Thesis (Ph.D.)--McMaster University, 2005. / Supervisor: Paul Harrison. Includes bibliographical references (leaves 192-207).

As sementes do cacaueiro (Theobroma cacao L.) constituem a única fonte de manteiga de cacau, matéria prima fundamental para as indústrias de chocolates e confeitos, farmacêutica e cosmética. Cerca de 50 % do peso seco das sementes é composto por gordura, caracterizada pelo alto nível de estearato (30-37%), em combinação com palmitato (24-31%) e de oleato (33-39%), conferindo-lhe uma composição triglicerídica única, responsável pelas suas propriedades de fusão, com aplicações específicas e especiais. Apesar dos genes que codificam as enzimas da via metabólica de biossíntese de ácidos graxos e triglicerídeos em plantas serem conhecidos, os mecanismos moleculares pelos quais as plantas controlam a produção de estearato e que diferenciam as plantas acumuladoras de estearato de todas as demais não estão claramente definidos. O objetivo deste trabalho foi analisar a composição de ácidos graxos nos frutos de Theobroma cacao e a expressão temporal de genes relacionados à via metabólica de ácidos graxos e triglicerídeos durante o desenvolvimento de sementes de T. cacao, com ênfase na acumulação de estearato. Em paralelo, foram eleitos os genes referências mais estáveis para os estudos em embriões e diversos tecidos de Theobroma cacao. Empregando-se a técnica de reação quantitativa da amplificação em cadeia de transcritos reversos de RNA (RT-qPCR), foram analisadas a expressão dos genes codificadores da proteína carregadora de acil A, B e C, \'beta\'-cetoacil-ACP sintase II, \'delta\'9estearoil-ACP desaturase A e B, Acil-ACP tioesterase A, acil-ACP tioesterase B, acil-CoA sintetase A e B e da proteína oleosina. Quando se estudou de expressão gênica apenas nos embriões de T. cacao, os três genes mais estáveis foram proteína ribossomal L35, proteína carregadora de acil A e gliceraldeído 3-fosfato desidrogenase. Quando se considerou diversos tecidos de plantas de Theobroma cacao, os melhores genes para a normalização dos valores de expressão foram os codificadores da proteína ribossomal L35, proteína carregadora de acil B e gliceraldeído 3-fosfato desidrogenase. A acumulação de transcritos da \'delta\'9estearoil-ACP desaturase foi relacionada ao aumento do ácido oleico. O aumento na quantidade deste ácido acontece pela ação conjunta da \'delta\'9estearoil-ACP desaturase, e acil-ACP tioesterase A, a qual mostra maiores níveis de transcritos entre 90 e 140 DAP com pico aos 100 DAP. O aumento de ácidos esteárico estaria relacionado com a ação conjunta e com transcrição temporalmente coordenada dos genes das enzimas \'beta\' -cetoacil-ACP sintase II, Acil-ACP tioesterase A e Acil-ACP tioesterase B. Transcritos da enzima \'beta\' -cetoacil-ACP sintase II apresenta pico aos 100 DAP, possivelmente com acúmulo máximo de substratos 18:0-ACP, que poderiam ser hidrolizado preferencialmente pela enzima acil-ACP tioesterase A, ou acil-ACP tioesterase B, O intervalo entre o pico de acúmulo de trasncritos entre \'beta\'-cetoacil-ACP sintase II (100 DAP) e Acil-ACP tioesterase A e \'delta\'9estearoil-ACP desaturase (110 DAP) sugere que poderia ocorrer um acúmulo de estearato resultante da ação dessas enzimas. Esses resultados corroboram o modelo de acumulação de estearato proposto por Silva (2005) / Cacao seeds (Theobroma cacao L.) are unique sources of cocoa butter, fundamental raw material for the chocolate, confectionary, cosmetic and pharmaceutical industries. Around 50% of the seed dry weight represents fat, characterized by the high levels of stearate (30-37%), in combination of palmitate (24-31%) and oleate (33-39%), giving a unique triacylglycerol compostion, responsible for the melting profile for special and specific applications. Despite the fact that genes encoding enzymes of the fatty acid and triglyceride biosynthetic pathway of plants are known, the mechanisms to control the accumulation of high levels of stearate, that differ from other species, are not clearly defined. The objective of this work was to analyse the composition of fatty acids and the expression of genes associated with fatty acid and triglyceride biosynthetic pathway during the development of cacao pods, with emphasis with stearate accumulation. In parallel, the establishment of stable reference genes to investigate gene expression in developing embryos and other cacao tissues were investigated. Using the quantitative amplification of reversed transcripts (RT-qPCR), the expresion of genes coding for the acyl-carrier protein A, B and C; \'beta\'-ketoacyl-ACP sinthase II; \'delta\'9stearoyl-ACP desaturase A and B; Acyl-ACP thioesterase A; Acyl-ACP thioesterase B; Acyl-CoA sintethase A and B; and oleosin. When gene expression was conductd only in developing cacao embryos, the three most stable genes were the ribosomal protein L35, acyl-carrier protein A and glyceraldehide 3-phosphate dehydrogenase. When various tissues were considered, the best reference genes for gene expression normalization were those encoding for the ribosomal protein L35, acyl carrier protein B and glyceraldehide 3-phosphate dehydrogenase. The accumulation of \'delta\'9stearoyl-ACP desaturase transcripts could be associated with the accumulation of oleate, together with the increase of acyl-ACP thioesterase A, with increased relative levels of transcripts between 90 and 140 DAP, peaking at 100 DAP. The increase in stearate might result from the joint activity of the \'delta\'9stearoyl-ACP desaturase and acyl-ACP thioesterase A, which presented higher accumulation of transcripts between 90 and 140 DAP, with peak at 110 DAP. The increase in stearate would associated with the joint and temporal coordinated expression of genes encoding \'beta\'-ketoacyl-ACP synthase II, and Acyl-ACP thioesterase A and B. Transcripts of the enzyme \'beta\'-ketoacyl-ACP synthase II peaked at 100 DAP, possibly with the maximum accumulation of substrates 18:0-ACP, that would be preferentially hydrolzyed by the enzyme acyl-ACP thioesterase A, or acyl-ACP thioesterase B, The gap between the peak in transcript accumulation between \'beta\'-ketoacyl-ACP synthase II (100 DAP) and acyl-ACP thioesterase A and \'delta\'9stearoyl-ACP desaturase (110 DAP) could lead to the accumulation of stearate. These results corroborated the model proposed by Silva (2005)

As sementes do cacaueiro (Theobroma cacao L.) constituem a única fonte de manteiga de cacau, matéria prima fundamental para as indústrias de chocolates e confeitos, farmacêutica e cosmética. Cerca de 50 % do peso seco das sementes é composto por gordura, caracterizada pelo alto nível de estearato (30-37%), em combinação com palmitato (24-31%) e de oleato (33-39%), conferindo-lhe uma composição triglicerídica única, responsável pelas suas propriedades de fusão, com aplicações específicas e especiais. Apesar dos genes que codificam as enzimas da via metabólica de biossíntese de ácidos graxos e triglicerídeos em plantas serem conhecidos, os mecanismos moleculares pelos quais as plantas controlam a produção de estearato e que diferenciam as plantas acumuladoras de estearato de todas as demais não estão claramente definidos. O objetivo deste trabalho foi analisar a composição de ácidos graxos nos frutos de Theobroma cacao e a expressão temporal de genes relacionados à via metabólica de ácidos graxos e triglicerídeos durante o desenvolvimento de sementes de T. cacao, com ênfase na acumulação de estearato. Em paralelo, foram eleitos os genes referências mais estáveis para os estudos em embriões e diversos tecidos de Theobroma cacao. Empregando-se a técnica de reação quantitativa da amplificação em cadeia de transcritos reversos de RNA (RT-qPCR), foram analisadas a expressão dos genes codificadores da proteína carregadora de acil A, B e C, \'beta\'-cetoacil-ACP sintase II, \'delta\'9estearoil-ACP desaturase A e B, Acil-ACP tioesterase A, acil-ACP tioesterase B, acil-CoA sintetase A e B e da proteína oleosina. Quando se estudou de expressão gênica apenas nos embriões de T. cacao, os três genes mais estáveis foram proteína ribossomal L35, proteína carregadora de acil A e gliceraldeído 3-fosfato desidrogenase. Quando se considerou diversos tecidos de plantas de Theobroma cacao, os melhores genes para a normalização dos valores de expressão foram os codificadores da proteína ribossomal L35, proteína carregadora de acil B e gliceraldeído 3-fosfato desidrogenase. A acumulação de transcritos da \'delta\'9estearoil-ACP desaturase foi relacionada ao aumento do ácido oleico. O aumento na quantidade deste ácido acontece pela ação conjunta da \'delta\'9estearoil-ACP desaturase, e acil-ACP tioesterase A, a qual mostra maiores níveis de transcritos entre 90 e 140 DAP com pico aos 100 DAP. O aumento de ácidos esteárico estaria relacionado com a ação conjunta e com transcrição temporalmente coordenada dos genes das enzimas \'beta\' -cetoacil-ACP sintase II, Acil-ACP tioesterase A e Acil-ACP tioesterase B. Transcritos da enzima \'beta\' -cetoacil-ACP sintase II apresenta pico aos 100 DAP, possivelmente com acúmulo máximo de substratos 18:0-ACP, que poderiam ser hidrolizado preferencialmente pela enzima acil-ACP tioesterase A, ou acil-ACP tioesterase B, O intervalo entre o pico de acúmulo de trasncritos entre \'beta\'-cetoacil-ACP sintase II (100 DAP) e Acil-ACP tioesterase A e \'delta\'9estearoil-ACP desaturase (110 DAP) sugere que poderia ocorrer um acúmulo de estearato resultante da ação dessas enzimas. Esses resultados corroboram o modelo de acumulação de estearato proposto por Silva (2005) / Cacao seeds (Theobroma cacao L.) are unique sources of cocoa butter, fundamental raw material for the chocolate, confectionary, cosmetic and pharmaceutical industries. Around 50% of the seed dry weight represents fat, characterized by the high levels of stearate (30-37%), in combination of palmitate (24-31%) and oleate (33-39%), giving a unique triacylglycerol compostion, responsible for the melting profile for special and specific applications. Despite the fact that genes encoding enzymes of the fatty acid and triglyceride biosynthetic pathway of plants are known, the mechanisms to control the accumulation of high levels of stearate, that differ from other species, are not clearly defined. The objective of this work was to analyse the composition of fatty acids and the expression of genes associated with fatty acid and triglyceride biosynthetic pathway during the development of cacao pods, with emphasis with stearate accumulation. In parallel, the establishment of stable reference genes to investigate gene expression in developing embryos and other cacao tissues were investigated. Using the quantitative amplification of reversed transcripts (RT-qPCR), the expresion of genes coding for the acyl-carrier protein A, B and C; \'beta\'-ketoacyl-ACP sinthase II; \'delta\'9stearoyl-ACP desaturase A and B; Acyl-ACP thioesterase A; Acyl-ACP thioesterase B; Acyl-CoA sintethase A and B; and oleosin. When gene expression was conductd only in developing cacao embryos, the three most stable genes were the ribosomal protein L35, acyl-carrier protein A and glyceraldehide 3-phosphate dehydrogenase. When various tissues were considered, the best reference genes for gene expression normalization were those encoding for the ribosomal protein L35, acyl carrier protein B and glyceraldehide 3-phosphate dehydrogenase. The accumulation of \'delta\'9stearoyl-ACP desaturase transcripts could be associated with the accumulation of oleate, together with the increase of acyl-ACP thioesterase A, with increased relative levels of transcripts between 90 and 140 DAP, peaking at 100 DAP. The increase in stearate might result from the joint activity of the \'delta\'9stearoyl-ACP desaturase and acyl-ACP thioesterase A, which presented higher accumulation of transcripts between 90 and 140 DAP, with peak at 110 DAP. The increase in stearate would associated with the joint and temporal coordinated expression of genes encoding \'beta\'-ketoacyl-ACP synthase II, and Acyl-ACP thioesterase A and B. Transcripts of the enzyme \'beta\'-ketoacyl-ACP synthase II peaked at 100 DAP, possibly with the maximum accumulation of substrates 18:0-ACP, that would be preferentially hydrolzyed by the enzyme acyl-ACP thioesterase A, or acyl-ACP thioesterase B, The gap between the peak in transcript accumulation between \'beta\'-ketoacyl-ACP synthase II (100 DAP) and acyl-ACP thioesterase A and \'delta\'9stearoyl-ACP desaturase (110 DAP) could lead to the accumulation of stearate. These results corroborated the model proposed by Silva (2005)

Ramnolipídeos (RLs) e polihidroxialcanoatos (PHAs) produzidos por Pseudomonas aeruginosa são compostos biodegradáveis e que podem ser obtidos a partir de matérias-primas renováveis. Com o objetivo de elucidar aspectos metabólicos e regulatórios da produção de RLs e PHAs, mutantes de P. aeruginosa LFM634 afetados na síntese desses compostos foram obtidos utilizando um transposon (ISlacZ/hah). Dentre 61 mutantes caracterizados, foram detectados vários super-produtores de RLs e/ou PHAs, bem como alguns nos quais nenhum RL foi detectado. Dois mutantes (p09-13 e p12-39) apresentaram capacidade reduzida de inserir ramnose em RLs e de direcionar intermediários da biossíntese de ácidos graxos para a síntese de RLs ou PHAs. O mutante p09-13 está afetado no gene crc, sugerindo um importante papel deste regulador global no processo de síntese de RLs e PHAs. / Rhamnolipids (RLs) and polyhydroxyalkanoates (PHAs) produced by Pseudomonas aeruginosa are biodegradable compounds and can be obtained from renewable raw materials. Aiming to elucidate metabolic and regulatory issues involved in the RLs and PHAs production, P. aeruginosa LFM634 mutants affected in their biosynthesis were obtained using a transposon (ISlacZ/hah). Out of 61mutants characterized, it was detected several overproducing RLs and/or PHA, as well as some in which no RLs was detected. Two mutants (p09-13 and p12-39) presented reduced capability of inserting rhamnose in RLs and of channeling intermediates from fatty acid biosynthesis to the synthesis of RLs and PHAs. The mutant p09-13 is affected on crc gene, suggesting an important role of this global regulator on the process of RLs and PHA synthesis.

Ramnolipídeos (RLs) e polihidroxialcanoatos (PHAs) produzidos por Pseudomonas aeruginosa são compostos biodegradáveis e que podem ser obtidos a partir de matérias-primas renováveis. Com o objetivo de elucidar aspectos metabólicos e regulatórios da produção de RLs e PHAs, mutantes de P. aeruginosa LFM634 afetados na síntese desses compostos foram obtidos utilizando um transposon (ISlacZ/hah). Dentre 61 mutantes caracterizados, foram detectados vários super-produtores de RLs e/ou PHAs, bem como alguns nos quais nenhum RL foi detectado. Dois mutantes (p09-13 e p12-39) apresentaram capacidade reduzida de inserir ramnose em RLs e de direcionar intermediários da biossíntese de ácidos graxos para a síntese de RLs ou PHAs. O mutante p09-13 está afetado no gene crc, sugerindo um importante papel deste regulador global no processo de síntese de RLs e PHAs. / Rhamnolipids (RLs) and polyhydroxyalkanoates (PHAs) produced by Pseudomonas aeruginosa are biodegradable compounds and can be obtained from renewable raw materials. Aiming to elucidate metabolic and regulatory issues involved in the RLs and PHAs production, P. aeruginosa LFM634 mutants affected in their biosynthesis were obtained using a transposon (ISlacZ/hah). Out of 61mutants characterized, it was detected several overproducing RLs and/or PHA, as well as some in which no RLs was detected. Two mutants (p09-13 and p12-39) presented reduced capability of inserting rhamnose in RLs and of channeling intermediates from fatty acid biosynthesis to the synthesis of RLs and PHAs. The mutant p09-13 is affected on crc gene, suggesting an important role of this global regulator on the process of RLs and PHA synthesis.

This thesis entitled ‘ Unusual Acylation Properties of Type II Fatty Acid Biosynthesis Acyl Carrier Proteins’ describes the discovery of self-acylation and malonyl transferase activity in acyl carrier proteins involved in type II fatty acid biosynthesis and assigns a physiological role to these processes inside the cellular milieu. Acyl carrier protein (ACP) is one of the most abundant proteins present inside the cell and almost 4% enzymes require it as a cofactor. Acyl carrier proteins can exist either as discrete proteins or as domains of large functional proteins. They function in a variety of synthases as central molecules to which growing acyl intermediates and nascent product molecules are covalently tethered during the elongation and modification steps required to produce the final product. A prototypical bacterial ACP is composed of 70-80 amino acids and is generally expressed in the apo form. It is post-translationally modified to active holo form by the addition of 4'-phosphopantetheine moiety to an absolutely conserved serine residue in a reaction catalyzed by holo-ACP synthase or 4'-phosphopantetheine transferase. Chapter 1 surveys literature related to carrier proteins inside the cell and describes the thesis objective. It also presents an overview of the acyl carrier proteins and their involvement in various metabolic pathways inside the cell. The chapter details the structural organization of acyl carrier proteins from various sources revealing the conservation in their structure and also details the molecular basis of interaction of ACP with other enzymes inside the cell. The discovery of unusual self-acylation property in acyl carrier proteins involved in polyketide biosynthesis and its absence in acyl carrier proteins involved in fatty acid biosynthesis prompted me to investigate the reasons for this selective behavior. Discovery of self-acylation property in acyl carrier proteins Plasmodium falciparum and chloroplast targeted Brassica napus acyl carrier proteins involved in type II fatty acid biosynthesis and the mechanism of this reaction forms the basis of Chapter 2. In this chapter it has been shown that self-acylation property is intrinsic to a given acyl carrier protein and is not dependent on the pathway in which it is involved. Based on primary sequence analysis and site directed mutagenesis studies presence of an aspartate/glutamate has been identified to be critical for the self-acylation event. Furthermore, it has also been shown that the self-acylation event in type II fatty acid biosynthesis acyl carrier proteins is highly specific in nature employing only dicarboxylic acid –CoAs as substrates unlike the polyketide biosynthesis acyl carrier proteins which utilize both dicarboxylic acid and β-keto acid thiol ester -CoAs as substrates. The detailed kinetics of these reactions has also been worked out. Combining all the results a plausible mechanism for the self-acylation reaction has been proposed. Chapter 3 describes the discovery of a novel malonyl transferase behavior in acyl carrier proteins involved in type II fatty acid biosynthesis. Malonyl transferase property in ACPs of type II FAS from a bacterium (Escherichia coli), a plant (Brassica napus) and a parasitic protozoon (Plasmodium falciparum) were investigated to present a unifying paradigm for the mechanism of malonyl transferase behavior in ACPs. Identification of malonyl transferase property in Plasmodium falciparum ACP and Escherichia coli ACP (EcACP) and the absence of this property in Brassica napus ACP has been described in this chapter. Detailed investigations demonstrated that presence of an arginine or a lysine in loop II and an arginine or glutamine at the start of helix III as the residues that are critical for the transferase activity. In order to assign a physiologic function to these unusual acylation properties, fabD(Ts) mutant strain of Escherichia coli was utilized for heterologous complementation by the various wild type and mutant ACPs that are able to catalyze either or both of the activities. Growth of the mutant strain at non-permissive temperature, when complemented with ACPs catalyzing both the reactions confirmed that these properties have a physiologic relevance. Extensive mutagenesis experiments in conjunction with complementation studies allowed me to propose a plausible mechanism on how the self-malonylation and malonyl transferase properties operate in tandem. Chapter 4 describes the thermodynamic characterization of self-acylation process using Isothermal Titration Calorimetry. Isothermal Titration Calorimetric studies on the binding of malonyl, succinyl, butyryl and methylmalonyl –CoA to Plasmodium falciparum and Brassica napus acyl carrier proteins were performed to investigate the role of thermodynamic parameters in the specificity of self-acylation reaction. Calculation of the parameters showed that the thermodynamics does not control the self-acylation reaction. The evolution of self-acylation property in various acyl carrier proteins and its possible significance in the evolution of various metabolic events is described in Chapter 5. Extensive bioinformatics search was performed and phylogenetic analysis on acyl carrier proteins from 60 different taxa was done using the MEGA4 program. Analysis showed that this property was first found in cyanobacterium. Later, during the course of evolution this property was lost in most acyl carrier proteins, and was retained either in acyl carrier proteins that are targeted to organelles of cyanobaterial orgin viz. apicoplast in apicomplexans and chlorplasts in plants or in acyl carrier proteins involved in secondary metabolic events such as polyketide biosynthesis. Chapter 6 summarizes the findings of the thesis. Acyl carrier protein from Plasmodium falciparum, Brassica napus and Escherichia coli were characterized for their self-acylation and malonyl transferase properties and a combined mechanism for these two properties is proposed. The work done also provides an in vivo rationale to these in vitro processes. Furthermore, the evolutionary significance of the self-acylation behavior is also discussed in the thesis. The thesis also probes into the thermodynamics of the self-acylation reaction in Plasmodium falciparum and Brassica napus acyl carrier proteins. Thus, the thesis adds a new dimension to the much unexplored ACP biology and paves the way to study in vivo roles of these processes in detail. Appendix I describes the Isothermal Titration calorimetric characterization of binding of various acyl-PO4 molecules to Escherichia coli PlsX (Acyl-phosphate acyltransferase). PlsX, the first enzyme of phosphatidic acid biosynthesis pathway catalyzes the conversion of acyl-ACP into acyl-PO4, which is further used by other enzymes leading to the formation of phosphatidic acid. ITC results presented in this section show that longer chain length acyl-PO4 molecules show better binding to PlsX, as compared to the smaller ones demonstrating that long chain acyl molecules serve as better substrates for phosphatidic acid synthesis.

Lipids are stored in a cell for providing energy. The main advantages of storing lipids over carbohydrates like glycogen is that, lipids yield more energy after oxidation because they represent the highly reduced form of carbon, needs less space and water for storage. Conservation of chemical energy in the form of biologically inert form is by storing molecules like triacylglycerol (TAG) and Steryl esters (SE). Triacylglycerol is the major storage form of energy in all eukaryotic cells. During the periods of nutritional excess and nutritional stress, all organisms like bacteria, yeast, animals, and plants can able to do the critical function of synthesizing the triacylglycerol. TAG is an energy store and a repository of essential and non-essential fatty acids and precursors for phospholipid biosynthesis. TAG synthesis mainly takes place in endoplasmic reticulum in mammals and in plants, it takes place in plastid and mitochondria. Triacylglycerol synthesis discovered by Kennedy starts with glycerol 3- phosphate. Glycerol 3-phosphate gets acylate to form lysophosphatic acid (LPA), which in turn acylate to form phosphatic acid (PA) and the reactions are catalyzed by glycerol 3-phosphate acyltransferase (GPAT) and LPA acyltransferase (LPAT) respectively. PA undergoes phosphorylation by PA phosphatase enzyme to give diacylglycerol (DAG). Further acylation of DAG gives rise to TAG and the reaction is catalyzed by diacylglycerol acyltransferase (DGAT). There are several DGAT classes were identified they are DGAT1, DGAT2, PDAT and bifunctional TAG/wax ester synthase. However all the enzymes involved in Kennedy TAG biosynthetic pathway as well as the enzymes of all different DGAT classes are membrane bound enzymes. Through our studies an another DGAT class that is soluble and cytosolic DGAT was first identified in peanut and also in yeast, Rhodotorula glutinis in which a soluble cytosolic complex itself has been identified. The biosynthesis of triacylglycerol (TAG) occurs in the microsomal membranes of eukaryotes. Here, we report the identification and functional characterization of diacylglycerol acyltransferase (DGAT), a member of the 10 S cytosolic TAG biosynthetic complex (TBC) in R. glutinis. Both a full-length and an N-terminally truncated cDNA clone of a single gene were isolated from R. glutinis. The DGAT activity of the protein encoded by RgDGAT was confirmed in vivo by the heterologous expression of cDNA in a Saccharomyces cerevisiae quadruple mutant (H1246) that is defective in TAG synthesis. RgDGAT overexpression in yeast was found to be capable of acylating diacylglycerol (DAG) in an acyl-CoA-dependent manner. Quadruple mutant yeast cells exhibit growth defects in the presence of oleic acid, but wild-type yeast cells do not. In an in vivo fatty acid supplementation experiment, RgDGAT expression rescued quadruple mutant growth in an oleate-containing medium. We describe a soluble acyl-CoA-dependent DAG acyltransferase from R. glutinis that belongs to the DGAT3 class of enzymes. The study highlights the importance of alternate TAG biosynthetic pathway in oleaginous yeasts. A key step in the triacylglycerol (TAG) biosynthetic pathway is the final acylation of diacylglycerol (DAG) by DAG acyltransferase. In silico analysis has revealed that the DCR (defective in cuticular ridges) (At5g23940) gene has a typical HX4D acyltransferase motif at the N-terminal end and a lipid binding motif VX2GF at the middle of the sequence. To understand the biochemical function, the gene was overexpressed in Escherichia coli, and the purified recombinant protein was found to acylate DAG specifically in an acyl-CoA-dependent manner. Overexpression of At5g23940 in a Saccharomyces cerevisiae quadruple mutant deficient in DAG acyltransferases resulted in TAG accumulation. At5g23940 rescued the growth of this quadruple mutant in the oleate-containing medium, whereas empty vector control did not. Lipid particles were localized in the cytosol of At5g23940-transformed quadruple mutant cells, as observed by oil red O staining. There was an incorporation of 16-hydroxyhexadecanoic acid into TAG in At5g23940-transformed cells of quadruple mutant. Here we report a soluble acyl-CoA-dependent DAG acyltransferase from Arabidopsis thaliana. Taken together, these data suggest that a broad specific DAG acyltransferase may be involved in the cutin as well as in the TAG biosynthesis by supplying hydroxy fatty acid.

Malaria, caused by the parasite Plasmodium, continues to exact high global morbidity and mortality rate next only to tuberculosis. It causes 300-500 million clinical infections out of which more than a million people succumb to death annually. Worst affected are the children below 5 years of age in sub-Saharan Africa. Plasmodium is a protozoan parasite classified under the phylum Apicomplexa that also includes parasites such as Toxoplasma, Lankestrella, Eimeria and Cryptosporidium. Of the four species of Plasmodium affecting man viz., P. falciparum, P. vivax, P. ovale and P. malariae, Plasmodium falciparum is the deadliest as it causes cerebral malaria. The situation has worsened recently with the emergence of drug resistance in the parasite. Therefore, deciphering new pathways in the parasite for developing lead antimalarial compounds is the need of the hour. The discovery of the type II fatty acid biosynthesis pathway in Plasmodium falciparum has opened up new avenues for the design of new antimalarials as this pathway is different from the one in human hosts. Although many biochemical pathways such as the purine, pyrimidine and carbohydrate metabolic pathways, and the phospholipid, folate and heme biosynthetic pathways operate in the malaria parasite and are being investigated for their amenability as antimalarial therapeutic targets, no antimalarial of commercial use based on the direct intervention of these biochemical pathways has emerged so far. This is due to the fact that the structure and function of the targets of these drugs overlaps with that of the human host. A description of the parasite, its metabolic pathways, efforts to use these pathways for antimalarial drug discovery, inhibitors targeting these pathways, introduction to fatty acid biosynthesis pathway, discovery of type II fatty acid biosynthesis pathway in Plasmodium falciparum and prospects of developing lead compounds towards antimalarial drug discovery is given in Chapter 1 of the thesis. In the exploration of newly discovered type II fatty acid biosynthesis pathway of P. falciparum as a drug target for antimalarial drug discovery, one of the enzymes; β-hydroxyacyl- acyl carrier protein dehydratase (PfFabZ) was cloned and being characterized in the lab. The atomic structure of PfFabZ was not known till that point of time. Chapter 2 describes the homology modeled structure of PfFabZ and docking of the discovered inhibitors with this structure to provide a rationale for their inhibitory activity. Despite low sequence identity of ~ 21% with the closest available atomic structure then, E. coli FabA, a good model of PfFabZ could be built. A comparison of the modeled structure with recently determined crystal structure of PfFabZ is provided and design of new potential inhibitors is described. This study provides insights to further improve the inhibition of this enzyme. Enoyl acyl carrier protein reductase (ENR) is the most important enzyme in the type II fatty acid biosynthesis pathway. It has been proved as an important target for antibacterial as well as antimalarial drug discovery. The most effective drug against tuberculosis – Isoniazid targets this enzyme in M. tuberculosis. The well known antibacterial compound – Triclosan, a diphenyl ether, also targets this enzyme in P. falciparum. I designed a number of novel diphenyl ether compounds. Some of these compounds could be synthesized in the laboratory. Chapter 3 describes the design, docking studies and inhibitory activity of these novel diphenyl ether compounds against PfENR and E. coli ENR. Some of these compounds inhibit PfENR in nanomolar concentrations and EcENR in low micromolar concentrations, and many of them inhibit the growth of parasites in culture also. The structure activity relationship of these compounds is discussed that provides important insights into the activity of this class of compounds which is a step towards developing this class of compounds into an antimalarial and antibacterial candidate drugs. Components of the green tea extract and polyphenols are well known for their medicinal properties since ages. Recently they have been shown to inhibit components of the bacterial fatty acid biosynthesis pathway. Some selected tea catechins and polyphenols were tested in the laboratory for their inhibitory activity against PfENR. I conducted docking studies to find their probable binding sites in PfENR. On kinetic analysis of their inhibition, these compounds were found to be competitive with respect to the cofactor NADH. This has an implication that they could potentiate inhibition of PfENR by Triclosan in a fashion similar to that of NADH. As a model case, one of the tea catechins; EGCG ((-) Epigalocatechin gallate) was tested for this property. Indeed, in the presence of EGCG, the inhibition of PfENR improved from nanomolar to picomolar concentration of Triclosan.conducted molecular modeling studies and propose a model for the formation of a ternary complex consisting of EGCG, Triclosan and PfENR. Docking studies of these inhibitors and a model for the ternary complex is described in Chapter 4. Docking simulations show that these compounds indeed occupy NADH binding site. This study provides insights for further improvements in the usage of diphenyl ethers in conjugation or combination with tea catechins as possible antimalarial therapeutics. In search for new lead compounds against deadly diseases, in silico virtual screening and high throughput screening strategies are being adopted worldwide. While virtual screening needs a large amount of computation time and hardware, high throughput screening proves to be quite expensive. I adopted an intermediate approach, a combination of both these strategies and discovered compounds with a 2-thioxothiazolidin-4-one core moiety, commonly known as rhodanines as a novel class of inhibitors of PfENR with antimalarial properties. Chapter 5 describes the discovery of this class of compounds as inhibitors of PfENR. A small but diverse set of 382 compounds from a library of ~2,00,000 compounds was chosen for high throughput screening. The best compound gave an IC50 of 6.0 µM with many more in the higher micromolar range. The compound library was searched again for the compounds similar in structure with this best compound, virtual screening was conducted and 32 new compounds with better binding energies compared to the first lead and reasonable binding modes were tested. As a result, a new compound with an IC50 of 240 nM was discovered. Many more compounds gave IC50 values in 3-15 µM range. The best inhibitor was tested in red blood cell cultures of Plasmodium, it was found to inhibit the growth of the malaria parasite at an IC50 value of 0.75 µM. This study provides a new scaffold and lead compounds for further exploration towards antimalarial drug discovery. The summary of the results and conclusions of studies described in various chapters is given in Chapter 6. This chapter concludes the work described in the thesis. Cloning, over-expression and purification of PanD from M. tuberculosis, FabA and FabZ from E. coli are described in the Appendix.