Biochemistry Department Masters Theses Collection

Proteolytic Regulation of CtrA, the Master Regulator of Cell Cycle in Caulobacter crescentus

Cantin, Amber M. — Fri, 23 Nov 2012 07:05:26 PST

Cell cycle progression in Caulobacter crescentus depends on the master regulator, CtrA. During the transition from swarmer to stalk cell (G1 to S phase), CtrA is degraded by the AAA+ protease ClpXP and levels rise again in the predivisional stage. The focus of this work is to explore how cyclic, regulated degradation is controlled. CtrA is known to bind to the origin of replication, thereby suppressing replication, so we first asked if DNA binding had an effect on CtrA stability. CtrA is readily degraded by ClpXP on its own, but when bound to DNA containing the proper binding sites, degradation is inhibited. Stabilization is dependent on DNA binding, as CtrA mutants deficient in DNA binding show the same degradation regardless of addition of DNA, as does CtrA in the presence of a mutant origin sequence lacking CtrA binding sites. Looking closely at CtrA degradation in the presence of auxiliary factors suggests that higher order complex formation may be a mechanism of protecting critical cell cycle regulators from premature proteolysis. In vivo study of over-expression of CtrA mutants revealed that accumulation of non-degradable CtrA, CtrA-DD, perturbs the cell cycle, leading to filamentation and a G2 arrest. Over-expression of the DNA-binding domain alone showed filamentation but no G2 arrest, suggesting that CtrA-DD is detrimental for reasons including, but likely not limited to, its ability to bind DNA. Exogenously expressing other domains of CtrA may further elucidate the mechanism of its regulated degradation in vivo.

Novel Adaptor-Dependent Domains Promote Processive Degradation by ClpXP

Rood, Keith L. — Mon, 21 Nov 2011 09:35:00 PST

Protein degradation by ATP dependent proteases is a universally conserved process. Recognition of substrates by such proteases commonly occurs via direct interaction or with the aid of a regulatory adaptor protein. An example of this regulation is found in Caulobacter crescentus, where key regulatory proteins are proteolysed in a cell-cycle dependent fashion. Substrates include essential transcription factors, structural proteins, and second messenger metabolism components. In this study, we explore sequence and structural requirements for regulated adaptor mediated degradation of PdeA, an important regulator of cyclic-di-GMP levels.

Robust degradation of PdeA is dependent on the response regulator CpdR in vivo and in vitro. Here, I structurally identify a novel PAS domain in PdeA that is necessary and sufficient for CpdR mediated PdeA degradation. The PAS domain was found to contain a unique dimerization element that is associated with PdeA function. I show specifically that PdeA engages ClpXP through C-terminal recognition motifs. Finally, we present evidence that PdeA contains cryptic ClpXP recognition sites that are revealed during partial processing. Due to these uncommon degradation characteristics of PdeA, unique proteolytic insights may be gained by investigating this model system.

Pharmacological Chaperoning in Fabry Disease

Rogich, Jerome — Mon, 21 Nov 2011 09:34:45 PST

Fabry Disease is an X-‐linked lysosomal storage disorder characterized by a variety of symptoms including hypohydrosis, seizures, cardiac abnormalities, skin lesions, and chronic pain. These symptoms stem from a lack of functional endogenous α-‐ Galactosidase A (α-GAL), which leads to an accrual of its natural substrate. The severity of the disease symptoms can be directly correlated with the amount of residual enzyme activity. It has been shown that an imino sugar, 1-deoxygalactonojirimycin (DGJ), can increase enzymatic activity and clear excess substrate. This pH-‐dependent chaperoning phenomenon is believed to arise from the presence of aspartic acid 170 in the active site. This key residue may become protonated at lower pH, preventing a buried salt bridge from being formed. We mutated this residue to an alanine, abolishing activity, and making traditional assays impractical. We have measured the KD of chaperone for this modified active site through crystallography. Previous crystallographic studies on this enzyme have also shown a preliminary second binding site on the surface of α-Galactosidase that prefers the β-Galactose anomer. When β-Galactose binds it buries a greater surface area than when α‐Galactose binds to the active site. Binding of this site by a small molecule should stabilize the native state of the enzyme, but would be sterically occluded from inhibiting active site. We have probed this second site by soaking crystals of α‐Galactosidase with a small library of compounds.

Probing the Activation Mechanism of Transcription-Coupled Repair Factor Mfd

Hsieh, Chih-Heng — Fri, 05 Nov 2010 09:16:36 PDT

Cells dedicate tremendous amounts of energy to express essential genes for survival. During transcription, RNA polymerase (RNAP) actively scans the template strand of DNA, stalling when it meets DNA damages. Stalled RNAP prevents repair by the nucleotide excision repair pathway (NER); a sub-pathway of NER named transcription-coupled repair (TCR) resolve this problem by removing RNAP and recruiting repair proteins. In Escherichia coli, a TCR protein named “Mutation Frequency Decline” (Mfd) couples removal of RNAP through its motor activity with recruitment of the NER repair proteins. Mfd can be divided into two functional halves; the N-terminal region (MfdN, domains 1-3) is essential for NER protein recruitment, and the C-terminal region (MfdC, domains 4-7) is responsible for RNAP-interaction and motor activity. Data suggest Mfd undergoes large conformational movement to activate RNAP removal and repair protein recruitment. To study the activation mechanism of Mfd, we created several full-length “hyperactive” mutants by perturbing interactions between MfdN and MfdC. In all mutants, residue 79 in domain 1 is changed from aspartic acid to arginine (D79R), disrupting a key salt bridge interaction with arginine 804 in domain 6. The linker connecting MfdN and MfdC was made cleavable to allow separation of MfdN and MfdC, which enable us to study activities in equal molar concentration. We have studied the effect of the D79R mutation in vivo (cytotoxicity and UV sensitivity) and in vitro (enzyme activity and thermal stability), and demonstrate that this single residues change render the enzyme “hyperactive”. This confirms our model of activation: activation of Mfd results from breaking communication between MfdN and MfdC

Dopamine Controls Locomotion by Modulating the Activity of the Cholinergic Motor Neurons in C. elegans

Allen, Andrew T. — Fri, 04 Sep 2009 12:26:11 PDT

Dopamine is an important neurotransmitter in the brain, where it plays a regulatory role in the coordination of movement and cognition by acting through two classes of G protein-coupled receptors to modulate synaptic activity. In addition, it has been shown these two receptor classes can exhibit synergistic or antagonistic effects on neurotransmission. However, while the pharmacology of the mammalian dopamine receptors have been characterized in some detail, less is known about the molecular pathways that act downstream of the receptors. As in mammals, the soil nematode Caenorhabditis elegans uses two classes of dopamine receptors to control neural activity and thus can serve as a genetic tool to identify the molecular mechanisms through which dopamine receptors exert their effects on neurotransmission. To identify novel components of mammalian dopamine signaling pathways, we conducted a genetic screen for C. elegans mutants defective in exogenous dopamine response. We screened 31,000 mutagenized haploid genomes and recovered seven mutants. Five of these mutants were in previously-identified dopamine signaling genes, including those encoding the Ga proteins GOA-1 (ortholog of human Gao) and EGL-30 (ortholog of human Gaq), the diacylglycerol kinase DGK-1 (ortholog of human DGK0), and the dopamine receptor DOP-3 (ortholog of human D2-like receptor). In addition to these known components, we identified mutations in the glutamate-gated cation channel subunit GLR-1 (ortholog of human AMPA receptor subunits) and the class A acetycholinesterase ACE-1 (ortholog of human acetylcholinesterase). Behavioral analysis of these mutants demonstrates that dopamine signaling controls acetylcholine release by modulating the excitability of the cholinergic motor neurons in C. elegans through two antagonistic dopamine receptor signaling pathways, and that this antagonism occurs within a single cell. In addition, a mutation in the putative Rab GTPase activating protein TBC-4 was identified, which may suggest a role for this Rab GAP in synaptic vesicle trafficking. Subsequent behavioral and genetic analyses of mutants in synaptic vesicular trafficking components implicate RAB-3-mediated vesicular trafficking in DOP-3 receptor signaling. These results together suggest a possible mechanism for the regulation of dopamine receptor signaling by vesicular trafficking components in the cholinergic motor neurons of C. elegans.

Probing for Conformational Changes in the Repair Enzyme Mfd Using Mutant Protein Constructs

Hunnewell, Mary E. — Fri, 22 Aug 2008 05:21:06 PDT

DNA repair is essential for survival, as damage to the genome can interrupt the precarious balance of cell functions, causing further mutations and possibly leading to cancer. The bacterial transcription repair coupling factor, Mfd, is capable of recognizing a stalled RNA polymerase at a site of DNA damage. The Mfd works both to remove the RNA polymerase through its motor function (utilizing the energy of ATP to translocate along DNA), and to recruit the DNA repair complex UvrA/B/C. To study conformational changes in the protein, we are creating multiple mutants of the full length Mfd protein. My approach is to use a cleavable mutant of full-length Mfd as a template for further mutations. This will allow us to probe for conformational changes by changing interactions at the interface of the two halves of Mfd, and then using the ability to cut with TEV protease as a sensor to identify and characterize the open state of the protein. By introducing this TEV protease cut site at residue 450 in the protein linker region between the N (amino-) and C (carboxy-) terminal domains, we can then assess the conformational changes Mfd must undergo to obtain activity. We can study the effect of further mutations on the full length and cut versions of the protein. Another approach attempted in this study involves using cysteine modification of the full length Mfd protein as a sensor for these conformational changes. Mfd acts as a model system for studying the DNA repair mechanisms found in humans, and the elucidation of functional and conformational changes in Mfd contributes to studying disease phenotypes resulting from aberrant transcription coupled repair.

Probing the Peptidyl Transferase Center of Ribosomes Containing Mutant 23S rRNA with Photoreactive tRNA

Caci, Nicole C. — Tue, 15 Apr 2008 05:53:03 PDT

There is strong crystallographic evidence that the 23S rRNA is the only catalytic entity in the peptidyl transferase center. Various mechanisms for the catalysis of peptidyl transfer have been proposed. Recently, attention has been given to the idea that the 23S rRNA simply acts to position the tRNA for spontaneous peptidyl transfer and that chemical catalysis may play only a secondary role. Conserved nucleotides U2585 and U2506 are thought to be involved in positioning the 3’ ends of A- and P-site substrates based on the crystallographic evidence, and because mutagenesis at these sites severely impairs peptide bond formation. In this study, pure populations of ribosomes with either U2585A or U2506G mutations in the 23S rRNA were analyzed to test the hypothesis that substitutions at nucleotides U2585 and U2506 in the peptidyl transferase center impair peptide bond formation by altering the position of the 3’ end of P-site tRNA relative to the 23S rRNA. Pure populations of mutant or wild-type ribosomes were obtained by an affinity tagging system and probed with 32P-labeled [2N3A76]tRNAPhe to determine how the 3’ end of tRNA interacts with the ribosomal proteins and 23S RNA at the peptidyl transferase center. Some of the data for the ribosomes with a G at position 2506 are consistent with a model suggested by Schmeing and coworkers in which nucleotide U2506 breaks from its original wobble base pair with nucleotide G2583 during A-site tRNA binding and swings towards the 3’ end of P-site tRNA, while nucleotide U2585 simultaneously moves away from the 3’ end of P-site tRNA.