Microbial Pathogenesis and Genetics Research

Microbial Pathogenesis

The study of microbial pathogens and the molecular genetics of microorganisms has always been a major focus of the Department of Microbiology. Research interests in these areas are diverse, including the study of important bacterial pathogens such as Mycobacterium tuberculosis, Streptococcus pneumoniae, Staphylococcus aureus, and Bacillus anthracis as well as model organisms like Escherichia coli and Saccharomyces cerevisiae. This research is designed to elucidate critical cellular functions necessary for virulence, interactions between pathogens and their hosts, and basic genetic mechanisms necessary for cellular adaptation and survival. A special emphasis in these studies is the design of new strategies for the prevention and treatment of disease. Furthermore, these studies are greatly enhanced by close collaborations with immunologists, structural biologists, bioinformaticists, and other scientists in the Department of Microbiology and at UAB.
David M. Bedwell, Ph.D.
The Bedwell laboratory uses molecular genetic approaches to study the basic features of protein synthesis (particularly translation termination) and the post-transcriptional regulation of gene expression in eukaryotic organisms.  Much of this work is done using a yeast model system.  We are also investigating whether compounds that suppress nonsense mutations can be used to treat various human genetic diseases.

David Briles, Ph.D.
The Briles lab studies the interactions of host defenses and bacterial virulence factors in the pathogenesis of bacteria. Our approach is to use both bacterial and animal genetics to identify and study important mechanisms in protection and virulence. We have identified a cell wall protein of pneumococci, PspA, which is important for pneumococcal virulence and which may be useful as a vaccine for very young children. Studies are underway to characterize the protection-eliciting portion of PspAs from different childhood strains of pneumococci, and to assemble these into an effective human vaccine with other pneumococcal proteins. We are studying the mode of action of several pneumococcal virulence factors including PspA, pneumolysin, PspC, PsaA, PcpA, and NanA, and are investigating the possibility of developing a pneumococcal vaccine that would prevent pneumococcal carriage. In other studies, we are investigating the effects of specific immunity and inflammation induced host immunity on the in vivo killing and growth rates of Streptococcus pneumoniae. In collaboration with Drs. Crain in Pediatrics and Nahm in Pathology, we have examined the changing distributions of capsular polysaccharides and protein antigens in human pneumococcal isolates.


David Chaplin, M.D., Ph.D.
Dr. Chaplin’s laboratory aims to define the ways innate immune stimuli modulate allergic inflammatory responses that are manifest in tissues through the action of the adaptive immune response. He has a special interest in the ways commensal and pathogenic microbes that are present in the lung alter allergic inflammatory responses such as those that underlie asthmatic inflammation. He is testing the hypothesis that airway microbes impact the quality and quantity of asthmatic inflammation largely through their induction of myeloid-derived regulatory cells (MDRC). Lung and airway MDRC, defined by Dr. Chaplin’s laboratory in 2011, constitute several discrete populations of cells that determine the overall inflammatory tone in the tissues through their production of cytokines, chemokines, and reactive nitrogen and oxygen free radical species. Dr. Chaplin’s laboratory demonstrated in studies using a mouse model that superoxide-producing MDRC dramatically accentuate airway hyperresponsiveness after exposure to aerosolized antigen. In contrast, populations of nitric oxide-producing MDRC blunt airway hyperresponsiveness, suggesting that the nitric oxide/superoxide axis may be a valuable target for future development of novel anti-asthmatic therapeutics.

Terje Dokland, Ph.D.
Molecular piracy and the mobilization of Staphylococcus aureus pathogenicity islands
Staphylococcus aureus is an opportunistic pathogen that can cause serious local and systemic infections in humans and livestock. The emergence of virulent strains of community-acquired S. aureus resistant to antibiotics (e.g. MRSA) has become a significant public health problem. Genes encoding virulence factors in these bacteria are frequently carried on mobile genetic elements, such as bacteriophages and pathogenicity islands (SaPIs). My research is focused on the process of mobilization of SaPIs. In particular, we are interested in the process of “molecular piracy”, by which SaPIs usurp gene products produced by specific bacteriophages ("helper" phages) in order to ensure their own mobilization, propagation and spread. These processes are studied by a combination of structural methods (cryo-EM, X-ray crystallography), genetics and biochemical approaches.

Kim Keeling, Ph.D.
My research focuses on finding treatments for protein deficiencies attributable to premature termination codons (PTCs).  Using this personalized medicine approach, we have identified drugs that suppress translation termination at PTCs and restore partial levels of functional protein in a mucopolysaccharidosis type I-Hurler (MPS I-H) disease model.  We are also investigating whether partial inhibition of nonsense-mediated mRNA decay, a pathway that degrades PTC-containing mRNAs, is another option for treating MPS I-H due to PTCs.

Elliot Lefkowitz, Ph.D.
My research interests are directed at contributing to the understanding of microbial genomics and evolution by developing and utilizing computational tools and bioinformatics techniques to mine sequence and other data for significant patterns characteristic of function and/or evolution. This work has included the development of new algorithms for the detection of genomic regulatory motifs; tools for the identification of microbial genes; the development and utilization of High Performance and Grid Computing tools for bioinformatics analysis; and the development and use of tools for analyzing patterns of microbial evolution. I have also been involved in the development of databases, web applications, and analysis tools for the sequencing and annotation of several complete bacterial and viral genomes. Research interests have include the annotation and comparative analysis of the complete genomic sequence of several different Mycoplasma bacteria; the annotation and comparative analysis of the complete genomes of several Streptococcus pneumoniae strains; and the development of bioinformatics resources to support biodefense research on microbial pathogens including poxviruses, viral hemorrhagic fevers, and emerging/re-emerging biological threats. The goals of the latter are to provide bioinformatics resources and analyses that can be used to support the development of environmental detectors, diagnostics, animal models, vaccines, and antimicrobial drugs; as well as provide a better understanding of the molecular biology, pathogenesis, and evolution of microbial pathogens.

Currently, as part of the Biomedical Informatics Component of the UAB Center for Clinical Sciences that I direct, my group is heavily involved in collaborative research projects utilizing next-generation sequencing technologies to help answer a wide variety of research questions. This effort includes the analysis of the human microbiome and its role in human health. Even when at the peak of health, our bodies are colonized by vast numbers of microorganisms. But these populations of microorganisms (our microbiome) may vary with, and contribute to human disease. We are developing and utilizing the computational tools needed to understand the role the microbiome plays in human health and disease.

Frances Lund, Ph.D.
One of the key research objectives of the Lund laboratory is to identify the key players that suppress or exacerbate pathologic pulmonary inflammation associated with chronic or acute infection. In one project, we are characterizing the role of the TRPM2 cation channel in regulating acute respiratory distress in response to pulmonary or systemic infection with gram-negative bacteria. TRPM2, although reported to induce inflammation in response to oxidative stress, actually protects the lung from damage following infection or exposure to LPS. Current experiments are directed at determining how TRPM2 acts as anti-oxidant and modulates the infected lung microenvironment.

Suzanne Michalek, Ph.D.
We are interested in determining how microbial pathogens evade the host’s immune system, and in identifying key virulence antigens for use in vaccine development.

Michael Niederweis, Ph.D.
Tuberculosis is caused by Mycobacterium tuberculosis and kills approximately two million people each year, more than any other bacterial pathogen. Yet, M. tuberculosis is one of the least understood bacterial pathogens. Virulence of M. tuberculosis is mainly associated with its ability to survive within macrophages. The outer membrane is an efficient permeability barrier for toxic molecules and plays a key role in protecting M. tuberculosis from the host immune system. To date, the molecular basis for the transport of most solutes across the outer membrane is unknown for M. tuberculosis. The aim of our research is to identify and characterize the outer membrane proteome of M. tuberculosis. The identification of proteins that enable transport of solutes across the outer membrane would represent a major breakthrough in our understanding of the physiology and drug resistance of M. tuberculosis.

The proteins which functionalize the outer membrane of M. tuberculosis are fascinating for several reasons:
(i) They fulfill essential biological functions.
(ii) The outer membrane proteins reside in a highly unusual lipid membrane. Therefore, their structures will be novel as we have already shown for MspA. This makes it likely that they also function by novel mechanisms.
iii) Some outer membrane proteins are likely to represent attractive drug targets because inhibitors do not have to cross the notoriously impermeable outer membrane, which is a major determinant of the intrinsic drug resistance of M. tuberculosis.
(iv) Many outer membrane proteins of pathogenic Gram-negative bacteria are involved in interactions with host cells. We assume that this will also be the case for M. tuberculosis.

Jan Novak, Ph.D.
Dr. Novak’s research interests in Microbial pathogenesis and genetics include biologically active compounds with anti-bacterial, anti-fungal, or anti-protozoal activity, streptococcal virulence factors, antibiotic resistance, protozoal metabolism, and bacterial glycosylation.

Andries Steyn, Ph.D.
M. tuberculosis, the etiological agent of TB is one of the most effective human pathogens and is responsible for 2.2 million deaths every year (1 death every 10 seconds). It is estimated that a total of 225 million new cases and 79 million deaths will occur between 1998 and 2030. Tuberculosis (TB) continues to pose a significant threat to mankind that cannot be conquered without an effective vaccine strategy, which remains unavailable to date. The prophylactic vaccine BCG (Bacille Calmette-Guerin), fails to protect against the most common form of disease, adult pulmonary tuberculosis, and its efficacy varies dramatically e.g., from 0% in South India to 80% in the UK. Since the lungs of an infected patient contain more than a billion bacilli, poor treatment compliance can easily lead to multi drug resistant (MDR) strains. The cost for treating a patient infected with MDR-TB (currently designated as Category C Priority pathogens) can approach $250,000 about 10-15 times the cost for treating a drug-sensitive case. One of the greatest risk factors for TB is HIV, which increases the risk of developing tuberculosis 30-fold.

Our long-term goal is to understand the mechanisms of M. tuberculosis virulence. The first project involves a gene, whiB3, which appears to play a unique role in the bacterium-host interaction. We established that WhiB3 interacts with the 4.2 domain of the principal sigma factor, RpoV in virulent M. tuberculosis, but not with RpoV of an attenuated strain containing a single point mutation (Arg515-His) in the 4.2 domain. Our studies showed that the M. tuberculosis whiB3 mutant behaved identical to the wild-type strain with respect to its ability to replicate in mice, but was attenuated in terms of host survival. In addition, the whiB3 mutant strain showed much reduced lung pathology, compared to wild type infected mice. Intriguingly, we showed that a whiB3 mutant of virulent Mycobacterium bovis was completely impaired for growth in guinea pigs. These mutants define a new class of virulence genes in M. tuberculosis and M. bovis. M. tuberculosis contains seven WhiB homologues that show strong similarity to Streptomyces spp. proteins that are required for sporulation. We hypothesize that WhiB3 controls a subset of genes required for virulence. It is notable that this virulence gene would not have been detected using conventional screens such as signature mutagenesis, which screen primarily for mutants defective in growth and not virulence.

A second project in the laboratory involves the development and application of "in vivo expression technology (IVET)" to rapidly identify M. tuberculosis genes that are specifically induced during infection in vivo. Since many bacterial virulence determinants share a unique phenotype - induction in the host; the development of such a system for mycobacteria would be of significance. Subsequently, we have successfully developed a genetic system, which uses the animal as a selective medium to identify M. tuberculosis genes specifically induced during infection. These in vivo induced genes are poorly expressed on laboratory medium, but exhibit elevated levels of expression in host tissues and suggest that they contribute to growth in restricted host tissues and thus enhance pathogenicity.

A third project in the laboratory is studying signal transduction pathways in M. tuberculosis. In most bacterial two-component systems, the signals or components of the two-component signaling pathways are mostly uncharacterized. We hypothesized that accessory proteins communicate directly, through direct protein-protein communication with the M. tuberculosis two component histidine kinases to modulate gene expression. Subsequently, we have shown that the sensing module of the M. tuberculosis histidine kinase KdpD specifically interacts with two membrane proteins, and that the N-terminal sensing module of KdpD and the histidine kinase domain of KdpD form a ternary complex with these membrane proteins. Our results suggest that the membrane proteins function as accessory or ligand-binding proteins that communicate directly with the sensing domain of KdpD to modulate kdp expression.

Charles Turnbough, Ph.D.
There are two major research projects in the Turnbough laboratory. The first project is to determine the structure and function of the outermost exosporium layer of Bacillus anthracis spores, an established weapon of bioterrorism that causes the lethal disease anthrax. The exosporium is a bipartite structure consisting of a paracrystalline basal layer and an external hair-like nap. The filaments of the nap are formed by trimers of the collagen-like glycoprotein BclA, while the basal layer contains approximately 20 different proteins. Most basal layer proteins are structural elements that undergo posttranslational modifications necessary for stable exosporium assembly. The mechanisms and functions of several of these modifications are currently being actively studied. These modifications include multi-site phosphorylation of basal layer protein ExsB, glycosylation of BclA, and the apparently spontaneous covalent attachment of BclA to the basal layer protein BxpB. Based on the BclA-BxpB attachment mechanism, the Turnbough lab is also developing a new generally applicable vaccine platform that promotes a strong, lasting, and potentially multivalent immune response.

The second project focuses on mechanisms of gene regulation in bacteria, particularly Escherichia coli, that involve reiterative transcription and/or transcription start site switching. Reiterative transcription is the repetitive addition of a nucleotide to the 3’ end of a nascent transcript due to slippage between the transcript and DNA template. Start site switching is the selection of alternative start sites at a single promoter, which results in the synthesis of transcripts with different potentials for translation. Previous studies have described control mechanisms in which reiterative transcription during initiation and start site switching act independently or together to regulate the expression of operons involved in pyrimidine biosynthesis and salvage. Recently, additional operons have been shown to use reiterative transcription and/or start site switching to regulate their expression by mechanisms unlike those previously described. These new mechanisms are presently being elucidated. In addition, studies are in progress to define the mechanisms of reiterative transcription and start site switching and the factors that modulate the extent of these reactions. Because the basic machinery of transcription is highly conserved throughout the biological world, it is possible that all life forms employ regulatory mechanisms analogous to those being unraveled in the Turnbough lab. Recent studies suggest that this is indeed the case and that such mechanisms contribute to human health.

Janet Yother, Ph.D.
Many bacteria elaborate capsular polysaccharides that serve to protect against environmental insults. As a paradigm for characterizing the mechanisms of capsule synthesis and regulation in bacteria, we study the human pathogen Streptococcus pneumoniae, which is a major cause of pneumonia, bacteremia, meningitis, sinusitis, and otitis media. Young children, the elderly, and those with chronic underlying disorders such as heart disease, certain malignancies, sickle cell anemia, and diabetes are particularly susceptible to pneumococcal infections. The capsule of S. pneumoniae protects the bacterium from host defenses and it is the basis for vaccines against this organism. Our work focuses on the genetics of capsule expression, the biochemical mechanisms of capsule synthesis, and the virulence properties associated with capsule production. Additionally, we study the regulation of multiple other virulence factors that are co-regulated with capsule and whose expression is influenced by factors found in different host niches in which the bacterium resides.