increasing muscle energy levels, HFD failed to restore the muscle mass and cross-sectional area to that of wild-type (WT) mice (104.95 ± 2.6 mg for WT mice on chow vs. 77.26 ± 1.7 mg for vdr-/- mice on HFD for GAS). Moreover, HFD disrupted glucose homeostasis in vdr-/- mice, while MBD restored it. We further analysed insulin response and pancreatic insulin levels of these mice to show that HFD led to reduced insulin levels in pancreatic beta cells of vdr-/- mice (mean intensity of 1.5 × 10-8 for WT mice on chow vs. 4.3 × 10-9 for vdr-/- mice on HFD). At the same time, MBD restored glucose-stimulated pancreatic insulin response (mean intensity of 9.2 × 10-9 ). CONCLUSIONS Skeletal muscles of vdr-/- mice are predisposed to utilize fatty acids as their primary energy source to circumvent their defective carbohydrate utilization. Thus, HFDs could restore energy levels in the skeletal muscles of vdr-/- mice. This study reveals that when mice are subjected to a lard-based HFD, VDR signalling is essential for maintaining insulin levels in pancreatic islets. Our data show a critical role of VDR in muscle metabolic flexibility and pancreatic insulin response.
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Affiliation(s)
- Anamica Das
- Molecular Genetics LaboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Neha Jawla
- Molecular Genetics LaboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Vaidehee Meena
- Molecular Genetics LaboratoryNational Institute of ImmunologyNew DelhiIndia
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Anand R, Kashif M, Pandit A, Babu R, Singh AP. Reprogramming in Candida albicans Gene Expression Network under Butanol Stress Abrogates Hyphal Development. Int J Mol Sci 2023; 24:17227. [PMID: 38139056 PMCID: PMC10743114 DOI: 10.3390/ijms242417227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 12/24/2023] Open
Abstract
Candida albicans is the causative agent of invasive fungal infections. Its hyphae-forming ability is regarded as one of the important virulence factors. To unravel the impact of butanol on Candida albicans, it was placed in O+ve complete human serum with butanol (1% v/v). The Candida transcriptome under butanol stress was then identified by mRNA sequencing. Studies including electron microscopy demonstrated the inhibition of hyphae formation in Candida under the influence of butanol, without any significant alteration in growth rate. The numbers of genes upregulated in the butanol in comparison to the serum alone were 1061 (20 min), 804 (45 min), and 537 (120 min). Candida cells exhibited the downregulation of six hypha-specific transcription factors and the induction of four repressor/regulator genes. Many of the hypha-specific genes exhibited repression in the medium with butanol. The genes related to adhesion also exhibited repression, whereas, among the heat-shock genes, three showed inductions in the presence of butanol. The fungal-specific genes exhibited induction as well as repression in the butanol-treated Candida cells. Furthermore, ten upregulated genes formed the core stress gene set in the presence of butanol. In the gene ontology analysis, enrichment of the processes related to non-coding RNA, ribosome biosynthesis, and metabolism was observed in the induced gene set. On the other side, a few GO biological process terms, including biofilm formation and filamentous growth, were enriched in the repressed gene set. Taken together, under butanol stress, Candida albicans is unable to extend hyphae and shows growth by budding. Many of the genes with perturbed expression may have fitness or virulence attributes and may provide prospective sites of antifungal targets against C. albicans.
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Affiliation(s)
- Rajesh Anand
- Infectious Disease Laboratory, National Institute of Immunology, New Delhi 110067, India; (R.A.)
| | - Mohammad Kashif
- Infectious Disease Laboratory, National Institute of Immunology, New Delhi 110067, India; (R.A.)
| | - Awadhesh Pandit
- Next Generation Sequencing Facility, National Institute of Immunology, New Delhi 110067, India
| | - Ram Babu
- Department of Botany, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Agam P. Singh
- Infectious Disease Laboratory, National Institute of Immunology, New Delhi 110067, India; (R.A.)
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Khanduja A, Kumar M, Mohanty D. ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes. Brief Bioinform 2023; 24:7079710. [PMID: 36988160 DOI: 10.1093/bib/bbad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/31/2023] [Accepted: 02/24/2023] [Indexed: 03/30/2023] Open
Abstract
Small open reading frames (smORFs) encoding proteins less than 100 amino acids (aa) are known to be important regulators of key cellular processes. However, their computational identification remains a challenge. Based on a comprehensive analysis of known prokaryotic small ORFs, we have developed the ProsmORF-pred resource which uses a machine learning (ML)-based method for prediction of smORFs in the prokaryotic genome sequences. ProsmORF-pred consists of two ML models, one for initiation site recognition in nucleic acid sequences upstream of putative start codons and the other uses translated amino acid sequences to decipher functional protein like sequences. The nucleotide sequence-based initiation site recognition model has been trained using longer ORFs (>100 aa) in the same genome while the ML model for identification of protein like sequences has been trained using annotated smORFs from Escherichia coli. Comprehensive benchmarking of ProsmORF-pred reveals that its performance is comparable to other state-of-the-art approaches on the annotated smORF set derived from 32 prokaryotic genomes. Its performance is distinctly superior to other tools like PRODIGAL and RANSEPS for prediction of newly identified smORFs which have a length range of 10-30 aa, where prediction of smORFs has been a major challenge. Apart from identification of smORFs in genomic sequences, ProsmORF-pred can also aid in functional annotation of the predicted smORFs based on sequence similarity and genomic neighbourhood similarity searches in ProsmORFDB, a well-curated database of known smORFs. ProsmORF-pred along with its backend database ProsmORFDB is available as a user-friendly web server (http://www.nii.ac.in/prosmorfpred.html).
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Affiliation(s)
- Akshay Khanduja
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manish Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasisa Mohanty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Rawat RS, Bansal P, Sharma P. A VPS15-like kinase regulates apicoplast biogenesis and autophagy by promoting PI3P generation in Toxoplasma gondii. PLoS Pathog 2022; 18:e1010922. [PMID: 36318587 PMCID: PMC9624415 DOI: 10.1371/journal.ppat.1010922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/07/2022] [Indexed: 01/24/2023] Open
Abstract
Phosphoinositides are important second messengers that regulate key cellular processes in eukaryotes. While it is known that a single phosphoinositol-3 kinase (PI3K) catalyses the formation of 3'-phosphorylated phosphoinositides (PIPs) in apicomplexan parasites like Plasmodium and Toxoplasma, how its activity and PI3P formation is regulated has remained unknown. Present studies involving a unique Vps15 like protein (TgVPS15) in Toxoplasma gondii provides insight into the regulation of phosphatidyl-3-phosphate (PI3P) generation and unravels a novel pathway that regulates parasite development. Detailed investigations suggested that TgVPS15 regulates PI3P formation in Toxoplasma gondii, which is important for the inheritance of the apicoplast-a plastid like organelle present in most apicomplexans and parasite replication. Interestingly, TgVPS15 also regulates autophagy in T. gondii under nutrient-limiting conditions as it promotes autophagosome formation. For both these processes, TgVPS15 uses PI3P-binding protein TgATG18 and regulates trafficking and conjugation of TgATG8 to the apicoplast and autophagosomes, which is important for biogenesis of these organelles. TgVPS15 has a protein kinase domain but lacks several key residues conserved in conventional protein kinases. Interestingly, two critical residues in its active site are important for PI3P formation and parasitic functions of this kinase. Collectively, these studies unravel a signalling cascade involving TgVPS15, a novel effector of PI3-kinase in T. gondii and possibly other Apicomplexa, that regulate critical processes like apicoplast biogenesis and autophagy.
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Affiliation(s)
- Rahul Singh Rawat
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
| | - Priyanka Bansal
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
| | - Pushkar Sharma
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
- * E-mail:
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Naz S, Dabral S, Nagarajan SN, Arora D, Singh LV, Kumar P, Singh Y, Kumar D, Varshney U, Nandicoori VK. Compromised base excision repair pathway in Mycobacterium tuberculosis imparts superior adaptability in the host. PLoS Pathog 2021; 17:e1009452. [PMID: 33740020 PMCID: PMC8011731 DOI: 10.1371/journal.ppat.1009452] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/31/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022] Open
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (Mtb) is a significant public health concern, exacerbated by the emergence of drug-resistant TB. To combat the host’s dynamic environment, Mtb encodes multiple DNA repair enzymes that play a critical role in maintaining genomic integrity. Mtb possesses a GC-rich genome, rendering it highly susceptible to cytosine deaminations, resulting in the occurrence of uracils in the DNA. UDGs encoded by ung and udgB initiate the repair; hence we investigated the biological impact of deleting UDGs in the adaptation of pathogen. We generated gene replacement mutants of uracil DNA glycosylases, individually (RvΔung, RvΔudgB) or together (RvΔdKO). The double KO mutant, RvΔdKO exhibited remarkably higher spontaneous mutation rate, in the presence of antibiotics. Interestingly, RvΔdKO showed higher survival rates in guinea pigs and accumulated large number of SNPs as revealed by whole-genome sequence analysis. Competition assays revealed the superior fitness of RvΔdKO over Rv, both in ex vivo and in vivo conditions. We propose that compromised DNA repair results in the accumulation of mutations, and a subset of these drives adaptation in the host. Importantly, this property allowed us to utilize RvΔdKO for the facile identification of drug targets. Mutation in the genome of bacteria contributes to the acquisition of drug resistance. Mutations in bacteria can arise due to exposures to antibiotics, oxidative, reductive, and many other stresses that bacteria encounter in the host. Mtb has multiple DNA repair mechanisms, including a base excision repair pathway to restore the damaged genome. Here we set out to determine the impact of deleting the Uracil DNA base excision pathway on pathogen adaptability to both antibiotic and host induced stresses. Combinatorial mutant of Mtb UDGs showed higher spontaneous rates of mutations when subjected to antibiotic stress and showed higher survival levels in the guinea pig model of infection. Whole-genome sequence analysis showed significant accumulation of SNPs, suggesting that mutations providing survival advantage may have been positively selected. We also showed that double mutant of Mtb UDGs would be an excellent means to identify antibiotic targets in the bacteria. Competition experiments wherein we pitted wild type and double mutant against each other demonstrated that double mutant has a decisive edge over the wild type. Together, data suggest that the absence of a base excision repair pathway leads to higher mutations and provides a survival advantage under stress. They could be an invaluable tool for identifying targets of new antibiotics.
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Affiliation(s)
- Saba Naz
- Signal Transduction Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
- Department of Zoology, University of Delhi, Delhi, India
| | - Shruti Dabral
- Cellular Immunology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | | | - Divya Arora
- Signal Transduction Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Lakshya Veer Singh
- Cellular Immunology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Pradeep Kumar
- Department of Microbiology & Cell Biology, Indian Institute of Sciences, Bangalore, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Umesh Varshney
- Department of Microbiology & Cell Biology, Indian Institute of Sciences, Bangalore, India
- * E-mail: (UV); (VKN)
| | - Vinay Kumar Nandicoori
- Signal Transduction Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail: (UV); (VKN)
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