Kartikeya Tiwari

Understanding pyrimidine and aspartate metabolism in the growth and infectivity of L. donovani A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY By Kartikeya Tiwari Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati Guwahati-781039, Assam, India July 2017 Understanding pyrimidine and aspartate metabolism in the growth and infectivity of L. donovani A Thesis Submitted By Kartikeya Tiwari (Roll No. 11610612) In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati Guwahati-781039, Assam, India July 2017 TH-1739_11610612 Dedicated to My ever amazing parents, inspiring mentors and curious researchers i TH-1739_11610612 INDIAN INSTITUTE OF TECHNOLOGY GUWAHATI DEPARTMENT OF BIOSCIENCES AND BIOENGINEERING STATEMENT I hereby declare that the matter embodied in this thesis titled “Understanding pyrimidine and aspartate metabolism in the growth and infectivity of L. donovani” is the result of investigations carried out by me in the Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India under the supervision of Prof. Vikash Kumar Dubey. In keeping with the general practice of reporting scientific observations, due acknowledgements have been made wherever the work of other investigators are referred. Further the data in the thesis are collected by me. I certify that there is no fabrication or manipulation of data in the thesis. Date: July, 2017 Kartikeya Tiwari (11610612) ii TH-1739_11610612 INDIAN INSTITUTE OF TECHNOLOGY GUWAHATI DEPARTMENT OF BIOSCIENCES AND BIOENGINEERING CERTIFICATE It is certified that the work described in this thesis “Understanding pyrimidine and aspartate metabolism in the growth and infectivity of L. donovani’’ by Mr. Kartikeya Tiwari (Roll No. 11610612), submitted to Indian Institute of Technology Guwahati, India for the award of degree of Doctor of Philosophy, is an authentic record of results obtained from the research work carried out under my supervision at the Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India and this work has not been submitted elsewhere for a degree. Prof. Vikash Kumar Dubey (Thesis Supervisor) iii TH-1739_11610612 Acknowledgement I feel delighted to present the dissertation on “Understanding pyrimidine and aspartate metabolism in the growth and infectivity of L. donovani”. This thesis would not have seen the light of day without the constant support of my thesis advisor Prof. Vikash Kumar Dubey. His constant motivation and supervision has led me to travel the treacherous path of research and to reach this version of work. Calling him just a thesis advisor would not do justice to the role he has played during my PhD. He was more like a guardian too me whose caring nature has made this journey a special one during my fruitful years spent at this prestigious institute. His disciplined nature, sincerity, hard work and an ambition of academic excellence has steered me to reach where I am today. He’s been an overall inspiration to me in my all academic pursuits. I would also like to extend my heartfelt thanks to my Doctoral committee members. Prof. Kannan Pakshirajan (Chairman, Doctoral committee), Dr. Shankar Prasad Kanaujia and Dr. Tamal Banerjee. Their constant support and constructive criticism that has helped me to progress in my research work. They have always motivated me to prove my mettle. I would also thank present Head of Department Prof. Kannan Pakshirajan and past HoD’s Prof. VV Dasu and Prof. Arun Goyal, under whose able administration I was able to carry out my research work in a collegial environment. Central Instrumentation Facility of IIT Guwahati is also acknowledged. Also big heartfelt thanks goes to the current lab members Dr. Jay Prakash, Dr. Sunita Yadav, Shyamali, Adarsh, Kamalesh, Gundappa, Jiban, Buddhadeb, Chayanika, Aamen and Hena. Also past lab members Dr. Sushant Kumar, Dr. Mousumi Das, Dr. Shalini Singh, Dr. Ruchika Bhardwaj, Dr. Ritesh Kumar, Arunima, Vidyadhar, Ashish, Ankur, Ekta, Sona, Prachi, Pratyajit, Sudipta, Bijoy, Dr. Suresh Kumar and Amartya. The lab has always been a fun filled experience; every one of them has made my stay in the campus a memorable one, it was another home away from home. Each and every part of this thesis bears the constant and endless efforts of all lab members, their intense discussions, and constructive criticisms have helped me to stretch my capabilities. The late lab nightouts, tea at banimandir, snacks at faculty gate and endless gossips has what made this a cherishable journey. iv TH-1739_11610612 Also mentionable are my friends Dr. Ganesh Thapa, Nandkishor, Suman and Nitin for making me believe in me. The serene and charming campus of IIT Guwahati has provided a perfect environment to think and innovate. And last but not the least my parents. I always feel short of words to describe what they mean to me. They are my guiding light. Their illuminated presence has always motivated to do something special. Many thanks to them for their unwavering support in me. For instilling a fighters spirit in me. For being with my side in all times. Whatever good have been done and whatever good is too be done from my side will always be a reflection of my parents and peers. As always this work is also not free from errors. I hope peers will forgive me for this. This is what I was able to do with my limited capacities. Finally I seek blessings from my parents and peers and dedicate this work to them. Kartikeya Tiwari July, 2017 v TH-1739_11610612 Abbreviations AnsA : L-cytoplasmic asparaginase (Type I) AnsB : L-asparaginase like protein (Type II) BLAST : Basic Local Alignment Search Tool BSA : Bovine Serum Albumin CL : Cutaneous Leishmaniasis CA-asp : N-Carbamoyl-L-Aspartate DHO : Dihydroorotate DHOase : Dihydroorotase DNA : Deoxyribonucleic Acid EDTA : Ethylene Diamine Tetra Acetic Acid FACS : Fluorescence Activated Cell Sorting FBS : Fetal Bovine Serum IPTG : Isopropyl β-D-1-thiogalactopyranoside LdDHOase : Dihydroorotase of Leishmania donovani MCL : Mucocutaneous Leishmaniasis mRNA : Messenger Ribonucleic Acid [(3-(4,5-Dimethylthiazol-2-yl)-2,5- MTT : Diphenyltetrazolium Bromide)] NaCl : Sodium chloride NCBI : National Center for Biotechnology Information PBS : Phosphate Buffered Saline PCR : Polymerase Chain Reaction PI : Propidium iodide PKDL : Post Kala Azar Dermal Leishmaniasis RNA : Ribonucleic Acid SDS : Sodium Dodecyl Sulphate Sodium Dodecyl Sulfate Polyacrylamide Gel SDS-PAGE : Electrophoresis vi TH-1739_11610612 List of Figures Figure Number Figure Name Figure 1.1 Life cycle of Leishmania donovani Figure 1.2 Extracellular vesicles of Leishmania donovani Figure 1.3 Vaccines for visceral leishmaniasis Figure 1.4 Regulation of de novo pyrimidine biosynthesis Figure 1.5 De novo pyrimidine biosynthesis pathway in Leishmania donovani Figure 1.6 Comparison of de novo pyrimidine pathway in mammals and L. donovani Figure 1.7 An outline of the work presented Figure 2.1 Schematic for cloning and expression of L. donovani dihydroorotase Figure 2.2 Cloning of dihydroorotase in pET 28a expression vector Figure 2.3 Expression and purification of L. donovani dihydroorotase Figure 2.4 Size exclusion chromatography of L. donovani dihydoorotase Figure 2.5 Kinetic characterization of L. donovani dihydroorotase Figure 2.6 pH optima studies on L. donovani dihydroorotase Figure 3.1 Schematic representing the workflow for the in silico studies done on L. donovani dihydroorotase Figure 3.2 Multiple sequence alignment of Homo sapiens and L. donovani dihydroorotase Figure 3.3 Active site differences between Homo sapiens and L. donovani dihydroorotase Figure 3.4 Multiple sequence alignment of L. donovani dihydroorotase Figure 3.5 L. donovani dihydroorotase modeled structure Figure 3.6 Ramachandran plot for L. donovani dihydroorotase Figure 3.7 In silico studies on L. donovani dihydroorotase vii TH-1739_11610612 Figure 4.1 Inhibition studies on L. donovani dihydroorotase Figure 4.2 Inhibition studies on L. donovani promastigotes Figure 4.3 Expression analysis of salvage and de novo pyrimidine biosynthesis pathway genes Figure 4.4 DNA content analysis of L. donovani in kaempferol and zebularine treated cells Figure 5.1 Cello v 2.5 based predictions for the subcellular localization of L. donovani cytoplasmic asparaginase like protein (right) and asparaginase like protein (left) Figure 5.2 Cloning of L. donovani asparaginase variants in pGL GFP vector Figure 5.3 Subcellular localization of L. donovani cytoplasmic asparaginase like protein (LDBPK_150440) Figure 5.4 Subcellular localization of L. donovani asparaginase like protein (LDBPK_364650) Figure 6.1 Summary of the thesis work viii TH-1739_11610612 List of Tables Table number Table Name Table 2.1 Kinetic parameters of Leishmania donovani dihydroorootase (LdDHOase) Table 3.1 Structure and binding energies of compounds docked with modeled LdDHOase Table 4.1 Primers used for qRT-PCR ix TH-1739_11610612 Contents Page No. CHAPTER I – Leishmania donovani: Biology in the context of pyrimidine and 1-46 aspartate metabolism 1.1 Introduction 2 1.2 Leishmaniasis: Historical perspective 2 1.3 Types of Leishmaniasis 3 1.4 Life cycle of Leishmania parasite 4 1.4.1 Flagellated Promastigotes in the sandfly 4 1.4.2 Amastigotes in the mammalian host 7 1.5 Evasion of host immune response 10 1.6 Extracellular vesicles of Leishmania 11 1.7 Control

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