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No description available.

Bacteria have developed various means of secreting proteins that can enter the host cell membrane. In this work I focus on two systems: cholesterol-dependent cytolysins and Type III Secretion. Cholesterol is a molecule that is critical for physiological processes and cell membrane function. Not only can improper regulation lead to disease, but also the role cholesterol plays in cell function indicates it is an important molecule to understand. In response to this need, probes have been developed that detect cholesterol molecules in membranes. However, it has been recently shown that there is a need for probes that only respond to cholesterol that is accessible at the membrane surface. Perfringolysin O (PFO) is a toxin secreted by Clostridium perfringens that has been developed into a probe capable of detecting accessible cholesterol. Recently, researchers have been expanding the capabilities of this probe by substituting residues, modifying residues, truncating the probe, or a combination of the three. However, lack of characterization of these new probes has led to controversial results. To understand the role of a conserved Cys residue, here we perform cholesterol binding assays and measure the pore formation activity of a Cys modified PFO derivative. The Type III Secretion (T3S) system is a syringe-like apparatus used by various pathogens to inject effector proteins into target cells. The apparatus spans both the inner and outer bacterial membrane, extending to make contact with the host cell where it forms a pore known as the translocon. In Pseudomonas aeruginosa, the translocon is made up of two proteins, PopB and PopD. While recent advances have been made on the structure of the needle and injectisome, information on the translocon remains sparse. In this work, the P. aeruginosa T3S translocon is analyzed using both in vivo and in vitro methods.

<p dir="ltr">The yeast zinc metalloprotease, Ste24, is involved in the maturation of the yeast mating pheromone <b>a</b>-factor by performing two distinct cleavages in the same precursor peptide substrate. Firstly, during the CaaX processing, Ste24 cleaves the three terminal residues of <b>a</b>-factor. CaaX processing is a well-studied process that involves the prenylation, proteolysis, and carboxyl-methylation of proteins ending with a cysteine (C), two aliphatic residues (aa), and one of several amino acids (X). The second cleavage step by Ste24 occurs after CaaX processing and involves an upstream cleavage N-terminal to the CaaX site. Another cleavage is performed by the enzyme Axl1 before the precursor peptide is transported from the cell to initiate mating processes. Inhibition of Ste24 typically results in ‘sterile’ cells which is how the term ‘Sterile 24’ was coined. In humans, defects in this metalloprotease or its substrate, Prelamin A, typically result in a range of progeroid disorders. Furthermore, the severity of these diseases has been directly linked to the catalytical activity of the enzyme. Treatments for these diseases are difficult to develop due to the limited knowledge available on the catalysis, substrate recognition, and functions of Ste24 and its homolog.</p><p dir="ltr">As such, these studies aim to define the substrate specificity of Ste24 and elucidate the binding site of Ste24. Identifying the substrate requirements of Ste24 has been an increasingly interesting topic due to the implication of Ste24 in a variety of unrelated functions. Previously, it has only been shown that yeast Ste24 is able to cleave the native substrate, the precursor of <b>a</b>-factor, and the substrate of its human homolog, prelamin A. This is an interesting finding because both substrates have dissimilar sequences at each cleavage site; so, it could be hypothesized that Ste24 may be able to recognize a wider range of sequences than expected. Further research has provided evidence that Ste24 is able to cleave both prenylated and non-prenylated substrates. It is also able to act as a translocon unclogger which may support its function in cleaving toxic islet amyloid polypeptides involved in cell failure in diabetes. Surprisingly, it was shown that this ‘unclogger ability’ was directly correlated to the activity level of Ste24, suggesting that the active site is directly involved in cleaving these peptides. With this information, it is clear that Ste24 has a broader substrate recognition ability than previously believed.</p><p dir="ltr">To elucidate the substrate specificity of Ste24, short peptide sequences containing varying CaaX sequences were developed and tested for C-terminal activity through a radioactive methyltransferase-coupled diffusion assay. Ste24 was able to recognize several sequences, however, a larger library is necessary to identify the specific requirements necessary for cleavage. Secondly, we tested the necessity of carboxylmethylation for the upstream N-terminal cleavage. The Distefano group designed three 33-mer analogs of <b>a</b>-factor, developed to mimic the C-terminally cleaved peptide. These peptides had either <b>a)</b> a methyl ester terminus representing the native substrate, <b>b)</b> a free carboxyl terminus representing the unmethylated precursor, and <b>c)</b> an amide terminus representing an unnatural end. All three peptides were tested using a FRET-based assay that allowed for the kinetic parameters of each peptide to be evaluated. We demonstrated that carboxylmethylation was not necessary for the upstream N-terminal cleavage; all three peptides presented similar kinetics. Finally, we interrogated the binding site of Ste24 through the use of a radioactive methyltransferase-coupled diffusion assay (C-terminal cleavage), a FRET-based assay (N-terminal cleavage), and photocrosslinking assays (binding). Together, these data presented a clearer image of residues necessary for the cleavage and binding of substrates within Ste24.</p>

Meprins are oligomeric cell-surface metalloproteinases that are expressed at high concentrations in the renal brush border membranes of mice. Meprins consist of two types of subunits, α and β, which are the products of two different genes. The β subunit cDNA was cloned and sequenced from mouse kidneys, and the membrane association and the in vivo proteolytic processing of mouse meprin subunits were investigated. The primary translation product of the meprin β subunit is composed of 704 amino acids, and contains several domains, including a signal sequence at the NH₂-terminus, a prosequence, a protease domain, an adhesion domain (MAM domain), an epidermal growth factor-like domain, a potential transmembrane-spanning domain, and a short cytoplasmic tail. The B subunit is evolutionarily related to the α subunit. The α and β subunit share about 42% overall sequence identity, and have a similar arrangement of functional domains; however, a 56 amino acid segment near the COOH-terminus of a is missing in β, and the signal sequences, transmembrane and cytoplasmic domains share no significant sequence similarity. The protease domains of o and B are 55% identical. NH₂-terminal protein sequencing of detergent-solubilized meprin subunits from mouse kidneys showed that the prosequence in a is removed in the mature subunit. By contrast, only the signal sequence is removed from the mature β subunit NH₂-terminus, and the β subunit retains the prosequence. Further, the mature α subunit, but not the β subunit, is proteolytically processed at the COOH-terminus and does not contain the transmembrane and the EGF-like domains encoded by the meprin α cDNA. The β subunit is a type I integral membrane protein. By contrast, α does not transverse the membrane, and its membrane association depends on disulfide bonds. The oligomeric organization of membrane-bound meprins was analyzed by SDSPAGE under non-reducing conditions, and by isoelectric focusing. ICR mouse kidneys express αβ heterodimers and α₂ homodimers; C3H/He mice contain β₂ dimers. Transfection of COS-1 cells with the full-length meprin α subunit cDNA resulted in the secretion of meprin dimers into the culture medium, indicating that the COOH-terminal transmembrane domain of meprin α subunits is posttranslationally removed from the protein in COS-1 cells, as it is in mouse kidney cells. Replacement of the COOH-terminal 137 amino acids of a with the COOH-terminus of B, or deletion of the 56 amino acid inserted domain in α, resulted in mutant proteins that were not secreted into the medium, but rather were membrane-bound, indicating that the inserted domain of α is essential for proteolytic cleavage and secretion. Deletion of the COOH-terminal 133 residues of a did not affect meprin α dimerization or intracellular transport. The meprin a subunits secreted from transfected COS-1 cells were catalytically inactive, but could be activated by limited proteolysis with trypsin. Thus, processing at the NH,-terminus differed in COS-1 cells and in mouse kidney. COS-1 cells did not remove the prosequence from the α subunit protein, and removal of the prosequence was essential for catalytic activity of the a subunit. These results have implications for the biosynthesis and regulation of a cell surface proteinase, and thus relate to the elucidation of the mechanisms by which biological events at the cell surface are regulated. / Ph. D.

Components of the bacterial spore germination apparatus are crucial for survival and for initiation of infection by some pathogens. While some components of the germination apparatus are well conserved in spore-forming species, such as the spoVA operon, each species may possess a different and possibly unique germinant recognition mechanism. The significance of several individual proteins in the germination process has been characterized. However, the mechanisms of how these proteins perform their functions and the network connecting these proteins in the complete germination process are still a mystery. In this study, we characterized a Bacillus subtilis superdormant spore population and investigated the abundance of 11 germination-related proteins. The relative quantities of these proteins in dormant, germinating and superdormant spores suggested that variation in the levels of proteins, other than germinant receptor proteins may result in superdormancy. Specifically, variation in the abundance of the GerD lipoprotein may contribute to heterogeneity of spore germination rates. Spore membrane proteomes of Bacillus anthracis and B. subtilis were characterized to generate a candidate protein list that can be further investigated. Proteins that were not previously known to be spore-associated were identified, and many of these proteins shared great similarity in both Bacillus species. A significant number of these proteins are implicated in functions that play major roles in spore formation and germination, such as amino acid or inorganic ion transport and protein fate determination. By analyzing the in vivo and in vitro activity of HtrC, we proved that the protease is responsible for YpeB proteolytic processing at specific sites during germination. However, without HtrC present in the spore, other proteases appear to degrade YpeB at a reduced rate. The activity of purified HtrC in vitro was stimulated by a relatively high concentration of Mn²⁺ or Ca²⁺ ions, but the mechanism behind the stimulation is not clear. We also demonstrated that YpeB and SleB, in the absence of their partner protein, were degraded by unknown proteases other than HtrC during spore formation. Identification and characterization of these unknown proteases would be a future direction for revealing the roles of proteases in spore germination. / Ph. D.

Yes / Human identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects’ DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European–American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts. / The Technology Commercialization Innovation Program (Contracts #121668, #132043) of the Utah Governors Office of Commercial Development, the Scholarship Activities

No / Gram-positive bacterial lipoproteins are a functionally diverse and important class of peripheral membrane proteins. Recent advances in molecular biology and the availability of whole genome sequence data have overturned many long-held assumptions about the export and processing of these proteins, most notably the recent discovery that not all lipoproteins are exported as unfolded substrates through the general secretion pathway. Here, we review recent discoveries concerning the export and processing of these proteins, their role in virulence in Gram-positive bacteria and their potential as vaccine candidates or targets for new antimicrobials. / Biotechnology and Biological Sciences Research Council (grant numbers F009224/1, F009429/1, EGH16082), the Medical Research Council (MRC), the Commission of the European Community (grant LSHG-CT-2004–005257) and The Royal Society.

Yes / Mislocalised membrane proteins (MLPs) present a risk to the cell due to exposed hydrophobic amino acids which cause MLPs to aggregate. Previous studies identified SGTA as a key component of the machinery that regulates the quality control of MLPs. Overexpression of SGTA promotes deubiqutination of MLPs resulting in their accumulation in cytosolic inclusions, suggesting SGTA acts in collaboration with deubiquitinating enzymes (DUBs) to exert these effects. However, the DUBs that play a role in this process have not been identified. In this study we have identified the ubiquitin specific peptidase 5 (USP5) as a DUB important in regulating the quality control of MLPs. We show that USP5 is in complex with SGTA, and this association is increased in the presence of an MLP. Overexpression of SGTA results in an increase in steady-state levels of MLPs suggesting a delay in proteasomal degradation of substrates. However, our results show that this effect is strongly dependent on the presence of USP5. We find that in the absence of USP5, the ability of SGTA to increase the steady state levels of MLPs is compromised. Moreover, knockdown of USP5 results in a reduction in the steady state levels of MLPs, while overexpression of USP5 increases the steady state levels. Our findings suggest that the interaction of SGTA with USP5 enables specific MLPs to escape proteasomal degradation allowing selective modulation of MLP quality control. These findings progress our understanding of aggregate formation, a hallmark in a range of neurodegenerative diseases and type II diabetes, as well as physiological processes of aggregate clearance.