Diversity of metabolic and energy-generating pathways.

Research Interests:

Our research examines the physiology, systematics and ecology of environmentally important microorganisms, but especially the methane-producing archaea and the marine alpha proteobacteria. Of special interest is to understand the complete organism, from the biochemical mechanisms it uses to accomplish its day-to-day tasks of living to its interactions with other organisms and its environment in general. Every organism has its own story.

The methanogens are strictly anaerobic autotrophs which obtain energy from the synthesis of methane gas. They catalyze the terminal step in the anaerobic decomposition of organic matter, and about 1.6 % of the CO2 fixed worldwide is released to the atmosphere by the activity of these bacteria. As autotrophs they are also unusual because they are commonly found closely associated with heterotrophic bacteria and protists. Our studies of the methanogens have focused on Methanococcus, which is common in estuarine environments. Currently, we are using genetic methods to elucidate novel biosynthetic pathways and mechanisms of H2 metabolism.

The roseobacters play important roles in the transformation of carbon and sulfur compounds in the ocean and estuarine environments. Currently, we are studying the metabolism of dimethylsulfonium propionate (DMSP), a common osmolyte and major source of atmospheric sulfur, by Siliicibacter pomeroyii. Studies of this model organism provide insights into the mechanisms of DMSP degradation in the natural environments.

Research Interests:

We have long studied bacterial plasmid-encoded resistance to inorganic

and organic mercury compounds (the mer locus) as a model for (a) gene

regulation by toxic metals, (b) microbial detoxification of

environmental hazards, and (c) the influence of toxic metals on the

commensal microbiota of vertebrates. Our present work on mer focuses on

structure-function and dynamic studies of the two major types of MerR

protein and on the unique interactions of the classical Tn21 MerR

regulator with RNA polymerase during repression and activation and with

MerD during shut-down of mer operon expression. In this work we

collaborate with the groups of Jeremy Smith and Liyuan Liang at the Oak

Ridge National Laboratory.

We also have a growing interest in the molecular basis of mercury

intoxication. With collaborators Sue Miller at UCSF and Mary Lipton at

the Pacific Northwest National Laboratory we have devised a

computational filter based on the seven stable isotopes of Hg to

identify, at the individual peptide scale using LC-MS/MS proteomics,

those proteins most vulnerable to forming adducts with

organo-mercurials. We are now beginning a new project to similarly

define the inorganic mercury "exposome" and to use this approach in

collaboration with Judy Wall at Missouri for high-throughput discovery

of proteins involved in mercury methylation by sulfate reducing bacteria.

We have also worked in the area of lateral gene transfer in prokaryotes

with special emphasis on the dissemination by plasmids and transposons

of genes for resistance to toxic metals and antibiotics. We are now

wrapping up two major sequencing projects on large, mobile plasmids of

meticillin-resistant Staphylococcus aureus (MRSA) and of several genera

of marine bacteria, agricultural pathogens, and bacteria important in

biofuel fermentation.

The Stabb Lab:     Researchers in Dr. Eric Stabb's lab study the light-organ symbiosis between the bioluminescent bacterium Vibrio fischeri and the squid Euprymna scolopes, as a model for natural bacteria-animal interactions. E. scolopes hatchlings lack V. fischeri, which they must obtain from their surroundings.  After infection, the squid carry V. fischeri, and only this bacterium, in epithelium-lined crypts of a specialized light-emitting organ. Several features make this symbiosis uniquely tractable. Notably, this natural infection can be reconstituted in the lab, so we are able to observe the bacteria and their gene expression in an ecologically relevant context inside its host.

One focus of the lab is how V. fischeri cells communicate using pheromone signals.  Such bacterial signaling is often termed "quorum sensing" and is typically depicted as regulation in response to high cell density or "quorum".  However, it is now clear that the pheromones are not simply census-taking molecules and can perform more complicated social roles.  The pheromones in V. fischeri control the lux genes responsible for bioluminescence, and the pheromones are controlled by themselves in positive-feedback loops and by environmentally responsive regulators, including ArcA/ArcB, Crp, Fur, and others.  This raises the intriguing possibility that in addition to reflecting cell density, bacterial pheromones may coordinate behaviors, such as the group decision to bioluminesce, in response to local environmental cues.  Interestingly, bioluminescence is induced upon entering the symbiosis, and dark (lux) mutants are attenuated in colonizing the E. scolopes light organ; however, the symbiotic role of bioluminescence remains unclear.   Studying pheromone-mediated regulation may help shed light on the purpose of bioluminescence.  We have embarked on a collaborative project to model and understand how V. fischeri uses multiple pheromones to underpin its cell-cell communication.

A second major focus of the lab is aimed at understanding the interspecies signaling by which the squid host recognizes and responds to V. fischeri.  Peptidoglycan and LPS can trigger changes in host development that parallel those seen during normal symbiotic infection.  We are interested in how and why V. fischeri releases peptidoglycan monomer, which acts as a morphogen on the host.  Currently, a project in the lab is using V. fischeri as a model to understand how new peptidoglycan structures can evolve in bacteria.

Many projects in the lab are underpinned by genetic approaches, and we are often developing genetic and genomic tools for V. fischeri.  For example, characterizing the small V. fischeri plasmid pES213 led to an array of shuttle vectors that is still expanding.  We have also pioneered improved methods for mutagenesis with mini-Tn5 in V. fischeri.

Finally, everyone in the Stabb lab contributes to the teaching mission at the University of Georgia, and we are involved in outreach efforts to K-12 students, spreading the word of the power of microbes and the wonders of bioluminescence.  Three Stabb labbers [Noreen Lyell, Richard M. (Mark) Jones, and Julie Stoudenmire] have earned the prestigious UGA Excellence in Teaching Award, which is given to only five teaching assistants across the entire university each year.  

Research Interests:

Research in the Neidle group centers on gene expression, metabolism, and chromosomal rearrangements in a soil bacterium, Acinetobacter baylyi ADP1.  A novel method to study and generate chromosomal gene amplification is used for metabolic engineering and experimental evolution. This research has medical implications because gene amplification is associated with drug resistance, bacterial virulence, cancer, and many human diseases, as published in review articles that we wrote in 2013 and 2007.

Additionally, there are important biotechnology and environmental applications of this work. Gene amplification in strain ADP1 was first discovered during studies of  the degradation of aromatic compounds, as we reported in 2003 and 2004. We are now investigating how these degradative pathways can be exploited to convert lignin-derived aromatic compounds into biofuels and other types of desirable compounds.  Pathways for aromatic compound catabolism also hold great promise for reducing pollution (bioremediation). We described the features of ADP1 that make it an ideal experimental bacterium for fundamental and applied research in 2011.

Complementary investigations of gene expression and metabolic regulation are ongoing. Two LysR-type transcriptional regulators, BenM and CatM, control the expression of many different genes and operons needed for aromatic compound catabolism. Together with Dr. Cory Momany and his research team, we are investigating the molecular details of the function and structure of LysR-type proteins, a large family of homologs that represent the most common type of bacterial transcriptional regulator.

Selected Publications:

Elliott, K.T., Cuff, L.E., and Neidle, E.L. (2013) Copy number change: evolving views on gene amplification. Future Microbiology 8:887-899.

Alanazi, A.M., Neidle, E.L., and Momany, C. (2013) The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N₁₁-A sequence motif by LysR-type transcriptional regulators. Acta Crystallographica Section D-Biological Crystallography 69:1995-2007.

Seaton, S.C., Elliott, K.T., Cuff, L.E., Laniohan, N.S., Patel, P.R., and Neidle, E.L. (2012) Genome-wide selection for increased copy number in Acinetobacter baylyi ADP1: locus and context-dependent variation in gene amplification. Molecular Microbiology 83:520-535.

Momany, C., and Neidle, E.L. (2012) Defying stereotypes: the elusive search for a universal model of LysR-type regulation. Molecular Microbiology 83:453-456.

Elliott, K.T., and Neidle, E.L. (2011) Acinetobacter baylyi ADP1: Transforming the Choice of Model Organism. IUBMB Life 63: 1075-1080.

Craven, S.H., Ezezika, O.C., Haddad, S., Hall, R.A., Momany, C., and Neidle, E.L. (2009) Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1. Molecular Microbiology 72: 881-894.

Research Interests

We refer to our lab as Computational Microbiology Laboratory and our research centers on comparative analyses of microbial (mainly prokaryotic) genomes. However, unlike standard comparative genomic studies, which compare gene contents among different genomes, our analyses focus mainly on genome properties other than protein- and RNA-coding genes. For example, different genomes often have distinct nucleotide and oligonucleotide compositions, repeat structures, and/or sequence patterns that affect structures of DNA or RNA molecules and physical organization of the chromosomes. Our goal is to understand how these genome features evolve and what physiological roles they play in the organisms. Our research relies to a large extent on statistics and computer science, and includes development of new methods, algorithms and software for sequence analysis. Our web site features a number of programs developed in our lab that we not only use in our research but also offer for use by other researchers.

     Our most recent project involved analyses of simple sequence repeats (SSRs), that is, uninterrupted tandem repeats of a single nucleotide or a short oligonucleotide like AAAAAAAA… or ATCCGATCCGATCCG… Such repeats are hypervariable due to slipped-strand mutations and a common source of phase variation, including antigenic variation in pathogens. By comparative analysis among hundreds of genomes, we found that repeats of mono-, di-, tri-, and tetranucleotides occur in different types of genomes (mostly host-adapted pathogens) than repeats of pentanucleotides and longer oligonucleotides (environmental organisms and opportunistic pathogens), and probably have different functions. Further investigation revealed that the function of SSRs is not limited to phase variation, and extends to genome reduction in host adapted pathogens, influence on DNA structure, and possibly expression of adjacent genes.

The sequestration and storage of metals, and the maturation and roles of metal-containing enzymes by bacterial pathogens are of keen interest. The bacterial pathogens under study include the persistent gastric pathogen Helicobacter pylori, other Helicobacters that colonize liver and colon environments, and some enteric diarrheal pathogens (e.g. Salmonella/Shigella). For example, all these bacteria sequester the metal nickel for use in nickel-containing enzymes, yet the mechanism of nickel storage and subsequent nickel allocation and insertion into the nickel enzyme sinks (hydrogenases and ureases) is not understood. Mutant analysis combined with pure protein studies and animal infection models are all used to study metal containing proteins in these pathogens. A key growth substrate used by all these pathogens in animals is molecular hydrogen produced by the host flora; the pathogens ability to use this small but highly energetic substrate is due to a nickel-containing H2-splitting enzyme. The nickel-dependent expression and maturation of this enzyme is studied, as well as unique ways (i.e. nickel chelation) to inhibit its activity. Another related area of research involves stress-combating proteins used by Helicobacter pylori to colonize the gastric mucosa of humans. Such colonization leads to a variety of inflammatory gastric diseases. The persistence of the pathogen in withstanding host defense mechanisms over a period of years or decades results in the most severe gastric diseases, including even gastric carcinomas. Growth of the bacterium in animals is partially inhibited by a battery of host-produced reactive oxygen species. Our goal is to identify and then characterize the expression of oxidative stress resistance proteins that enable the gastric pathogen to persistently survive the harsh host environment.

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Research Interests: The goal of the research in my laboratory is to characterize the regulation of bacterial gene expression at multiple levels, from DNA rearrangements that alter the DNA template to RNA repair, thereby contributing to a complete picture of gene regulation in bacteria.

Current areas of focus:

1) Gene regulation by the DEDD-motif family of specialized DNA recombinases. We previously identified a unique family of DNA recombinases, the DEDD-motif family, that mediate DNA rearrangements and frequently control expression of genes involved in interactions of bacteria with their environment. We utilize genetic and biochemical approaches to define the mechanisms for recombination mediated by the DEDD-motif recombinases and to characterize the genes regulated by the recombinase systems. The recombinase systems that we study include Irg mediated integration of the Meningococcal Disease Associated (MDA) phage in Neisseria meningitidis, and MooV-mediated site-specific integration and excision of IS492 in the marine bacterium Pseudomonas atlantica to control extracellularpolysaccharide production and biofilm formation.

2) Gene regulation through the activity of the alternative sigma factor, RpoN. We are utilizing genomics, genetics, and molecular biology approaches to define the RpoN regulon of Salmonella enterica subspecies enterica serovar Typhimurium. Transcription of many operons that encode proteins and structural RNAs involved in diverse cellular processes are dependent on RpoN-RNA polymerase holoenzyme. Our research has also revealed numerous intragenic, RpoN-dependent promoters and RpoN binding sites that appear to regulate expression of genes within different sigma factor regulatory networks through transcriptional interference, expression of regulatory small RNAs, or repression. The novel regulatory roles for RpoN in the global regulatory networks of S. Typhimurium are being investigated.

3) Potential gene regulation by the RNA repair system of S. Typhimurium. In a RpoN-dependent operon, S. Typhimurium encodes homologs of human and archaeal RNA ligase (RtcB) and RNA 3' phosphate cyclase (RtcA); these enzymes are involved in tRNA splicing and RNA repair pathways in humans and archaea, but their physiological functions in bacteria are unknown. We are using transcriptomics, proteomics, genetics, and molecular biology approaches to characterize the RNA repair system and its function in S. Typhimurium.

Research Interests:

Helicobacter pylori is a bacterial pathogen that colonizes the human gastric mucosa where it can cause a variety of stomach diseases, including peptic ulcer disease and gastric cancer. H. pylori uses a cluster of polar flagella for motility which is essential for colonization of the gastric musoca. All three of the sigma factors in H. pylori (RpoD, RpoN and FliA) are used to coordinate the expression of over 60 genes encoding structural components, enzymes and regulatory proteins needed for assembly and function of the flagellum. Current work in the lab is directed at characterizing the mechanisms by which expression of the various sets of flagellar genes are regulated.

A second project in the lab focuses on RpoN (σ⁵⁴) regulon of Salmonella enterica serovar Typhimurium (S. Typhimurium), which is a major food-borne pathogen. Transcription by σ⁵⁴-RNA polymerase holoenzyme (σ⁵⁴-holoenzyme) requires an activator protein.  S. Typhimurium possesses 13 RpoN-dependent activators, each targeting a specific set of genes.  Functions for many of the genes of the S. Typhimurium RpoN regulon are unknown, and one of the goals of the project is to determine the physiological roles of these genes.  In addition, we are characterizing RpoN-dependent promoters and other intragenic σ⁵⁴-holoenzyme binding sites in the S. Typhimurium genome to identify core and contextual sequences that are important for promoter activity, as well as determining the functions of these sites.