201 results on '"Waters CM"'
Search Results
2. Risks to carbon dynamics in semi-arid woodlands of eastern Australia under current and future climates
- Author
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Nolan, RH, Sinclair, J, Waters, CM, Mitchell, PJ, Eldridge, DJ, Paul, KI, Roxburgh, S, Butler, DW, and Ramp, D
- Subjects
Climate Change ,Australia ,Bayes Theorem ,Forests ,Environmental Sciences ,Carbon - Abstract
© 2019 Elsevier Ltd Extreme disturbance events, such as wildfire and drought, have large impacts on carbon storage and sequestration of forests and woodlands globally. Here, we present a modelling approach that assesses the relative impact of disturbances on carbon storage and sequestration, and how this will alter under climate change. Our case study is semi-arid Australia where large areas of land are managed to offset over 122 million tonnes of anthropogenic carbon emissions over a 100-year period. These carbon offsets include mature vegetation that has been protected from clearing and regenerating vegetation on degraded agricultural land. We use a Bayesian Network model to combine multiple probabilistic models of the risk posed by fire, drought, grazing and recruitment failure to carbon dynamics. The model is parameterised from a review of relevant literature and additional quantitative analyses presented here. We found that the risk of vegetation becoming a net source of carbon due to a mortality event, or failing to realise maximum sequestration potential, through recruitment failure in regenerating vegetation, was primarily a function of rainfall in this semi-arid environment. However, the relative size of an emissions event varied across vegetation communities depending on plant attributes, specifically resprouting capacity. Modelled climate change effects were variable, depending on the climate change projection used. Under ‘best-case’ or ‘most-likely’ climate scenarios for 2050, similar or increased projections of mean annual precipitation, associated with a build-up of fuel, were expected to drive an increase in fire activity (a 40–160% increase), but a decrease in drought (a 20–35% decrease). Under a ‘worst-case’ climate scenario, fire activity was expected to decline (a 37% decrease), but drought conditions remain similar (a 5% decrease). These projected changes to the frequency of drought and fire increase the risk that vegetation used for carbon offsetting will fail to provide anticipated amounts of carbon abatement over their lifetime.
- Published
- 2019
3. Steady-state pleural fluid flow and pressure and the effects of lung buoyancy
- Author
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Haber, R, Grotberg, J, Glucksberg, M, Miserocchi, G, Venturoli, D, Del Fabbro, M, Waters, C, Grotberg, JB, Glucksberg, MR, Waters, CM, Haber, R, Grotberg, J, Glucksberg, M, Miserocchi, G, Venturoli, D, Del Fabbro, M, Waters, C, Grotberg, JB, Glucksberg, MR, and Waters, CM
- Abstract
Both theoretical and experimental studies of pleural fluid dynamics and lung buoyancy during steady-state, apneic conditions are presented. The theory, shows that steady-state, top-to-bottom pleural-liquid flow, creates a pressure distribution that opposes lung buoyancy. These two forces may, balance, permitting dynamic lung floating, but when they, do not, pleural-pleural contact is required. The animal experiments examine pleural-liquid pressure distributions in response to simulated reduced gravity, achieved by, lung inflation with perfluorocarbon liquid as compared to air The resulting decrease in lung buoyancy modifies the force balance in the pleural fluid, which is reflected in its vertical pressure gradient. The data and model show that the decrease in buoyancy with perfluorocarbon inflation causes the vertical pressure gradient to approach hydrostatic. In the microgravity analogue, the pleural pressures would be toward a more uniform distribution, consistent with ventilation studies during spaceflight. The pleural liquid turnover predicted by the model is computed and found to be comparable to experimental values from the literature. The model provides the flow field, which can be used to develop a full transport theory for molecular and cellular constituents that are found in pleural fluid.
- Published
- 2001
4. Changes in c-myc expression and the kinetics of dexamethasone-induced programmed cell death (apoptosis) in human lymphoid leukaemia cells
- Author
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Wood, AC, primary, Waters, CM, additional, Garner, A, additional, and Hickman, JA, additional
- Published
- 1994
- Full Text
- View/download PDF
5. End-of-life care directives among African Americans: lessons learned -- a need for community-centered discussion and education.
- Author
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Waters CM
- Abstract
African Americans appear to be less likely to know about advance directives and, even if known, to complete them. This small, exploratory study used a community-centered educational group discussion to assess African Americans' knowledge, attitudes, and utilization of end-of-life care directives before the occurrence of a health crisis. McNemar and paired t tests were computed to detect immediate changes in participants' initial and final perceptions about advance directives before and after the group discussion. Findings indicated further education is needed to clarify the terms used for advance directives. African Americans rely on a family-centered approach to end-of-life decision making, especially in the absence of written advance directives. They are open to community forums to discuss end-of-life care choices if presented the opportunity. Culture plays an essential role in this issue. There is a need for community health nurses to develop community-based educational programs that are not a 'one-size-fits-all' approach. [ABSTRACT FROM AUTHOR]
- Published
- 2000
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6. A Vibrio cholerae Type IV restriction system targets glucosylated 5-hydroxymethylcytosine to protect against phage infection.
- Author
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Gomez JB and Waters CM
- Subjects
- Genomic Islands, Bacterial Proteins genetics, Bacterial Proteins metabolism, Vibrio cholerae virology, Vibrio cholerae genetics, 5-Methylcytosine metabolism, 5-Methylcytosine analogs & derivatives, Bacteriophages genetics, Bacteriophages physiology
- Abstract
A major challenge faced by Vibrio cholerae is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, V. cholerae has acquired and/or evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized that more were encoded in V. cholerae given the low diversity of phages that have been isolated, which infect this species. Using a V. cholerae genomic library, we identified a Type IV restriction system consisting of two genes within a 16-kB region of the Vibrio pathogenicity island-2, which we name TgvA and TgvB ( T ype I-embedded g mrSD -like system of V PI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modifications are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff, becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We also show that the Type I restriction-modification system that embeds the tgvAB genes protects against phage T3, secΦ18, secΦ27, and λ, suggesting that this region is a phage defense island. Our study uncovers a novel Type IV restriction system in V. cholerae , increasing our understanding of the evolution and ecology of V. cholerae, while highlighting the evolutionary interplay between restriction systems and phage genome modification.IMPORTANCEBacteria are constantly being predated by bacteriophage (phage). To counteract this predation, bacteria have evolved a myriad of defense systems. Some of these systems specifically digest infecting phage by recognizing unique base modifications present on the phage DNA. In this study, we discover a Type IV restriction system encoded in V. cholerae, which we name TgvAB, and demonstrate it recognizes and restricts phage that have 5-hydroxymethylcytosine glucosylated DNA. Moreover, the evolution of resistance to TgvAB render phage susceptible to other Type IV restriction systems, demonstrating a significant evolutionary tradeoff. These results enhance our understanding of the evolution of V. cholerae and more broadly how bacteria evade phage predation., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
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7. Combinatorial control of Pseudomonas aeruginosa biofilm development by quorum-sensing and nutrient-sensing regulators.
- Author
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Chen G, Fanouraki G, Anandhi Rangarajan A, Winkelman BT, Winkelman JT, Waters CM, and Mukherjee S
- Subjects
- Signal Transduction, Mutation, Nutrients metabolism, Repressor Proteins genetics, Repressor Proteins metabolism, Biofilms growth & development, Quorum Sensing genetics, Pseudomonas aeruginosa physiology, Pseudomonas aeruginosa genetics, Bacterial Proteins genetics, Bacterial Proteins metabolism, Gene Expression Regulation, Bacterial
- Abstract
The human pathogen Pseudomonas aeruginosa , a leading cause of hospital-acquired infections, inhabits and forms sessile antibiotic-resistant communities called biofilms in a wide range of biotic and abiotic environments. In this study, we examined how two global sensory signaling pathways-the RhlR quorum-sensing system and the CbrA/CbrB nutritional adaptation system-intersect to control biofilm development. Previous work has shown that individually these two systems repress biofilm formation. Here, we used biofilm analyses, RNA-seq, and reporter assays to explore the combined effect of information flow through RhlR and CbrA on biofilm development. We find that the Δ rhlR Δ cbrA double mutant exhibits a biofilm morphology and an associated transcriptional response distinct from wildtype and the parent Δ rhlR and Δ cbrA mutants indicating codominance of each signaling pathway. The Δ rhlR Δ cbrA mutant gains suppressor mutations that allow biofilm expansion; these mutations map to the crc gene resulting in loss of function of the carbon catabolite repression protein Crc. Furthermore, the combined absence of RhlR and CbrA leads to a drastic reduction in the abundance of the Crc antagonist small RNA CrcZ. Thus, CrcZ acts as the molecular convergence point for quorum- and nutrient-sensing cues. We find that in the absence of antagonism by CrcZ, Crc promotes the expression of biofilm matrix components-Pel exopolysaccharide, and CupB and CupC fimbriae. Therefore, this study uncovers a regulatory link between nutritional adaption and quorum sensing with potential implications for anti-biofilm targeting strategies.IMPORTANCEBacteria often form multicellular communities encased in an extracytoplasmic matrix called biofilms. Biofilm development is controlled by various environmental stimuli that are decoded and converted into appropriate cellular responses. To understand how information from two distinct stimuli is integrated, we used biofilm formation in the human pathogen Pseudomonas aeruginosa as a model and studied the intersection of two global sensory signaling pathways-quorum sensing and nutritional adaptation. Global transcriptomics on biofilm cells and reporter assays suggest parallel regulation of biofilms by each pathway that converges on the abundance of a small RNA antagonist of the carbon catabolite repression protein, Crc. We find a new role of Crc as it modulates the expression of biofilm matrix components in response to the environment. These results expand our understanding of the genetic regulatory strategies that allow P. aeruginosa to successfully develop biofilm communities., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
- Full Text
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8. Negative feedback of cyclic di-GMP levels optimizes switching between sessile and motile lifestyles in Vibrio cholerae .
- Author
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Rangarajan AA, Schroeder JW, Hurto RL, Severin GB, Pell ME, Hsieh ML, Waters CM, and Freddolino L
- Abstract
The signaling molecule cyclic di-GMP (cdG) controls the switch between bacterial motility and biofilm production, and fluctuations in cellular levels of cdG have been implicated in Vibrio cholerae pathogenesis. Intracellular concentrations of cdG are controlled by the interplay of diguanylate cyclase (DGC) enzymes, which synthesize cdG to promote biofilms, and phosphodiesterase (PDE) enzymes, which hydrolyse cdG to drive motility. To track the complete regulatory logic of how V. cholerae responds to changing cdG levels, we followed a timecourse of overexpression of either the V. harveyi diguanylate cyclase QrgB or a variant of QrgB lacking catalytic activity (QrgB*). We find that QrgB increases cdG levels relative to QrgB* for 30 minutes after overexpression, but the effect of QrgB on cdG levels plateaus at 30 minutes, indicating tight adaptive control of cdG levels. In contrast, loss of VpsR, a master regulator activating biofilm formation upon binding to cdG, leads to higher baseline levels of cdG and continuously increasing cdG through 60 minutes after QrgB induction, revealing the existence of a negative feedback loop on cdG levels operating through VpsR. Through a combination of RNA polymerase ChIP-seq, RNA-seq, and genetic approaches, we show that transcription of a gene encoding a PDE, cdgC , is activated by VpsR at high cdG concentrations, mediating this negative feedback on cdG levels. We further identify a transcript encoded within, and antisense to, the cdgC open reading frame which we name sRNA negative regulator of CdgC (SnrC). RNA polymerase ChIP-seq and RNA-seq demonstrate SnrC to be expressed specifically under conditions of high cdG in the absence of VpsR. Ectopic SnrC expression increases cdG levels in a manner dependent on CdgC, demonstrating that its effect on cdG levels is likely through interference with CdgC production. Further, although cells lacking cdgC exhibit enhanced biofilm formation, these mutants are outcompeted by wild type V. cholerae in colonization assays that reward a combination of attachment, dispersal, and motility behaviors. These results underscore the importance of negative feedback regulation of cdG to maintain appropriate homeostatic levels for efficient transitioning between biofilm formation and motility, both of which are necessary over the course of the V. cholerae infection cycle.
- Published
- 2024
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9. National Beef Quality Audit-2022: in-plant assessments of quality and yield determining carcass characteristics of fed steers and heifers.
- Author
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Mayer TR, Borders SE, Schwartz TE, Gehring KB, Griffin DB, Kerth CR, Belk KE, Scanga JA, Nair MN, Pfeiffer MM, Mafi GG, Harr KM, Lawrence TE, Tennant TC, Lucherk LW, O'Quinn TG, Beyer ES, Bass PD, Garcia LG, Bohrer BM, Pempek JA, Garmyn AJ, Maddock RJ, Carr CC, Pringle TD, Scheffler TL, Scheffler JM, Stelzleni AM, Gonzalez JM, Underwood KR, Harsh BN, Waters CM, and Savell JW
- Abstract
The National Beef Quality Audit - 2022 serves as a benchmark of the current fed steer and heifer population of the U.S. beef industry and allows comparison to previous audits as a method of monitoring industry progress. In-plant cooler assessments and collections of beef carcass data took place from July 2021 to November 2022. During in-plant evaluations, 10% of 1-d production was surveyed for quality and yield indicating characteristics of fed beef carcasses ( n = 9,746 beef carcasses). Distributions of sex classes among sampled carcasses were steer (65.0%) and heifer (35.0%), whereas distributions of breed type were native (87.7%), dairy (11.3%), and Bos indicus (0.9%). Mean values were observed for USDA Yield Grades ( YG ; 3.3), USDA Quality Grade ( QG ; Choice
16 ), marbling score (Small98 ), ribeye area (91.0 cm2 ), adjusted fat thickness (1.49 cm), hot carcass weight (401.9 kg), and KPH (2.5%). Mean overall maturity was A66 , with a mean lean maturity of A56 and mean skeletal maturity of A72 . There were 28.1% of carcasses identified for use in a USDA-certified beef G-Schedule Program. Defects, such as dark cutting and blood splash, were observed at 1.8% and 0.5%, respectively. Distributions of USDA YG were YG 1 (8.2%), YG 2 (30.7%), YG 3 (40.2%), YG 4 (16.6%), and YG 5 (4.3%). USDA QGs were observed at 7.5% Prime, 69.2% Choice, 16.4% Select, and 6.8% other. The results of this study provide an updated look at the current grading trends of beef carcasses in the United States to drive progress in the fed beef industry., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Society of Animal Science.)- Published
- 2024
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10. Slings and arrows: sRNAs mediate intragenomic competition.
- Author
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Ferrell MJ and Waters CM
- Subjects
- RNA, Small Untranslated genetics, RNA, Small Untranslated metabolism, Genome, Bacterial, Bacteriophages genetics, Bacteriophages physiology, Gene Expression Regulation, Bacterial, RNA, Bacterial genetics, RNA, Bacterial metabolism, Vibrio cholerae genetics, Prophages genetics, Prophages physiology
- Abstract
Bacterial genomes are littered with exogenous: competing DNA elements. Here, Sprenger et al. demonstrate that the Vibrio cholerae prophage VP882 modulates host functions via production of regulatory sRNAs to promote phage development. Alternatively, host sRNAs inhibit the VP882 lytic phase by specifically regulating phage genes., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
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11. Plasmid-free cheater cells commonly evolve during laboratory growth.
- Author
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Bedore AM and Waters CM
- Subjects
- Humans, Plasmids genetics, beta-Lactamases genetics, Penicillins pharmacology, Anti-Bacterial Agents pharmacology, Bacteria genetics
- Abstract
It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, extracellular beta-lactamases produced by resistant cells that subsequently degrade penicillin and related antibiotics allow neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show in multiple bacterial species that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface-grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss was still observed. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.IMPORTANCEPlasmids are routinely used in microbiology as readouts of cell biology or tools to manipulate cell function. Central to these studies is the assumption that all cells in an experiment contain the plasmid. Plasmid maintenance in a host cell typically depends on a plasmid-encoded antibiotic resistance marker, which provides a selective advantage when the plasmid-containing cell is grown in the presence of antibiotic. Here, we find that growth of plasmid-containing bacteria on a surface and to a lesser extent in liquid culture in the presence of three distinct antibiotic families leads to the evolution of a significant number of plasmid-free cells, which rely on the resistance mechanisms of the plasmid-containing cells. This process generates a heterogenous population of plasmid-free and plasmid-containing bacteria, an outcome which could confound further experimentation., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
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12. A Vibrio cholerae Type IV restriction system targets glucosylated 5-hydroxyl methyl cytosine to protect against phage infection.
- Author
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Gomez JB and Waters CM
- Abstract
A major challenge faced by Vibrio cholerae is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, V. cholerae has evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized more were encoded in V. cholerae given the relative paucity of phage that have been isolated which infect this species. Using a V. cholerae genomic library, we identified a Type IV restriction system consisting of two genes within a 16kB region of the Vibrio pathogenicity island-2 that we name TgvA and TgvB ( T ype I-embedded g mrSD-like system of V PI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modification are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We show that additional phage defense genes are encoded in VPI-2 that protect against other phage like T3, secΦ18, secΦ27 and λ. Our study uncovers a novel Type IV restriction system in V. cholerae , increasing our understanding of the evolution and ecology of V. cholerae while highlighting the evolutionary interplay between restriction systems and phage genome modification., Competing Interests: Declarations of interest: none
- Published
- 2024
- Full Text
- View/download PDF
13. National Beef Quality Audit-2022: Transportation, mobility, live cattle, and hide assessments to determine producer-related defects that affect animal welfare and the value of market cows and bulls at processing facilities.
- Author
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Borders SE, Schwartz TE, Mayer TR, Gehring KB, Griffin DB, Kerth CR, Belk KE, Edwards-Callaway L, Scanga JA, Nair MN, Morgan JB, Douglas JB, Pfeiffer MM, Mafi GG, Harr KM, Lawrence TE, Tennant TC, Lucherk LW, O'Quinn TG, Beyer ES, Bass PD, Garcia LG, Bohrer BM, Pempek JA, Garmyn AJ, Maddock RJ, Carr CC, Pringle TD, Scheffler TL, Scheffler JM, Stelzleni AM, Gonzalez JM, Underwood KR, Harsh BN, Waters CM, and Savell JW
- Abstract
The National Beef Quality Audit (NBQA)-2022 serves as a benchmark of the current market cow and bull sectors of the U.S. beef industry and allows comparison to previous audits as a method of monitoring industry progress. From September 2021 through May 2022, livestock trailers ( n = 125), live animals ( n = 5,430), and post-slaughter hide-on animals ( n = 6,674) were surveyed at 20 commercial beef processing facilities across the U.S. Cattle were transported in a variety of trailer types for an average distance of 490.6 km and a mean transport time of 6.3 h. During transit, cattle averaged 2.3 m
2 of trailer space per animal indicating sufficient space was provided according to industry guidelines. Of all trailers surveyed, 55.3% transported cattle from an auction barn to a processing facility. When surveyed, 63.6% of all truck drivers reported to be Beef Quality Assurance certified. The majority (77.0%) of cattle were sound when evaluated for mobility. Mean body condition scores (9-point scale) for beef cows and bulls were 3.8 and 4.4, respectively, whereas mean body condition scores (5-point scale) for dairy cows and bulls were 2.3 and 2.6, respectively. Of the cattle surveyed, 45.1% had no visible live animal defects, and 37.9% had only a single defect. Of defects present in cows, 64.6% were attributed to an udder problem. Full udders were observed in 47.5% of all cows. Nearly all cattle were free of visible abscesses and knots (97.9% and 98.2%, respectively). No horns were observed in 89.4% of all cattle surveyed. Beef cattle were predominantly black-hided (68.9% and 67.4% of cows and bulls, respectively). Holstein was the predominant dairy animal observed and accounted for 85.7% of the cows and 98.0% of the bulls. Only 3.1% of all animals had no form of identification. Findings from the NBQA-2022 show improvements within the industry and identify areas that require continued education and research to improve market cow and bull welfare and beef quality., Competing Interests: There are no known conflicts of interest by any of the authors., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Society of Animal Science.)- Published
- 2024
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14. pGpG-signaling regulates virulence and global transcriptomic targets in Erwinia amylovora .
- Author
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Kharadi RR, Hsueh BY, Waters CM, and Sundin GW
- Abstract
Cyclic-di-GMP (c-di-GMP) is a critical bacterial second messenger that enables the physiological phase transition in Erwinia amylovora , the phytopathogenic bacterium that causes fire blight disease. C-di-GMP generation is dependent on diguanylate cyclase enzymes while the degradation of c-di-GMP can occur through the action of phosphodiesterase (PDE) enzymes that contain an active EAL and/or a HD-GYP domain. The HD-GYP-type PDEs, which are absent in E. amylovora , can directly degrade c-di-GMP into two GMP molecules. PDEs that contain an active EAL domain, as found in all active PDEs in E. amylovora, degrade c-di-GMP into pGpG. The signaling function of pGpG is not fully understood in bacterial systems. A transcriptomic approach revealed that elevated levels of pGpG in E. amylovora impacted several genes involved in metabolic and regulatory functions including several type III secretion and extracellular appendage related genes. The heterologous overexpression of an EAL or HD-GYP-type PDE in different background E. amylovora strains with varying c-di-GMP levels revealed that in contrast to the generation of pGpG, the direct breakdown of c-di-GMP into GMP by the HD-GYP-type PDE led to an elevation in amylovoran production and biofilm formation despite a decrease in c-di-GMP levels. The breakdown of c-di-GMP into pGpG (as opposed to GTP) also led to a decrease in virulence in apple shoots. The expression of hrpS was significantly increased in response to the breakdown of c-di-GMP into pGpG. Further, our model suggests that a balance in the intracellular ratio of pGpG and c-di-GMP is essential for biofilm regulation in E. amylovora.
- Published
- 2024
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15. Deficiency of Acute-Phase Serum Amyloid A Exacerbates Sepsis-Induced Mortality and Lung Injury in Mice.
- Author
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Ji A, Trumbauer AC, Noffsinger VP, Meredith LW, Dong B, Wang Q, Guo L, Li X, De Beer FC, Webb NR, Tannock LR, Starr ME, Waters CM, and Shridas P
- Subjects
- Animals, Mice, Serum Amyloid A Protein genetics, Lung pathology, Chemokines, Mice, Inbred C57BL, Disease Models, Animal, Lung Injury pathology, Sepsis pathology
- Abstract
Serum amyloid A (SAA) is a family of proteins, the plasma levels of which may increase >1000-fold in acute inflammatory states. We investigated the role of SAA in sepsis using mice deficient in all three acute-phase SAA isoforms (SAA-TKO). SAA deficiency significantly increased mortality rates in the three experimental sepsis mouse models: cecal ligation and puncture (CLP), cecal slurry (CS) injection, and lipopolysaccharide (LPS) treatments. SAA-TKO mice had exacerbated lung pathology compared to wild-type (WT) mice after CLP. A bulk RNA sequencing performed on lung tissues excised 24 h after CLP indicated significant enrichment in the expression of genes associated with chemokine production, chemokine and cytokine-mediated signaling, neutrophil chemotaxis, and neutrophil migration in SAA-TKO compared to WT mice. Consistently, myeloperoxidase activity and neutrophil counts were significantly increased in the lungs of septic SAA-TKO mice compared to WT mice. The in vitro treatment of HL-60, neutrophil-like cells, with SAA or SAA bound to a high-density lipoprotein (SAA-HDL), significantly decreased cellular transmigration through laminin-coated membranes compared to untreated cells. Thus, SAA potentially prevents neutrophil transmigration into injured lungs, thus reducing exacerbated tissue injury and mortality. In conclusion, we demonstrate for the first time that endogenous SAA plays a protective role in sepsis, including ameliorating lung injury.
- Published
- 2023
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16. Scratching the Surface of Individual Aerosol Particle Properties.
- Author
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Ault AP and Waters CM
- Published
- 2023
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17. Activation of a Vibrio cholerae CBASS anti-phage system by quorum sensing and folate depletion.
- Author
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Severin GB, Ramliden MS, Ford KC, Van Alst AJ, Sanath-Kumar R, Decker KA, Hsueh BY, Chen G, Yoon SH, Demey LM, O'Hara BJ, Rhoades CR, DiRita VJ, Ng W-L, and Waters CM
- Subjects
- Quorum Sensing physiology, Signal Transduction, Vibrio cholerae metabolism, Bacteriophages genetics
- Abstract
Importance: To counteract infection with phage, bacteria have evolved a myriad of molecular defense systems. Some of these systems initiate a process called abortive infection, in which the infected cell kills itself to prevent phage propagation. However, such systems must be inhibited in the absence of phage infection to prevent spurious death of the host. Here, we show that the cyclic oligonucleotide based anti-phage signaling system (CBASS) accomplishes this by sensing intracellular folate molecules and only expressing this system in a group. These results enhance our understanding of the evolution of the seventh Vibrio cholerae pandemic and more broadly how bacteria defend themselves against phage infection., Competing Interests: The authors declare no conflict of interest.
- Published
- 2023
- Full Text
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18. Vibrio cholerae phage ICP3 requires O1 antigen for infection.
- Author
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Beckman DA and Waters CM
- Subjects
- Humans, Environment, Membrane Proteins, Vibrio cholerae genetics, Cholera, Bacteriophages genetics
- Abstract
In its natural aquatic environment, the bacterial pathogen Vibrio cholerae , the causative agent of the enteric disease cholera, is in constant competition with bacterial viruses known as phages. Following ICP3 infection, V. cholerae cultures that exhibited phage killing always recovered overnight, and clones isolated from these regrowth populations exhibited complete resistance to subsequent infections. Whole-genome sequencing of these resistant mutants revealed seven distinct mutations in genes encoding for enzymes involved in O1 antigen biosynthesis, demonstrating that the O1 antigen is a previously uncharacterized putative receptor of ICP3. To further elucidate the specificity of the resistance conferred by these mutations, they were challenged with the V. cholerae -specific phages ICP1 and ICP2. All seven O1 antigen mutants demonstrated pan-resistance to ICP1 but not ICP2, which utilizes the OmpU outer membrane protein as a receptor. We show that resistant mutations to ICP1 and ICP3 evolve at a significantly higher frequency than ICP2, but these mutations have a significant fitness tradeoff to V. cholerae and are unable to evolve in the presence of an antimicrobial that mimics host cell defensins., Competing Interests: The authors declare no conflict of interest.
- Published
- 2023
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19. Replication cycle timing determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system.
- Author
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Hsueh BY, Ferrell MJ, Sanath-Kumar R, Bedore AM, and Waters CM
- Subjects
- Cytidine Deaminase, Bacteria, Nucleotides, RNA, Antitoxins, Bacteriophages genetics
- Abstract
Toxin-antitoxin (TA) systems are ubiquitous two-gene loci that bacteria use to regulate cellular processes such as phage defense. Here, we demonstrate the mechanism by which a novel type III TA system, avcID, is activated and confers resistance to phage infection. The toxin of the system (AvcD) is a deoxycytidylate deaminase that converts deoxycytidines (dC) to dexoyuridines (dU), while the RNA antitoxin (AvcI) inhibits AvcD activity. We have shown that AvcD deaminated dC nucleotides upon phage infection, but the molecular mechanism that activated AvcD was unknown. Here we show that the activation of AvcD arises from phage-induced inhibition of host transcription, leading to degradation of the labile AvcI. AvcD activation and nucleotide depletion not only decreases phage replication but also increases the formation of defective phage virions. Surprisingly, infection of phages such as T7 that are not inhibited by AvcID also lead to AvcI RNA antitoxin degradation and AvcD activation, suggesting that depletion of AvcI is not sufficient to confer protection against some phage. Rather, our results support that phage with a longer replication cycle like T5 are sensitive to AvcID-mediated protection while those with a shorter replication cycle like T7 are resistant., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Hsueh et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
- Full Text
- View/download PDF
20. Plasmid-free cheater cells commonly evolve during laboratory growth.
- Author
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Bedore AM and Waters CM
- Abstract
It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, secretion of beta-lactamase from resistant cells, and subsequent degradation of nearby penicillin and related antibiotics, allows neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss still occurred. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.
- Published
- 2023
- Full Text
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21. Spatial metabolomics reveals glycogen as an actionable target for pulmonary fibrosis.
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Conroy LR, Clarke HA, Allison DB, Valenca SS, Sun Q, Hawkinson TR, Young LEA, Ferreira JE, Hammonds AV, Dunne JB, McDonald RJ, Absher KJ, Dong BE, Bruntz RC, Markussen KH, Juras JA, Alilain WJ, Liu J, Gentry MS, Angel PM, Waters CM, and Sun RC
- Subjects
- Mice, Animals, Humans, Glycogen, Metabolomics methods, Polysaccharides, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization methods, Pulmonary Fibrosis
- Abstract
Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high-dimensionality reduction/spatial clustering and histopathological annotation of matrix assisted laser desorption/ionization imaging datasets to assess tissue metabolic heterogeneity in human lung diseases. Using metabolic features identified from this pipeline, we hypothesize that metabolic channeling between glycogen and N-linked glycans is a critical metabolic process favoring pulmonary fibrosis progression. To test our hypothesis, we induced pulmonary fibrosis in two different mouse models with lysosomal glycogen utilization deficiency. Both mouse models displayed blunted N-linked glycan levels and nearly 90% reduction in endpoint fibrosis when compared to WT animals. Collectively, we provide conclusive evidence that lysosomal utilization of glycogen is required for pulmonary fibrosis progression. In summary, our study provides a roadmap to leverage spatial metabolomics to understand foundational biology in pulmonary diseases., (© 2023. The Author(s).)
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- 2023
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22. Cervical spinal cord injury leads to injury and altered metabolism in the lungs.
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Huffman EE, Dong BE, Clarke HA, Young LEA, Gentry MS, Allison DB, Sun RC, Waters CM, and Alilain WJ
- Abstract
High-cervical spinal cord injury often disrupts respiratory motor pathways and disables breathing in the affected population. Moreover, cervically injured individuals are at risk for developing acute lung injury, which predicts substantial mortality rates. While the correlation between acute lung injury and spinal cord injury has been found in the clinical setting, the field lacks an animal model to interrogate the fundamental biology of this relationship. To begin to address this gap in knowledge, we performed an experimental cervical spinal cord injury (N = 18 ) alongside sham injury ( N = 3) and naïve animals ( N = 15) to assess lung injury in adult rats. We demonstrate that animals display some early signs of lung injury two weeks post-spinal cord injury. While no obvious histological signs of injury were observed, the spinal cord injured cohort displayed significant signs of metabolic dysregulation in multiple pathways that include amino acid metabolism, lipid metabolism, and N-linked glycosylation. Collectively, we establish for the first time a model of lung injury after spinal cord injury at an acute time point that can be used to monitor the progression of lung damage, as well as identify potential targets to ameliorate acute lung injury., Competing Interests: The authors report no competing interests., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Guarantors of Brain.)
- Published
- 2023
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23. Activation of TREK-1 ( K 2P 2.1 ) potassium channels protects against influenza A-induced lung injury.
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Zyrianova T, Lopez B, Zou K, Gu C, Pham D, Talapaneni S, Waters CM, Olcese R, and Schwingshackl A
- Subjects
- Animals, Humans, Mice, Chemokine CXCL10 metabolism, Interleukin-6 metabolism, Lung metabolism, Acute Lung Injury pathology, Influenza A virus, Influenza, Human pathology, Orthomyxoviridae Infections pathology, Potassium Channels, Tandem Pore Domain genetics, Potassium Channels, Tandem Pore Domain metabolism
- Abstract
Influenza-A virus (IAV) infects yearly an estimated one billion people worldwide, resulting in 300,000-650,000 deaths. Preventive vaccination programs and antiviral medications represent the mainstay of therapy, but with unacceptably high morbidity and mortality rates, new targeted therapeutic approaches are urgently needed. Since inflammatory processes are commonly associated with measurable changes in the cell membrane potential (Em), we investigated whether Em hyperpolarization via TREK-1 ( K
2P 2.1 ) K+ channel activation can protect against influenza-A virus (IAV)-induced pneumonia. We infected mice with IAV, which after 5 days caused 10-15% weight loss and a decrease in spontaneous activity, representing a clinically relevant infection. We then started a 3-day intratracheal treatment course with the novel TREK-1 activating compounds BL1249 or ML335. We confirmed TREK-1 activation with both compounds in untreated and IAV-infected primary human alveolar epithelial cells (HAECs) using high-throughput fluorescent imaging plate reader (FLIPR) assays. In mice, TREK-1 activation with BL1249 and ML335 counteracted IAV-induced histological lung injury and decrease in lung compliance and improved BAL fluid total protein levels, cell counts, and inflammatory IL-6, IP-10/CXCL-10, MIP-1α, and TNF-α levels. To determine whether these anti-inflammatory effects were mediated by activation of alveolar epithelial TREK-1 channels, we studied the effects of BL1249 and ML335 in IAV-infected HAEC, and found that TREK-1 activation decreased IAV-induced inflammatory IL-6, IP-10/CXCL10, and CCL-2 secretion. Dissection of TREK-1 downstream signaling pathways and construction of protein-protein interaction (PPI) networks revealed NF-κB1 and retinoic acid-inducible gene-1 (RIG-1) cascades as the most likely targets for TREK-1 protection. Therefore, TREK-1 activation may represent a novel therapeutic approach against IAV-induced lung injury.- Published
- 2023
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24. ACE-Inhibitor or ARB-Induced Refractory Hypotension Treated With Vasopressin in Patients Undergoing General Anesthesia for Dentistry: Two Case Reports.
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Waters CM, Pelczar K, Adlesic EC, Schwartz PJ, and Giovannitti JA
- Subjects
- Anesthesia, General adverse effects, Angiotensin Receptor Antagonists adverse effects, Angiotensin-Converting Enzyme Inhibitors adverse effects, Dentistry, Humans, Postoperative Complications etiology, Retrospective Studies, Vasopressins adverse effects, Anesthetics, General adverse effects, Hypotension chemically induced, Hypotension drug therapy
- Abstract
Two case reports present the use of vasopressin for treating refractory hypotension associated with continued angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB) therapy prior to general anesthesia for oral surgery. Both patients were treated in an ambulatory dental surgery clinic and took either their ACEI or ARB medication for hypertension within 24 hours prior to undergoing an intubated general anesthetic. Persistent profound hypotension was encountered intraoperatively that was refractory to treatment with traditional methods. However, the ACEI- or ARB-induced refractory hypotension was successfully managed with the administration of vasopressin., (© 2022 by the American Dental Society of Anesthesiology.)
- Published
- 2022
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25. Double take: A dual-functional Hypr GGDEF synthesizes both cyclic di-GMP and cyclic GMP-AMP to control predation in Bdellovibrio bacteriovorus.
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Rangarajan AA and Waters CM
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- Antibiosis, Bacterial Proteins genetics, Bacterial Proteins metabolism, Cyclic GMP, Gene Expression Regulation, Bacterial, Nucleotides, Cyclic, Bdellovibrio metabolism, Bdellovibrio bacteriovorus genetics, Bdellovibrio bacteriovorus metabolism
- Abstract
Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2022
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26. The 27th Annual Midwest Microbial Pathogenesis Conference in the Age of COVID.
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Hammer ND and Waters CM
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- Humans, Pandemics prevention & control, RNA, Viral, Universities, COVID-19 prevention & control, SARS-CoV-2
- Abstract
Michigan State University was honored to host in-person the 27th Annual Midwest Microbial Pathogenesis Conference from 17 to 19 September 2021 in East Lansing, MI. Here, we report the precautions that were used to host a safe, in-person meeting during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) pandemic and the research on microbial pathogenesis that was presented at the meeting. One of the most significant impacts of the SARS-CoV2 pandemic on the scientific community is the cancelation of many in-person scientific conferences. This has limited the ability of scientists, especially those who are early in their careers, to present their research and establish scientific networks and collaborations. Using a series of safety precautions, we describe here how we implemented a highly successful in-person meeting of 280 attendees in September 2021. Six of the research projects presented at this meeting are being published together in this issue of the Journal of Bacteriology .
- Published
- 2022
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27. Public Health Nurses: The Most Essential Single Factor.
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Monsen KA, Waters CM, and McCauley LA
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- Humans, Nurse's Role, Public Health Nursing, Nurses, Nurses, Public Health
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- 2022
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28. Public Health Nursing's Impact on Strengthening Community Resilience.
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Waters CM
- Subjects
- Humans, Public Health, Public Health Nursing
- Published
- 2022
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29. Public Health Nursing: Difference Is Power Mural.
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Waters CM
- Subjects
- Humans, Public Health Nursing
- Published
- 2022
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30. Nursing and Public Health Special Issue.
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McCauley LA, Waters CM, and Monsen KA
- Subjects
- Humans, Public Health, Public Health Nursing
- Published
- 2022
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31. Simple, accurate calculation of mechanical power in pressure controlled ventilation (PCV).
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Trinkle CA, Broaddus RN, Sturgill JL, Waters CM, and Morris PE
- Abstract
Background: Mechanical power is a promising new metric to assess energy transfer from a mechanical ventilator to a patient, which combines the contributions of multiple parameters into a single comprehensive value. However, at present, most ventilators are not capable of calculating mechanical power automatically, so there is a need for a simple equation that can be used to estimate this parameter at the bedside. For volume-controlled ventilation (VCV), excellent equations exist for calculating power from basic ventilator parameters, but for pressure-controlled ventilation (PCV), an accurate, easy-to-use equation has been elusive., Results: Here, we present a new power equation and evaluate its accuracy compared to the three published PCV power equations. When applied to a sample of 50 patients on PCV with a non-zero rise time, we found that our equation estimated power within an average of 8.4% ± 5.9% (mean ± standard deviation) of the value obtained by numerical integration of the P-V loop. The other three equations estimated power with an error of 19.4% ± 12.9% (simplified Becher equation), 10.0% ± 6.8% (comprehensive Becher equation), and 16.5% ± 14.6% (van der Meijden equation)., Conclusions: Our equation calculates power more accurately than the other three published equations, and is much easier to use than the only previously published equation with similar accuracy. The proposed new mechanical power equation is accurate and simple to use, making it an attractive option to estimate power in PCV cases at the bedside., (© 2022. The Author(s).)
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- 2022
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32. The Vibrio cholerae master regulator for the activation of biofilm biogenesis genes, VpsR, senses both cyclic di-GMP and phosphate.
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Hsieh ML, Kiel N, Jenkins LMM, Ng WL, Knipling L, Waters CM, and Hinton DM
- Subjects
- Bacterial Proteins genetics, Bacterial Proteins metabolism, Biofilms, Cyclic GMP analogs & derivatives, Cyclic GMP metabolism, DNA-Binding Proteins genetics, DNA-Directed RNA Polymerases genetics, DNA-Directed RNA Polymerases metabolism, Gene Expression Regulation, Bacterial, Phosphates metabolism, Sigma Factor genetics, Sigma Factor metabolism, Vibrio cholerae metabolism
- Abstract
Vibrio cholerae biofilm formation/maintenance is controlled by myriad factors; chief among these are the regulator VpsR and cyclic di-guanosine monophosphate (c-di-GMP). VpsR has strong sequence similarity to enhancer binding proteins (EBPs) that activate RNA polymerase containing sigma factor σ54. However, we have previously shown that transcription from promoters within the biofilm biogenesis/maintenance pathways uses VpsR, c-di-GMP and RNA polymerase containing the primary sigma factor (σ70). Previous work suggested that phosphorylation of VpsR at a highly conserved aspartate, which is phosphorylated in other EBPs, might also contribute to activation. Using the biofilm biogenesis promoter PvpsL, we show that in the presence of c-di-GMP, either wild type or the phospho-mimic VpsR D59E activates PvpsL transcription, while the phospho-defective D59A variant does not. Furthermore, when c-di-GMP levels are low, acetyl phosphate (Ac∼P) is required for significant VpsR activity in vivo and in vitro. Although these findings argue that VpsR phosphorylation is needed for activation, we show that VpsR is not phosphorylated or acetylated by Ac∼P and either sodium phosphate or potassium phosphate, which are not phosphate donors, fully substitutes for Ac∼P. We conclude that VpsR is an unusual regulator that senses phosphate directly, rather than through phosphorylation, to aid in the decision to form/maintain biofilm., (Published by Oxford University Press on behalf of Nucleic Acids Research 2022.)
- Published
- 2022
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33. Quorum-Sensing Master Regulator VfmE Is a c-di-GMP Effector That Controls Pectate Lyase Production in the Phytopathogen Dickeya dadantii.
- Author
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Banerjee B, Zeng Q, Yu M, Hsueh BY, Waters CM, and Yang CH
- Subjects
- Cyclic GMP analogs & derivatives, Cyclic GMP metabolism, Dickeya, Enterobacteriaceae metabolism, Polysaccharide-Lyases, Bacterial Proteins genetics, Bacterial Proteins metabolism, Gene Expression Regulation, Bacterial
- Abstract
Dickeya dadantii is a phytopathogenic bacterium that causes diseases on a wide range of host plants. The pathogen secretes pectate lyases (Pel) through the type II secretion system (T2SS) that degrades the cell wall in host plants. The virulence of D. dadantii is controlled by the second messenger cyclic diguanylate monophosphate (c-di-GMP), and the homeostasis of c-di-GMP is maintained by a number of diguanylate cyclases and phosphodiesterases. Deletion of a phosphodiesterase ecpC repressed pelD transcription, and such repression can be suppressed by an additional deletion in vfmE . VfmE is an AraC type of transcriptional regulator in the Vfm quorum-sensing system. Our results suggest that VfmE is a c-di-GMP effector that functions as an activator of pel at low c-di-GMP concentrations and a repressor of pel at high c-di-GMP concentrations through regulation of the transcriptional activator SlyA. Multiple sequence alignment with known c-di-GMP effectors identified an RWIWR motif in VfmE that we demonstrate is required for the c-di-GMP binding. Mutation of R93D in the RxxxR motif eliminates the c-di-GMP-related phenotypes in Pel activity. Our results show that VfmE is not only a quorum-sensing regulator but also a c-di-GMP effector, suggesting that D. dadantii integrates the c-di-GMP signaling network with the Vfm quorum-sensing pathway during environmental adaptation. IMPORTANCE How bacteria integrate environmental cues from multiple sources to appropriately regulate adaptive phenotypes is a central question in microbiology. In Dickeya dadantii, the quorum-sensing regulator VfmE controls the key virulence factor pectate lyase (Pel). Here, we demonstrate that VfmE also binds to c-di-GMP, resulting in VfmE functioning as an activator of pel at low c-di-GMP concentrations and repressor of pel at high c-di-GMP concentrations. The RWIWR motif in VfmE is required for c-di-GMP binding, and mutation of the motif in the mutant R93D eliminates the c-di-GMP-related phenotypes in Pel activity. We propose that VfmE is an important mediator to integrate quorum-sensing signals with c-di-GMP to collectively regulate D. dadantii pathogenesis.
- Published
- 2022
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34. NrnA Is a Linear Dinucleotide Phosphodiesterase with Limited Function in Cyclic Dinucleotide Metabolism in Listeria monocytogenes.
- Author
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Gall AR, Hsueh BY, Siletti C, Waters CM, and Huynh TN
- Subjects
- Biofilms, Mutation, Phosphoric Diester Hydrolases genetics, Virulence Factors, Gene Expression Regulation, Bacterial physiology, Gene Expression Regulation, Enzymologic physiology, Listeria monocytogenes enzymology, Nucleotides, Cyclic metabolism, Phosphoric Diester Hydrolases metabolism
- Abstract
Listeria monocytogenes produces both c-di-AMP and c-di-GMP to mediate many important cellular processes, but the levels of both nucleotides must be regulated. c-di-AMP accumulation attenuates virulence and diminishes stress response, and c-di-GMP accumulation impairs bacterial motility. An important regulatory mechanism to maintain c-di-AMP and c-di-GMP homeostasis is to hydrolyze them to the linear dinucleotides pApA and pGpG, respectively, but the fates of these hydrolytic products have not been examined in L. monocytogenes. We found that NrnA, a stand-alone DHH-DHHA1 phosphodiesterase, has a broad substrate range but with a strong preference for linear dinucleotides over cyclic dinucleotides. Although NrnA exhibited detectable cyclic dinucleotide hydrolytic activities in vitro , NrnA had negligible effects on their levels in the bacterial cell, even in the absence of the c-di-AMP phosphodiesterases PdeA and PgpH. The Δ nrnA mutant had a mammalian cell infection defect that was fully restored by Escherichia coli Orn. Together, our data indicate that L. monocytogenes NrnA is functionally orthologous to Orn, and its preferred physiological substrates are most likely linear dinucleotides. Furthermore, our findings revealed that, unlike some other c-di-AMP- and c-di-GMP-producing bacteria, L. monocytogenes does not employ their hydrolytic products to regulate their phosphodiesterases, at least at the pApA and pGpG levels in the Δ nrnA mutant. Finally, the Δ nrnA infection defect was overcome by constitutive activation of PrfA, the master virulence regulator, suggesting that accumulated linear dinucleotides inhibit the expression, stability, or function of PrfA-regulated virulence factors. IMPORTANCE Listeria monocytogenes produces both c-di-AMP and c-di-GMP and encodes specific phosphodiesterases that degrade them into pApA and pGpG, respectively, but the metabolism of these products has not been characterized in this bacterium. We found that L. monocytogenes NrnA degrades a broad range of nucleotides. Among the tested cyclic and linear substrates, it exhibits a strong biochemical and physiological preference for the linear dinucleotides pApA, pGpG, and pApG. Unlike in some other bacteria, these oligoribonucleotides do not appear to interfere with cyclic dinucleotide hydrolysis. The absence of NrnA is well tolerated by L. monocytogenes in broth cultures but impairs its ability to infect mammalian cells. These findings indicate a separation of cyclic dinucleotide signaling and oligoribonucleotide metabolism in L. monocytogenes.
- Published
- 2022
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35. The Campylobacter jejuni Response Regulator and Cyclic-Di-GMP Binding CbrR Is a Novel Regulator of Flagellar Motility.
- Author
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Cox CA, Bogacz M, El Abbar FM, Browning DD, Hsueh BY, Waters CM, Lee VT, and Thompson SA
- Abstract
A leading cause of bacterial gastroenteritis, Campylobacter jejuni is also associated with broad sequelae, including extragastrointestinal conditions such as reactive arthritis and Guillain-Barré Syndrome (GBS). CbrR is a C. jejuni response regulator that is annotated as a diguanylate cyclase (DGC), an enzyme that catalyzes the synthesis of c-di-GMP, a universal bacterial second messenger, from GTP. In C. jejuni DRH212, we constructed an unmarked deletion mutant, cbrR
- , and complemented mutant, cbrR+ . Motility assays indicated a hyper-motile phenotype associated with cbrR- , whereas motility was deficient in cbrR+ . The overexpression of CbrR in cbrR+ was accompanied by a reduction in expression of FlaA, the major flagellin. Biofilm assays and scanning electron microscopy demonstrated similarities between DRH212 and cbrR- ; however, cbrR+ was unable to form significant biofilms. Transmission electron microscopy showed similar cell morphology between the three strains; however, cbrR+ cells lacked flagella. Differential radial capillary action of ligand assays (DRaCALA) showed that CbrR binds GTP and c-di-GMP. Liquid chromatography tandem mass spectrometry detected low levels of c-di-GMP in C. jejuni and in E. coli expressing CbrR. CbrR is therefore a negative regulator of FlaA expression and motility, a critical virulence factor in C. jejuni pathogenesis.- Published
- 2021
- Full Text
- View/download PDF
36. Au naturale: use of biologically derived cyclic di-nucleotides for cancer immunotherapy.
- Author
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Waters CM
- Subjects
- Biological Factors chemistry, Biological Factors pharmacology, Biological Factors therapeutic use, Gene Expression Regulation, Neoplastic drug effects, Humans, Immunity, Innate, Immunotherapy, Molecular Structure, Neoplasms immunology, Nucleotides, Cyclic chemistry, Nucleotides, Cyclic pharmacology, Second Messenger Systems, Interferon Type I metabolism, Membrane Proteins metabolism, Neoplasms drug therapy, Nucleotides, Cyclic therapeutic use
- Abstract
Cyclic di-nucleotides (CDNs) are widespread second messenger signalling molecules that regulate fundamental biological processes across the tree of life. These molecules are also potent modulators of the immune system, inducing a Type I interferon response upon binding to the eukaryotic receptor STING. Such a response in tumours induces potent immune anti-cancer responses and thus CDNs are being developed as a novel cancer immunotherapy. In this review, I will highlight the use, challenges and advantages of using naturally occurring CDNs to treat cancer.
- Published
- 2021
- Full Text
- View/download PDF
37. CsrA Enhances Cyclic-di-GMP Biosynthesis and Yersinia pestis Biofilm Blockage of the Flea Foregut by Alleviating Hfq-Dependent Repression of the hmsT mRNA.
- Author
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Silva-Rohwer AR, Held K, Sagawa J, Fernandez NL, Waters CM, and Vadyvaloo V
- Subjects
- Animals, Cyclic GMP biosynthesis, Host-Pathogen Interactions, RNA, Messenger metabolism, Siphonaptera anatomy & histology, Yersinia pestis pathogenicity, Biofilms growth & development, Cyclic GMP analogs & derivatives, Gastrointestinal Tract microbiology, Host Factor 1 Protein genetics, RNA, Messenger genetics, Siphonaptera microbiology, Yersinia pestis metabolism
- Abstract
Plague-causing Yersinia pestis is transmitted through regurgitation when it forms a biofilm-mediated blockage in the foregut of its flea vector. This biofilm is composed of an extracellular polysaccharide substance (EPS) produced when cyclic-di-GMP (c-di-GMP) levels are elevated. The Y. pestis diguanylate cyclase enzymes HmsD and HmsT synthesize c-di-GMP. HmsD is required for biofilm blockage formation but contributes minimally to in vitro biofilms. HmsT, however, is necessary for in vitro biofilms and contributes to intermediate rates of biofilm blockage. C-di-GMP synthesis is regulated at the transcriptional and posttranscriptional levels. In this, the global RNA chaperone, Hfq, posttranscriptionally represses hmsT mRNA translation. How c-di-GMP levels and biofilm blockage formation is modulated by nutritional stimuli encountered in the flea gut is unknown. Here, the RNA-binding regulator protein CsrA, which controls c-di-GMP-mediated biofilm formation and central carbon metabolism responses in many Gammaproteobacteria, was assessed for its role in Y. pestis biofilm formation. We determined that CsrA was required for markedly greater c-di-GMP and EPS levels when Y. pestis was cultivated on alternative sugars implicated in flea biofilm blockage metabolism. Our assays, composed of mobility shifts, quantification of mRNA translation, stability, and abundance, and epistasis analyses of a csrA hfq double mutant strain substantiated that CsrA represses hfq mRNA translation, thereby alleviating Hfq-dependent repression of hmsT mRNA translation. Additionally, a csrA mutant exhibited intermediately reduced biofilm blockage rates, resembling an hmsT mutant. Hence, we reveal CsrA-mediated control of c-di-GMP synthesis in Y. pestis as a tiered, posttranscriptional regulatory process that enhances biofilm blockage-mediated transmission from fleas. IMPORTANCE Yersinia pestis, the bacterial agent of bubonic plague, produces a c-di-GMP-dependent biofilm-mediated blockage of the flea vector foregut to facilitate its transmission by flea bite. However, the intricate molecular regulatory processes that underlie c-di-GMP-dependent biofilm formation and thus, biofilm-mediated blockage in response to the nutritional environment of the flea are largely undefined. This study provides a novel mechanistic understanding of how CsrA transduces alternative sugar metabolism cues to induce c-di-GMP-dependent biofilm formation required for efficient Y. pestis regurgitative transmission through biofilm-mediated flea foregut blockage. The Y. pestis-flea interaction represents a unique, biologically relevant, in vivo perspective on the role of CsrA in biofilm regulation.
- Published
- 2021
- Full Text
- View/download PDF
38. Host-emitted amino acid cues regulate bacterial chemokinesis to enhance colonization.
- Author
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Robinson CD, Sweeney EG, Ngo J, Ma E, Perkins A, Smith TJ, Fernandez NL, Waters CM, Remington SJ, Bohannan BJM, and Guillemin K
- Subjects
- Animals, Bacteria genetics, Bacteria isolation & purification, Bacterial Proteins genetics, Bacterial Proteins metabolism, Biofilms growth & development, Cues, Cyclic GMP analogs & derivatives, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Host Microbial Interactions, Phosphorus-Oxygen Lyases genetics, Symbiosis, Zebrafish microbiology, Amino Acids metabolism, Bacteria metabolism, Chemokines metabolism
- Abstract
Animal microbiomes are assembled predominantly from environmental microbes, yet the mechanisms by which individual symbionts regulate their transmission into hosts remain underexplored. By tracking the experimental evolution of Aeromonas veronii in gnotobiotic zebrafish, we identify bacterial traits promoting host colonization. Multiple independently evolved isolates with increased immigration harbored mutations in a gene we named sensor of proline diguanylate cyclase enzyme (SpdE) based on structural, biochemical, and phenotypic evidence that SpdE encodes an amino-acid-sensing diguanylate cyclase. SpdE detects free proline and to a lesser extent valine and isoleucine, resulting in reduced production of intracellular c-di-GMP, a second messenger controlling bacterial motility. Indeed, SpdE binding to amino acids increased bacterial motility and host colonization. Hosts serve as sources of SpdE-detected amino acids, with levels varying based on microbial colonization status. Our work demonstrates that bacteria use chemically regulated motility, or chemokinesis, to sense host-emitted cues that trigger active immigration into hosts., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)
- Published
- 2021
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39. Correction: Quorum sensing provides a molecular mechanism for evolution to tune and maintain investment in cooperation.
- Author
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Bruger EL, Snyder DJ, Cooper VS, and Waters CM
- Published
- 2021
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- View/download PDF
40. Recommendations for Demonstrators, Law Enforcement Agencies, and Public Health Agencies for Reducing SARS-CoV-2 Transmission During Civil Protests.
- Author
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Eisenman DP, Wiley DJ, Pollock BH, Rutherford GW, Rimoin AW, Bibbins-Domingo K, Checkoway H, Hurd T, Waters CM, and Dawson-Rose C
- Subjects
- Humans, SARS-CoV-2, COVID-19 prevention & control, Civil Disorders, Communicable Disease Control methods, Disease Transmission, Infectious prevention & control, Law Enforcement, Public Health
- Published
- 2021
- Full Text
- View/download PDF
41. Quorum sensing provides a molecular mechanism for evolution to tune and maintain investment in cooperation.
- Author
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Bruger EL, Snyder DJ, Cooper VS, and Waters CM
- Subjects
- Phenotype, Quorum Sensing, Vibrio genetics
- Abstract
As selection frequently favors noncooperating defectors in mixed populations with cooperators, mechanisms that promote cooperation stability clearly exist. One potential mechanism is bacterial cell-to-cell communication, quorum sensing (QS), which can allow cooperators to prevent invasion by defectors. However, the impact of QS on widespread maintenance of cooperation in well-mixed conditions has not been experimentally demonstrated over extended evolutionary timescales. Here, we use wild-type (WT) Vibrio campbellii that regulates cooperation with QS and an unconditional cooperating (UC) mutant to examine the evolutionary origins and dynamics of novel defectors during a long-term evolution experiment. We found that UC lineages were completely outcompeted by defectors, whereas functioning QS enabled the maintenance of cooperative variants in most WT populations. Sequencing evolved populations revealed multiple luxR mutations that swept the UC lineages. However, the evolution of mutant lineages with reduced levels of bioluminescence (dims) occurred in many WT lineages. These dim variants also decreased other cooperative phenotypes regulated by QS, including protease production, indicating they result from changes to QS regulation. This diminished investment phenotype optimizes a tradeoff between cooperative input and growth output and suggests that decreasing the cost of QS could be a favorable strategy for maintaining the cooperative behaviors it regulates.
- Published
- 2021
- Full Text
- View/download PDF
42. K 2P 2.1 (TREK-1) potassium channel activation protects against hyperoxia-induced lung injury.
- Author
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Zyrianova T, Lopez B, Olcese R, Belperio J, Waters CM, Wong L, Nguyen V, Talapaneni S, and Schwingshackl A
- Subjects
- Alveolar Epithelial Cells drug effects, Alveolar Epithelial Cells metabolism, Animals, Bronchoalveolar Lavage Fluid, Calcium metabolism, Cell Line, Cytokines metabolism, Inflammation Mediators metabolism, Intracellular Space metabolism, Membrane Potentials drug effects, Mice, Inbred C57BL, Tetrahydronaphthalenes pharmacology, Tetrazoles pharmacology, Acute Lung Injury etiology, Acute Lung Injury metabolism, Hyperoxia complications, Ion Channel Gating drug effects, Potassium Channels, Tandem Pore Domain metabolism, Protective Agents metabolism
- Abstract
No targeted therapies exist to counteract Hyperoxia (HO)-induced Acute Lung Injury (HALI). We previously found that HO downregulates alveolar K
2P 2.1 (TREK-1) K+ channels, which results in worsening lung injury. This decrease in TREK-1 levels leaves a subset of channels amendable to pharmacological intervention. Therefore, we hypothesized that TREK-1 activation protects against HALI. We treated HO-exposed mice and primary alveolar epithelial cells (AECs) with the novel TREK-1 activators ML335 and BL1249, and quantified physiological, histological, and biochemical lung injury markers. We determined the effects of these drugs on epithelial TREK-1 currents, plasma membrane potential (Em), and intracellular Ca2+ (iCa) concentrations using fluorometric assays, and blocked voltage-gated Ca2+ channels (CaV ) as a downstream mechanism of cytokine secretion. Once-daily, intra-tracheal injections of HO-exposed mice with ML335 or BL1249 improved lung compliance, histological lung injury scores, broncho-alveolar lavage protein levels and cell counts, and IL-6 and IP-10 concentrations. TREK-1 activation also decreased IL-6, IP-10, and CCL-2 secretion from primary AECs. Mechanistically, ML335 and BL1249 induced TREK-1 currents in AECs, counteracted HO-induced cell depolarization, and lowered iCa2+ concentrations. In addition, CCL-2 secretion was decreased after L-type CaV inhibition. Therefore, Em stabilization with TREK-1 activators may represent a novel approach to counteract HALI.- Published
- 2020
- Full Text
- View/download PDF
43. Cyclic di-GMP-Mediated Regulation of Extracellular Mannuronan C-5 Epimerases Is Essential for Cyst Formation in Azotobacter vinelandii.
- Author
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Martínez-Ortiz IC, Ahumada-Manuel CL, Hsueh BY, Guzmán J, Moreno S, Cocotl-Yañez M, Waters CM, Zamorano-Sánchez D, Espín G, and Núñez C
- Subjects
- Alginates metabolism, Azotobacter vinelandii genetics, Azotobacter vinelandii growth & development, Azotobacter vinelandii metabolism, Bacterial Proteins genetics, Carbohydrate Epimerases genetics, Cyclic GMP metabolism, Escherichia coli Proteins genetics, Escherichia coli Proteins metabolism, Gene Expression Regulation, Bacterial, Phosphorus-Oxygen Lyases genetics, Phosphorus-Oxygen Lyases metabolism, Pseudomonas aeruginosa enzymology, Pseudomonas aeruginosa genetics, Pseudomonas aeruginosa metabolism, Azotobacter vinelandii enzymology, Bacterial Proteins metabolism, Carbohydrate Epimerases metabolism, Cyclic GMP analogs & derivatives
- Abstract
The genus Azotobacter, belonging to the Pseudomonadaceae family, is characterized by the formation of cysts, which are metabolically dormant cells produced under adverse conditions and able to resist desiccation. Although this developmental process has served as a model for the study of cell differentiation in Gram-negative bacteria, the molecular basis of its regulation is still poorly understood. Here, we report that the ubiquitous second messenger cyclic dimeric GMP (c-di-GMP) is critical for the formation of cysts in Azotobacter vinelandii Upon encystment induction, the levels of c-di-GMP increased, reaching a peak within the first 6 h. In the absence of the diguanylate cyclase MucR, however, the levels of this second messenger remained low throughout the developmental process. A. vinelandii cysts are surrounded by two alginate layers with variable proportions of guluronic residues, which are introduced into the final alginate chain by extracellular mannuronic C-5 epimerases of the AlgE1 to AlgE7 family. Unlike in Pseudomonas aeruginosa , MucR was not required for alginate polymerization in A. vinelandii Conversely, MucR was necessary for the expression of extracellular alginate C-5 epimerases; therefore, the MucR-deficient strain produced cyst-like structures devoid of the alginate capsule and unable to resist desiccation. Expression of mucR was partially dependent on the response regulator AlgR, which binds to two sites in the mucR promoter, enhancing mucR transcription. Together, these results indicate that the developmental process of A. vinelandii is controlled through a signaling module that involves activation by the response regulator AlgR and c-di-GMP accumulation that depends on MucR. IMPORTANCE A. vinelandii has served as an experimental model for the study of the differentiation processes to form metabolically dormant cells in Gram-negative bacteria. This work identifies c-di-GMP as a critical regulator for the production of alginates with specific contents of guluronic residues that are able to structure the rigid laminated layers of the cyst envelope. Although allosteric activation of the alginate polymerase complex Alg8-Alg44 by c-di-GMP has long been recognized, our results show a previously unidentified role during the polymer modification step, controlling the expression of extracellular alginate epimerases. Our results also highlight the importance of c-di-GMP in the control of the physical properties of alginate, which ultimately determine the desiccation resistance of the differentiated cell., (Copyright © 2020 American Society for Microbiology.)
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- 2020
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44. Increased c-di-GMP Levels Lead to the Production of Alginates of High Molecular Mass in Azotobacter vinelandii.
- Author
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Ahumada-Manuel CL, Martínez-Ortiz IC, Hsueh BY, Guzmán J, Waters CM, Zamorano-Sánchez D, Espín G, and Núñez C
- Subjects
- Alginates chemistry, Azotobacter vinelandii enzymology, Azotobacter vinelandii genetics, Bacterial Proteins genetics, Bacterial Proteins metabolism, Cyclic GMP metabolism, Escherichia coli Proteins genetics, Escherichia coli Proteins metabolism, Gene Expression Regulation, Bacterial, Molecular Weight, Oxygen metabolism, Phosphoric Diester Hydrolases genetics, Phosphoric Diester Hydrolases metabolism, Phosphorus-Oxygen Lyases genetics, Phosphorus-Oxygen Lyases metabolism, Polysaccharides, Bacterial chemistry, Alginates metabolism, Azotobacter vinelandii metabolism, Cyclic GMP analogs & derivatives, Polysaccharides, Bacterial biosynthesis
- Abstract
Azotobacter vinelandii produces the linear exopolysaccharide alginate, a compound of significant biotechnological importance. The biosynthesis of alginate in A. vinelandii and Pseudomonas aeruginosa has several similarities but is regulated somewhat differently in the two microbes. Here, we show that the second messenger cyclic dimeric GMP (c-di-GMP) regulates the production and the molecular mass of alginate in A. vinelandii The hybrid protein MucG, containing conserved GGDEF and EAL domains and N-terminal HAMP and PAS domains, behaved as a c-di-GMP phosphodiesterase (PDE). This activity was found to negatively affect the amount and molecular mass of the polysaccharide formed. On the other hand, among the diguanylate cyclases (DGCs) present in A. vinelandii , Av GReg, a globin-coupled sensor (GCS) DGC that directly binds to oxygen, was identified as the main c-di-GMP-synthesizing contributor to alginate production. Overproduction of Av GReg in the parental strain phenocopied a Δ mucG strain with regard to alginate production and the molecular mass of the polymer. MucG was previously shown to prevent the synthesis of high-molecular-mass alginates in response to reduced oxygen transfer rates (OTRs). In this work, we show that cultures exposed to reduced OTRs accumulated higher levels of c-di-GMP; this finding strongly suggests that at least one of the molecular mechanisms involved in modulation of alginate production and molecular mass by oxygen depends on a c-di-GMP signaling module that includes the PAS domain-containing PDE MucG and the GCS DGC Av GReg. IMPORTANCE c-di-GMP has been widely recognized for its essential role in the production of exopolysaccharides in bacteria, such as alginate produced by Pseudomonas and Azotobacter spp. This study reveals that the levels of c-di-GMP also affect the physical properties of alginate, favoring the production of high-molecular-mass alginates in response to lower OTRs. This finding opens up new alternatives for the design of tailor-made alginates for biotechnological applications., (Copyright © 2020 American Society for Microbiology.)
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- 2020
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45. Earning the Trust of African American Communities to Increase Representation in Dementia Research.
- Author
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Portacolone E, Palmer NR, Lichtenberg P, Waters CM, Hill CV, Keiser S, Vest L, Maloof M, Tran T, Martinez P, Guerrero J, and Johnson JK
- Subjects
- Black or African American statistics & numerical data, Aged, Beneficence, Female, Focus Groups, Humans, Interpersonal Relations, Male, Middle Aged, Black or African American psychology, Clinical Trials as Topic psychology, Dementia, Patient Selection, Trust
- Abstract
Black/African American populations are underrepresented as participants in dementia research. A major barrier to participation of African American older adults in dementia research is a tendency to distrust research institutions owing to both historical and contemporary racism. Building on the Ford framework, the objective of our study was to examine factors that influence participation in dementia research among African American older adults and caregivers, with an emphasis on understanding factors related to trust. Data were collected during January 2019 and March 2020 from 10 focus groups with African American older adults (n=91), 5 focus groups with caregivers (n=44), and interviews with administrators of community-based organizations (n=11), and meetings with our Community Advisory Board. Inductive/deductive content analysis was used to identify themes. The results identified an overall tension between distrust of researchers and a compelling desire to engage in dementia research. This overarching theme was supported by six themes that provided insights about the multiple layers of distrust, as well as expectations about the appropriate conduct of researchers and academic institutions. Strong commitment to the community was identified as a priority. The findings suggest that a paradigm shift is needed to increase the representation of African Americans in dementia research. In this new paradigm, earning the trust of African American communities becomes a systemic endeavor, with academic, state, and national institutions deeply committed to earning the trust of African American communities and guiding researchers in this endeavor. The findings also generated actionable recommendations to help improve representation of African American older adults in dementia research., Competing Interests: Competing Interests: None declared., (Copyright © 2020, Ethnicity & Disease, Inc.)
- Published
- 2020
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46. Vibrio cholerae adapts to sessile and motile lifestyles by cyclic di-GMP regulation of cell shape.
- Author
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Fernandez NL, Hsueh BY, Nhu NTQ, Franklin JL, Dufour YS, and Waters CM
- Subjects
- Bacterial Proteins genetics, Biofilms, Cyclic GMP analogs & derivatives, Gene Expression Regulation, Bacterial, Humans, Second Messenger Systems, Vibrio cholerae genetics, Cell Shape physiology, Cyclic GMP metabolism, Life Style, Vibrio cholerae metabolism
- Abstract
The cell morphology of rod-shaped bacteria is determined by the rigid net of peptidoglycan forming the cell wall. Alterations to the rod shape, such as the curved rod, occur through manipulating the process of cell wall synthesis. The human pathogen Vibrio cholerae typically exists as a curved rod, but straight rods have been observed under certain conditions. While this appears to be a regulated process, the regulatory pathways controlling cell shape transitions in V. cholerae and the benefits of switching between rod and curved shape have not been determined. We demonstrate that cell shape in V. cholerae is regulated by the bacterial second messenger cyclic dimeric guanosine monophosphate (c-di-GMP) by posttranscriptionally repressing expression of crvA , a gene encoding an intermediate filament-like protein necessary for curvature formation in V. cholerae. This regulation is mediated by the transcriptional cascade that also induces production of biofilm matrix components, indicating that cell shape is coregulated with V. cholerae 's induction of sessility. During microcolony formation, wild-type V. cholerae cells tended to exist as straight rods, while genetically engineering cells to maintain high curvature reduced microcolony formation and biofilm density. Conversely, straight V. cholerae mutants have reduced swimming speed when using flagellar motility in liquid. Our results demonstrate regulation of cell shape in bacteria is a mechanism to increase fitness in planktonic and biofilm lifestyles., Competing Interests: The authors declare no competing interest.
- Published
- 2020
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47. Triclosan depletes the membrane potential in Pseudomonas aeruginosa biofilms inhibiting aminoglycoside induced adaptive resistance.
- Author
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Maiden MM and Waters CM
- Subjects
- Animals, Anti-Infective Agents, Local pharmacology, Biofilms growth & development, Female, Male, Mice, Mice, Hairless, Pseudomonas Infections microbiology, Pseudomonas aeruginosa growth & development, Aminoglycosides pharmacology, Biofilms drug effects, Drug Resistance, Bacterial drug effects, Membrane Potentials drug effects, Pseudomonas Infections drug therapy, Pseudomonas aeruginosa drug effects, Triclosan pharmacology
- Abstract
Biofilm-based infections are difficult to treat due to their inherent resistance to antibiotic treatment. Discovering new approaches to enhance antibiotic efficacy in biofilms would be highly significant in treating many chronic infections. Exposure to aminoglycosides induces adaptive resistance in Pseudomonas aeruginosa biofilms. Adaptive resistance is primarily the result of active antibiotic export by RND-type efflux pumps, which use the proton motive force as an energy source. We show that the protonophore uncoupler triclosan depletes the membrane potential of biofilm growing P. aeruginosa, leading to decreased activity of RND-type efflux pumps. This disruption results in increased intracellular accumulation of tobramycin and enhanced antimicrobial activity in vitro. In addition, we show that triclosan enhances tobramycin effectiveness in vivo using a mouse wound model. Combining triclosan with tobramycin is a new anti-biofilm strategy that targets bacterial energetics, increasing the susceptibility of P. aeruginosa biofilms to aminoglycosides., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2020
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48. One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity.
- Author
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Mhatre E, Snyder DJ, Sileo E, Turner CB, Buskirk SW, Fernandez NL, Neiditch MB, Waters CM, and Cooper VS
- Subjects
- Bacterial Proteins metabolism, Burkholderia cenocepacia growth & development, Cyclic GMP analogs & derivatives, Cyclic GMP genetics, Directed Molecular Evolution methods, Gene Expression Regulation, Bacterial genetics, Mutation genetics, Phenotype, Signal Transduction genetics, Virulence genetics, Biofilms growth & development, Burkholderia cenocepacia genetics, Quorum Sensing genetics
- Abstract
Many bacteria cycle between sessile and motile forms in which they must sense and respond to internal and external signals to coordinate appropriate physiology. Maintaining fitness requires genetic networks that have been honed in variable environments to integrate these signals. The identity of the major regulators and how their control mechanisms evolved remain largely unknown in most organisms. During four different evolution experiments with the opportunist betaproteobacterium Burkholderia cenocepacia in a biofilm model, mutations were most frequently selected in the conserved gene rpfR RpfR uniquely integrates two major signaling systems-quorum sensing and the motile-sessile switch mediated by cyclic-di-GMP-by two domains that sense, respond to, and control the synthesis of the autoinducer cis-2-dodecenoic acid (BDSF). The BDSF response in turn regulates the activity of diguanylate cyclase and phosphodiesterase domains acting on cyclic-di-GMP. Parallel adaptive substitutions evolved in each of these domains to produce unique life history strategies by regulating cyclic-di-GMP levels, global transcriptional responses, biofilm production, and polysaccharide composition. These phenotypes translated into distinct ecology and biofilm structures that enabled mutants to coexist and produce more biomass than expected from their constituents grown alone. This study shows that when bacterial populations are selected in environments challenging the limits of their plasticity, the evolved mutations not only alter genes at the nexus of signaling networks but also reveal the scope of their regulatory functions., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)
- Published
- 2020
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49. VpsR Directly Activates Transcription of Multiple Biofilm Genes in Vibrio cholerae.
- Author
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Hsieh ML, Waters CM, and Hinton DM
- Subjects
- Bacterial Proteins genetics, Gene Expression Regulation, Bacterial, Operon, Promoter Regions, Genetic, Bacterial Proteins metabolism, Biofilms, Cyclic GMP metabolism, DNA-Directed RNA Polymerases metabolism, Sigma Factor metabolism, Vibrio cholerae genetics
- Abstract
Vibrio cholerae biofilm biogenesis, which is important for survival, dissemination, and persistence, requires multiple genes in the Vibrio polysaccharides ( vps ) operons I and II as well as the cluster of ribomatrix ( rbm ) genes. Transcriptional control of these genes is a complex process that requires several activators/repressors and the ubiquitous signaling molecule, cyclic di-GMP (c-di-GMP). Previously, we demonstrated that VpsR directly activates RNA polymerase containing σ
70 (σ70 -RNAP) at the vpsL promoter (PvpsL ), which precedes the vps -II operon, in a c-di-GMP-dependent manner by stimulating formation of the transcriptionally active, open complex. Using in vitro transcription, electrophoretic mobility shift assays, and DNase I footprinting, we show here that VpsR also directly activates σ70 -RNAP transcription from other promoters within the biofilm formation cluster, including PvpsU , at the beginning of the vps -I operon, PrbmA , at the start of the rbm cluster, and PrbmF , which lies upstream of the divergent rbmF and rbmE genes. In this capacity, we find that VpsR is able to behave both as a class II activator, which functions immediately adjacent/overlapping the core promoter sequence (PvpsL and PvpsU ), and as a class I activator, which functions farther upstream (PrbmA and PrbmF ). Because these promoters vary in VpsR-DNA binding affinity in the absence and presence of c-di-GMP, we speculate that VpsR's mechanism of activation is dependent on both the concentration of VpsR and the level of c-di-GMP to increase transcription, resulting in finely tuned regulation. IMPORTANCE Vibrio cholerae , the bacterial pathogen that is responsible for the disease cholera, uses biofilms to aid in survival, dissemination, and persistence. VpsR, which directly senses the second messenger c-di-GMP, is a major regulator of this process. Together with c-di-GMP, VpsR directly activates transcription by RNA polymerase containing σ70 from the vpsL biofilm biogenesis promoter. Using biochemical methods, we demonstrate for the first time that VpsR/c-di-GMP directly activates σ70 -RNA polymerase at the first genes of the vps and ribomatrix operons. In this regard, it functions as either a class I or class II activator. Our results broaden the mechanism of c-di-GMP-dependent transcription activation and the specific role of VpsR in biofilm formation., (Copyright © 2020 American Society for Microbiology.)- Published
- 2020
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50. Surface sensing stimulates cellular differentiation in Caulobacter crescentus .
- Author
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Snyder RA, Ellison CK, Severin GB, Whitfield GB, Waters CM, and Brun YV
- Subjects
- Cell Cycle, Cyclic GMP analogs & derivatives, Cyclic GMP metabolism, DNA Replication, Fimbriae, Bacterial physiology, Models, Biological, Mutation, Bacterial Physiological Phenomena, Caulobacter crescentus physiology, Gram-Negative Bacterial Infections microbiology
- Abstract
Cellular differentiation is a fundamental strategy used by cells to generate specialized functions at specific stages of development. The bacterium Caulobacter crescentus employs a specialized dimorphic life cycle consisting of two differentiated cell types. How environmental cues, including mechanical inputs such as contact with a surface, regulate this cell cycle remain unclear. Here, we find that surface sensing by the physical perturbation of retracting extracellular pilus filaments accelerates cell-cycle progression and cellular differentiation. We show that physical obstruction of dynamic pilus activity by chemical perturbation or by a mutation in the outer-membrane pilus secretin CpaC stimulates early initiation of chromosome replication. In addition, we find that surface contact stimulates cell-cycle progression by demonstrating that surface-stimulated cells initiate early chromosome replication to the same extent as planktonic cells with obstructed pilus activity. Finally, we show that obstruction of pilus retraction stimulates the synthesis of the cell-cycle regulator cyclic diguanylate monophosphate (c-di-GMP) through changes in the activity and localization of two key regulatory histidine kinases that control cell fate and differentiation. Together, these results demonstrate that surface contact and sensing by alterations in pilus activity stimulate C. crescentus to bypass its developmentally programmed temporal delay in cell differentiation to more quickly adapt to a surface-associated lifestyle., Competing Interests: The authors declare no competing interest.
- Published
- 2020
- Full Text
- View/download PDF
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