Research
Deciphering a histone-like code in bacteria
Recently, lysine acetylation was realized to be a widespread bacterial post-translational modification, contrary to the historical notion that this was a rare occurrence. With the advancement of mass spectrometry instrumentation and improvements in the quality of anti-acetyllysine antibodies, the acetylomes of more than 40 different bacterial species have now been characterized. Our work, in collaboration with Dr. Cristea, in this field began with one of the first characterizations of the acetylome of a Gram-positive organism, Bacillus subtilis. We found that acetylation is prevalent, identifying over 2300 unique acetylation sites on more than 750 proteins. The acetylated proteins functioned in a diverse array of important biological processes, including DNA replication, nucleoid organization, translation, cell shape and central carbon metabolism. We made several important early contributions to this rapidly growing field. First, we identified changes in acetylation were placed in the context of the overall proteome changes during cell growth, providing an early picture of temporal regulation. Second, we provided an improved workflow for acetylome characterizations, as we identified an increased number of acetylated sites and proteins than previous B. subtilis studies. Third, due to our large dataset, we were able to identify potential acetylation motifs, including one enriched specifically in stationary phase. Finally, we were one of the first to perform a follow up study to validate our acetylome data. We showed that acetylation of K240 of MreB, a cell-shape determining protein, was important in restricting cell wall growth and cell diameter. Our acetylome data revealed that the essential, histone-like protein HBsu was acetylated at seven sites, including one that changed in abundance depending on growth phase. HBsu belongs to the HU-family of proteins, which are the most widely conserved nucleoid-associated proteins (NAPs). In bacteria, NAPs are largely responsible for chromosome compaction and the coordination of DNA transactions. Despite lack of sequence or structural homology, the HU-family is generally considered to represent functional homologs of histones. As HBsu is a functional homolog of histones, this raised the exciting question: Is there a histone-like code in bacteria? The major goals of my laboratory now are to explore the roles of HBsu acetylation during growth, development and in response to drug challenge to continue to decipher a potential “code.” We also are characterizing the mechanisms of HBsu acetylation and exploring the mechanism(s) of deacetylation.
Exploring novel therapies to combat multidrug-resistant (MDR) Acinetobacter baumannii
Acinetobacter baumannii is an environmental, opportunistic pathogen with the ability to colonize hospitalized patients and cause disease in the critically ill. Multiple outbreaks have been reported from around the world, with ongoing transmission lasting months to years, which is a testimony to the adaptive resilience of these bacteria and their ability to survive in adverse environments. Acinetobacter species can be part of the human skin flora, but they also naturally inhabit soil, water and sewage. A. baumannii is one of the six ESKAPE pathogens, which represent the most common drug-resistant bacterial species that cause hospital-acquired infections (HAIs). These bacteria evolve quickly and readily gain resistance to antibiotics. Further compounding this problem is the emergence of so called “super bugs” that are multidrug resistant (MDR), extensively-drug resistant (XDR, only susceptible to two or fewer classes of drugs) or pan-drug resistant (PDR, resistant to every available drug). Alarmingly, this includes a rise in resistance to last line drugs, like the carbapenems, colistin and tigecycline. The Centers for Disease Control and Prevention (CDC) and World Health Organization (WHO) classify MDR A. baumannii as a serious threat to humans, prompting continuous public health surveillance and prioritizing research to prevent transmission and treat A. baumannii infections. Therefore, there is a great need to develop new antimicrobial therapies and strategies for treatment of these highly resistant infections. Our lab is examining the efficacy of novel combinations of drugs against MDR, XDR and PDR strains of A. baumannii. We work in collaboration with Dr. Fraimow and Dr. Nahra at Cooper University Hospital. We have a collection of ~150 patient isolates collected from 2003-2019. Currently, we are focusing on determining the efficacy of novel combinations of 22 standard-of-care antibiotics with four newly released drugs to the market against our collection of strains. In addition, we are exploring the possibility of using bacteriophage as a therapeutic agent, alone and in combination with antibiotics. For this work, we are collaborating with Dr. Barr (Monash University). We are also interested in understanding the underlying mechanisms of evolution of resistance to environmental stresses that A. baumannii naturally encounters and the potential emergence of cross-resistance to other toxicants or antibiotics.
Design of new antimicrobial surfaces to combat biofilm-based infections
Prosthetics and indwelling medical devices are used to reinforce, replace, or repair damaged tissues and organs. Due to an increase in the aging population and advances in biomaterials, the use of biomaterial-based medical devices has drastically increased in recent times. While these devices have significantly improved the quality of life and prolonged the lives of many patients, biomaterial implants, such as titanium artificial knee joints or pacemakers, pose a risk for microbial colonization and subsequent complications. Bacterial colonization of surgical implants or prosthetic medical devices leads to device failure, chronic infections, and increased morbidity and mortality. Treatment of severe bacterial infections includes a high dose administration of antibiotics and eventual removal and replacement of the infected implant. This process is costly and often ineffective due to the prevalence of antibiotic-resistant bacterial strains and there is an increased risk for reinfection of the new implant. Infections of medical devices are typically caused by biofilms, which are highly structured multicellular communities of bacteria that are encased in an extracellular matrix of polysaccharides, DNA, and proteins. The biofilm affords the bacteria protection against host immune responses, biocides and antibiotics, making them inherently difficult to treat. Biofilms are a source for recurrent bloodstream infections, further highlighting the need to prevent biofilm formation on indwelling medical devices. It is estimated that Staphylococcus aureus accounts for two-thirds of all indwelling medical device infections. We collaborate with Dr. Vega (Rowan University, Biomedical Engineering) for this work. We are exploring the use of a combination of antimicrobial peptides (AMPs) tethered to a biomaterial surface and examining their ability to kill and prevent S. aureus biofilms. AMPs are a diverse class of amino acid sequences that are effective in mitigating biofilm formation in model systems. Our goal is to be able to design a new surface that can be used to coat surgically implanted medical devices and prevent biofilm-based infections.
