The aromatic beta-glucosides of plant origin, salicin and arbutin, serve as carbon sources for the sustenance of bacteria when ‘preferred’ sugars are absent in the environment. In the family Enterobacteriaceae, there are varied patterns for utilization of these beta-glucosides, wherein, in some members the ability to utilize salicin or arbutin is cryptic while in others it is completely absent. Escherichia coli harbors silent or cryptic genetic systems for the utilization of arbutin and salicin, which are activated by spontaneous mutation(s). Of these systems, the bgl operon of E.coli has been used as a paradigm for silent genes and extensive studies have been carried out to understand its silencing and activating mechanisms. Mutational activation of the wild type bgl operon in E.coli leads to the acquisition of the ability to utilize both arbutin and salicin. Preliminary studies have shown that aromatic beta-glucoside utilization in Shigella sonnei, which is evolutionarily related to E.coli, shows a two-step activation process wherein the wild type strain first becomes Arb+, which subsequently mutates to Sal+. The genetic systems responsible for beta-glucoside utilization, including the bgl operon, are conserved in S.sonnei to a large extent. A major difference is that the bglB gene encoding the phosphor-β-glucosidase B is insertionally inactivated in S.sonnei. As a result, activation of the bgl operon in the first stage leads to expression of the permease, BglF, which along with the phosphor-β-glucosidase A expressed from an unlinked constitutive gene, bglA, confers an Arb+phenotype. Salicin is not a substrate for the enzyme BglA and therefore a second mutational event is required for the acquisition of the Sal+ phenotype. Interestingly, the insertion within bglB is retained in AK102, the Sal+ second step mutant of S.sonnei. Therefore, the locus involved in conferring salicin utilization ability is unknown. However, S.sonnei is not amenable to routine genetic echniques and an E.coli bglB model was generated by creating an insertion in the bglB gene to identify the locus involved in conferring the Sal+ phenotype. Like S.sonnei, this E.coli strain, SD-1.3, also showed a two-step activation process for the utilization of salicin. Utilization of salicin in the Sal+ second step mutant of SD-1.3 could require activation of other silent genetic systems such as the asc operon and the chb operon or mutation in loci such as bglB or bglA. Linkage analysis by P1 transduction showed that activation of the asc operon is required for conferring a Sal+ phenotype in the second step mutant. The asc operon comprises of two genes, ascF encoding a PTS permease and ascB encoding a phosphor-β-glucosidaseB.The Precise mechanism of activation of the asc operon is not known but, it has been speculated that AscG, encoded by an upstream gene, acts as a repressor. Results presented in this thesis show that BglF is responsible for the transport of salicin and AscB provides the phosphor-β-glucosidase B in the Sal+ second step mutant of the E.coli strain SD-1.3. Analysis of the expression of the ascFB operon by measuring the transcripts as well as the activity of phosphor-β-glucosidase B showed that it is enhanced in the Sal+ second step mutant of SD-1.3 in the presence of the inducer. The expression of the ascFB operon is also increased constitutively when ascG is replaced by an antibiotic cassette in the parent strain SD-1.3 and the Arb+ first step mutant, indicating that AscG acts as a repressor for the asc operon. Moreover, inactivation of ascG in the parent leads to utilization of salicin in a single step by the activation of the bgl operon to provide the transport function, indicating that the inactivation of ascG is sufficient to activate the expression of ascB. Similarly, loss of AscG–mediated repression of the asc operon confers salicin utilization ability to the Arb+ first step mutant of SD-1.3. Interestingly, measurement of phosphor-β-glucosidase B activity in a Sal+ second step mutant derivative deleted for ascG showed a constitutive increase in the expression of the ascFB operon. Thus, AscG mediates the induction of the asc operon in response to salicin. In order to study the mechanism of activation of the asc operon, the ascB gene was cloned from the Arb+ first step mutant and the Sal+ second step mutant of SD-1.3 in a low copy number vector. Both these constructs were able to confer a Sal+ phenotype to the Arb+ first step mutant indicating absence of any genetic change in ascB in the Sal+ second step mutant. This was also confirmed by sequencing of ascB gene from the strains that showed no changes in the nucleotide sequence. Absence of any insertions within ascG showed that activation of the ascoperon is not achieved through disruption of ascG in the Sal+ second step mutants analyzed. AscG belongs to the GalR family of repressors in which some members require a mutation to enable the binding of sugar to mediate induction. Nucleotide sequence analysis showed that there was no change in the ascG gene in the Sal+ mutants analyzed. However, when the upstream regulatory region of the ascFB operon was analyzed a mutation was found in the -10 sequence of the putative promoter of the ascFB genes. This change leads to a stronger promoter as it brings the -10 sequence closer to the consensus sequence. Therefore, salicin utilization is achieved in the Sal+ second step mutant analyzed by an increase in expression of the asc operon by a promoter-up mutation. The negative effect of binding of AscG on expression of the ascFB operon is relieved in presence of the inducer, salicin. The possible role of the asc operon in salicin utilization in S.sonnei was tested by replacing the ascB gene by anantibiotic cassette in AK102, the Sal+ second step mutant of S. sonnei. This did not lead to loss of salicin utilization. By gene targeting approach it was also found that none of the phosphor-β-glucosidases known in E.coli are involved in degradation of salicin in AK102. A search of the S. sonnei genome database indicated the presence of two putative phosphor-β-glucosidases encoded by glvG and SSO1595. Replacement of glvG gene by anantibiotic cassette in AK102 did not lead to loss of salicin utilization. However, a similar replacement of SSO1595 in AK102 resulted in a Sal+ phenotype indicating that SSO1595 provides the phosphor-β-glucosidase in the Sal+ second step mutant of S. sonnei. A homolog of this enzyme is not present in E.coliorinany of the other members of the Shigella genus. Transcription alanalysis as well as measurement of phosphor-β-glucosidase B activity showed that expression of SSO1595 is enhanced constitutively in AK102. To study the mechanism of mutational activation for achieving salicin utilization in S. sonnei, SSO1595 was cloned from AK101, theArb+ first step mutant and AK102, the Sal+ second step mutant in a low copy numbe rvector. Both these constructs were able to confer a Sal+ phenotype to AK101 indicating an absence of genetic change in SSO1595 in AK102. This was also confirmed by sequencing of SSO1595 gene from the strains. Analysis of the upstream regulatory region of SSO1595 in AK102 indicated a deletion of around 1.0kbp sequence. This was also confirmed by nucleotide sequencing of the region. By primer extension analysis it was found that a new transcriptional start site is generated upstream to the deletion in the Sal+ second stepmutant of S.sonnei. Acquisition of the Sal+ phenotype in AK102 is therefore the resultof the SSO1595 gene being brought under a new promoter as a result of a DNA rearrangement. Overall, this study suggests that a high degree of similarity at the genomic level between organisms does not always ensure similarity in genetic mechanisms as two distinct pathways are responsible for conferring utilization of salicinin S. sonnei and E.coli.

The chb operon constitutes the genes essential for utilization of chitooligosaccharides in Escherichia coli and related species. The six genes of the operon code for a transcriptional regulator (ChbR) of the operon, a permease (ChbBCA), a monodeacetylase (ChbG), and a phospho-beta-glucosidase (ChbF). In the absence of the substrate, the operon is maintained in a transcriptionally repressed state, while presence of the substrate leads to transcriptional activation. Regulation of the chb operon is brought about by the concerted action of three proteins, the negative regulator NagC coded by the nag operon, the dual function regulator ChbR coded by the chb operon and the universal regulatory protein CRP. Mutations that lead to alterations in the regulation of the operon can facilitate utilization of cellobiose, in addition to chitooligosaccharides by E. coli. The studies presented in Chapter II were aimed at understanding the evolution of cellobiose utilization in Shigella sonnei, which is phylogenetically very close to E. coli. Cel+ mutants were isolated from a Cel- wild type S. sonnei strain. Interestingly, Cel+ mutants arose relatively faster on MacConkey cellobiose agar from the S. sonnei wild type strain compared to E. coli. Similar to E. coli, the Cel+ phenotype in S. sonnei mutants was linked to the chb operon. Deletion of the phospho-β-glucosidase gene, chbF also resulted in loss of the Cel+ phenotype, indicating that ChbF is responsible for hydrolysis of cellobiose in these mutants. Previous work from the lab has shown that acquisition of two classes of mutations is necessary and sufficient to give rise to Cel+ mutants in E. coli. The first class of mutations either within the nagC locus or at the NagC binding site within the chb promoter, lead to NagC derepression. The second class consisting of gain-of-function mutations in chbR enable the recognition of cellobiose as an inducer by ChbR and subsequent activation of the operon. However, in S. sonnei a single mutational event of an IS element insertion resulted in acquisition of this phenotype. Depending on the type and location of the insertion, the mutants were grouped as Type I, and Type II. In Type I mutants an 1S600 insertion between the inherent -10 and -35 elements within the chb promoter leads to ChbR-independent constitutive activation of the operon, while in Type II mutants, an IS2/600 insertion at -113/-114, leads to ChbR-dependent, cellobiose-inducible expression of the operon. The results presented also indicate that in addition to relieving NagC mediated repression, the insertion in Type II mutants also leads to increase in basal transcription from the chb promoter. Constitutive expression of the chb operon also results in utilization of the aromatic β-glucosides salicin and arbutin, in addition to cellobiose in Type I mutants, which indicates the promiscuous nature of permease and hydrolysis enzyme of the chb operon. This part of the thesis essentially demonstrates the different trajectories taken for the evolution of new metabolic function under conditions of nutrient stress by two closely related species. It emphasizes the significance of the strain background, namely the diversity of transposable elements in the acquisition of the novel function. The second part of this research investigation, detailed in Chapter III deals with experiments to characterize the eukaryotic orthologs of the last gene of the chb operon. The chbG gene of E. coli codes for a monodeacetylase of chitooligosaccharides like chitobiose and chitotriose. The protein belongs to a highly conserved, but less explored family of proteins called YdjC, whose orthologs are present in many prokaryotes and eukaryotes including mammals. The human YDJC locus located on chromosome 22 is linked to a variety of inflammatory diseases and the transcript levels are relatively high in stem cells and a few cancer cells. In silico analysis suggested that the mammalian YdjC orthologs possess sequence and structural similarity with the prokaryotic counterpart. The full length mouse YdjC ortholog, which is 85% identical to the human ortholog was cloned into a bacterial vector and expressed in a chbG deletion strain of E. coli. The mouse YdjC ortholog could neither promote growth of the strain on chitobiose nor induce transcription from the chb promoter. The purified mouse YdjC ortholog could not deacetylate chitobiose in vitro as well, suggesting that the mouse ortholog failed to complement the function of the E. coli counterpart, ChbG under the conditions tested in this study. In order to characterize the mammalian YdjC orthologs more elaborately, further experimentation was performed in mammalian cell lines. The results indicate that YdjC is expressed in mammalian cell lines of different tissue origin and the expression was seen throughout the cell. Overexpression of mouse Ydjc in a few mammalian cells also resulted in increased proliferation and migration, indicating a direct or indirect role of this protein in cell growth/proliferation. The mammalian orthologs of ChbG therefore appear to have related but distinct activities and substrates compared to the bacterial counterpart that need to be elucidated further.