Controlling the substrate specificity of α-isopropylmalate synthase and related enzymes
Degree GrantorUniversity of Canterbury
Degree NameDoctor of Philosophy
The enzyme α-isopropylmalate synthase (IPMS) catalyses the reaction between acetyl coenzyme A (AcCoA) and α-ketoisovalerate (KIV) to produce free coenzyme A and α isopropylmalate (IPM). This reaction is a key control point in the biosynthesis of a leucine, a pathway absent in animals but present in plants, fungi and bacteria. As a result, IPMS is a antibiotic and herbicidal target that has been validated by knockout studies for M. tuberculosis, the causative agent of tuberculosis. Engineered IPMSs have also been used in the fermentative production of long chain alcohols for use as fuels. IPMS belongs to a family of related enzymes called α-ketoacid: AcCoA re-aldolases (KARAs), with each subfamily differing in the specific α-ketoacid that AcCoA is reacted with. The known KARA subfamilies are IPMS, citramalate synthases (CMSs), homocitrate synthases (HCSs), methylthioalkylmalate synthases (MAMSs) and re-citrate synthases (RCSs), respectively involved in the biosynthesis of isoleucine, lysine, glucosinolates and TCA cycle intermediates.
This thesis describes work aimed at improving understanding of both specific subfamilies of KARA enzymes and also the genetic and functional relationships between the subfamilies. A particular emphasis is placed on relating primary structure to function, allowing the inference of function from a very small subset of residues.
IPMSs are divided into two classes, the Mtu-like IPMSs and the much less studied Eco-like IPMSs. Chapter 2 details the expression and characterisation of the Eco like IPMS from N. meningitidis (NmeIPMS). Overall NmeIPMS showed similar properties to MtuIPMS, but unlike that enzyme NmeIPMS is inhibited by high divalent metal ion concentrations, does not require monovalent metal ions, and shows some activity with the α-ketoacid 3-methyl α ketovalerate. Several previous results showing inhibitory activity of Zn2+, Cd2+ and bromopyruvate were also found to be the results of interference with the assay system and all three were found to be much weaker inhibitors than previously determined. Phylogenetic analysis of the different KARA subfamilies revealed certain specific positions that were believed to control substrate specificity. Chapter 3 details mutagenesis experiments on MtuIPMS that probe the function of these residues. Once the importance of the residues had been established, substitutions were made in which IPMS residues were replaced with their equivalents from HCSs and CMSs in order to change substrate specificity. The most successful result was the Y169L substitution based on HCS, which decreased the specificity constant with KIV by four orders of magnitude while improving other activities, successfully shifting the best activity to the unbranched α-ketoacid α-ketobutyrate.
Chapter 4 of this thesis details the purification and functional testing of the RCS from C. saccharolyticus (CscRCS), the first thermophilic RCS characterised. CscRCS was found to have an extremely low Km for its substrate oxaloacetate (1.7 µM), believed to be an adaptation to the instability of oxaloacetate at the temperatures CscRCS operates at in vivo. The enzyme also showed competitive affinity by α-ketoglutarate, the end product of the pathway. Unlike other characterised RCSs, CscRCS showed no oxygen sensitivity.
The phylogenetic analysis conducted for this thesis identified a subfamily of KARAs dubbed pseudo-IPMSs (PIPMSs) that showed no substantial homology to any studied subfamily. In Chapter 5 the PIPMS from T. thermophilus (TthPIPMS) was expressed and characterised. TthPIPMS showed many features of a CMS, being most active with the same substrate (pyruvate) and sensitive to the same inhibitor (isoleucine). Unlike the previously studied CMS subfamilies, TthPIPMS possesses a nanomolar IC50 for its inhibitor, and also shows substantial activity as an RCS.
The results of these chapters are then drawn together in Chapter 6 to create a picture of the relationships between the KARA enzymes, in terms of their functional characteristics as well as the sequence and evolutionary relationships between them that have bought about their diverse functions.