Manganese-dependent transcription regulation by MntR and PerR in Thermus thermophilus HB8.

Bacteria contain conserved mechanisms to control the intracellular levels of metal ions. Metalloregulatory transcription factors bind metal cations and play a central role in regulating gene expression of metal transporters. Often, these transcription factors regulate transcription by binding to a specific DNA sequence in the promoter region of target genes. Understanding the preferred DNA-binding sequence for transcriptional regulators can help uncover novel gene targets and provide insight into the biological role of the transcription factor in the host organism. Here, we identify consensus DNA-binding sequences and subsequent transcription regulatory networks for two metalloregulators from the ferric uptake regulator (FUR) and diphtheria toxin repressor (DtxR) superfamilies in Thermus thermophilus HB8. By homology search, we classify the DtxR homolog as a manganese-specific, MntR (TtMntR), and the FUR homolog as a peroxide-sensing, PerR (TtPerR). Both transcription factors repress separate ZIP transporter genes in vivo, and TtPerR acts as a bifunctional transcription regulator by activating the expression of ferric and hemin transport systems. We show TtPerR and TtMntR bind DNA in the presence of manganese in vitro and in vivo; however, TtPerR is unable to bind DNA in the presence of iron, likely due to iron-mediated histidine oxidation. Unlike canonical PerR homologs, TtPerR does not appear to contribute to peroxide detoxification. Instead, the TtPerR regulon and DNA binding sequence are more reminiscent of Fur or Mur homologs. Collectively, these results highlight the similarities and differences between two metalloregulatory superfamilies and underscore the interplay of manganese and iron in transcription factor regulation.

A CsoR family transcriptional regulator, TTHA1953, controls the sulfur oxidation pathway in Thermus thermophilus HB8.

Transcription regulation is a critical means by which microorganisms sense and adapt to their environments. Bacteria contain a wide range of highly conserved families of transcription factors that have evolved to regulate diverse sets of genes. It is increasingly apparent that structural similarities between transcription factors do not always equate to analogous transcription regulatory networks. For example, transcription factors within the copper-sensing operon repressor (CsoR)-resistance to cobalt and nickel repressor family have been found to repress a wide range of gene targets, including various metal efflux genes, as well as genes involved in sulfide and formaldehyde detoxification machinery. In this study, we identify the preferred DNA-binding sequence for the CsoR-like protein, TTHA1953, from the model extremophile Thermus thermophilus HB8 using the iterative selection approach, restriction endonuclease, protection, selection, and amplification. By mapping significant DNA motifs to the T. thermophilus HB8 genome, we identify potentially regulated genes that we validate with in vitro and in vivo methodologies. We establish TTHA1953 as a master regulator of the sulfur oxidation pathway, providing the first link between CsoR-like proteins and Sox regulation.

Using Restriction Endonuclease, Protection, Selection, and Amplification to Identify Preferred DNA-Binding Sequences of Microbial Transcription Factors.

Regulation of gene expression is a vital component of cellular biology. Transcription factor proteins often bind regulatory DNA sequences upstream of transcription start sites to facilitate the activation or repression of RNA polymerase. Research laboratories have devoted many projects to understanding the transcription regulatory networks for transcription factors, as these regulated genes provide critical insight into the biology of the host organism. Various in vivo and in vitro assays have been developed to elucidate transcription regulatory networks. Several assays, including SELEX-seq and ChIP-seq, capture DNA-bound transcription factors to determine the preferred DNA-binding sequences, which can then be mapped to the host organism's genome to identify candidate regulatory genes. In this protocol, we describe an alternative in vitro, iterative selection approach to ascertaining DNA-binding sequences of a transcription factor of interest using restriction endonuclease, protection, selection, and amplification (REPSA). Contrary to traditional antibody-based capture methods, REPSA selects for transcription factor-bound DNA sequences by challenging binding reactions with a type IIS restriction endonuclease. Cleavage-resistant DNA species are amplified by PCR and then used as inputs for the next round of REPSA. This process is repeated until a protected DNA species is observed by gel electrophoresis, which is an indication of a successful REPSA experiment. Subsequent high-throughput sequencing of REPSA-selected DNAs accompanied by motif discovery and scanning analyses can be used for determining transcription factor consensus binding sequences and potential regulated genes, providing critical first steps in determining organisms' transcription regulatory networks. IMPORTANCE Transcription regulatory proteins are an essential class of proteins that help maintain cellular homeostasis by adapting the transcriptome based on environmental cues. Dysregulation of transcription factors can lead to diseases such as cancer, and many eukaryotic and prokaryotic transcription factors have become enticing therapeutic targets. Additionally, in many understudied organisms, the transcription regulatory networks for uncharacterized transcription factors remain unknown. As such, the need for experimental techniques to establish transcription regulatory networks is paramount. Here, we describe a step-by-step protocol for REPSA, an inexpensive, iterative selection technique to identify transcription factor-binding sequences without the need for antibody-based capture methods.

Identification of the Preferred DNA-Binding Sequence and Transcription Regulatory Network for the Thermophilic Zinc Uptake Regulator TTHA1292.

D-block metal cations are essential for most biological processes; however, excessive metal exposure can be deleterious to the survival of microorganisms. To tightly control heavy metal regulation, prokaryotic organisms have developed several mechanisms to sense and adapt to changes in intracellular and extracellular metal concentrations. The ferric uptake regulator superfamily of transcription factors associates with DNA when complexed with a regulatory metal cofactor and often represses the transcription of genes involved in metal transport, thus providing a genomic response to an environmental stressor. Although extensively studied in mesothermic organisms, there is little information describing ferric uptake regulator homologs in thermophiles. In this study, we biochemically characterize the ferric uptake regulator homolog TTHA1292 in the extreme thermophile Thermus thermophilus HB8. We identify the preferred DNA-binding sequence of TTHA1292 using the combinatorial approach, restriction endonuclease, protection, selection, and amplification (REPSA). We map this sequence to the Thermus thermophilus HB8 genome and identify the TTHA1292 transcription regulatory network, which includes the zinc ABC transporter subunit genes TTHA0596 and TTHA0453/4. We formally implicate TTHA1292 as a zinc uptake regulator and show that zinc coordination is critical for the multimerization of TTHA1292 dimers on DNA in vitro and transcription repression in vivo. IMPORTANCE Discovering how organisms sense and adapt to their environments is paramount to understanding biology. Thermophilic organisms have adapted to survive at elevated temperatures (>50°C); however, our understanding of how these organisms adapt to changes in their environment is limited. In this study, we identify a zinc uptake regulator in the extreme thermophile Thermus thermophilus HB8 that provides a genomic response to fluctuations in zinc availability. These results provide insights into thermophile biology, as well as the zinc uptake regulator family of proteins.

Biolayer interferometry for DNA-protein interactions.

Biolayer interferometry (BLI) is a widely utilized technique for determining macromolecular interaction dynamics in real time. Using changes in the interference pattern of white light reflected off a biosensor tip, BLI can determine binding parameters for protein-protein (e.g., antibody-substrate kinetics) or protein-small molecule (e.g., drug discovery) interactions. However, a less-appreciated application for BLI analysis is DNA-protein interactions. DNA-binding proteins play an immense role in cellular biology, controlling critical processes including transcription, DNA replication, and DNA repair. Understanding how proteins interact with DNA often provides important insight into their biological function, and novel technologies to assay DNA-protein interactions are of broad interest. Currently, a detailed protocol utilizing BLI for DNA-protein interactions is lacking. In the following protocol, we describe the use of BLI and biotinylated-DNA probes to determine the binding kinetics of a transcription factor to a specific DNA sequence. The experimental steps include the generation of biotinylated-DNA probes, the execution of the BLI experiment, and data analysis by scientific graphing and statistical software (e.g., GraphPad Prism). Although the example experiment used throughout this protocol involves a prokaryotic transcription factor, this technique can be easily translated to any DNA-binding protein. Pitfalls and potential solutions for investigating DNA-binding proteins by BLI are also presented.

Discovering the DNA-Binding Consensus of the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359.

Transcription regulatory proteins, also known as transcription factors, function as molecular switches modulating the first step in gene expression, transcription initiation. Cyclic-AMP receptor proteins (CRPs) and fumarate and nitrate reduction regulators (FNRs) compose the CRP/FNR superfamily of transcription factors, regulating gene expression in response to a spectrum of stimuli. In the present work, a reverse-genetic methodology was applied to the study of TTHA1359, one of four CRP/FNR superfamily transcription factors in the model organism Thermus thermophilus HB8. Restriction Endonuclease Protection, Selection, and Amplification (REPSA) followed by next-generation sequencing techniques and bioinformatic motif discovery allowed identification of a DNA-binding consensus for TTHA1359, 5'-AWTGTRA(N)6TYACAWT-3', which TTHA1359 binds to with high affinity. By bioinformatically mapping the consensus to the T. thermophilus HB8 genome, several potential regulatory TTHA1359-binding sites were identified and validated in vitro. The findings contribute to the knowledge of TTHA1359 regulatory activity within T. thermophilus HB8 and demonstrate the effectiveness of a reverse-genetic methodology in the study of putative transcription factors.

Determination and Dissection of DNA-Binding Specificity for the Thermus thermophilus HB8 Transcriptional Regulator TTHB099.

Transcription factors (TFs) have been extensively researched in certain well-studied organisms, but far less so in others. Following the whole-genome sequencing of a new organism, TFs are typically identified through their homology with related proteins in other organisms. However, recent findings demonstrate that structurally similar TFs from distantly related bacteria are not usually evolutionary orthologs. Here we explore TTHB099, a cAMP receptor protein (CRP)-family TF from the extremophile Thermus thermophilus HB8. Using the in vitro iterative selection method Restriction Endonuclease Protection, Selection and Amplification (REPSA), we identified the preferred DNA-binding motif for TTHB099, 5'-TGT(A/g)NBSYRSVN(T/c)ACA-3', and mapped potential binding sites and regulated genes within the T. thermophilus HB8 genome. Comparisons with expression profile data in TTHB099-deficient and wild type strains suggested that, unlike E. coli CRP (CRPEc), TTHB099 does not have a simple regulatory mechanism. However, we hypothesize that TTHB099 can be a dual-regulator similar to CRPEc.

Application of the Environmental Relative Moldiness Index in Indoor Marijuana Grow Operations.

OBJECTIVES: Indoor marijuana grow operations (IMGOs) are increasing due to legalization of recreational and medicinal cannabis at the state level. However, the potential exposures of IMGO workers have not been well studied. Mold exposure has been identified as a major occupational health concern. Mold-specific quantitative polymerase chain reaction (MSQPCR) can provide quantitative exposure data for fungi at the species level. The purpose of this study was to characterize the airborne fungal burden using MSQPCR and to evaluate the applicability of an airborne Environmental Relative Moldiness Index (ERMI) in IMGOs. METHODS: Air and dust samples were collected inside and outside the IMGOs and then analyzed via MSQPCR. These data were then used to calculate IMGO-specific ERMI scores. Culturable air samples were collected on agar plates and analyzed via microscopy. Differences were evaluated between indoor and outdoor concentrations, as well as between air and dust samples. The agreement between MSQPCR and culture-based methods was also evaluated. RESULTS: Based on the geometric means for non-zero values of each fungal species across all IMGOs, the total airborne concentration was approximately 9100 spore equivalent (SE) m-3 with an interquartile range (IQR) of 222 SE m-3. The indoor/outdoor ratio of geometric means across all 36 species per IMGO ranged from 0.4 to 6.2. Significantly higher indoor concentrations of fungal species, including Aspergillus spp., were observed. An average airborne ERMI score of 7 (IQR = 7.6) indicated a relatively high burden of mold across a majority of operations. The ERMI scores were driven by the high concentrations of Group 1 species with a mean of 15.8 and an IQR of 13. There were 63 additional species identified in the culturable air samples not included in the ERMI. CONCLUSIONS: High concentrations of airborne fungi were identified in IMGOs. Our evaluation of the ERMI based on MSQPCR as a rapid diagnostic and risk assessment tool for industrial hygienists in the IMGO setting is equivocal. ERMI did not identify all relevant fungal species associated with this specific occupational environment. We identified several issues with using the ERMI calculation. At this time, the catalog of fungal species needs to optimized for the occupational setting to ensure adequate coverage, especially for those species expected to be found in this burgeoning industry. Further research is necessary to elucidate the link between the ERMI score of airborne samples, worker exposure and health effects in grows to generate an acceptable index score for use in occupational exposure assessments.

General and Genomic DNA-Binding Specificity for the Thermus thermophilus HB8 Transcription Factor TTHB023.

Transcription factors are proteins that recognize specific DNA sequences and affect local transcriptional processes. They are the primary means by which all organisms control specific gene expression. Understanding which DNA sequences a particular transcription factor recognizes provides important clues into the set of genes that they regulate and, through this, their potential biological functions. Insights may be gained through homology searches and genetic means. However, these approaches can be misleading, especially when comparing distantly related organisms or in cases of complicated transcriptional regulation. In this work, we used a biochemistry-based approach to determine the spectrum of DNA sequences specifically bound by the Thermus thermophilus HB8 TetR-family transcription factor TTHB023. The consensus sequence 5'-(a/c)Y(g/t)A(A/C)YGryCR(g/t)T(c/a)R(g/t)-3' was found to have a nanomolar binding affinity with TTHB023. Analyzing the T. thermophilus HB8 genome, several TTHB023 consensus binding sites were mapped to the promoters of genes involved in fatty acid biosynthesis. Notably, some of these were not identified previously through genetic approaches, ostensibly given their potential co-regulation by the Thermus thermophilus HB8 TetR-family transcriptional repressor TTHA0167. Our investigation provides additional evidence supporting the usefulness of a biochemistry-based approach for characterizing putative transcription factors, especially in the case of cooperative regulation.

Identification and Characterization of Preferred DNA-Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA0973.

Advances in genomic sequencing have allowed the identification of a multitude of genes encoding putative transcriptional regulatory proteins. Lacking, often, is a fuller understanding of the biological roles played by these proteins, the genes they regulate or regulon. Conventionally this is achieved through a genetic approach involving putative transcription factor gene manipulation and observations of changes in an organism's transcriptome. However, such an approach is not always feasible or can yield misleading findings. Here, we describe a biochemistry-centric approach, involving identification of preferred DNA-binding sequences for the Thermus thermophilus HB8 transcriptional repressor TTHA0973 using the selection method Restriction Endonuclease Protection, Selection and Amplification (REPSA), massively parallel sequencing, and bioinformatic analyses. We identified a consensus TTHA0973 recognition sequence of 5'-AACnAACGTTnGTT-3' that exhibited nanomolar binding affinity. This sequence was mapped to several sites within the T. thermophilus HB8 genome, a subset of which corresponded to promoter regions regulating genes involved in phenylacetic acid degradation. These studies further demonstrate the utility of a biochemistry-centric approach for the facile identification of potential biological functions for orphan transcription factors in a variety of organisms.

A Systematic Review of the Epidemiologic Literature Assessing Health Outcomes in Populations Living near Oil and Natural Gas Operations: Study Quality and Future Recommendations.

A systematic method was used to review the existing epidemiologic literature and determine the state of the scientific evidence for potential adverse health outcomes in populations living near oil and natural gas (ONG) operations in the United States. The review utilized adapted systematic review frameworks from the medical and environmental health fields, such as Grading of Recommendations, Assessment, Development and Evaluations (GRADE), the Navigation Guide, and guidance from the National Toxicology Program's Office of Health Assessment and Translation (OHAT). The review included 20 epidemiologic studies, with 32 different health outcomes. Studies of populations living near ONG operations provide limited evidence (modest scientific findings that support the outcome, but with significant limitations) of harmful health effects including asthma exacerbations and various self-reported symptoms. Study quality has improved over time and the highest rated studies within this assessment have primarily focused on birth outcomes. Additional high-quality studies are needed to confirm or dispute these correlations.

Exposures and Health Risks from Volatile Organic Compounds in Communities Located near Oil and Gas Exploration and Production Activities in Colorado (U.S.A.).

The study objective was to use a preliminary risk based framework to evaluate the sufficiency of existing air data to answer an important public health question in Colorado: Do volatile organic compounds (VOCs) emitted into the air from oil and gas (OG) operations result in exposures to Coloradoans living at or greater than current state setback distances (500 feet) from OG operations at levels that may be harmful to their health? We identified 56 VOCs emitted from OG operations in Colorado and compiled 47 existing air monitoring datasets that measured these VOCs in 34 locations across OG regions. From these data, we estimated acute and chronic exposures and compared these exposures to health guideline levels using maximum and mean air concentrations. Acute and chronic non-cancer hazard quotients were below one for all individual VOCs. Hazard indices combining exposures for all VOCs were slightly above one. Lifetime excess cancer risk estimates for benzene were between 1.0 × 10-5⁻3.6 × 10-5 and ethylbenzene was 7.3 × 10-6. This evaluation identified a small sub-set of VOCs, including benzene and n-nonane, which should be prioritized for additional exposure characterization in site-specific studies that collect comprehensive time-series measurements of community scale exposures to better assess community exposures.

Coagulase-Negative Staphylococcal Strain Prevents Staphylococcus aureus Colonization and Skin Infection by Blocking Quorum Sensing.

Coagulase-negative staphylococci (CoNS) and Staphylococcus aureus are part of the natural flora of humans and other mammals. We found that spent media from the CoNS species Staphylococcus caprae can inhibit agr-mediated quorum sensing by all classes of S. aureus. A biochemical assessment of the inhibitory activity suggested that the S. caprae autoinducing peptide (AIP) was responsible, and mass spectrometric analysis identified the S. caprae AIP as an eight-residue peptide (YSTCSYYF). Using a murine model of intradermal MRSA infection, the therapeutic efficacy of synthetic S. caprae AIP was evident by a dramatic reduction in both dermonecrotic injury and cutaneous bacterial burden relative to controls. Competition experiments between S. caprae and MRSA demonstrated a significant reduction in MRSA burden using murine models of both skin colonization and intradermal infection. Our findings indicate that important interactions occur between commensals that can impact disease outcomes and potentially shape the composition of the natural flora.

Clinical tool for disease phenotyping in granulomatous lung disease.

BACKGROUND: Exposure to beryllium may lead to granuloma formation and fibrosis in those who develop chronic beryllium disease (CBD). Although disease presentation varies from mild to severe, little is known about CBD phenotypes. This study characterized CBD disease phenotypes using longitudinal measures of lung function. METHODS: Using a case-only study of 207 CBD subjects, subject-specific trajectories over time were estimated from longitudinal pulmonary function and exercise-tolerance tests. To estimate linear combinations of the 30-year values that define underlying patterns of lung function, we conducted factor analysis. Cluster analysis was then performed on all the predicted lung function values at 30 years. These estimates were used to identify underlying features and subgroups of CBD. RESULTS: Two factors, or composite measures, explained nearly 70% of the co-variation among the tests; one factor represented pulmonary function in addition to oxygen consumption and workload during exercise, while the second factor represented exercise tests related to gas exchange. Factors were associated with granulomas on biopsy, exposure, steroid use and lung inflammation. Three clusters of patients (n = 53, n = 59 and, n = 95) were identified based on the collection of test values. Lower levels of each of the factor composite scores and cluster membership were associated with baseline characteristics of patients. CONCLUSIONS: Using factor analysis and cluster analysis, we identified disease phenotypes that were associated with baseline patient characteristics, suggesting that CBD is a heterogeneous disease with varying severity. These clinical tools may be used in future basic and clinical studies to help define the mechanisms and risk factors for disease severity.

Identification and characterization of preferred DNA-binding sites for the Thermus thermophilus transcriptional regulator FadR.

One of the primary transcriptional regulators of fatty acid homeostasis in many prokaryotes is the protein FadR. To better understand its biological function in the extreme thermophile Thermus thermophilus HB8, we sought to first determine its preferred DNA-binding sequences in vitro using the combinatorial selection method Restriction Endonuclease Protection, Selection, and Amplification (REPSA) and then use this information to bioinformatically identify potential regulated genes. REPSA determined a consensus FadR-binding sequence 5´-TTRNACYNRGTNYAA-3´, which was further characterized using quantitative electrophoretic mobility shift assays. With this information, a search of the T. thermophilus HB8 genome found multiple operons potentially regulated by FadR. Several of these were identified as encoding proteins involved in fatty acid biosynthesis and degradation; however, others were novel and not previously identified as targets of FadR. The role of FadR in regulating these genes was validated by physical and functional methods, as well as comparative genomic approaches to further characterize regulons in related organisms. Taken together, our study demonstrates that a systematic approach involving REPSA, biophysical characterization of protein-DNA binding, and bioinformatics can be used to postulate biological roles for potential transcriptional regulators.

Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA.

One of the first steps towards elucidating the biological function of a putative transcriptional regulator is to ascertain its preferred DNA-binding sequences. This may be rapidly and effectively achieved through the application of a combinatorial approach, one involving very large numbers of randomized oligonucleotides and reiterative selection and amplification steps to enrich for high-affinity nucleic acid-binding sequences. Previously, we had developed the novel combinatorial approach Restriction Endonuclease Protection, Selection and Amplification (REPSA), which relies not on the physical separation of ligand-nucleic acid complexes but instead selects on the basis of ligand-dependent inhibition of enzymatic template inactivation, specifically cleavage by type IIS restriction endonucleases. Thus, no prior knowledge of the ligand is required for REPSA, making it more amenable for discovery purposes. Here we describe using REPSA, massively parallel sequencing, and bioinformatics to identify the preferred DNA-binding sites for the transcriptional regulator SbtR, encoded by the TTHA0167 gene from the model extreme thermophile Thermus thermophilus HB8. From the resulting position weight matrix, we can identify multiple operons potentially regulated by SbtR and postulate a biological role for this protein in regulating extracellular transport processes. Our study provides a proof-of-concept for the application of REPSA for the identification of preferred DNA-binding sites for orphan transcriptional regulators and a first step towards determining their possible biological roles.

Association Between Occupational Exposures and Sarcoidosis: An Analysis From Death Certificates in the United States, 1988-1999.

BACKGROUND: Sarcoidosis is a disease that is associated with occupational and environmental antigens, in the setting of a susceptible host. The aim of this study was to examine the association between sarcoidosis mortality and previously reported occupational exposures based on sex and race. METHODS: The decedents enrolled in this study were derived from United States death certificates from 1988-1999. Cause of death was coded according to ICD-9 and ICD-10. The usual occupation was coded with Bureau of the Census Occupation Codes. Mortality odds ratio (MOR) were determined and multiple Poisson regression were performed to evaluate the independent exposure effects after adjustment for age, sex, race and other occupational exposures. RESULTS: Of the 7,118,535 decedents in our study, 3,393 were identified as sarcoidosis-related, including 1,579 identified as sarcoidosis being the underlying cause of death. The sarcoidosis-related MOR of any occupational exposure was 1.52 (95% CI, 1.35-1.71). Women with any exposure demonstrated an increased MOR compared to women without (MOR 1.65, 95% CI, 1.45-1.89). The mortality risk was significantly elevated in those with employment involving metal working, health care, teaching, sales, banking, and administration. Higher sarcoidosis-related mortality risks associated with specific exposures were noted in women vs men and blacks vs whites. CONCLUSIONS: Findings of prior occupations and risk of sarcoidosis were verified using sarcoidosis mortality rates. There were significant differences in risk for sarcoidosis mortality by occupational exposures based on sex and race.

Developing effective worker health and safety training materials: hazard awareness, identification, recognition, and control for the salon industry.

OBJECTIVE: In addition to formaldehyde, workers in salons can be exposed to other chemical irritants, sensitizers, carcinogens, reproductive hazards, infectious agents, ergonomic, and other physical hazards. Worker health and safety training is challenging because of current product labeling practices and the myriad of hazards portending risk for a wide variety of health effects. METHODS: Through a Susan B. Harwood Targeted Topic Training grant from the Occupational Safety and Health Administration and assistance from salon development and training partners, we developed, delivered, and validated a health and safety training program using an iterative five-pronged approach. RESULTS: The training was well received and resulted in knowledge gain, improved workplace safety practices, and increased communication about health and safety. CONCLUSIONS: These training materials are available for download from the Occupational Safety and Health Administration's Susan B. Harwood Training Grant Program Web site.

Staphylococcus epidermidis agr quorum-sensing system: signal identification, cross talk, and importance in colonization.

Staphylococcus epidermidis is an opportunistic pathogen that is one of the leading causes of medical device infections. Global regulators like the agr quorum-sensing system in this pathogen have received a limited amount of attention, leaving important questions unanswered. There are three agr types in S. epidermidis strains, but only one of the autoinducing peptide (AIP) signals has been identified (AIP-I), and cross talk between agr systems has not been tested. We structurally characterized all three AIP types using mass spectrometry and discovered that the AIP-II and AIP-III signals are 12 residues in length, making them the largest staphylococcal AIPs identified to date. S. epidermidis agr reporter strains were developed for each system, and we determined that cross-inhibitory interactions occur between the agr type I and II systems and between the agr type I and III systems. In contrast, no cross talk was observed between the type II and III systems. To further understand the outputs of the S. epidermidis agr system, an RNAIII mutant was constructed, and microarray studies revealed that exoenzymes (Ecp protease and Geh lipase) and low-molecular-weight toxins were downregulated in the mutant. Follow-up analysis of Ecp confirmed the RNAIII is required to induce protease activity and that agr cross talk modulates Ecp activity in a manner that mirrors the agr reporter results. Finally, we demonstrated that the agr system enhances skin colonization by S. epidermidis using a porcine model. This work expands our knowledge of S. epidermidis agr system function and will aid future studies on cell-cell communication in this important opportunistic pathogen.