Structural and Related Studies on Mycobacterial Lectins
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This thesis is concerned with the first ever X-ray crystallographic and complimentary solution studies on mycobacterial lectins. Lectins, described as multivalent carbohydrate binding proteins of non-immune origin, are found in all kingdoms of life. As explained in the introductory chapter, those from plants and animals are the best characterized in terms of structure and function. Although not that extensive, important studies have been carried out on viral, fungal and parasite lectins as well. Bacterial lectins studied so far can be classified in to fimbrial, surface and secretory (or toxic). Applications of lectins include blood typing, cell separation and purification of glycoconjugates, mitogenic stimulation of lymphocytes, mapping of neuronal pathways and drug targeting and delivery. The work reported in the thesis lies at the intersection of two major long range programs in this laboratory, one on lectins and the other on mycobacterial proteins. Three putative lectins Rv1419 and Rv2813 from M. tuberculosis and MSMEG_3662 from M. smegmatis were chosen for exploratory studies on the basis of preliminary genomic searches. Exploratory studies on Rv1419, Rv2813 and MSMEG_3662 are described in the second chapter. MSMEG_3662 contains two domains, a LysM domain and a lectin domain (MSL) connected by a long polypeptide chain. The two M. tuberculosis proteins, full length MSMEG_3662 and MSL were cloned, expressed, purified and characterized. Rv2813 did not show any appreciable agglutination activity. It showed ATPase activity. Clearly the protein was not a lectin. Rv1419, full length MSMEG_3662 and MSL exhibited lectin characteristics. Among them, Rv1419 and MSL could be crystallized. Preliminary X-ray diffraction studies on them were carried out. Rv1419 could be successfully expressed only once. However, that was enough for the determination of crystal structure and the glycan array analysis of the lectin (Chapter 3). The monomeric lectin has a β-trefoil fold. It has high affinity for LacNAc and its Neu5Ac derivatives. Modeling studies using complexes of homologous structures, led to the identification of two carbohydrate binding sites on the lectins. Sequence comparisons of Rv1419 with homologous proteins with known structures and phylogenetic analysis involving them provide interesting insights into the relationship among trefoil lectins from different sources. X-ray crystal structure analysis of MSL and its complexes with mannose and methyl-α-mannose, the first comprehensive effort of its kind on a mycobacterial lectin, reveals a structure very similar to β-prism II fold lectins from plant sources, but with extensive unprecedented domain swapping in dimer formation (Chapter 4). The two subunits in a dimer often show small differences in structure, but the two domains, not always related by 2-fold symmetry, have the same structure. Each domain carries three sugar-binding sites, similar to those in plant lectins, one on each Greek key motif. The occurrence of β-prism II fold lectins in bacteria, with characteristics similar to those from plants, indicates that this family of lectins is of ancient origin and had evolved into a mature system before bacteria and plants diverged. In plants, the number of binding sites per domain varies between one and three, whereas the number is two in the recently reported lectin domains from Pseudomonas putida and Pseudomonas aeruginosa. An analysis of the sequences of the lectins and the lectin domains shows that the level of sequence similarity among the three Greek keys in each domain has a correlation with the number of binding sites in it. Furthermore, sequence conservation among the lectins from different species is the highest for that Greek key which carries a binding site in all of them. Thus, it would appear that carbohydrate binding influences the course of the evolution of the lectin. LysM domains have been recognized in bacteria and eukaryotes as carbohydrate-binding protein modules, but the mechanism of their binding to chitooligosaccharides is underexplored. Binding of a full length MSMEG_3662 containing LysM and lectin (MSL) domains to chitooligosaccharides has been studied using isothermal titration calorimetry and fluorescence titration (Chapter 5). This investigation demonstrates the presence of two binding sites of non-identical affinities per dimeric MSL-LysM molecule. Affinity of the molecule for chitooligosaccharides correlates with the length of the carbohydrate chain. Its binding to chitooligosaccharides is characterized by negative cooperativity in the interactions of the two domains. Apparently, the flexibility of the long linker that connects the LysM and MSL domains plays a facilitating role in this recognition. The LysM domain in MSL-LysM, like other bacterial domains but unlike plant LysM domains, recognizes equally well peptidoglycan fragments as well as chitin polymers. Interestingly, in the present case two LysM domains are enough for binding to peptidoglycan in contrast to the three reportedly required by the LysM domains of Bacillus subtilis and Lactococcus lactis. Also, the affinity of MSL-LysM for chitooligosaccharides is higher than that of LysM-chitooligosaccharide interactions reported so far. A part of the work presented in this thesis has been reported in the following publications: • Patra D, Mishra P, Surolia A, Vijayan M. 2014. Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis. Glycobiology, 24:956-965. • Patra D, Sharma A, Chandran D, Vijayan M. 2011. Cloning, expression, purification, crystallization and preliminary X-ray studies of the mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis. Acta Crystallogr Sect F Struct Biol Cryst Commun, 67:596-599. • Patra D, Srikalaivani R, Misra A, Singh DD, Selvaraj M, Vijayan M. 2010. Cloning, expression, purification, crystallization and preliminary X-ray studies of a secreted lectin (Rv1419) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun, 66:1662-1665.
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