@article {8882, title = {Role of Mating Receptivity Peptides in Helicoverpa armigera: Molecular and Evolutionary Perspectives [Mass Spectrometry - Proteomics Facility]}, journal = {Journal of Advances in Biology \& Biotechnology}, volume = {27 }, year = {2024}, month = {08/2024}, chapter = {1427}, abstract = {

Previous studies have implicated the role of peptides/proteins in male accessory glands (MAGs), responsible for the induction of behavioral and reproductive changes in\ Helicoverpa armigera\ females. Our and several other studies have seen the MAG showed post-mating behaviors such as accelerated unreceptivity to re-mating and other post-mating traits. We have reported several peptides responsible for reduced mating receptivity, including a putative 4.9 kDa, a novel peptide with various functions in female post-copulatory reproductive behavior (PMR). In this study, we report a detailed analysis of the proteins from a biochemical, physiological, molecular and evolutionary perspective. 5 major classes of multigene family proteins were detected after protein database searches. All proteins were found to bind nucleic acids, possess signal peptides, and undergo posttranslational modification by seminal fluid proteins (SFPs). The Porphobilinogen synthetase protein (PBGS) was unique to the lepidopteran order. Our molecular studies support the observation that the molecular weight of MAG proteins varies significantly across species, suggesting the existence of different target sites or faster evolution of SFP. MAG proteins not only ensure male reproductive fitness by constantly evolving under postcopulatory sexual selection (PCSS), but also maintain species-specific barriers to fertilization thus potentially contribute to the formation of new species and mediate reproductive conflicts between the sexes.

}, doi = {doi.org/10.9734/jabb/2024/v27i81266}, url = {https://journaljabb.com/index.php/JABB/article/view/1266$\#$:~:text=MAG\%20proteins\%20not\%20only\%20ensure,reproductive\%20conflicts\%20between\%20the\%20sexes.}, author = {Rama Thyloor and Kiran Kumar Halagur Bhogegowda and Saraswathi Saraswathi and Doddamane Manjulakumari} } @article {1716, title = {ROS Dependent Antifungal and Anticancer Modulations of Piper colubrinum Osmotin [Bio-Incubation Core Equipment/Protein Expression Facility]}, journal = {Molecules}, volume = {26}, year = {2021}, abstract = {

Osmotin, a plant defense protein, has functional similarity to adiponectin, an insulin sensitizingsensitising hormone secreted by adipocytes. We speculated that Piper colubrinum Osmotin (PcOSM) could have functional roles in obesity-related cancers, especially breast cancer. Immunofluorescence assays, flow cytometry, cell cycle analysis and a senescence assay were employed to delineate the activity in MDAMB231 breast cancer cell line. PcOSM pre-treated P. nigrum leaves showed significant reduction in disease symptoms correlated with high ROS production. In silico analysis predicted that PcOSM has higher binding efficiency with adiponectin receptor compared to adiponectin. PcOSM was effectively taken up by MDAMB231 cancer cells which resulted in marked increase in intracellular ROS levels leading to senescence and cell cycle arrest in G2/M stage. This study provides evidence on the ROS mediated direct inhibitory activity of the plant derived osmotin protein on the phytopathogen Phytophthora capsici, and the additional functional roles of this plant defense protein on cancer cells through inducing ROS associated senescence. The strong leads produced from this study could be pursued further to obtain more insights into the therapeutic potential of osmotin in human cancers.

}, issn = {1420-3049}, doi = {10.3390/molecules26082239}, url = {https://www.mdpi.com/1420-3049/26/8/2239}, author = {Geetha, Rajeswari Gopal and Krishnankutty Nair Chandrika, Sivakumar and Saraswathy, Gayathri G. and Nair Sivakumari, Asha and Sakuntala, Manjula} } @article {1627, title = {RNA-binding proteins La and HuR cooperatively modulate translation repression of PDCD4 mRNA [Mass Spectrometry Facility - Proteomics]}, journal = {J Biol Chem .}, volume = {doi: 10.1074/jbc.RA120.014894. Online ahead of print.}, year = {2020}, month = {12/2020}, abstract = {

Post-transcriptional regulation of gene expression plays a critical role in controlling the inflammatory response. An uncontrolled inflammatory response results in chronic inflammation, often leading to tumorigenesis. Programmed cell death 4 (PDCD4) is a pro-inflammatory tumor-suppressor gene which helps to prevent the transition from chronic inflammation to cancer. PDCD4 mRNA translation is regulated by an interplay between the oncogenic microRNA miR-21 and the RNA-binding protein (RBP) HuR in response to LPS stimulation, but the role of other regulatory factors remain unknown. Here we report that the RBP Lupus antigen (La) interacts with the 3{\textquoteright}UTR of PDCD4 mRNA and prevents miR-21-mediated translation repression. While LPS causes nuclear-cytoplasmic translocation of HuR, it enhances cellular La expression. Remarkably, La and HuR were found to bind cooperatively to the PDCD4 mRNA and mitigate miR-21-mediated translation repression. The cooperative action of La and HuR reduced cell proliferation and enhanced apoptosis, reversing the pro-oncogenic function of miR-21. Together, these observations demonstrate a cooperative interplay between two RBPs, triggered differentially by the same stimulus, which exerts a synergistic effect on PDCD4 expression and thereby helps maintain a balance between inflammation and tumorigenesis.

}, author = {Kumar, Ravi and Poria, Dipak Kumar and Ray, Partho Sarothi} } @article {1079, title = {ROS Inhibits Cell Growth by Regulating 4EBP and S6K, Independent of TOR, during Development [Transgenic Fly Facility].}, journal = {Dev Cell}, volume = {49}, year = {2019}, month = {2019 May 06}, pages = {473-489.e9}, abstract = {

Reactive oxygen species (ROS), despite having damaging roles, serve as signaling molecules regulating diverse biological and physiological processes. Employing in\ vivo genetic studies in Drosophila, we show that besides causing G1-S arrest by activation of Dacapo, ROS can simultaneously inhibit cell growth by regulating the expression of 4EBP and S6K. This is achieved by triggering a signaling cascade that includes Ask1, JNK, and FOXO independent of the Tsc-TOR growth regulatory pathway. Qualitative and quantitative differences in the types of ROS molecules generated dictate whether cells undergo G1-S arrest only or experience blocks in both cell proliferation and growth. Importantly, during normal development, this signaling cascade is triggered by ecdysone in late larval fat body cells to restrict their growth prior to pupation by antagonizing insulin signaling. The present work reveals an unexpected role of ROS in systemic control of growth in response to steroid hormone signaling to establish organismal size.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2019.04.008}, author = {Toshniwal, Ashish G and Gupta, Sakshi and Mandal, Lolitika and Mandal, Sudip} } @article {891, title = {RagC phosphorylation autoregulates mTOR complex 1. [Drosophila Facility]}, journal = {EMBO J}, year = {2018}, month = {2018 Dec 14}, abstract = {

The mechanistic (or mammalian) target of rapamycin complex 1 (mTORC1) controls cell growth, proliferation, and metabolism in response to diverse stimuli. Two major parallel pathways are implicated in mTORC1 regulation including a growth factor-responsive pathway mediated via TSC2/Rheb and an amino acid-responsive pathway mediated via the Rag GTPases. Here, we identify and characterize three highly conserved growth factor-responsive phosphorylation sites on RagC, a component of the Rag heterodimer, implicating cross talk between amino acid and growth factor-mediated regulation of mTORC1. We find that RagC phosphorylation is associated with destabilization of mTORC1 and is essential for both growth factor and amino acid-induced mTORC1 activation. Functionally, RagC phosphorylation suppresses starvation-induced autophagy, and genetic studies in reveal that RagC phosphorylation plays an essential role in regulation of cell growth. Finally, we identify mTORC1 as the upstream kinase of RagC on S21. Our data highlight the importance of RagC phosphorylation in its function and identify a previously unappreciated auto-regulatory mechanism of mTORC1 activity.

}, issn = {1460-2075}, doi = {10.15252/embj.201899548}, author = {Yang, Guang and Humphrey, Sean J and Murashige, Danielle S and Francis, Deanne and Wang, Qiao-Ping and Cooke, Kristen C and Neely, Greg and James, David E} } @article {814, title = {Recovery of Five Complete Influenza A(H1N1)pdm09 Genome Sequences from the 2015 Influenza Outbreak in India by Metagenomic Sequencing. [Next Gen Genomics Facility (INT)]}, journal = {Genome Announc}, volume = {6}, year = {2018}, month = {2018 Jun 28}, abstract = {

Five complete (H1N1)pdm09 viral sequences were recovered from hospitalized individuals during the 2015 influenza outbreak by metagenomic sequencing. Four of the genomes are from oropharyngeal swabs, and one is from an isolate. All five sequences belong to an emerging 6B clade. Studying them further is critical for outbreak preparedness.

}, issn = {2169-8287}, doi = {10.1128/genomeA.00511-18}, author = {Dash, Paban Kumar and Pattabiraman, Chitra and Tandel, Kundan and Sharma, Shashi and Kumar, Jyoti S and Siddappa, Shilpa and Gowda, Malali and Krishna, Sudhir and Parida, Manmohan} } @article {767, title = {Regulation of Global Transcription in by Rsd and 6S RNA. [Next Gen Genomics Facility (INT)]}, journal = {G3 (Bethesda)}, year = {2018}, month = {2018 Apr 23}, abstract = {

In , the sigma factor σ directs RNA polymerase to transcribe growth-related genes, while σ directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to σ, and the non-coding 6S RNA which binds to the RNA polymerase-σ holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial. Here we use RNA-Seq in five phases of growth to elucidate their function on a genome-wide scale. We show for the first time that Rsd and 6S RNA facilitate σ activity throughout bacterial growth, while 6S RNA also regulates widely different genes depending upon growth phase. We discover novel interactions between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. Finally, we present a mathematical model of transcription which highlights the crosstalk between Rsd and 6S RNA as a crucial factor in controlling sigma factor competition and global gene expression.

}, issn = {2160-1836}, doi = {10.1534/g3.118.200265}, author = {Lal, Avantika and Krishna, Sandeep and Seshasayee, Aswin Sai Narain} } @article {742, title = {The role of ZA channel water-mediated interactions in the design of bromodomain-selective BET inhibitors.}, journal = {J Mol Graph Model}, volume = {81}, year = {2018}, month = {2018 Mar 22}, pages = {197-210}, abstract = {

The Bromodomain and Extra-Terminal domain (BET) family of proteins are involved in the regulation of gene transcription, and their dysregulation is implicated in several diseases including cancer. BET proteins contain two tandem bromodomains (BD1 and BD2) that independently recognize acetylated-lysine residues and appear to have distinct biological roles. We compared several published co-crystal structures and found five positions near the substrate binding pocket that vary between BET bromodomains. One position located in the ZA loop has unique properties. In BRD2-4, this residue is glutamine in BD1 and lysine in BD2; in BRDT, this residue is arginine in BD1 and asparagine in BD2. Using molecular modeling, we identified differences in the water-mediated network at this position between bromodomains. Molecular dynamics simulations helped rationalize the observed bromodomain selectivity for exemplar BET inhibitors and a congeneric series of tetrahydroquinolines (THQ) that differed by a single heteroatom near the ZA channel. The 2-furan SJ830599, the most BD2-selective THQ analog, did not disrupt the water-mediated networks in either domain, but was electrostatically-repulsed by the specific arrangement of the W5 water dipole in BD1. Our work underscores the value of exploring water-mediated interactions to study ligand binding, and highlights the difficulty of optimizing polar interactions due to high desolvation penalties. Finally, we suggest further modifications to THQ-based BET inhibitors that would increase BD2-selectivity in BRD2-4, while minimizing affinity for one or both bromodomains of BRDT.

}, issn = {1873-4243}, doi = {10.1016/j.jmgm.2018.03.005}, author = {Bharatham, Nagakumar and Slavish, Peter J and Young, Brandon M and Shelat, Anang A} } @article {533, title = {A rapid, nonradioactive assay for measuring heparan sulfate C-5 epimerase activity using hydrogen/deuterium exchange-mass spectrometry.}, journal = {Methods Mol Biol}, volume = {1229}, year = {2015}, month = {2015}, pages = {209-19}, abstract = {

Heparin and heparan sulfate (HS) glycosaminoglycans have important roles in anticoagulation, human development, and human diseases. HS C5-epimerase, which catalyzes the epimerization of GlcA to IdoA, is a crucial enzyme involved in the biosynthesis of heparin-related biomolecules. Here, we describe a detailed method for measuring the total activity of HS C5-epimerase that involves the following steps: H/D exchange upon epimerization of the substrate with HS C5-epimerase, low-pH nitrous acid treatment of the substrate, the separation of low-pH nitrous acid-cleaved disaccharides using HPLC, and mass spectrometry analysis. This nonradioactive method is rapid and sensitive and, importantly, allows us to study the reversible nature of HS C5-epimerase.

}, keywords = {Animals, Biocatalysis, Carbohydrate Epimerases, Chromatography, Ion Exchange, Chromatography, Liquid, Deuterium Exchange Measurement, Disaccharides, Enzyme Assays, Glucuronic Acid, Heparitin Sulfate, Humans, Iduronic Acid, Mass Spectrometry, Sf9 Cells}, issn = {1940-6029}, doi = {10.1007/978-1-4939-1714-3_19}, author = {Babu, Ponnusamy and Victor, Xylophone V and Raman, Karthik and Kuberan, Balagurunathan} } @article {472, title = {RDGBα, a PtdIns-PtdOH transfer protein, regulates G-protein-coupled PtdIns(4,5)P2 signalling during Drosophila phototransduction.[Drosophila Facility]}, journal = {J Cell Sci}, volume = {128}, year = {2015}, month = {2015 Sep 01}, pages = {3330-44}, abstract = {

Many membrane receptors activate phospholipase C (PLC) during signalling, triggering changes in the levels of several plasma membrane lipids including phosphatidylinositol (PtdIns), phosphatidic acid (PtdOH) and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2]. It is widely believed that exchange of lipids between the plasma membrane and endoplasmic reticulum (ER) is required to restore lipid homeostasis during PLC signalling, yet the mechanism remains unresolved. RDGBα (hereafter RDGB) is a multi-domain protein with a PtdIns transfer protein (PITP) domain (RDGB-PITPd). We find that, in vitro, the RDGB-PITPd binds and transfers both PtdOH and PtdIns. In Drosophila photoreceptors, which experience high rates of PLC activity, RDGB function is essential for phototransduction. We show that binding of PtdIns to RDGB-PITPd is essential for normal phototransduction; however, this property is insufficient to explain the in vivo function because another Drosophila PITP (encoded by vib) that also binds PtdIns cannot rescue the phenotypes of RDGB deletion. In RDGB mutants, PtdIns(4,5)P2 resynthesis at the plasma membrane following PLC activation is delayed and PtdOH levels elevate. Thus RDGB couples the turnover of both PtdIns and PtdOH, key lipid intermediates during G-protein-coupled PtdIns(4,5)P2 turnover.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Eye Proteins, Light Signal Transduction, Membrane Proteins, Phosphatidic Acids, Phosphatidylinositol 4,5-Diphosphate, Type C Phospholipases}, issn = {1477-9137}, doi = {10.1242/jcs.173476}, author = {Yadav, Shweta and Garner, Kathryn and Georgiev, Plamen and Li, Michelle and Gomez-Espinosa, Evelyn and Panda, Aniruddha and Mathre, Swarna and Okkenhaug, Hanneke and Cockcroft, Shamshad and Raghu, Padinjat} } @article {684, title = {Role of Homothorax in region specific regulation of Deformed in embryonic neuroblasts.}, journal = {Mech Dev}, volume = {138 Pt 2}, year = {2015}, month = {2015 Nov}, pages = {190-7}, abstract = {

The expression and regulation of Hox genes in developing central nervous system (CNS) lack important details like specific cell types where Hox genes are expressed and the transcriptional regulatory players involved in these cells. In this study we have investigated the expression and regulation of Drosophila Hox gene Deformed (Dfd) in specific cell types of embryonic CNS. Using Dfd neural autoregulatory enhancer we find that Dfd autoregulates itself in cells of mandibular neuromere. We have also investigated the role of a Hox cofactor Homothorax (Hth) for its role in regulating Dfd expression in CNS. We find that Hth exhibits a region specific role in controlling the expression of Dfd, but has no direct role in mandibular Dfd neural autoregulatory circuit. Our results also suggest that homeodomain of Hth is not required for regulating Dfd expression in embryonic CNS.

}, keywords = {Animals, Central Nervous System, Drosophila, Drosophila Proteins, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Genes, Homeobox, Homeodomain Proteins, Neural Stem Cells, Organogenesis}, issn = {1872-6356}, doi = {10.1016/j.mod.2015.09.003}, author = {Kumar, Raviranjan and Chotaliya, Maheshvari and Vuppala, Sruthakeerthi and Auradkar, Ankush and Palasamudrum, Kalyani and Joshi, Rohit} } @article {537, title = {Redox proteomics of thiol proteins in mouse heart during ischemia/reperfusion using ICAT reagents and mass spectrometry.}, journal = {Free Radic Biol Med}, volume = {58}, year = {2013}, month = {2013 May}, pages = {109-17}, abstract = {

There is strong evidence for the involvement of reactive oxygen species in ischemia/reperfusion injury. Although oxidation of individual thiol proteins has been reported, more extensive redox proteomics of hearts subjected to ischemia/reperfusion has not been performed. We have carried out an exploratory study using mass spectrometry with isotope-coded affinity tags (ICAT) aimed at identifying reversible oxidative changes to protein thiols in Langendorff perfused isolated mouse hearts subjected to 20 min ischemia with or without aerobic reperfusion for 5 or 30 min. Reduced thiols were blocked by adding N-ethylmaleimide during protein extraction, then reversibly oxidized thiols in extracts of control perfused and treated hearts were reduced and labeled with the light and heavy ICAT reagents, respectively. Protein extracts were mixed in equal amounts and relative proportions of the isotope-labeled peaks were used to quantify oxidative changes between the control and the treated groups. Approximately 300 peptides with ICAT signatures were reliably identified in each sample, with 181 peptides from 118 proteins common to all treatments. A proportion showed elevated ICAT ratios, consistent with reversible thiol oxidation. This was most evident after early reperfusion, with apparent reversal after longer reperfusion. In comparison, there was gradual accumulation of protein carbonyls and loss of GSH with longer reperfusion. Many of the thiol changes were in mitochondrial proteins, including components of electron transport complexes and enzymes involved in lipid metabolism. The results are consistent with mitochondria being a major site of oxidant generation during early cardiac reperfusion and mitochondrial thiol proteins being targets for oxidation.

}, keywords = {Animals, Isotope Labeling, Mass Spectrometry, Mice, Mitochondrial Proteins, Myocardium, Oxidation-Reduction, Proteomics, Reactive Oxygen Species, Reperfusion Injury, Sulfhydryl Compounds}, issn = {1873-4596}, doi = {10.1016/j.freeradbiomed.2013.01.021}, author = {Kumar, Vikas and Kleffmann, Torsten and Hampton, Mark B and Cannell, Mark B and Winterbourn, Christine C} }