Browsing by Author "Lal, Sneha"
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Item A Holistic View of Cancer Bioenergetics: Mitochondrial Function and Respiration Play Fundamental Roles in the Development and Progression of Diverse Tumors(Springer) Alam, Md Maksudul; Lal, Sneha; FitzGerald, Keely E.; Zhang, Li; Alam, Md Maksudul; Lal, Sneha; FitzGerald, Keely E.; Zhang, LiSince Otto Warburg made the first observation that tumor cells exhibit altered metabolism and bioenergetics in the 1920s, many scientists have tried to further the understanding of tumor bioenergetics. Particularly, in the past decade, the application of the state-of the-art metabolomics and genomics technologies has revealed the remarkable plasticity of tumor metabolism and bioenergetics. Firstly, a wide array of tumor cells have been shown to be able to use not only glucose, but also glutamine for generating cellular energy, reducing power, and metabolic building blocks for biosynthesis. Secondly, many types of cancer cells generate most of their cellular energy via mitochondrial respiration and oxidative phosphorylation. Glutamine is the preferred substrate for oxidative phosphorylation in tumor cells. Thirdly, tumor cells exhibit remarkable versatility in using bioenergetics substrates. Notably, tumor cells can use metabolic substrates donated by stromal cells for cellular energy generation via oxidative phosphorylation. Further, it has been shown that mitochondrial transfer is a critical mechanism for tumor cells with defective mitochondria to restore oxidative phosphorylation. The restoration is necessary for tumor cells to gain tumorigenic and metastatic potential. It is also worth noting that heme is essential for the biogenesis and proper functioning of mitochondrial respiratory chain complexes. Hence, it is not surprising that recent experimental data showed that heme flux and function are elevated in non-small cell lung cancer (NSCLC) cells and that elevated heme function promotes intensified oxygen consumption, thereby fueling tumor cell proliferation and function. Finally, emerging evidence increasingly suggests that clonal evolution and tumor genetic heterogeneity contribute to bioenergetic versatility of tumor cells, as well as tumor recurrence and drug resistance. Although mutations are found only in several metabolic enzymes in tumors, diverse mutations in signaling pathways and networks can cause changes in the expression and activity of metabolic enzymes, which likely enable tumor cells to gain their bioenergetic versatility. A better understanding of tumor bioenergetics should provide a more holistic approach to investigate cancer biology and therapeutics. This review therefore attempts to comprehensively consider and summarize the experimental data supporting our latest view of cancer bioenergetics.Item Heme Promotes Transcriptional and Demethylase Activities of Gis1, a Member of the Histone Demethylase JMJD2/KDM4 Family(Oxford University Press, 2018-10-22) Lal, Sneha; Comer, Jonathan M.; Konduri, Purna C.; Shah, Ajit; Wang, Tianyuan; Lewis, Anthony; Shoffner, Grant; Guo, Feng; Zhang, Li; Lal, Sneha; Comer, Jonathan M.; Konduri, Purna C.; Wang, Tianyuan; Lewis, Anthony; Zhang, LiThe yeast Gis1 protein is a transcriptional regulator belonging to the JMJD2/KDM4 subfamily of demethylases that contain a JmjC domain, which are highly conserved from yeast to humans. They have important functions in histone methylation, cellular signaling and tumorigenesis. Besides serving as a cofactor in many proteins, heme is known to directly regulate the activities of proteins ranging from transcriptional regulators to potassium channels. Here, we report a novel mechanism governing heme regulation of Gis1 transcriptional and histone demethylase activities. We found that two Gis1 modules, the JmjN + JmjC domain and the zinc finger (ZnF), can bind to heme specifically in vitro. In vivo functional analysis showed that the ZnF, not the JmjN + JmjC domain, promotes heme activation of transcriptional activity. Likewise, measurements of the demethylase activity of purified Gis1 proteins showed that full-length Gis1 and the JmjN + JmjC domain both possess demethylase activity. However, heme potentiates the demethylase activity of full-length Gis1, but not that of the JmjN + JmjC domain, which can confer heme activation of transcriptional activity in an unrelated protein. These results demonstrate that Gis1 represents a novel class of multi-functional heme sensing and signaling proteins, and that heme binding to the ZnF stimulates Gis1 demethylase and transcriptional activities.Item Molecular Mechanisms Underlying Aerobic Respiration and Heme Regulation in Yeast(2017-12) Lal, Sneha; Zhang, LiHeme is an important signaling molecule with diverse functions in living organisms ranging from regulating gene transcription to circadian rhythm. In yeast, heme serves as a secondary messenger of oxygen, as heme synthesis depends on the intracellular levels of oxygen. Yeast and higher eukaryotes have adapted to adverse conditions including low oxygen or hypoxia. To understand the molecular mechanisms underlying hypoxia tolerance on a genome-wide scale, protein localization was studied using green fluorescence protein (GFP) tagged library of yeast genes under normoxia and hypoxia by Henke and colleagues. This study identified more than 200 proteins that change their localization under hypoxia. Among them were proteins of the chromatin remodeling SWI/SNF complex. Six proteins of the SWI/SNF complex- Swi3, Snf5, Snf6, Snf11, Snf12 and Swp82 relocalized under hypoxia. One of the objectives of this dissertation was to study the mechanism of regulation of cellular bioenergetics and respiration by the SWI/SNF proteins. Measurement of oxygen consumption rate and promoter activity show that Swi3, not Swi2, regulates aerobic gene expression and oxygen consumption. The levels of mitochondrial respiratory chain complex proteins were found to be increased in Δswi3 cells as compared to the parent cells. Deletion of SWI3 also induced the expression of aerobic respiration genes under high heme conditions. Computational analysis of the promoters of the genes bound by the human homologs of Swi3, BAF155 and BAF170 also show that they modulate aerobic respiration genes. In the next part of the dissertation, we have studied the regulation of a transcription factor Gis1 which was initially identified as a stress response regulator. In the previous genome-wide study of protein sub-cellular localization under hypoxia, Gis1 was identified as one of the fast responders to hypoxia and reoxygenation. Here we have studied the regulation of the transcriptional activity of Gis1 by heme. Gis1 belongs to the JmjC family of histone demethylases. Gis1 protein has two heme regulatory motifs (HRM). We show that the DNA binding zinc finger domain of Gis1 promotes the heme activation of its transcriptional activity, although heme does not affect Gis1 binding to DNA. These results have identified a new class of heme signaling proteins.Item The Swi3 Protein Plays A Unique Role In Regulating Respiration In Eukaryotes(2016-06-30) Lal, Sneha; Alam, Md Maksudul; Hooda, Jagmohan; Shah, Ajit; Cao, Thai M.; Xuan, Zhenyu; Zhang, Li; Lal, Sneha; Alam, Md Maksudul; Hooda, Jagmohan; Shah, Ajit; Cao, Thai M.; Xuan, Zhenyu; Zhang, LiRecent experimental evidence increasingly shows that the dysregulation of cellular bioenergetics is associated with a wide array of common human diseases, including cancer, neurological diseases and diabetes. Respiration provides a vital source of cellular energy for most eukaryotic cells, particularly high energy demanding cells. However, the understanding of how respiration is globally regulated is very limited. Interestingly, recent evidence suggests that Swi3 is an important regulator of respiration genes in yeast. In this report, we performed an array of biochemical and genetic experiments and computational analysis to directly evaluate the function of Swi3 and its human homologues in regulating respiration. First, we showed, by computational analysis and measurements of oxygen consumption and promoter activities, that Swi3, not Swi2, regulates genes encoding functions involved in respiration and oxygen consumption. Biochemical analysis showed that the levels of mitochondrial respiratory chain complexes were substantially increased in Delta swi3 cells, compared with the parent cells. Additionally, our data showed that Swi3 strongly affects haem/oxygen-dependent activation of respiration gene promoters whereas Swi2 affects only the basal, haem-independent activities of these promoters. We found that increased expression of aerobic expression genes is correlated with increased oxygen consumption and growth rates in Delta swi3 cells in air. Furthermore, using computational analysis and RNAi knockdown, we showed that the mammalian Swi3 BAF155 and BAF170 regulate respiration in HeLa cells. Together, these experimental and computational data demonstrated that Swi3 and its mammalian homologues are key regulators in regulating respiration.