Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2004. / Title from PDF t.p. (viewed Nov. 14, 2008). Source: Dissertation Abstracts International, Volume: 66-01, Section: B, page: 0082. Chair: Yves V. Brun.

Mu is a temperate bacteriophage which infects Escherichia coli and several other Gram negative enteric bacteria. It is an extraordinary phage in several respects and has carved a special niche for itself both as a genetic tool and a paradigm in phage biology, almost rivaling phage lambda. It is also a predator that has adapted its hunting skills well in order to have an extraordinarily wide host range. While phage Mu finds a mention in almost every genetics textbook for several of its unique and well-studied characteristics, there are a few aspects of its biology that are far from understood. In this thesis, light has been shed on one such less understood feature of Mu biology, namely its anti-restriction function. The enigmatic mom gene of bacteriophage Mu is the center of this thesis work. Bacteriophages, through their sheer number and versatility of attack tactics, constitute an overwhelming threat to bacteria in the natural environment. While it is not always possible to completely prevent the entry of foreign DNA into the cell, it is in the interest of the bacterium to tame the xenogeneic DNA, whose expression may have adverse effects on bacterial fitness. Bacterial nucleoid associated proteins (NAPs) participate in chromosome structuring and global transcriptional regulation. Besides this canonical role, they furnish the job of regulating xenogeneic DNA as well. NAPs are known to regulate the expression of toxin-antitoxin modules, pathogenicity islands and other horizontally transferred DNA and have a profound role in regulating transposon dynamics and the lifestyle of many phages. Chapter 1 introduces the role of bacterial NAPs in silencing foreign DNA, especially after the DNA establishes itself in the host. This thesis examines the role of a bacterial NAP namely Fis in fine-tuning an immune evasion function of bacteriophage Mu. A general introduction to phage Mu and its host expansion strategies, with special focus on its DNA modification function is also presented. Owing to the various immune evasion strategies, phages often have an upper hand on their hosts in the ongoing evolutionary arms race. One such strategy is DNA modification which bacteriophages have evolved as a means to protect their genomes from restriction enzymes of the host. While most phages employ the commonplace methylation modification for their anti-restriction function, phage Mu employs an unusual acetamido modification, catalysed by its protein Mom. Mom modified DNA is refractory to several restriction enzymes from different bacterial species. However, the modification is toxic to the host and thus mom expression needs to be precisely regulated to prevent untimely expression. A crowded multifactorial regulatory circuit has evolved to ensure the expression of mom without jeopardizing the welfare of the bacterial host. Chapter 2 uncovers a new player in mom regulation. The study shows that the bacterial chromatin architectural protein Fis is a transcriptional repressor of mom promoter and that Fis mediates its repressive effect by denying access to RNA polymerase at mom promoter. Two distinct roles of Fis have been known previously in Mu biology. In addition to bringing about the overall downregulation of transposition events and transcription of early genes of phage Mu, Fis also stimulates tail fiber flipping by aiding the activity of a site-specific recombinase. The present study thus presents a novel facet of Fis function in Mu biology. While the regulation of mom has been a matter of intense investigation over the past few decades, most biochemical and structural aspects of the Mom protein per se have remained mysterious owing to the difficulties in cloning this toxic gene. Chapter 3 describes the expression, purification and biophysical characterization of Mom. A variety of techniques show Mom to be folded and dimeric in solution. SPR studies with Mom indicate its high affinity binding to DNA. Chapter 4 deals with the attempts to identify the elusive co-factor of Mom. To begin with, the in vivo activity of Mom was demonstrated by employing a simple plasmid cleavage assay based on the resistance of Mom modified DNA to certain restriction endonucleases. A variety of disparate in silico structure prediction tools such as I-TASSER, Robetta and PHYRE indicate Mom to be related to the GCN5-related N-acetyltransferase superfamily. Mutation of residues deemed important from this analysis indeed abolished or reduced Mom activity in vivo, validating the bioinformatics based prediction and shed light on the possible active site of Mom. However, acetyltransferases are not known to transfer acetamido groups. It was also necessary to establish beyond doubt, the chemical structure of the Mom modified nucleoside. High resolution mass spectrometry data showed the modification to be acetamido, corroborating the earlier sole report on this aspect. Based on the biochemical reactions that acetyl coenzyme A is known to participate in, it is difficult to explain the involvement of acetyl coenzyme A in acetamido addition. Notwithstanding the converging predictions of different bioinformatics tools, caution is recommended when inferring function from structurally similar family members. It is possible that a different chemistry might have converged on the same (acetyltransferase) fold, given that none of the known pathways utilizing acetyl coenzyme A can explain the Mom modification. Several likely candidates such as carboxy-SAM, glyoxylic acid and glycine were also tested for being donors of the two carbon entity transferred on adenine by Mom. Since these candidates tested negative in our genetic assays, a genome-wide genetic screen was subsequently devised to identify the host genes involved in mom modification. The assay exploited the phenotype of lethality associated with overexpression of Mom in E. coli in order to screen for mutations in the host genome that rescued the toxicity. However, the survivors which were obtained in this assay had emerged through mutations in the mom gene rather than abrogation of the co-factor synthesis pathway of the host. The results point at two possibilities: (i) utilization of essential gene(s) or (ii) existence of redundant pathways for the Mom modification reaction. Chapter 5 is an account of our attempts to trace the lineage of mom and its regulatory region, employing updated DNA and protein sequence databases. Despite the selective advantage conferred on the phage by the anti-restriction function of mom, in many Mu-like phages, mom is either absent or substituted with methyltransferases. However, in Mu-like genomes that do encode mom, in spite of a significant overall sequence divergence from Mu, the core elements of the mom regulatory circuit seem to have either co-evolved or have been selectively conserved. Although Mu appears to be unique in the possession of a regulatory circuit tailored for the purpose of mom regulation, recently discovered Mu-like genomes show that different types of regulatory features evolved several times in closely related genomes. It is very likely that a toxic gene like mom has earned its place in the phage genome by carrying along with itself a baggage of regulatory elements. Failure to sustain sufficient regulatory pressure may trigger the loss or replacement of the advantageous but potentially lethal mom function.

Mycobacterial populations are known for the heterogeneity in terms of cell size, morphology, and metabolic status, which are believed to help the population survive under stress conditions. Such population heterogeneity had been observed in TB patients, in animal models, and in in vitro cultures. Also, the physiological relevance of population heterogeneity under nutrient starvation has been studied. However, the physiological significance of population heterogeneity in oxidative and nitrite stress has not been addressed yet. Our laboratory had earlier shown that a subpopulation of mycobacterial mid-log phase cultures divide by highly deviated asymmetric division, generating short cells and normal-sized/long cells. This proportion has been found to be consistent and reproducible, and has been found in the freshly diagnosed pulmonary tuberculosis patients’ sputum, which is known to have high levels of oxidative stress. The highly deviated asymmetric cell division has been found to be one of the mechanisms that mycobacteria use to generate cell size heterogeneity in the population. However, the physiological significance of the population heterogeneity generated by the highly deviated asymmetric division remained to be addressed. Therefore, in the present study, we addressed the physiological significance of the generation of population heterogeneity in terms of cell size in Mycobacterium smegmatis and Mycobacterium tuberculosis. In this regard, we explored whether the minor subpopulation of short cells generated in the population has any relevance in the response of mycobacteria to oxidative and nitrite stress for survival. The Chapter 1, which forms the Introduction to the thesis, gives an extensive literature survey on the phenotypic heterogeneity in diverse bacterial systems and the physiological significance of such heterogeneity. Subsequently, an account of the phenotypic heterogeneity reported in mycobacteria is given, with examples of its significance implicated for survival under nutrient stress. Then an account of various studies on the oxidative and nitrite stress response of mycobacteria and on the genes involved in those processes are given. Further, the present study is justified by stating that so far there has not been any study to find out the physiological relevance of phenotypic heterogeneity on oxidative and nitrite stress response in mycobacteria. Finally, the Introduction is concluded by stating that the present study investigates and reports for the first time the physiological significance of the minor subpopulation of short cells for survival under oxidative and nitrite stress conditions. The Chapter 2 forms the Materials and Methods used in the present study. Here a detailed description of the methods used for the separation of the short cells, their characterisation, stress response, and so on are given in great detail. The Chapter 3 forms the first data chapter that presents results on the nature of response of Mycobacterium smegmatis and Mycobacterium tuberculosis against oxidative and nitrite stress. Here the cell size natural distribution, in terms of short cells and normal-sized/long cells in the mid-log phase population, the fractionation and enrichment of these subpopulations, differential susceptibility of the cells in the fractions to the stress conditions, the enhanced survival of the population upon mixing of these cell populations at the natural proportion, and the decreased survival upon mixing them at unnatural proportion are presented. The differential survival of the short cells and normal-sized/long cells was studied at a variety of stress concentrations for oxidative (H2O2) and nitrite (acidified sodium nitrite, pH 5), cell densities and exposure time to show the robustness of the phenomenon. Enhanced survival upon extended exposure to stress also has been documented. Essentially the data in this chapter shows that although the different sized populations show differential stress susceptibility to the stress conditions, their combined presence at the proportion that naturally exists in the mid-log phase population enhances the survival of the population, at the cost of the highly susceptible short cells for the enhanced survival of the less susceptible normal-sized/long cells, kin selection and altruism. The Chapter concludes with a discussion on the results. The Chapter 4 delineates the mechanism of the altruistic phenomenon that results in the enhanced survival of the population at the sacrifice of the minor subpopulation of short cells. Here we present evidence that hydroxyl radical generated through Fenton reaction is responsible for the enhanced survival through the induction of the synthesis of catalase-peroxidase (KatG) for the degradation of H2O2. The free iron deficient short cells acquire more iron, which in turn becomes stoichiometrically detrimental to them due to the high levels of hydroxyl generation in the presence of H2O2. On the contrary, the free iron containing normal-sized/long cells do not acquire iron and hence the hydroxyl radical produced in the population becomes stoichiometrically beneficial to them. Thus, the deficiency of free iron which consequentially necessitates the short cells to acquire more iron becomes a maladaptive trait in the presence of H2O2 but gets co-opted in kin selection, for the survival of the normal-sized/long cells that form major proportion of the population – a phenomenon reminiscent of altruism. The Chapter concludes with a model depicting the entire phenomenon and a discussion on the results and their implications.

The transition to flowering is an important decision for plants since seed-setting and the survival of the progeny depend on the environmental conditions prevalent during this transition. Therefore, to ensure maximum reproductive success, plants have evolved several regulatory mechanisms to enable them flower at the most appropriate time. Environmental parameters such as light, temperature and nutrient availability as well as endogenous factors such as age and hormonal status of the plant profoundly affect floral transition (Boss et al., 2004; Srikanth and Schmid, 2011). Studies in Arabidopsis and other model plant species have identified several distinct genetic pathways that integrate the information from the endogenous and environmental cues to regulate flowering (Boss et al., 2004; Srikanth and Schmid, 2011). Many components and gene regulatory networks identified in Arabidopsis are conserved in other commercially important species including rice, maize, sorghum, potato and tomato. Therefore, it is important to understand the basic mechanisms that modulate the flowering response in model plants such as Arabidopsis thaliana, the knowledge from which can be used to develop better adapted and high-yielding varieties of crop plants in the wake of challenges like global warming and increasing food demand. In the present study, we have studied the function of VLB1 and VLB2, genes that code for plant-specific Zn-finger transcription factors. Previous studies from our laboratory (Pratibha Choudhary, Ph.D thesis, 2011) and by other research groups have reported that VLBs redundantly promote flowering in A. thaliana (Yasui et al., 2012; Celesnik et al., 2013). However, the underlying mechanism of this regulation is not well understood. Our data suggests that VLBs redundantly promote the transition to flowering specifically in the photoperiod pathway, the major floral induction pathway in A. thaliana. CO, which is the 93 key regulatory gene in this pathway, is regulated by various factors at the transcriptional as well as post-transcriptional level (Suarez-Lopez et al., 2001; Yanovsky and Kay, 2002; Srikanth and Schmid, 2011). Using genetics, we show that VLBs and CO function together to promote flowering in the photoperiod pathway. Further, our BiFC results reveal that VLBs and CO interact physically. Nevertheless, the physical interaction between VLBs and CO needs to be further validated by in vitro and in vivo by co-immunoprecipitation experiments. We hypothesize that the interaction between VLBs and CO is important to regulate FT expression and hence, flowering. However, whether VLBs interact with CO and promote the CO-stability, or facilitates its recruitment to the FT promoter region, still needs to be determined. Apart from its role in flowering, VLBs have been recently shown to regulate biotic and abiotic responses in Arabidopsis (Nakai et al., 2013a; Nakai et al., 2013b). Also, even though it has been demonstrated that VLBs code for transcription factors, no direct targets of VLBs have been reported till date. We performed a whole genome trancriptome-profiling and found that several important classes of genes including WRKY, RLPs, NBS-LRR and JAZs were affected suggesting that, in addition to their role in floral transition, VLBs have important functions in other plant processes as well. In fact, vlb1vlb2 mutant showed an early senescence phenotype and many senescence-associated genes (SAGs) were up-regulated in our microarray experiments, which was further validated by qRT-PCR analysis. By comparing the differentially-regulated genes and PatMatch analysis, we have identified 82 putative direct targets of VLBs in the Arabidopsis genome which need to be validated by chromatin immunoprecipitation (ChIP) assay and functional studies. 94 Results of global transcriptome analysis revealed that the expression of several JA-signaling and response genes was significantly down-regulated. JA is an important phytohormone involved in plant defense and other developmental processes such as stamen development, root growth and senescence (Wasternack, 2007). Results from the JA-induced expression analysis and root inhibition assay confirmed that JA-signaling and response are indeed compromised in the vlb1vlb2 double mutant. Moreover, in vitro DNA-binding assay showed that MYC2, the key transcriptional regulator of JA-responsive gene expression, is a direct transcriptional target of VLB2. A recent study reported that loss-of-function of VLB genes impairs plant defense while their overexpression confers biotic stress tolerance in Arabidopsis (Nakai et al., 2013a; Nakai et al., 2013b). Compromised JA signaling in the vlb1vlb2 double mutant might partly explain this reduced tolerance to pathogens. However, whether VLBs are associated with the MYC2 promoter in planta needs to be tested by performing ChIP and other in vivo assays. In conclusion, our study shows that VLBs have important regulatory roles in diverse processes including control of flowering time, senescence and JA signaling in Arabidopsis. The validation and functional characterization of the direct targets of VLBs will shed more light on the role of VLBs. Since VLBs are conserved in vascular plants, it will be interesting to see if the function of VLBs is also conserved across species and what might be its ancestral function in evolution.

Astrocytoma is defined as the neoplasia of astrocytes, the most abundant non-neuronal glial cells in brain. According to the WHO classification, the different grades of astrocytoma are- gradeI/pilocytic astrocytoma (benign form), grade II/diffuse astrocytoma (DA), grade III/anaplastic astrocytoma (AA) and grade IV/Glioblastoma (GBM). Patients with grade II astrocytoma have median survival time of 6-8 years after surgical intervention. While the more aggressive grade III has a median survival of 2-3 years. Grade IV is the most malignant form and has a median survival of 15 months approximately. In spite of all the progress in the fields of diagnosis and therapy, the prognosis of GBM still remains very poor. The aggressiveness and poor survival of GBM is due to the recurrence which is primarily because of intratumoral heterogeneity, presence of glioma stem cells and infiltration of the tumor cells into the normal brain parenchyma. Apart from the role of genetic mechanisms in triggering tumorigenesis, epigenetic modifications particularly the DNA methylation and histone modifications, are now recognized as frequent alterations playing a crucial role in the development and progression of human malignancies. There are two distinct DNA methylation abnormalities. The first is the reduction in genome-wide DNA methylation levels (global hypomethylation) and the second is the hypermethylation in the CpG island of specific gene promoters. Hypomethylation is believed to induce proto-oncogene activation and chromosomal instability, whereas hypermethylation is strongly associated with silencing of tumor suppressor genes. Thus, DNA methylation can function as a “switch” to activate or repress gene transcription, providing an essential mechanism for overexpressed or silenced genes involved in the regulation of cell cycle, DNA repair, growth signalling, angiogenesis, apoptosis, migration, invasion and thus in the initiation and progression of astrocytoma. Recent studies have identified biomarkers with prognostic impact which would include promoter methylation of O⁶-methyl guanine-DNA methyltransferase methylation (MGMT), isocitrate dehydrogenase 1(IDH1) mutation and a glioma CpG-island methylator (G-CIMP) phenotype. In the current study, we have characterized the DNA methylation profile for the different grades of astrocytoma and analysed the significance of methylation events occurring commonly in all the grades or uniquely only in grade IV. One of the GBM-specific hypomethylated and upregulated genes, Fibromodulin (FMOD), was extensively investigated in terms of its role in glioma pathogenesis and its regulation. FMOD was found to induce F-actin stress fibre formation and promote glioma cell migration. We also found that FMOD-mediated glioma cell migration is dependent on Integrin/FAK/Src/Small Rho GTPases signalling cascade. We further found that TGFβ pathway regulates FMOD expression through a process involving active demethylation and chromatin state transitions on FMOD promoter. This work has been divided into three parts: Part I: Characterization of DNA methylome during progression of Astrocytoma To investigate the aberrant methylation pattern on a genome-wide scale, 17 Grade II, 16 Grade III and 36 Grade IV tumor samples as well as 9 control brain tissues were analysed using Infinium Human Methylation 450K Bead Array on Illumina platform. The analysis was carried out in two parts. Firstly, we validated the dataset with already existing TCGA dataset. Upon comparison, the methylation profile of our dataset was highly correlated to the TCGA dataset with correlation coefficient of 0.99. In addition, we also checked the methylation status of few known hypermethylated and hypomethylated genes which showed the similar type of differential methylation. Then, we characterized the differentially methylated CpGs based on their spatial distribution in the human genome, for different grades of astrocytoma. CpG-rich regions show more of hypermethylation while the non-CpG rich regions, like open sea or gene body, are observed to be hypomethylated. Secondly, we also analysed the differentially methylated genes which contribute to physiological events in gliomagenesis. We hypothesized that the methylation specific events that occur in grade II and remain similarly methylated in grade IV are the ones probably contributing to the initial astrocyte transformation. However, the methylation specific events responsible for the aggressive nature of grade IV may occur as differentially methylated genes only in grade IV (and not in grade II). In this analysis, we have identified differentially methylated genes that play a role in initial transformation process (293 genes hypermethylated and downregulated while 23 genes were hypomethylated and upregulated) and also those that play a role in tumor aggressiveness (459 genes hypermethylated and downregulated while 350 genes were hypomethylated and upregulated). The differentially methylated genes that were common in both grade II and grade IV showed an enrichment of cell proliferation pathways while the differentially methylated genes uniquely present in grade IV showed enrichment in pathways related to the aggressiveness phenotype of tumorigenesis like cell motility and angiogenesis. Part II: Fibromodulin (FMOD), a GBM-specific hypomethylated and upregulated gene, is essential for glioma cell migration Among differentially methylated genes specifically in GBM, fibromodulin (FMOD) is one of the top most hypomethylated genes. FMOD is a member of leucine – rich repeat proteoglycan that is widely distributed in interstitial connective tissues. We found that FMOD is hypomethylated and upregulated only in grade IV/GBM, not in the grade II. FMOD promoter methylation status is significantly negatively correlated to its transcript levels.Towards identifying functions of FMOD in glioma cells, total RNA derived from U251 cells transfected with either non-targeting siRNA or FMOD siRNA was subjected to transcriptome profiling. There were 872 genes upregulated and 299 genes downregulated in FMOD silenced cells than in control cells. PANTHER pathway analysis using the differentially regulated genes identified several pathways to be associated with FMOD. Cytoskeleton regulation by Rho GTPase, which is known to be involved in cell motility and migration, is enriched with highest significance. In coherence with the pathway analysis, modulating FMOD levels in glioma cells affected in glioma cell migration. Upon FMOD overexpression, there was significant increase in migration than in control cells. Conversely, when FMOD is silenced, there was delay in migration than in control cells and the delayed migration was rescued by the addition of recombinant purified FMOD protein. Prior neutralization with FMOD specific antibody inhibited cell migration suggesting that secreted FMOD promotes glioma cell migration. Overexpression of FMOD in glioma cells induced actin stress fibre formation required for the migration of cells. On the contrary, FMOD silencing resulted in the loss of F-actin stress fibres which was restored upon addition of FMOD purified protein exogenously to the media. To investigate further the role and the requirement of specific Rho GTPase in FMOD-mediated migration, each of members of Rho GTPase family was silenced and their effect on FMOD-induced silencing was studied. FMOD mediated glioma cell migration was delayed when RhoA, Rac1 and Cdc42 were silenced. In order to understand whether FMOD activates Integrin mediated signalling pathway, we performed western blot analysis to check the levels of phospho-FAK in either FMOD overexpressing or knockdown condition. We observed phospho-FAK levels increased upon FMOD overexpression and decreased upon FMOD silencing compared to the respective controls. Additional experiments revealed that inhibitors to Integrin, FAK and Src were able to abrogate the FMOD induced glioma cell migration. These results suggest that FMOD utilizes a pathway that involves Integrins, FAK, Src and Rho GTPases in promoting glioma cell migration. To comprehend the effect of FMOD promoter methylation status and its expression in GBM patient scenario, we stratified the patients into either high or low FMOD expression and promoter hypermethylation or hypomethylation. The GBM patients with low FMOD transcript levels and promoter hypermethylation showed better survival than the other group. Part III: Regulation of FMOD expression through TGFβ-dependent epigenetic remodelling in glioma To study how FMOD is regulated in glioma, we investigated the promoter sequence of FMOD by MatInspector. Several Smad-binding sites were located in FMOD promoter which indicated that FMOD might be regulated via TGFβ signalling pathway. Firstly, we checked active TGFβ signalling in glioma cell lines – LN229, U87 and U251. TGFβ-dependent signalling was active in U251 and U87 cells compared to LN229 cells as seen by the levels of phospho-Smad2. Moreover, FMOD transcript level was found to be high in U251 compared to LN229 cells. Further, TGFβ treatment increased FMOD promoter luciferase activity as well as FMOD transcript level in LN229 cells. In contrast, U251 cells that were treated with TGFβ RI inhibitor showed a significant decrease in FMOD promoter luciferase activity as well as FMOD transcript level. We correlated these findings with Smad2 occupancy at FMOD promoter by chromatin immunoprecipitation (ChIP). Smad2 association at FMOD promoter is found to be relatively higher in U251 cells than in LN229 cells which suggested that TGFβ induced transcription factor, Smad2, drives FMOD expression in U251 cells. Next, we investigated the role of TGFβ in FMOD promoter demethylation and chromatin state transition. Upon TGFβ treatment in LN229 cells, we found that there was gradual demethylation of FMOD promoter in a time-dependent manner. TGFβ treatment also altered the chromatin state by increasing the active marks (H3K4me3 and H3K9Ac) and decreasing the repressive mark (H3K27me3) with a simultaneous increase in Smad2 occupancy in the FMOD promoter. In contrast, TGFβ RI inhibitor treatment of U251 cells resulted in methylation of FMOD promoter in a time-dependent manner. Further, we observed a significant enrichment of repressive histone marks (H3K27me3) and loss of active chromatin marks (H3K4me3 and H3K9Ac) with a concomitant decrease in Smad2 occupancy at FMOD promoter. DNMT3A/B and EZH2 enzymes play a key role in DNA methylation and H3K27 trimethylation respectively. Accordingly, we examined the transcript levels of DNMT3A/B and EZH2 in LN229 cells treated with TGFβ as well as U251 cells treated with TGFβ RI inhibitor. In presence of TGFβ, DNMT3A/B and EZH2 transcript levels were significantly downregulated than in untreated cells in a time-dependent manner. Conversely, in U251 cells treated with TGFβ RI inhibitor, there was a significant increase in DNMT3A/B and EZH2 transcript levels when compared to untreated cells. TGFβ is known to promote glioma cell migration. In order to understand whether TGFβ-mediated glioma cell migration occurs via FMOD, we performed migration assay in U251 cells with or without TGFβ RI inhibitor followed by addition of either BSA control or FMOD purified protein. Upon TGFβ RI inhibitor treatment, there was delay in the migration of U251 cells than in untreated control cells which was rescued when purified FMOD protein was added, indicating that FMOD is essential for TGFβ signalling cascade to induce glioma cell migration. Therefore, we conclude from these results that epigenetically regulated FMOD is essential for TGFβ mediated glioma cell migration.

In order to identify new players in fruit development, a forward genetic screen was performed on EMS mutagenized plants. A mutant named elongated gynophore (egy) was identified in the M2 population based on altered fruit morphology. Genetic analysis established that the egy phenotype is due to a monogenic and recessive mutation. The egy plants show additional developmental defects including shorter root, narrower cotyledons and malformed leaf lamina. Molecular mapping and whole genome sequencing analyses showed a G/C deletion at the position 4414980 on the AT5G13680 gene locus which is predicted to encode the ELONGATA2 (ELO2) protein. ELO2 is a constituent member of the elongator complex which helps in transcriptional elongation in association with the phosphorylated form of RNA polymerase II. This complex has been implicated in controlling development, abiotic stress and biotic stress. Genetic complementation test confirmed that egy is indeed allelic to elo2-3. Surprisingly, the EGY overexpression line 35S::EGY showed loss-of-function phenotype, suggesting transgene silencing. In angiosperms, fruit is derived from the fertilized ovary. The initiation of the female reproductive organ commences with a lump of cells which eventually develops into the gynoecium with a stigma, a style, two fused ovaries and a gynophore, arranged from the apical to basal axis in that order. Genetic networks faithfully shapes up the carpel primordium into predetermined gynoecium shape. Following fertilization, siliques elongate concomitantly with developing embryos. Here we show that the egy mutant has apical basal patterning defect with longer gynophore at the base. This gynophore phenotype resembles the phenotype found in the mutants with altered auxin and cytokinin levels/signaling. We show that egy is hypersensitive to cytokinin treatment; egy fruits treated with cytokinin display phenotype similar to the plants expressing IPT7 under fruit-specific promoter. These results suggest that broadened shoulders at the apical region of egy gynoecium possibly results from higher cytokinin level/response. Genetic interaction studies have shown that EGY act independent of AGAMOUS and PEAPOD to suppress the medio-lateral growth of the apical gynoecium region. Genetic and expression studies suggest that PINOID and TMO5/T5L1 work downstream to EGY, while ETTIN acts in parallel to EGY. We also observed larger seeds in the egy mutant and show that this is controlled maternally. Thus, the gametic lethality in egy can possibly be accounted for by the defective ovules. We show that egy primary roots are shorter compared to Col-0, though egy seeds have longer embryonic root to begin with, suggesting a defect in cell division. The root cells are arranged radially in a stereotypic pattern in root meristem from the outer epidermis to the inner stele specific the vascular bundles. The four QC cells are also surrounded by stem cells of various identities. This stereotypic pattern of cell arrangement is perturbed in the egy root. The stele, composed of pericycle and vascular bundles is reduced in the egy mutant, suggesting a positive role of EGY in vascular cell division. Confocal microscopic studies and real-time PCR data suggest that TMO5/T5L1 work downstream to EGY. Thus, the Arabidopsis „ELONGATOR‟ complex regulates the transcription of target genes that are necessary for plant growth and development. A proposed genetic network for the role of EGY in fruit and root development. Based on the genetic interaction studies and expression analysis, we have placed EGY in the existing molecular network that control fruit and root vascular development in Arabidopsis

Mycobacterium are important human pathogens and their strength lies in establishing acute infections, latent infections as well as co-existing with other dreadful infectious agents like HIV. The success of mycobacterium infection often relies in its ability to evade immune-surveillance mechanisms mediated by sentinels of host immunity by modulating host signal transduction pathways and expression of immune regulatory molecules. In this scenario, the role of pattern recognition receptors (PRRs) in orchestrating host immune responses assumes central importance. Of the PRRs, the Toll-like receptors (TLRs) or intracellular surveillance receptors such as retinoic acid-inducible gene 1 (RIG-I)-like receptors (RLRs) govern key immune-surveillance mechanisms in recognition as well as control of mycobacterial or viral infections. The first part of this study illustrates the role of SHH signaling in macrophage induced neutrophil recruitment during mycobacterial infections. The present investigation demonstrates that, in response to mycobacterium infection, macrophages displayed robust activation of TLR2 dependent SHH signaling. By utilizing the well-documented experimental air pouch model, we show that the ability of pathogenic mycobacterium infected macrophages to recruit polymorph nuclear leukocytes (PMNs) like neutrophils to the infected site was dependent on SHH signaling. The activated SHH signaling differentially regulated the expression of proteolytic enzymes, MMP-9 and MMP-12 that would contribute to PMN migration. Interestingly, SHH-responsive krüppel-like family (KLF) of transcription factors, KLF4 and KLF5 were found to modulate these chemokine effectors to regulate neutrophil recruitment. Subsequent chapters describe novel functions of SHH signaling during RIG-I mediated anti-viral immunity and RIG-I mediated modulation of TLR2 anti-inflammatory signature in mycobacteria infected macrophages. In this perspective, we demonstrate that RIG-I ligand robustly induces the activation of SHH signaling via the phosphatidylinositide 3-kinase (PI3K) pathway in macrophages. Furthermore, we show that the sustained inhibition of PKA-GSK-3β-SUFU negative regulatory axis upon RIG-I engagement with 5'3pRNA is critical for the activation of SHH signaling. Gain or loss of function studies implicate the necessity of RIG-I triggered MAVS-TBK1 canonical axis in the inhibition of PKA-GSK-3β-SUFU negative regulatory axis that contributes to SHH signaling activation. The RIG-I activated SHH signaling drives the production of anti-viral type 1 interferons leading to the inhibition Japanese encephalitis virus (JEV) replication. Further, RIG-I-mediated anti-viral type 1 interferon production and subsequent control of viral replication suggested the involvement of two transcriptional factors, IRF3 and YY1 in the response along a SHH axis. Further, mounting evidence clearly depicts a significant cross talk among the molecular events initiated by given TLRs and RLRs like RIG-I. Clearly, these studies present an interesting challenge in delineating the events during polymicrobial infection of host immune cells like macrophages or DCs. Altogether, our results improve our understanding of mycobacteria associated confections’ and may add significantly to the current knowledge of the delicate balance that determines a successful mycobacterial infection.

Melanosome biogenesis is a highly regulated endosomal maturation process wherein structural fibers harbouring immature melanosomes acquires its biosynthetic proteins through the secretory pathway and finally matures into a functional organelle. These processes were shown to be dependent on several cytosolic protein complexes such as AP (adaptor protein)-1, AP-3, BLOC (biogenesis of lysosome-related organelles complex)-1, -2 and -3; in addition to kinesin motor KIF13A and Rab GTPases 7, 32 or 38. Mutations in the subunits of these complexes or Rab38 result into defective melanosome maturation leading to occulocutaneous albinism, a clinical phenotype commonly observed in Hermansky-Pudlak syndrome (HPS). Moreover, molecular function of these complexes in regulating the biogenesis of melanosome is partially known. The delivery of cargo to maturing melanosomal membranes requires fusion machinery that includes Rab GTPases, tethering factors and SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins. However, the SNAREs involved in the transport of cargo to melanosomes is poorly understood. In this study entitled as “understanding the SNARE dynamics during melanosome biogenesis” we focus on functional role of endosomal Qa-SNARE protein, Syntaxin 13 (formally called STX12, herein referred to as STX13) in the organelle biogenesis and its transport in and out of melanosome. Moreover, these studies show that STX13-mediated cargo transport require a melanosomal membrane localized R-SNARE VAMP7 and these SNAREs are interdependent on each other in regulating their steady state distribution. In addition, this study illustrated the possible mechanism of SNARE recycling which occurs indirectly through AP-3 complex. Thus, these studies underscore the STX13‟s role in cargo transport to maturating melanosomes and its trafficking routes to and from the melanosomes. Chapter-I describes the literature review on melanosome biogenesis; Chapter-II lists the experimental procedures used in this study and Chapter-III to V focuses on results and discussion, segregated into three sections. Chapter-III: Screening and identification of endosomal SNAREs involved in the trafficking of melanosomal proteins. Our preliminary RNAi screen for SNAREs involved in melanosome biogenesis revealed STX13 as one of the Qa-SNARE affecting pigmentation and cargo transport. STX13, a recycling endosomal SNARE has been reported to interact with pallidin, a subunit of BLOC-1; however the functional role of this interaction in pigment formation is unknown. In addition, previous studies from our lab have shown that STX13 colocalize with endosomal Rab11 and partially with EEA1- or Rab5-positive organelles in melanocytes. Together, these observations insinuated us to characterize the functional role of STX13 in melanosome biogenesis. Upon STX13 inactivation, wild type mouse melanocytes showed hypopigmentation due to mistargeting of cargo such as TYRP1 and TYR to lysosomes. Knockdown of STX13 dramatically decrease the population of immature and mature melanosomes. Moreover, STX13 associate with the melanosome cargo on endosomal tubular structures. In addition, deletion of regulatory domain in STX13 increases the cargo transport to melanosomes due to its increased SNARE activity. This is possibly due to loss in intracellular regulation of SNARE occur through multiple factors such as SM (Sec1p/Munc18) proteins. Together this data suggests that STX13 mediates cargo transport to melanosomes from recycling endosomes. Chapter-IV: Functional characterization of the SNAREs involved in melanosomal maturation. Several in vitro studies have shown that a set of four SNAREs such as Qa, Qb, Qc (or Qbc) and R control the membrane fusion event duing the cargo transport. Additionally, this process is further regulated by SM proteins in in vivo. Electron microscopic studies in melanocytes have shown that melanosomal proteins were delivered to the melanosomal membrane through recycling endosomal tubular domains. Moreover, our RNAi screen show that STX13 possibly acts as Qa-SNARE in mediating the fusion events between melanosomal membranes and the endosomal tubular or vesicular intermediates. However, the role of other SNAREs for this membrane transport is unknown. It has been shown that the expression of VAMP family SNAREs such as VAMP3, VAMP7 and VAMP8 increased with melanogenesis upon differentiation of melanoma cells. VAMPs belong to the class of R-SNAREs, in which VAMP7 is known to interact with VARP (abbreviation) and AP-3 (mediates the trafficking of TYR) separately, and these molecules are known to regulate the cargo transport to melanosomes. However, the precise role of VAMP7 in pigment granule maturation is unknown. Therefore, we set out to characterize the functional role of VAMP7 in melanosome biogenesis. VAMP7 has been shown to localizes to multiple sub-cellular compartments and regulate the several transport steps in other cell types. Our study found that GFP-epitope tagged either human or rat VAMP7 localize to melanosomes at steady state in wild type mouse melanocytes. Knockdown of VAMP7 causes hypopigmentation of melanocytes and misroutes the cargo to lysosomes. Further, the inactivation of VAMP7 in melanocytes phenocopies the STX13 depletion, suggesting both the SNAREs are required for the melanosome biogenesis. In addition, knockdown of STX13 target the VAMP7 to lysosomes; while inactivation of VAMP7 affect the localization of STX13 to recycling tubular structures. Subsequently, the dominant active mutants of STX13 were not able to rescue the pigmentation or cargo transport defects in VAMP7 knockdown melanocytes. Together, the data suggests that STX13 functions from recycling endosomes and VAMP7 on melanosome membrane for the transport of cargo to melanosomes Chapter-V: Understanding the mechanism of STX13 recycling during melanosome biogenesis. At steady state, SNAREs are localized to the membranes of specific organelles where they mediate or regulate the membrane fusion. During this process, three or two Q-SNAREs on one membrane (in a trans-SNARE complex, possibly formed by Qa, Qb, Qc or Qbc) interact with a R-SNARE on another member to form a SNAREpin complex. Post-fusion, SNAREs are disassembled by SNAP and NSF proteins and then recycled back to the original compartment for next round of fusion. Here, we address the mechanism of post-fusion recycling of STX13 from melanosomes to endosomes. Previous studies have shown that STX13 mislocalize to melanosomes in AP-3-deficient melanocytes, suggesting a role for AP-3 in recycling the SNARE from melanosomes. Bioinformatic analysis of the N-terminal region of STX13 revealed the presence of two canonical adaptor binding motifs 3YGP6L and KETNE80L81L, resembling the tyrosine-based (YXXø) and dileucine-based motif [DE]XXXL[LI], recognized by several adaptor proteins. Point mutagenesis of these motifs in STX13 had no effect on their steady state distribution indicating that STX13 possibly uses non-canonical residues for its recycling. Further, deletion of the N-terminal region (either 1-129 or 14-129 aa) in STX13 redistributes the SNARE to melanosomes. Moreover, the activity and the trafficking of recycling defective STX13 mutants are dependent on another HPS complex, BLOC-2 and the SNARE, VAMP7. Absence of 1-129 region in STX13 or mutations in the subunits of AP-3 perturbs the steady state localization of STX13 suggesting an indirect role for AP-3 in recycling of STX13 to endosome via non canonical motifs present in its 1-129 aa region.

Recycling embosoms (REs) are transient intermediates of endosomal network, constantly generated from early/sorting endosomes (EEs/SEs). Conventionally, these organelles function in recycling of many growth/nutrient/signalling receptors from SEs to the cell surface and maintain the cellular homeostasis in all cell types. Recent studies have shown that REs slightly diverted their function in specialized cells such as melanocytes for the delivery of melanogenic cargo to a set of lysosome-related organelles (LROs) called melanosomes. However, it is unknown how melanocytes modulate the trafficking routes of REs towards the biogenesis of melanosomes. Any alterations in this process result in occulocutaneous albinism, commonly observed in autosomal recessive disorder, Hermansky-Pudlak Syndrome (HPS). HPS is caused by mutations in nine genes in human and fifteen genes in mouse and the protein products of these genes were grouped in multiple endosomal protein complexes; BLOC (Biogenesis of Lysosome-related Organelles Complex)-1, -2, -3, AP (Adaptor Protein)-3 and HOPS (homotypic fusion and protein sorting). Studies from our laboratory and others have shown that REs deliver the melanin-synthesizing enzymes to melanosome in BLOC-1 and BLOC-2 dependent manner. On the other side, studies in fibroblasts have shown that the adaptor AP-1 and microtubule-dependent motor, KIF13A also regulates the formation of REs. In these studies, it was proposed that AP-1 binds to the cargo tails and interacts with motor KIF13A to generate the RE tubules, where BLOC-1 initiates the biogenesis. Nevertheless, the mechanism behind the biogenesis of REs and how these molecules synergistically control these processes is largely unknown. Additionally, the role of BLOC-2 in REs biogenesis never been implicated. Here we have attempted to study the mechanism of RE biogenesis and their role in pigment granule formation using HeLa and mouse melanocytes as model systems. In general, Rab GTPases (Rabs) regulate the several process of membrane trafficking including cargo sorting, membrane domain organization, tethering and fusion. We hypothesized that the biogenesis of RE is also regulated by one of the endosome localized Rab GTPases. Our RNAi screening against Rabs involved in regulating the RE length/number showed Rab22A as a potential candidate. Thus, we aim to study the role of Rab22A in RE biogenesis and its regulation in melanocyte pigmentation. The current study entitled as “Understanding the role of Rab22A in recycling endosome biogenesis and melanocyte pigmentation” is divided into five chapters. Chapter-I outlines the review of literature on cell biology of intracellular organelles such as endocytic network and melanosomes. Chapter-II details the experimental procedures used in the study. Chapter-III to Chapter-V describes the results and discussion. Chapter-III: Identification of endosomal Rab GTPases required for the dynamics of recycling endosomes Endosomal Rabs are known to regulate various functions such as vesicle biogenesis, transport, tethering and fusion, but their role in generation of tubulo-vesicular carriers of endocytic system, REs is unknown. It has been shown that REs possibly derived from EEs/SEs and characterized by the association/localization of multiple proteins such as transferrin receptor (TfR), SNARE STX13, Rab11 and motor KIF13A. In this study, we have used YFP-KIF13A as a marker to label the REs. YFP-KIF13A in HeLa cells localized to long tubular structures throughout the cell and also to the clusters of peripheral endosomes. To identify the endosomal Rabs that regulate the RE dynamics (both length and number), we have transfected the HeLa cells with shRNA against endosomal Rabs such as Rab4A, Rab5A, Rab5B, Rab5C, Rab7A, Rab9A, Rab11A, Rab14A and Rab22A. Post transfection and shRNA selection, cells were transfected with YFP-KIF13A, analyzed and quantified the RE dynamics using ImageJ. Here, we have measured two parameters for the identification of Rab/s that potentially regulates the REs biogenesis: first, average number of tubules per cell and second, average length of tubules per cell. These studies identified Rab22A as a potential candidate, depletion of this Rab affects both number and average length of KIF13A-positive tubules. As described above, REs deliver several melanocyte specific cargoes to melanosomes in melanocytes. However, the function of Rab22A in controlling these transport steps to melanosome/its biogenesis or pigmentation has not been addressed. Thus, we have studied the mechanism of Rab22A in RE biogenesis and its role in pigmentation in the following sections. Chapter-IV: Characterization of Rab22A function in regulating the recycling endosomes Initially, we tested whether Rab22A localizes to the REs. Our co-expression studies show that Rab22A localizes to KIF13A- or STX13-positive RE compartments in HeLa or melanocytes, respectively. In general, Rab GTPases mediate their function through cycling between GTP (membrane bound) and GDP (cytosol) bound state. These states can be achieved by point mutation of active site residues in the protein. We have generated Rab22A constitutive active mutant (Rab22AQ64L, defective in GTP hydrolysis) and dominant negative mutant (Rab22AS19N, defective in GTP binding) to understand the role of Rab22A in regulating REs. Interestingly, overexpression of Rab22AQ64L mutant in HeLa cells increases the average number of KIF13A-positive REs relative to the wild-type Rab22A (Rab22AWT). As predicted, overexpression of Rab22AS19N mutant reduces the number as well as length of RE tubules relative to the control HeLa cells. Consistent to these studies, Rab22A-knockdown did not affect the endogenous KIF13A protein levels or its recruitment to endosomes, however recycling of TfR (measured through Tf-Alexa 594) was significantly affected in these cells. These studies suggest that Rab22A possibly regulates the formation or function of REs. Likewise, overexpression of Rab22AQ64L and Rab22AS19N mutants in melanocytes resulted in reduction of total melanin content in the cells. To confirm these results, we have performed immunofluorescence microscopy (IFM) analysis, which showed Rab22AQ64L localized to the enlarged vacuolar structures, positive for melanosomal cargo TYRP1 (tyrosinase-related protein 1), whereas Rab22AS19N localized to the cytosol. Further, Rab22A depletion in melanocytes causes the hypopigmentation in the cells concurrently reduces the stability of TYRP1 but not other melanocyte specific proteins, indicating a role for Rab22A in regulating TYRP1 transport to melanosomes. Altogether, our studies suggests that Rab22A regulates the TfR recycling in HeLa cells and TYRP1 transport in melanocytes by controlling the RE dynamics. Chapter-V: Molecular mechanism of recycling endosome biogenesis: a role for Rab22A Rabs perform their function by recruiting specific effector/s to the membrane upon Rab activation. It is unknown, how Rab22A regulates REs through its effectors. We hypothesize that Rab22A may regulate the recruitment and function of BLOC-1 and BLOC-2 complexes during RE formation. To validate these hypothesis, we carried out the knockdown of individual BLOC-1 and -2 subunits (destabilize the entire complex) separately in HeLa and studied the dynamics of RE through YFP-KIF13A expression. As expected, the length and number of KIF13A-postive tubules were significantly reduced in both BLOC-1- and BLOC-2-deficient HeLa cells and was phenocopying the Rab22A knockdown cells. Moreover, subcellular fractionation in HeLa, co-fractionated Rab22A with BLOC-1 (Muted) or BLOC-2 (HPS6) subunits along with KIF13A. Additionally, endogenous subunit levels of BLOC-1 and BLOC-2 were moderately reduced in Rab22A knockdown HeLa cells. Consistent to these results, recycling kinetics of Transferrin (Tf) was altered in Rab22A depleted cells as similar to BLOC-1- or BLOC-2-deficient cells as reported earlier. Likewise, Rab22A knockdown in melanocytes affected STX13-positive tubules and also the stability of endogenous BLOC-1 subunit, Pallidin, suggesting that Rab22A possibly works with BLOC-1 and BLOC-2 independent of cell types. To understand the regulation among these molecules, we overexpressed Rab22A in BLOC-1-deficient cells and analyzed the cells for BLOC-1-deficient rescue phenotypes such as pigmentation and cargo localization. However, Rab22A could not compensate the BLOC-1 function, suggesting that Rab22A possibly functions upstream of BLOC-1. Our subcellular and membrane associated fractionation studies of homogenates depleted with Rab22A, BLOC-1 and BLOC-2 showed that subunit levels of BLOC-1 and BLOC-2 in the membrane pool were significantly reduced upon Rab22A depletion compared to control cells. However, membrane association of Rab22A in BLOC-1 deficient cells was not affected. Further, our biochemical interaction studies showed that Rab22A interacts physically with BLOC-1 and BLOC-2 subunits as well as with KIF13A. Thus, these studies indicate that Rab22A possibly recruits and interacts with BLOC-1 and BLOC-2 for the generation of REs. We have summarized the study by proposing a model wherein Rab22A localizes to the limiting membrane of endosomes that are positive for KIF13A and then recruits and associates with BLOC-1 and BLOC-2 complexes which subsequently pulled by KIF13A for the generation of RE tubules.

Polioviruses, Coxsackieviruses, and Echoviruses belonging to the Picornaviridae family of positive-stranded, non-enveloped viruses, are highly infectious and associated with a range of illnesses in children from minor febrile illness to severe, potentially fatal conditions (eg, aseptic meningitis, encephalitis, paralysis and myocarditis). The viruses encodes 11 viral proteins along with the transient set of intermediates unique to viral propagation. 3A, one of the non-structural proteins, plays a crucial role in viral replication by anchoring the replication complex to the membrane vesicle and by recruiting essential cellular factors to the site of replication. It is an 89 amino-acid longprotein, and consists of a soluble N-terminal region and a hydrophobicC-terminal region. The soluble region contains two amphipathic alphahelices that form a hairpin, which are flanked by unstructured regions.Since, Enteroviruses have limited coding capacity,viral protein interactions with cellular proteins and lipids are essentialin viral replication, translation, polyprotein processing andpathogenesis. Understanding these interactions is essential inunderstanding the molecular mechanisms associated pathogenesis, andidentifying drug targets. Our studies are aimed at identifying hostfactors interacting with 3A protein and their functional significance invirus replication.We have identified thepotential 3A-interacting cellular candidate proteins using pull-down followed by liquid chromatography associated mass spectrometry. Gene ontology analysis revealed asignificant enrichment in cellular pathways, functions, and proteindomains in comparison with the control. Further studies were focused on Sec12 (guanine nucleotideexchange factor), ACBD3 (acyl-CoA binding domain containing 3) andPhosphatidylinositol 4-kinase beta (PI4KIIIß) interactions with the 3Aprotein, and their significance in viral replication. Sec12 (GEF) initiates the COPII vesicle-mediated ER-to-Golgi membrane trafficking by recruiting and activating the small GTP binding protein Sar1A to the membrane, which further recruits Sec23/24, cargo and Sec13/31 coat proteins to form functional COPII vesicles.We demonstrated that Sec12 and 3A interact directly in the ER through their C-terminal hydrophobic regions in oligomerization independent manner, leading toreduced the level of recruitment of individual COPII components such as Sar1A, Sec24A, and Sec31A to the membranes, thereby inhibiting virus replication. But in infected cells, other viral proteins such as 2B and 2BC likely stabilize the membrane-recruited Sar1A to support the viral replication. The viral proteins, ACBD3, PI4KIIIß interacted and co-localized with the Echovirus 3A protein.Knockdown of Sec12 or PI4KIIIß and expression of 3A or DN-Sar1A inhibited Echovirus replication, unlike proteins which support the COPII vesicle mediated ER-to-Golgi trafficking.Our results collectively indicate Sec12 is a crucial component in the anterograde membrane trafficking and is a novel host factor in Echovirus replication.