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Burke Ó, Zeden MS, O'Gara JP. The pathogenicity and virulence of the opportunistic pathogen Staphylococcus epidermidis. Virulence 2024; 15:2359483. [PMID: 38868991 DOI: 10.1080/21505594.2024.2359483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024] Open
Abstract
The pervasive presence of Staphylococcus epidermidis and other coagulase-negative staphylococci on the skin and mucous membranes has long underpinned a casual disregard for the infection risk that these organisms pose to vulnerable patients in healthcare settings. Prior to the recognition of biofilm as an important virulence determinant in S. epidermidis, isolation of this microorganism in diagnostic specimens was often overlooked as clinically insignificant with potential delays in diagnosis and onset of appropriate treatment, contributing to the establishment of chronic infection and increased morbidity or mortality. While impressive progress has been made in our understanding of biofilm mechanisms in this important opportunistic pathogen, research into other virulence determinants has lagged S. aureus. In this review, the broader virulence potential of S. epidermidis including biofilm, toxins, proteases, immune evasion strategies and antibiotic resistance mechanisms is surveyed, together with current and future approaches for improved therapeutic interventions.
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Affiliation(s)
- Órla Burke
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | | | - James P O'Gara
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
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2
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Gao S, Wang Y, Yuan S, Zuo J, Jin W, Shen Y, Grenier D, Yi L, Wang Y. Cooperation of quorum sensing and central carbon metabolism in the pathogenesis of Gram-positive bacteria. Microbiol Res 2024; 282:127655. [PMID: 38402726 DOI: 10.1016/j.micres.2024.127655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/25/2024] [Accepted: 02/17/2024] [Indexed: 02/27/2024]
Abstract
Quorum sensing (QS), an integral component of bacterial communication, is essential in coordinating the collective response of diverse bacterial pathogens. Central carbon metabolism (CCM), serving as the primary metabolic hub for substances such as sugars, lipids, and amino acids, plays a crucial role in the life cycle of bacteria. Pathogenic bacteria often utilize CCM to regulate population metabolism and enhance the synthesis of specific cellular structures, thereby facilitating in adaptation to the host microecological environment and expediting infection. Research has demonstrated that QS can both directly or indirectly affect the CCM of numerous pathogenic bacteria, thus altering their virulence and pathogenicity. This article reviews the interplay between QS and CCM in Gram-positive pathogenic bacteria, details the molecular mechanisms by which QS modulates CCM, and lays the groundwork for investigating bacterial pathogenicity and developing innovative infection treatment drugs.
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Affiliation(s)
- Shuji Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Yuxin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Shuo Yuan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Jing Zuo
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Wenjie Jin
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Yamin Shen
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Quebec City, Quebec, Canada
| | - Li Yi
- Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China; College of Life Science, Luoyang Normal University, Luoyang 471934, China.
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China.
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Xiao Y, Wan C, Wu X, Xu Y, Chen Y, Rao L, Wang B, Shen L, Han W, Zhao H, Shi J, Zhang J, Song Z, Yu F. Novel small-molecule compound YH7 inhibits the biofilm formation of Staphylococcus aureus in a sarX-dependent manner. mSphere 2024; 9:e0056423. [PMID: 38170984 PMCID: PMC10826350 DOI: 10.1128/msphere.00564-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
The emergence of antibiotic-resistant and biofilm-producing Staphylococcus aureus isolates presents major challenges for treating staphylococcal infections. Biofilm inhibition is an important anti-virulence strategy. In this study, a novel maleimide-diselenide hybrid compound (YH7) was synthesized and demonstrated remarkable antimicrobial activity against methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) in both planktonic cultures and biofilms. The minimum inhibitory concentration (MIC) of YH7 for S. aureus isolates was 16 µg/mL. Quantification of biofilms demonstrated that the sub-MIC (4 µg/mL) of YH7 significantly inhibits biofilm formation in both MSSA and MRSA. Confocal laser scanning microscopy analysis further confirmed the biofilm inhibitory potential of YH7. YH7 also significantly suppressed bacterial adherence to A549 cells. Moreover, YH7 treatment significantly inhibited S. aureus colonization in nasal tissue of mice. Preliminary mechanistic studies revealed that YH7 exerted potent biofilm-suppressing effects by inhibiting polysaccharide intercellular adhesin (PIA) synthesis, rather than suppressing bacterial autolysis. Real-time quantitative PCR data indicated that YH7 downregulated biofilm formation-related genes (clfA, fnbA, icaA, and icaD) and the global regulatory gene sarX, which promotes PIA synthesis. The sarX-dependent antibiofilm potential of YH7 was validated by constructing S. aureus NCTC8325 sarX knockout and complementation strains. Importantly, YH7 demonstrated a low potential to induce drug resistance in S. aureus and exhibited non-toxic to rabbit erythrocytes, A549, and BEAS-2B cells at antibacterial concentrations. In vivo toxicity assays conducted on Galleria mellonella further confirmed that YH7 is biocompatible. Overall, YH7 demonstrated potent antibiofilm activity supports its potential as an antimicrobial agent against S. aureus biofilm-related infections. IMPORTANCE Biofilm-associated infections, characterized by antibiotic resistance and persistence, present a formidable challenge in healthcare. Traditional antibacterial agents prove inadequate against biofilms. In this study, the novel compound YH7 demonstrates potent antibiofilm properties by impeding the adhesion and the polysaccharide intercellular adhesin production of Staphylococcus aureus. Notably, its exceptional efficacy against both methicillin-resistant and methicillin-susceptible strains highlights its broad applicability. This study highlights the potential of YH7 as a novel therapeutic agent to address the pressing issue of biofilm-driven infections.
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Affiliation(s)
- Yanghua Xiao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Public Health, Nanchang University, Nanchang, China
| | - Cailing Wan
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Public Health, Nanchang University, Nanchang, China
| | - Xiaocui Wu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yanlei Xu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yao Chen
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lulin Rao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bingjie Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Li Shen
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Weihua Han
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Huilin Zhao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Junhong Shi
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiao Zhang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zengqiang Song
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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Oliveira AS, Saraiva LM, Carvalho SM. Staphylococcus epidermidis biofilms undergo metabolic and matrix remodeling under nitrosative stress. Front Cell Infect Microbiol 2023; 13:1200923. [PMID: 37469594 PMCID: PMC10352803 DOI: 10.3389/fcimb.2023.1200923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/05/2023] [Indexed: 07/21/2023] Open
Abstract
Staphylococcus epidermidis is a commensal skin bacterium that forms host- and antibiotic-resistant biofilms that are a major cause of implant-associated infections. Most research has focused on studying the responses to host-imposed stresses on planktonic bacteria. In this work, we addressed the open question of how S. epidermidis thrives on toxic concentrations of nitric oxide (NO) produced by host innate immune cells during biofilm assembly. We analyzed alterations of gene expression, metabolism, and matrix structure of biofilms of two clinical isolates of S. epidermidis, namely, 1457 and RP62A, formed under NO stress conditions. In both strains, NO lowers the amount of biofilm mass and causes increased production of lactate and decreased acetate excretion from biofilm glucose metabolism. Transcriptional analysis revealed that NO induces icaA, which is directly involved in polysaccharide intercellular adhesion (PIA) production, and genes encoding proteins of the amino sugar pathway (glmM and glmU) that link glycolysis to PIA synthesis. However, the strains seem to have distinct regulatory mechanisms to boost lactate production, as NO causes a substantial upregulation of ldh gene in strain RP62A but not in strain 1457. The analysis of the matrix components of the staphylococcal biofilms, assessed by confocal laser scanning microscopy (CLSM), showed that NO stimulates PIA and protein production and interferes with biofilm structure in a strain-dependent manner, but independently of the Ldh level. Thus, NO resistance is attained by remodeling the staphylococcal matrix architecture and adaptation of main metabolic processes, likely providing in vivo fitness of S. epidermidis biofilms contacting NO-proficient macrophages.
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Malviya J, Alameri AA, Al-Janabi SS, Fawzi OF, Azzawi AL, Obaid RF, Alsudani AA, Alkhayyat AS, Gupta J, Mustafa YF, Karampoor S, Mirzaei R. Metabolomic profiling of bacterial biofilm: trends, challenges, and an emerging antibiofilm target. World J Microbiol Biotechnol 2023; 39:212. [PMID: 37256458 DOI: 10.1007/s11274-023-03651-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/17/2023] [Indexed: 06/01/2023]
Abstract
Biofilm-related infections substantially contribute to bacterial illnesses, with estimates indicating that at least 80% of such diseases are linked to biofilms. Biofilms exhibit unique metabolic patterns that set them apart from their planktonic counterparts, resulting in significant metabolic reprogramming during biofilm formation. Differential glycolytic enzymes suggest that central metabolic processes are markedly different in biofilms and planktonic cells. The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is highly expressed in Staphylococcus aureus biofilm progenitors, indicating that changes in glycolysis activity play a role in biofilm development. Notably, an important consideration is a correlation between elevated cyclic di-guanylate monophosphate (c-di-GMP) activity and biofilm formation in various bacteria. C-di-GMP plays a critical role in maintaining the persistence of Pseudomonas aeruginosa biofilms by regulating alginate production, a significant biofilm matrix component. Furthermore, it has been demonstrated that S. aureus biofilm development is initiated by several tricarboxylic acid (TCA) intermediates in a FnbA-dependent manner. Finally, Glucose 6-phosphatase (G6P) boosts the phosphorylation of histidine-containing protein (HPr) by increasing the activity of HPr kinase, enhancing its interaction with CcpA, and resulting in biofilm development through polysaccharide intercellular adhesion (PIA) accumulation and icaADBC transcription. Therefore, studying the metabolic changes associated with biofilm development is crucial for understanding the complex mechanisms involved in biofilm formation and identifying potential targets for intervention. Accordingly, this review aims to provide a comprehensive overview of recent advances in metabolomic profiling of biofilms, including emerging trends, prevailing challenges, and the identification of potential targets for anti-biofilm strategies.
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Affiliation(s)
- Jitendra Malviya
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, India
| | - Ameer A Alameri
- Department of Chemistry, College of Science, University of Babylon, Babylon, Iraq
| | - Saif S Al-Janabi
- Medical Laboratory Techniques Department, Al-Maarif University College, Ramadi, Iraq
| | | | | | - Rasha Fadhel Obaid
- Department of Biomedical Engineering, Al-Mustaqbal University College, Babylon, Iraq
| | - Ali A Alsudani
- College of Science, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Ameer S Alkhayyat
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Jitendra Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, 281406, U. P., India
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, 41001, Iraq
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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Horizontal Transfer of Bacteriocin Biosynthesis Genes Requires Metabolic Adaptation To Improve Compound Production and Cellular Fitness. Microbiol Spectr 2023; 11:e0317622. [PMID: 36472430 PMCID: PMC9927498 DOI: 10.1128/spectrum.03176-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread among bacterial isolates and are important genetic determinants of competitive fitness within a given habitat. Staphylococci produce a tremendous diversity of compounds, and the corresponding BGCs are frequently associated with mobile genetic elements, suggesting gain and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenging, and many BGC recipients initially produce small amounts of compound or show reduced growth rates. To assess whether transfer of BGCs between closely related Staphylococcus aureus strains can be instantly effective or requires elaborate metabolic adaptation, we investigated the intraspecies transfer of a BGC encoding the ribosomally synthesized and posttranslationally modified peptide (RiPP) micrococcin P1 (MP1). We found that acquisition of the BGC by S. aureus RN4220 enabled immediate MP1 production but also imposed a metabolic burden, which was relieved after prolonged cultivation by adaptive mutation. We used a multiomics approach to study this phenomenon and found adaptive evolution to select for strains with increased activity of the tricarboxylic acid cycle (TCA), which enhanced metabolic fitness and levels of compound production. Metabolome analysis revealed increases of central metabolites, including citrate and α-ketoglutarate in the adapted strain, suggesting metabolic adaptation to overcome the BGC-associated growth defects. Our results indicate that BGC acquisition requires genetic and metabolic predispositions, allowing the integration of bacteriocin production into the cellular metabolism. Inappropriate metabolic characteristics of recipients can entail physiological burdens, negatively impacting the competitive fitness of recipients within natural bacterial communities. IMPORTANCE Human microbiomes are critically associated with human health and disease. Importantly, pathogenic bacteria can hide in human-associated communities and can cause disease when the composition of the community becomes unbalanced. Bacteriocin-producing commensals are able to displace pathogens from microbial communities, suggesting that their targeted introduction into human microbiomes might prevent pathogen colonization and infection. However, to develop probiotic approaches, strains are needed that produce high levels of bioactive compounds and retain cellular fitness within mixed bacterial communities. Our work offers insights into the metabolic burdens associated with the production of the bacteriocin micrococcin P1 and highlights evolutionary strategies that increase cellular fitness in the context of production. Metabolic adaptations are most likely broadly relevant for bacteriocin producers and need to be considered for the future development of effective microbiome editing strategies.
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Interplay of CodY and CcpA in Regulating Central Metabolism and Biofilm Formation in Staphylococcus aureus. J Bacteriol 2022; 204:e0061721. [PMID: 35735992 PMCID: PMC9295537 DOI: 10.1128/jb.00617-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Staphylococcus aureus is a medically important pathogen with high metabolic versatility allowing it to infect various niches within a host. S. aureus utilizes two major transcriptional regulators, namely, CodY and CcpA, to remodel metabolic and virulence gene expression in response to changing environmental conditions. Previous studies revealed that inactivation of either codY or ccpA has a pronounced impact on different aspects of staphylococcal physiology and pathogenesis. To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development, we constructed and characterized the codY ccpA double mutant in S. aureus UAMS-1. In line with previous studies, we found that CcpA and CodY control the cellular metabolic status by altering carbon flux through the central and overflow metabolic pathways. Our results demonstrate that ccpA inactivation impairs biofilm formation and decreases incorporation of extracellular DNA (eDNA) into the biofilm matrix, whereas disrupting codY resulted in a robust structured biofilm tethered together with eDNA and polysaccharide intercellular adhesin (PIA). Interestingly, inactivation of both codY and ccpA decreases biofilm biomass and reduces eDNA release in the double mutant. Compared with the inactivation of codY, the codY ccpA mutant did not overexpress toxins but maintained overexpression of amino acid metabolism pathways. Furthermore, the codY ccpA mutant produced large amounts of PIA, in contrast to the wild-type strain and ccpA mutant. Combined, the results of this study suggest that the coordinated action of CodY and CcpA modulate central metabolism, virulence gene expression, and biofilm-associated genes to optimize growth on preferred carbon sources until starvation sets in. IMPORTANCE Staphylococcus aureus is a leading cause of biofilm-associated infections, including infective endocarditis, worldwide. A greater understanding of metabolic forces driving biofilm formation in S. aureus is essential for the identification of novel therapeutic targets and for the development of new strategies to combat this medically important pathogen. This study characterizes the interplay and regulation of central metabolism and biofilm development by two global transcriptional regulators, CodY and CcpA. We found that the lack of CcpA and/or CodY have different impacts on intracellular metabolic status leading to a formation of morphologically altered biofilms. Overall, the results of this study provide new insights into our understanding of metabolism-mediated regulation of biofilm development in S. aureus.
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Identification of novel biofilm genes in avian pathogenic Escherichia coli by Tn5 transposon mutant library. World J Microbiol Biotechnol 2022; 38:130. [PMID: 35688968 DOI: 10.1007/s11274-022-03314-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
Avian pathogenic Escherichia coli (APEC) is the main pathogens that inflict the poultry industry. Biofilm as the pathogenic factors of APEC, which can enhance the anti-host immune system of APEC and improve its survival in the environment. In order to screen for new genes related to APEC biofilm. The APEC strain APEC81 was used to construct a mutant library by Tn5 insertion mutagenesis. Moreover the 28 mutant strains with severely weakened biofilm were successfully screened from 1500 mutant strains by crystal violet staining, in which 17 genes were obtained by high-efficiency thermal asymmetric interlaced PCR. The reported genes include 3 flagella genes (fliS, fliD, and fliR), 4 curli fimbriae genes (csgD, csgA, csgF, and csgG) and 3 type 1 fimbriae genes (fimA, fimD, and fimC). The novel genes include 3 coenzyme genes (gltA, bglX, and mltF) and 4 putative protein genes (yehE, 07045, 11735, 11255). To investigate whether these 17 genes co-regulate the biofilm, the 17 identified genes were deleted from APEC strain APEC81. The results showed that except for the 11735 and 11255 genes, the deletion of 15 genes significantly reduced the biofilm formation ability of APEC81 (P < 0.05). The result of rdar (red, dry and rough) colony morphology showed that curli fimbriae genes (csgD, csgA, csgF, and csgG) and other functional genes (fimC, glxK, yehE, 07045, and 11255) affected the colony morphology. In particular, the hypothetical protein YehE had the greatest influence on the biofilm. It was predicted to have the same structure as the type 1 fimbria protein. When yehE was deleted, the fimE transcription was up-regulated, and the fimA and fimB transcription were down-regulated, resulting in a decrease in type 1 fimbriae. Hence, the yehE mutant significantly reduced the biofilm and the adhesion and invasion ability to cells (P < 0.05). This study identified 5 novel genes (gltA, bglX, mltF, yehE, and 07045) related to biofilm formation and confirmed that yehE affects biofilm formation by type 1 fimbriae, which will benefit further study of the mechanism of biofilm regulation in APEC.
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Characterization of Staphylococcus aureus biofilms via crystal violet binding and biochemical composition assays of isolates from hospitals, raw meat, and biofilm-associated gene mutants. Microb Pathog 2022; 167:105554. [DOI: 10.1016/j.micpath.2022.105554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022]
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Transition of Dephospho-DctD to the Transcriptionally Active State via Interaction with Dephospho-IIA
Glc. mBio 2022; 13:e0383921. [PMID: 35311533 PMCID: PMC9040800 DOI: 10.1128/mbio.03839-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Exopolysaccharides (EPSs), biofilm-maturing components of Vibrio vulnificus, are abundantly produced when the expression of two major EPS gene clusters is activated by an enhancer-binding transcription factor, DctD2, whose expression and phosphorylation are induced by dicarboxylic acids. Surprisingly, when glucose was supplied to V. vulnificus, similar levels of expression of these clusters occurred, even in the absence of dicarboxylic acids. This glucose-dependent activation was also mediated by DctD2, whose expression was sequentially activated by the transcription regulator NtrC. Most DctD2 in cells grown without dicarboxylic acids was present in a dephosphorylated state, known as the transcriptionally inactive form. However, in the presence of glucose, a dephosphorylated component of the glucose-specific phosphotransferase system, d-IIAGlc, interacted with dephosphorylated DctD2 (d-DctD2). While d-DctD2 did not show any affinity to a DNA fragment containing the DctD-binding sequences, the complex of d-DctD2 and d-IIAGlc exhibited specific and efficient DNA binding, similar to the phosphorylated DctD2. The d-DctD2-mediated activation of the EPS gene clusters’ expression was not fully achieved in cells grown with mannose. Furthermore, the degrees of expression of the clusters under glycerol were less than those under mannose. This was caused by an antagonistic and competitive effect of GlpK, whose expression was increased by glycerol, in forming a complex with d-DctD2 by d-IIAGlc. The data demonstrate a novel regulatory pathway for V. vulnificus EPS biosynthesis and biofilm maturation in the presence of glucose, which is mediated by d-DctD2 through its transition to the transcriptionally active state by interacting with available d-IIAGlc.
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Gao L, Zhu H, Chen Y, Yang Y. Antibacterial pathway of cefquinome against Staphylococcus aureus based on label-free quantitative proteomics analysis. J Microbiol 2021; 59:1112-1124. [PMID: 34751907 DOI: 10.1007/s12275-021-1201-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 09/02/2021] [Accepted: 09/13/2021] [Indexed: 10/19/2022]
Abstract
Cefquinome (CEQ) is a novel β-lactam antibiotic that exhibits excellent antibacterial activity against Staphylococcus aureus. However, the bacterial protein targets of CEQ are unclear. To evaluate the relationship between the pharmacokinetic/pharmacodynamic (PK/PD) parameters of CEQ and strains with varying degrees of resistance and to elucidate bacterial protein responses to CEQ treatment, label-free quantitative proteomics analysis was conducted. The sensitive S. aureus ATCC6538 and the resistant 2MIC and 8MIC were tested for differentially expressed proteins. An in vitro model was treated with different concentrations of CEQ (3, 5, or 10 µg/ml) with different terminal half-lives (2.5 or 5 h) at different intervals (12 or 24 h). Differentially expressed proteins were evaluated using Gene Ontology analysis followed by KEGG pathway enrichment analysis and STRING network analysis. RT-qPCR was performed to validate the differentially expressed proteins at the molecular level. The results showed that the degree of resistance increased in a cumulative manner and increased gradually with the extension of administration time. The resistant strain would not have appeared in the model only if %T > mutant prevention concentration ≥ 50%. The expression of 45 proteins significantly changed following CEQ treatment, among which 42 proteins were obviously upregulated and 3 were downregulated. GO analysis revealed that the differentially expressed proteins were mainly present on cells and the cell membrane, participated in metabolic and intracellular processes, and had catalytic and binding activities. The RPSO, SDHB, CITZ, ADK, and SAOUHSC 00113 genes in S. aureus may play important roles in the development of resistance to CEQ. These results provided important reference candidate proteins as targets for overcoming S. aureus resistance to CEQ.
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Affiliation(s)
- Linglin Gao
- Hainan Key Laboratory of Tropical Animal Breeding and Disease Research, College of Animal Science and Technology, Hainan University, Hainan, P. R. China
| | - Hao Zhu
- Hainan Key Laboratory of Tropical Animal Breeding and Disease Research, College of Animal Science and Technology, Hainan University, Hainan, P. R. China
| | - Yun Chen
- Hainan Key Laboratory of Tropical Animal Breeding and Disease Research, College of Animal Science and Technology, Hainan University, Hainan, P. R. China
| | - Yuhui Yang
- Hainan Key Laboratory of Tropical Animal Breeding and Disease Research, College of Animal Science and Technology, Hainan University, Hainan, P. R. China.
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Kang S, Park H, Lee KJ, Lee KH. Transcription activation of two clusters for exopolysaccharide biosynthesis by phosphorylated DctD in Vibrio vulnificus. Environ Microbiol 2021; 23:5364-5377. [PMID: 34110060 DOI: 10.1111/1462-2920.15636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 11/28/2022]
Abstract
NtrC-mediated production of exopolysaccharides (EPS), essential components for Vibrio vulnificus biofilms, is highly increased in the presence of dicarboxylic or tricarboxylic acids. Gel-shift assays showed that regulation of the EPS-gene cluster I (EPS-I cluster) by NtrC was direct via binding of phosphorylated NtrC (p-NtrC) to the regulatory region of the EPS-I cluster. In contrast, p-NtrC did not bind to the EPS-II and EPS-III clusters, suggesting that NtrC regulation was not direct and another transcription factor belonging to an NtrC-regulon might play a role in activating their transcription. A candidate transcription factor, DctD, of which expression was induced by NtrC, activated the expression of the EPS-II and EPS-III clusters via direct binding to their upstream regions. Under growth conditions with either dicarboxylic or tricarboxylic acids, the expression of NtrC was induced and the transcription of dctD was activated. Furthermore, DctD exhibited higher transcriptional activity under the conditions with dicarboxylic acids than with tricarboxylic acids. Therefore, this study demonstrates that under dicarboxylate-rich conditions, both the abundance and activity of DctD were markedly induced, which activates the expression of two EPS clusters to maximize biosynthesis of EPS facilitating biofilm maturation in V. vulnificus.
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Affiliation(s)
- Sebin Kang
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Hana Park
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kyung-Jo Lee
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kyu-Ho Lee
- Department of Life Science, Sogang University, Seoul, South Korea
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Loza-Correa M, Yousuf B, Ramirez-Arcos S. Staphylococcus epidermidis undergoes global changes in gene expression during biofilm maturation in platelet concentrates. Transfusion 2021; 61:2146-2158. [PMID: 33904608 DOI: 10.1111/trf.16418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Staphylococcus epidermidis forms surface-attached aggregates (biofilms) when grown in platelet concentrates (PCs). Comparative transcriptome analyses were undertaken to investigate differential gene expression of S. epidermidis biofilms grown in PCs. STUDY DESIGN AND METHODS Two S. epidermidis strains isolated from human skin (AZ22 and AZ39) and one strain isolated from contaminated PCs (ST02) were grown in glucose-supplemented Trypticase Soy Broth (TSBg) and PCs. RNA was extracted and sequenced using Illumina HiSeq. Differential expression analysis was done using DESeq, and significantly differentially expressed genes (DEGs) were selected. DEGs were subjected to Kyoto encyclopedia of genes and genomes and Gene Ontology analyses. Differential gene expression was validated with quantitative reverse transcription-PCR. RESULTS A total of 436, 442, and 384 genes were expressed in AZ22, AZ39, and ST02, respectively. DEG analysis showed that 170, 172, and 117 genes were upregulated in PCs in comparison to TSBg, whereas 120, 135, and 89 genes were downregulated (p < .05) in mature biofilms of AZ22, AZ39, and ST02, respectively. Twenty-seven DEGs were shared by all three strains. While 76 DEGs were shared by AZ22 and AZ39, only 34 and 21 DEGs were common between ST02, and AZ22 and AZ39, respectively. Significant transcriptional expression changes were observed in genes involved in platelet-bacteria interaction, biofilm formation, production of virulence factors, and resistance to antimicrobial peptides and antibiotics. CONCLUSION Differential gene expression in S. epidermidis is triggered by the stressful PC storage environment. Upregulation of virulence and antimicrobial resistance genes could have clinical implications for transfusion patients.
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Affiliation(s)
- Maria Loza-Correa
- Centre for Innovation, Canadian Blood Services, Ottawa, Ontario, Canada
| | - Basit Yousuf
- Centre for Innovation, Canadian Blood Services, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Sandra Ramirez-Arcos
- Centre for Innovation, Canadian Blood Services, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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14
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Inactivation of the Pta-AckA pathway impairs fitness of Bacillus anthracis during overflow metabolism. J Bacteriol 2021; 203:JB.00660-20. [PMID: 33593944 PMCID: PMC8092162 DOI: 10.1128/jb.00660-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Under conditions of glucose excess, aerobically growing bacteria predominantly direct carbon flux towards acetate fermentation, a phenomenon known as overflow metabolism or the bacterial 'Crabtree effect'. Numerous studies of the major acetate-generating pathway, the Pta-AckA, revealed its important role in bacterial fitness through the control of central metabolism to sustain balanced growth and cellular homeostasis. In this work, we highlight the contribution of the Pta-AckA pathway to fitness of the spore-forming bacterium, Bacillus anthracis We demonstrate that disruption of the Pta-AckA pathway causes a drastic growth reduction in the mutants and alters the metabolic and energy status of the cells. Our results revealed that inactivation of the Pta-AckA pathway increases the glucose consumption rate, affects intracellular ATP, NAD+ and NADH levels and leads to a metabolic block at the pyruvate and acetyl-CoA nodes. Consequently, accumulation of intracellular acetyl-CoA and pyruvate forces bacteria to direct carbon into the TCA and/or glyoxylate cycles as well as fatty acid and poly(3-hydroxybutyrate) (PHB) biosynthesis pathways. Notably, the presence of phosphate butyryltransferase in B. anthracis partially compensates for the loss of phosphotransacetylase activity. Furthermore, overexpression of the ptb gene not only eliminates the negative impact of the pta mutation on B. anthracis fitness, but also restores normal growth in the pta mutant of the non-butyrate-producing bacterium, Staphylococcus aureus Taken together, the results of this study demonstrate the importance of the Pta-AckA pathway for B. anthracis fitness by revealing its critical contribution to the maintenance of metabolic homeostasis during aerobic growth under conditions of carbon overflow.IMPORTANCE B. anthracis, the etiologic agent of anthrax, is a highly pathogenic, spore-forming bacterium that causes acute, life-threatening disease in both humans and livestock. A greater understanding of the metabolic determinants governing fitness of B. anthracis is essential for the development of successful therapeutic and vaccination strategies aimed at lessening the potential impact of this important biodefense pathogen. This study is the first to demonstrate the vital role of the Pta-AckA pathway in preserving energy and metabolic homeostasis in B. anthracis under conditions of carbon overflow, therefore, highlighting this pathway as a potential therapeutic target for drug discovery. Overall, the results of this study provide important insight into understanding the metabolic processes and requirements driving rapid B. anthracis proliferation during vegetative growth.
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15
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Martínez-García S, Peralta H, Betanzos-Cabrera G, Chavez-Galan L, Rodríguez-Martínez S, Cancino-Diaz ME, Cancino-Diaz JC. Proteomic comparison of biofilm vs. planktonic Staphylococcus epidermidis cells suggests key metabolic differences between these conditions. Res Microbiol 2021; 172:103796. [PMID: 33412274 DOI: 10.1016/j.resmic.2020.103796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 11/16/2022]
Abstract
Previous studies have shown that biofilm-forming bacteria are deficient in tricarboxylic acid (TCA) cycle metabolites, suggesting a relationship between these cellular processes. In this work, we compared the proteomes of planktonic vs biofilm cells from a clinical strain of Staphylococcus epidermidis using LC-MS/MS. A total of 168 proteins were identified from both growth conditions. The biofilm cells showed enrichment of proteins participating in glycolysis for the formation of pyruvate; however, the absence of TCA cycle proteins and the presence of lactate dehydrogenase, formate acetyltransferase, and acetoin reductase suggested that pyruvate was catabolized to their respective products: lactate, formate and acetoin. On the other hand, planktonic cells showed proteins participating in glycolysis and the TCA cycle, the pentose phosphate pathway, gluconeogenesis, ATP generation and the oxidative stress response. Functional networks with higher interconnection were predicted for planktonic proteins. We propose that in S. epidermidis, the relative absence of TCA cycle proteins is associated with the formation of biofilms and that lactate, formate and acetoin are the end products of partial glucose metabolism.
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Affiliation(s)
- Sergio Martínez-García
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Cd. México, Mexico
| | - Humberto Peralta
- Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Cuernavaca, Morelos, Mexico
| | | | - Leslie Chavez-Galan
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Cd. México, Mexico
| | - Sandra Rodríguez-Martínez
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Cd. México, Mexico
| | - Mario E Cancino-Diaz
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Cd. México, Mexico.
| | - Juan C Cancino-Diaz
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Cd. México, Mexico.
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16
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Rudra P, Boyd JM. Metabolic control of virulence factor production in Staphylococcus aureus. Curr Opin Microbiol 2020; 55:81-87. [PMID: 32388086 DOI: 10.1016/j.mib.2020.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/27/2022]
Abstract
As investigators decipher the underlining mechanisms of Staphylococcus aureus pathogenesis, it is becoming apparent that perturbations in central metabolism alter virulence factor production and infection outcomes. It is also evident that S. aureus has the ability to metabolically adapt to improve colonization and overcome challenges imparted by the immune system. Altered metabolite pools modify virulence factor production suggesting that proper functioning of a core metabolic network is necessary for successful niche colonization and pathogenesis. Herein we discuss four examples of transcriptional regulators that monitor metabolic status. These regulatory systems sense perturbations in the metabolic network and respond by altering the transcription of genes utilized for central metabolism, energy generation and pathogenesis.
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Affiliation(s)
- Paulami Rudra
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA.
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17
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Genetic and Biochemical Analysis of CodY-Mediated Cell Aggregation in Staphylococcus aureus Reveals an Interaction between Extracellular DNA and Polysaccharide in the Extracellular Matrix. J Bacteriol 2020; 202:JB.00593-19. [PMID: 32015143 DOI: 10.1128/jb.00593-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/24/2020] [Indexed: 12/14/2022] Open
Abstract
The global regulator CodY links nutrient availability to the regulation of virulence factor gene expression in Staphylococcus aureus, including many genes whose products affect biofilm formation. Antithetical phenotypes of both biofilm deficiency and accumulation have been reported for codY-null mutants; thus, the role of CodY in biofilm development remains unclear. codY mutant cells of a strain producing a robust biofilm elaborate proaggregation surface-associated features not present on codY mutant cells that do not produce a robust biofilm. Biochemical analysis of the clinical isolate SA564, which aggregates when deficient for CodY, revealed that these features are sensitive to nuclease treatment and are resistant to protease exposure. Genetic analyses revealed that disrupting lgt (the diacylglycerol transferase gene) in codY mutant cells severely weakened aggregation, indicating a role for lipoproteins in the attachment of the biofilm matrix to the cell surface. An additional and critical role of IcaB in producing functional poly-N-acetylglucosamine (PIA) polysaccharide in extracellular DNA (eDNA)-dependent biofilm formation was shown. Moreover, overproducing PIA is sufficient to promote aggregation in a DNA-dependent manner regardless of source of nucleic acids. Taken together, our results point to PIA synthesis as the primary determinant of biofilm formation when CodY activity is reduced and suggest a modified electrostatic net model for matrix attachment whereby PIA associates with eDNA, which interacts with the cell surface via covalently attached membrane lipoproteins. This work counters the prevailing view that polysaccharide- and eDNA/protein-based biofilms are mutually exclusive. Rather, we demonstrate that eDNA and PIA can work synergistically to form a biofilm.IMPORTANCE Staphylococcus aureus remains a global health concern and exemplifies the ability of an opportunistic pathogen to adapt and persist within multiple environments, including host tissue. Not only does biofilm contribute to persistence and immune evasion in the host environment, it also may aid in the transition to invasive disease. Thus, understanding how biofilms form is critical for developing strategies for dispersing biofilms and improving biofilm disease-related outcomes. Using biochemical, genetic, and cell biology approaches, we reveal a synergistic interaction between PIA and eDNA that promotes cell aggregation and biofilm formation in a CodY-dependent manner in S. aureus We also reveal that envelope-associated lipoproteins mediate attachment of the biofilm matrix to the cell surface.
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18
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Alreshidi MM, Dunstan RH, Macdonald MM, Gottfries J, Roberts TK. The Uptake and Release of Amino Acids by Staphylococcus aureus at Mid-Exponential and Stationary Phases and Their Corresponding Responses to Changes in Temperature, pH and Osmolality. Front Microbiol 2020; 10:3059. [PMID: 32038532 PMCID: PMC6990410 DOI: 10.3389/fmicb.2019.03059] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 12/18/2019] [Indexed: 01/21/2023] Open
Abstract
Staphylococcus aureus is an important pathogen that is associated with nosocomial infections, as well as food poisoning. This bacterium is resistant to antimicrobial agents and can survive in a wide range of environmental conditions. The aim of this study was to measure the uptake and release of amino acids by S. aureus at mid-exponential and stationary phases of growth following exposure to a combination of conditions including variations in temperature, pH and NaCl. Bacterial cells were grown up to mid-exponential and stationary phases in tryptic soy broth (TSB), where the supernatants were collected for analyses of amino acids to determine the uptake and release characteristics. The uptake/release of amino acids was estimated by subtracting the initial levels of the free amino acids in the media from those measured at mid-exponential and stationary phases of growth. When cells were grown at ideal conditions, the analyses revealed that significant uptake of amino acids had occurred by stationary phase compared with the mid-exponential phase. A substantial release of valine and tyrosine into the external media was observed by cells at stationary phase. At both phases, the uptake and release patterns were significantly different between cells grown under ideal control conditions, when compared with those grown under various combinations of sub-optimal environmental conditions. The analyses of the supernatants harvested from controls and treatment groups at exponential phase indicated that the total uptake of amino acids was reduced approximately five times by cells grown with addition of 2.5% NaCl or with pH6 at 35°C, and 2-fold by cells grown at pH8 at 35°C. However, the final quantities of amino acids taken up by cells grown to stationary phase did not significantly alter between control and treated samples. Valine was found to be the most abundant amino acid that was significantly released into the media at stationary phase by both control and treated samples. It was evident that diverse environmental conditions resulted in differential patterns of amino acid uptake and release during adaptation to designated conditions.
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Affiliation(s)
- Mousa M Alreshidi
- Department of Biology, College of Sciences, University of Ha'il, Ha'il, Saudi Arabia
| | - R Hugh Dunstan
- Metabolic Research Group, Faculty of Science, School of Environmental and Life Sciences, University Drive, Callaghan, NSW, Australia
| | - Margaret M Macdonald
- Metabolic Research Group, Faculty of Science, School of Environmental and Life Sciences, University Drive, Callaghan, NSW, Australia
| | - Johan Gottfries
- Department of Chemistry, University of Gothenburg, Gothenburg, Sweden
| | - Tim K Roberts
- Metabolic Research Group, Faculty of Science, School of Environmental and Life Sciences, University Drive, Callaghan, NSW, Australia
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19
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CidR and CcpA Synergistically Regulate Staphylococcus aureus cidABC Expression. J Bacteriol 2019; 201:JB.00371-19. [PMID: 31501288 DOI: 10.1128/jb.00371-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022] Open
Abstract
The death and lysis of a subpopulation of Staphylococcus aureus cells during biofilm development benefit the whole bacterial population through the release of an important component of the biofilm matrix, extracellular DNA. Previously, we have demonstrated that these processes are affected by the gene products of the cidABC operon, the expression of which is controlled by the LysR-type transcriptional regulator, CidR. In this study, we characterized cis- and trans-acting elements essential for the induction of the cidABC operon. In addition to a CidR-binding site located within the cidABC promoter region, sequence analysis revealed the presence of a putative catabolite responsive element (cre box), suggestive of the involvement of the catabolite control protein A (CcpA) in the regulation of cidABC expression. This was confirmed using electrophoretic mobility shift assays and real-time reverse transcriptase PCR analysis demonstrating the direct positive control of cidABC transcription by the master regulator of carbon metabolism. Furthermore, the importance of CcpA and the identified cre site for the induction of the cidABC operon was demonstrated by examining the expression of P cidABC-lacZ reporter fusions in various mutant strains in which the genes involved in carbon metabolism and carbon catabolite repression were disrupted. Together the results of this study demonstrate the necessity of both transcriptional regulators, CidR and CcpA, for the induction of the cidABC operon and reveal the complexity of molecular interactions controlling its expression.IMPORTANCE This work focuses on the characterization of cis- and trans-acting elements essential for the induction of the cidABC operon in S. aureus The results of this study are the first to demonstrate the synergistic control of cidABC expression by transcriptional regulators CidR and CcpA during carbohydrate metabolism. We established that the full induction of cidABC expression depends on the metabolic state of bacteria and requires both CidR and CcpA. Together, these findings delineate regulatory control of cidABC expression under different metabolic conditions and provide important new insights into our understanding of cell death mechanisms during biofilm development in S. aureus.
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20
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Yan Q, Robert S, Brooks JP, Fong SS. Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model. BMC Bioinformatics 2019; 20:227. [PMID: 31060515 PMCID: PMC6501404 DOI: 10.1186/s12859-019-2826-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/17/2019] [Indexed: 12/31/2022] Open
Abstract
Background Serratia marcescens is a chitinolytic bacterium that can potentially be used for consolidated bioprocessing to convert chitin to value-added chemicals. Currently, S. marcescens is poorly characterized and studies on intracellular metabolic and regulatory mechanisms would expedite development of bioprocessing applications. Results In this study, our goal was to characterize the metabolic profile of S. marcescens to provide insight for metabolic engineering applications and fundamental biological studies. Hereby, we constructed a constraint-based genome-scale metabolic model (iSR929) including 929 genes, 1185 reactions and 1164 metabolites based on genomic annotation of S. marcescens Db11. The model was tested by comparing model predictions with experimental data and analyzed to identify essential aspects of the metabolic network (e.g. 138 essential genes predicted). The model iSR929 was refined by integrating RNAseq data of S. marcescens growth on three different carbon sources (glucose, N-acetylglucosamine, and glycerol). Significant differences in TCA cycle utilization were found for growth on the different carbon substrates, For example, for growth on N-acetylglucosamine, S. marcescens exhibits high pentose phosphate pathway activity and nucleotide synthesis but low activity of the TCA cycle. Conclusions Our results show that S. marcescens model iSR929 can provide reasonable predictions and can be constrained to fit with experimental values. Thus, our model may be used to guide strain designs for metabolic engineering to produce chemicals such as 2,3-butanediol, N-acetylneuraminic acid, and n-butanol using S. marcescens. Electronic supplementary material The online version of this article (10.1186/s12859-019-2826-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, West Hall, Room 422, 601 West Main Street, P.O. Box 843028, Richmond, VA, 23284-3028, USA.
| | - Seth Robert
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, West Hall, Room 422, 601 West Main Street, P.O. Box 843028, Richmond, VA, 23284-3028, USA
| | - J Paul Brooks
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA, 23284, USA.,Center for the study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Stephen S Fong
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, West Hall, Room 422, 601 West Main Street, P.O. Box 843028, Richmond, VA, 23284-3028, USA. .,Center for the study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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21
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Soumya KR, Jishma P, Sugathan S, Mathew J, Radhakrishnan EK. Biofilm Changes of Clinically Isolated Coagulase Negative Staphylococci. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s40011-019-01096-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Lerch MF, Schoenfelder SMK, Marincola G, Wencker FDR, Eckart M, Förstner KU, Sharma CM, Thormann KM, Kucklick M, Engelmann S, Ziebuhr W. A non-coding RNA from the intercellular adhesion (ica) locus of Staphylococcus epidermidis controls polysaccharide intercellular adhesion (PIA)-mediated biofilm formation. Mol Microbiol 2019; 111:1571-1591. [PMID: 30873665 DOI: 10.1111/mmi.14238] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2019] [Indexed: 12/15/2022]
Abstract
Polysaccharide intercellular adhesin (PIA)-associated biofilm formation is mediated by the intercellular adhesin (ica) locus and represents a major pathomechanism of Staphylococcus epidermidis. Here, we report on a novel long non-coding (nc)RNA, named IcaZ, which is approximately 400 nucleotides in size. icaZ is located downstream of the ica repressor gene icaR and partially overlaps with the icaR 3' UTR. icaZ exclusively exists in ica-positive S. epidermidis, but not in S. aureus or other staphylococci. Inactivation of the gene completely abolishes PIA production. IcaZ is transcribed as a primary transcript from its own promoter during early- and mid-exponential growth and its transcription is induced by low temperature, ethanol and salt stress. IcaZ targets the icaR 5' UTR and hampers icaR mRNA translation, which alleviates repression of icaADBC operon transcription and results in PIA production. Interestingly, other than in S. aureus, posttranscriptional control of icaR mRNA in S. epidermidis does not involve icaR mRNA 5'/3' UTR base pairing. This suggests major structural and functional differences in icaADBC operon regulation between the two species that also involve the recruitment of ncRNAs. Together, the IcaZ ncRNA represents an unprecedented novel species-specific player involved in the control of PIA production in NBSP S. epidermidis.
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Affiliation(s)
- Maike F Lerch
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Sonja M K Schoenfelder
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Gabriella Marincola
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Freya D R Wencker
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Martin Eckart
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Konrad U Förstner
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany.,Faculty of Information Science and Communication Studies, TH Köln, Cologne, D-50678, Germany.,ZB MED-Information Centre for Life Sciences, Cologne, Germany
| | - Cynthia M Sharma
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Kai M Thormann
- Institute of Microbiology and Molecular Biology, University of Gießen, Heinrich-Buff-Ring 26, Gießen, 35392, Germany
| | - Martin Kucklick
- Helmholtz Centre for Infection Research, Microbial Proteomics, Inhoffenstraße 7, Braunschweig, 38124, Germany.,Institute of Microbiology, Technical University Braunschweig, Spielmannstr. 7, Braunschweig, 38106, Germany
| | - Susanne Engelmann
- Helmholtz Centre for Infection Research, Microbial Proteomics, Inhoffenstraße 7, Braunschweig, 38124, Germany.,Institute of Microbiology, Technical University Braunschweig, Spielmannstr. 7, Braunschweig, 38106, Germany
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
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23
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Marincola G, Wencker FDR, Ziebuhr W. The Many Facets of the Small Non-coding RNA RsaE (RoxS) in Metabolic Niche Adaptation of Gram-Positive Bacteria. J Mol Biol 2019; 431:4684-4698. [PMID: 30914292 DOI: 10.1016/j.jmb.2019.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 01/01/2023]
Abstract
Small regulatory RNAs (sRNAs) are increasingly recognized as players in the complex regulatory networks governing bacterial gene expression. RsaE (synonym RoxS) is an sRNA that is highly conserved in bacteria of the Bacillales order. Recent analyses in Bacillus subtilis, Staphylococcus aureus and Staphylococcus epidermidis identified RsaE/RoxS as a potent riboregulator of central carbon metabolism and energy balance with many molecular RsaE/RoxS functions and targets being shared across species. Similarities and species-specific differences in cellular processes modulated by RsaE/RoxS suggest that this sRNA plays a prominent role in the adaptation of Gram-positive bacteria to niches with varying nutrient availabilities and environmental cues. This review summarizes recent findings on the molecular function of RsaE/RoxS and its interaction with mRNA targets. Special emphasis will be on the integration of RsaE/RoxS into metabolic regulatory circuits and, derived from this, the role of RsaE/RoxS as a putative driver to generate phenotypic heterogeneity in bacterial populations. In this respect, we will particularly discuss heterogeneous RsaE expression in S. epidermidis biofilms and its possible contribution to metabolic niche diversification, programmed bacterial lysis and biofilm matrix production.
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Affiliation(s)
- Gabriella Marincola
- Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Freya D R Wencker
- Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany.
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24
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Bronesky D, Desgranges E, Corvaglia A, François P, Caballero CJ, Prado L, Toledo-Arana A, Lasa I, Moreau K, Vandenesch F, Marzi S, Romby P, Caldelari I. A multifaceted small RNA modulates gene expression upon glucose limitation in Staphylococcus aureus. EMBO J 2019; 38:e99363. [PMID: 30760492 PMCID: PMC6418428 DOI: 10.15252/embj.201899363] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 12/17/2018] [Accepted: 01/21/2019] [Indexed: 01/10/2023] Open
Abstract
Pathogenic bacteria must rapidly adapt to ever-changing environmental signals resulting in metabolism remodeling. The carbon catabolite repression, mediated by the catabolite control protein A (CcpA), is used to express genes involved in utilization and metabolism of the preferred carbon source. Here, we have identified RsaI as a CcpA-repressed small non-coding RNA that is inhibited by high glucose concentrations. When glucose is consumed, RsaI represses translation initiation of mRNAs encoding a permease of glucose uptake and the FN3K enzyme that protects proteins against damage caused by high glucose concentrations. RsaI also binds to the 3' untranslated region of icaR mRNA encoding the transcriptional repressor of exopolysaccharide production and to sRNAs induced by the uptake of glucose-6 phosphate or nitric oxide. Furthermore, RsaI expression is accompanied by a decreased transcription of genes involved in carbon catabolism pathway and an activation of genes involved in energy production, fermentation, and nitric oxide detoxification. This multifaceted RNA can be considered as a metabolic signature when glucose becomes scarce and growth is arrested.
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Affiliation(s)
- Delphine Bronesky
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Emma Desgranges
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Anna Corvaglia
- Genomic Research Laboratory, Department of Medical Specialties, Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Department of Medical Specialties, Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | | | - Laura Prado
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-GN, Navarra, Spain
| | | | - Inigo Lasa
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
| | - Karen Moreau
- CIRI, Centre international de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Univ Lyon, Lyon, France
| | - François Vandenesch
- CIRI, Centre international de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Univ Lyon, Lyon, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
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Schoenfelder SMK, Lange C, Prakash SA, Marincola G, Lerch MF, Wencker FDR, Förstner KU, Sharma CM, Ziebuhr W. The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities. PLoS Pathog 2019; 15:e1007618. [PMID: 30870530 PMCID: PMC6435200 DOI: 10.1371/journal.ppat.1007618] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/26/2019] [Accepted: 02/04/2019] [Indexed: 12/15/2022] Open
Abstract
RsaE is a conserved small regulatory RNA (sRNA) which was previously reported to represent a riboregulator of central carbon flow and other metabolic pathways in Staphylococcus aureus and Bacillus subtilis. Here we show that RsaE contributes to extracellular (e)DNA release and biofilm-matrix switching towards polysaccharide intercellular adhesin (PIA) production in a hypervariable Staphylococcus epidermidis isolate. Transcriptome analysis through differential RNA sequencing (dRNA-seq) in combination with confocal laser scanning microscopy (CLSM) and reporter gene fusions demonstrate that S. epidermidis protein- and PIA-biofilm matrix producers differ with respect to RsaE and metabolic gene expression. RsaE is spatiotemporally expressed within S. epidermidis PIA-mediated biofilms, and its overexpression triggers a PIA biofilm phenotype as well as eDNA release in an S. epidermidis protein biofilm matrix-producing strain background. dRNA-seq and Northern blot analyses revealed RsaE to exist as a major full-length 100-nt transcript and a minor processed species lacking approximately 20 nucleotides at the 5'-end. RsaE processing results in expansion of the mRNA target spectrum. Thus, full-length RsaE interacts with S. epidermidis antiholin-encoding lrgA mRNA, facilitating bacterial lysis and eDNA release. Processed RsaE, however, interacts with the 5'-UTR of icaR and sucCD mRNAs, encoding the icaADBC biofilm operon repressor IcaR and succinyl-CoA synthetase of the tricarboxylic acid (TCA) cycle, respectively. RsaE augments PIA-mediated biofilm matrix production, most likely through activation of icaADBC operon expression via repression of icaR as well as by TCA cycle inhibition and re-programming of staphylococcal central carbon metabolism towards PIA precursor synthesis. Additionally, RsaE supports biofilm formation by mediating the release of eDNA as stabilizing biofilm matrix component. As RsaE itself is heterogeneously expressed within biofilms, we consider this sRNA to function as a factor favoring phenotypic heterogeneity and supporting division of labor in S. epidermidis biofilm communities. Bacterial biofilms are highly organized structures which functionally emulate multicellular organisms, last but not least through heterogeneous gene expression patterns displayed by biofilm subpopulations. Here we analyzed the functions of the non-coding RNA RsaE in Staphylococcus epidermidis biofilm communities. RsaE exerted unexpected influences on S. epidermidis biofilm matrix composition by triggering localized eDNA release and facilitating PIA expression. RsaE accomplishes these effects by targeting mRNAs involved in bacterial lysis control, icaADBC expression and TCA cycle activity, with RsaE undergoing processing to exploit its full target potential. Interestingly, RsaE interaction with lysis-engaged lrgA mRNA is specific for S. epidermidis lrgA, but does not occur with lrgA mRNA from S. aureus, suggesting species-specific differences in staphylococcal lysis control. We speculate that RsaE-mediated bacterial lysis might represent a form of bacterial altruism contributing to biofilm structuring by providing nutrients to neighboring bacterial cells as well as by releasing eDNA as stabilizing biofilm matrix component. Due to its heterogeneous expression, we consider RsaE as a supporting factor that facilitates population diversity. Together, the data give insight into an unanticipated role of sRNAs as players in S. epidermidis biofilm organization.
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Affiliation(s)
| | - Claudia Lange
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | | | - Gabriella Marincola
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Maike F. Lerch
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Freya D. R. Wencker
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Konrad U. Förstner
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Cynthia M. Sharma
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Wilma Ziebuhr
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
- * E-mail:
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Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput Biol 2019; 15:e1006644. [PMID: 30625152 PMCID: PMC6326480 DOI: 10.1371/journal.pcbi.1006644] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/14/2018] [Indexed: 12/15/2022] Open
Abstract
S. aureus is classified as a serious threat pathogen and is a priority that guides the discovery and development of new antibiotics. Despite growing knowledge of S. aureus metabolic capabilities, our understanding of its systems-level responses to different media types remains incomplete. Here, we develop a manually reconstructed genome-scale model (GEM-PRO) of metabolism with 3D protein structures for S. aureus USA300 str. JE2 containing 854 genes, 1,440 reactions, 1,327 metabolites and 673 3-dimensional protein structures. Computations were in 85% agreement with gene essentiality data from random barcode transposon site sequencing (RB-TnSeq) and 68% agreement with experimental physiological data. Comparisons of computational predictions with experimental observations highlight: 1) cases of non-essential biomass precursors; 2) metabolic genes subject to transcriptional regulation involved in Staphyloxanthin biosynthesis; 3) the essentiality of purine and amino acid biosynthesis in synthetic physiological media; and 4) a switch to aerobic fermentation upon exposure to extracellular glucose elucidated as a result of integrating time-course of quantitative exo-metabolomics data. An up-to-date GEM-PRO thus serves as a knowledge-based platform to elucidate S. aureus’ metabolic response to its environment. Environmental perturbations (e.g., antibiotic stress, nutrient starvation, oxidative stress) induce systems-level perturbations of bacterial cells that vary depending on the growth environment. The generation of omics data is aimed at capturing a complete view of the organism’s response under different conditions. Genome-scale models (GEMs) of metabolism represent a knowledge-based platform for the contextualization and integration of multi-omic measurements and can serve to offer valuable insights of system-level responses. This work provides the most up to date reconstruction effort integrating recent advances in the knowledge of S. aureus molecular biology with previous annotations resulting in the first quantitatively and qualitatively validated S. aureus GEM. GEM guided predictions obtained from model analysis provided insights into the effects of medium composition on metabolic flux distribution and gene essentiality. The model can also serve as a platform to guide network reconstructions for other Staphylococci as well as direct hypothesis generation following the integration of omics data sets, including transcriptomics, proteomics, metabolomics, and multi-strain genomic data.
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Affiliation(s)
- Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Nathan Mih
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Cristal Zuniga
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Jared Broddrick
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Karsten Zengler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America
- * E-mail:
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De Backer S, Sabirova J, De Pauw I, De Greve H, Hernalsteens JP, Goossens H, Malhotra-Kumar S. Enzymes Catalyzing the TCA- and Urea Cycle Influence the Matrix Composition of Biofilms Formed by Methicillin-Resistant Staphylococcus aureus USA300. Microorganisms 2018; 6:microorganisms6040113. [PMID: 30380651 PMCID: PMC6313315 DOI: 10.3390/microorganisms6040113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/17/2018] [Accepted: 10/25/2018] [Indexed: 11/21/2022] Open
Abstract
In methicillin-sensitive Staphylococcus aureus (MSSA), the tricarboxylic acid (TCA) cycle is known to negatively regulate production of the major biofilm-matrix exopolysaccharide, PIA/PNAG. However, methicillin-resistant S. aureus (MRSA) produce a primarily proteinaceous biofilm matrix, and contribution of the TCA-cycle therein remains unclear. Utilizing USA300-JE2 Tn-mutants (NARSA) in genes encoding TCA- and urea cycle enzymes for transduction into a prolific biofilm-forming USA300 strain (UAS391-Erys), we studied the contribution of the TCA- and urea cycle and of proteins, eDNA and PIA/PNAG, to the matrix. Genes targeted in the urea cycle encoded argininosuccinate lyase and arginase (argH::Tn and rocF::Tn), and in the TCA-cycle encoded succinyl-CoA synthetase, succinate dehydrogenase, aconitase, isocitrate dehydrogenase, fumarate hydratase class II, and citrate synthase II (sucC::Tn, sdhA/B::Tn, acnA::Tn, icd::Tn, fumC::Tn and gltA::Tn). Biofilm formation was significantly decreased under no flow and flow conditions by argH::Tn, fumC::Tn, and sdhA/B::Tn (range OD492 0.374−0.667; integrated densities 2.065−4.875) compared to UAS391-EryS (OD492 0.814; integrated density 10.676) (p ≤ 0.008). Cellular and matrix stains, enzymatic treatment (Proteinase K, DNase I), and reverse-transcriptase PCR-based gene-expression analysis of fibronectin-binding proteins (fnbA/B) and the staphylococcal accessory regulator (sarA) on pre-formed UAS391-Erys and Tn-mutant biofilms showed: (i) < 1% PIA/PNAG in the proteinaceous/eDNA matrix; (ii) increased proteins under no flow and flow in the matrix of Tn mutant biofilms (on average 50 and 51 (±11)%) compared to UAS391-Erys (on average 22 and 25 (±4)%) (p < 0.001); and (iii) down- and up-regulation of fnbA/B and sarA, respectively, in Tn-mutants compared to UAS391-EryS (0.62-, 0.57-, and 2.23-fold on average). In conclusion, we show that the biofilm matrix of MRSA-USA300 and the corresponding Tn mutants is PIA/PNAG-independent and are mainly composed of proteins and eDNA. The primary impact of TCA-cycle inactivation was on the protein component of the biofilm matrix of MRSA-USA300.
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Affiliation(s)
- Sarah De Backer
- Department of Medical Microbiology, Vaccine & Infectious Diseases Institute, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Julia Sabirova
- Department of Medical Microbiology, Vaccine & Infectious Diseases Institute, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Ines De Pauw
- Department of Medical Microbiology, Vaccine & Infectious Diseases Institute, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Henri De Greve
- Structural & Molecular Microbiology, VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
| | | | - Herman Goossens
- Department of Medical Microbiology, Vaccine & Infectious Diseases Institute, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Surbhi Malhotra-Kumar
- Department of Medical Microbiology, Vaccine & Infectious Diseases Institute, University of Antwerp, 2610 Wilrijk, Belgium.
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Galac MR, Stam J, Maybank R, Hinkle M, Mack D, Rohde H, Roth AL, Fey PD. Complete Genome Sequence of Staphylococcus epidermidis 1457. GENOME ANNOUNCEMENTS 2017; 5:e00450-17. [PMID: 28572323 PMCID: PMC5454206 DOI: 10.1128/genomea.00450-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/12/2017] [Indexed: 02/07/2023]
Abstract
Staphylococcus epidermidis 1457 is a frequently utilized strain that is amenable to genetic manipulation and has been widely used for biofilm-related research. We report here the whole-genome sequence of this strain, which encodes 2,277 protein-coding genes and 81 RNAs within its 2.4-Mb genome and plasmid.
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Affiliation(s)
- Madeline R Galac
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jason Stam
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mary Hinkle
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Dietrich Mack
- Institut für Medizinische Diagnostik GmbH, Bioscientia Labor Ingelheim, Ingelheim, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie & Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Amanda L Roth
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Paul D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
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29
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Taha M, Culibrk B, Kalab M, Schubert P, Yi QL, Goodrich R, Ramirez-Arcos S. Efficiency of riboflavin and ultraviolet light treatment against high levels of biofilm-derived Staphylococcus epidermidis in buffy coat platelet concentrates. Vox Sang 2017; 112:408-416. [PMID: 28378343 DOI: 10.1111/vox.12519] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/03/2017] [Accepted: 03/05/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND OBJECTIVES Staphylococcus epidermidis forms surface-attached aggregates (biofilms) in platelet concentrates (PCs), which are linked to missed detection during PC screening. This study was aimed at evaluating the efficacy of riboflavin-UV treatment to inactivate S. epidermidis biofilms in buffy coat (BC) PCs. MATERIALS AND METHODS Biofilm and non-biofilm cells from S. epidermidis ST-10002 and S. epidermidis AZ-66 were individually inoculated into whole blood (WB) units (~106 colony-forming units (CFU)/ml) (N = 4-5). One spiked and three unspiked WB units were processed to produce a BC-PC pool. Riboflavin was added to the pool which was then split into two bags: one for UV treatment and the second was untreated. Bacterial counts were determined before and after treatment. In vitro PC quality was assessed by flow cytometry and dynamic light scattering. RESULTS Bacterial counts were reduced during BC-PC production from ~106 CFU/ml in WB to 103 -104 CFU/ml in PCs (P < 0·0001). Riboflavin-UV treatment resulted in significantly higher reduction of S. epidermidis AZ-66 than strain ST-10002 (≥3·5 log reduction and 2·6-2·8 log reduction, respectively, P < 0·0001). Remaining bacteria post-treatment were able to proliferate in PCs. No differences in S. epidermidis inactivation were observed in PCs produced from WB inoculated with biofilm or non-biofilm cells (P > 0·05). Platelet activation was enhanced in PCs produced with WB inoculated with biofilms compared to non-biofilm cells (P < 0·05). CONCLUSION Riboflavin-UV treatment was similarly efficacious in PCs produced from WB inoculated with S. epidermidis biofilm or non-biofilm cells. Levels of biofilm-derived S. epidermidis ≥103 CFU/ml were not completely inactivated; however, further testing is necessary with lower (real-life) bacterial levels.
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Affiliation(s)
- M Taha
- Canadian Blood Services, Ottawa, ON, Canada
| | - B Culibrk
- Canadian Blood Services, Ottawa, ON, Canada
| | - M Kalab
- Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - P Schubert
- Canadian Blood Services, Ottawa, ON, Canada
| | - Q-L Yi
- Canadian Blood Services, Ottawa, ON, Canada
| | - R Goodrich
- Infectious Disease Research Center, Colorado State University, Fort Collins, CO, USA
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Dotto C, Lombarte Serrat A, Cattelan N, Barbagelata MS, Yantorno OM, Sordelli DO, Ehling-Schulz M, Grunert T, Buzzola FR. The Active Component of Aspirin, Salicylic Acid, Promotes Staphylococcus aureus Biofilm Formation in a PIA-dependent Manner. Front Microbiol 2017; 8:4. [PMID: 28167931 PMCID: PMC5253544 DOI: 10.3389/fmicb.2017.00004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 01/03/2017] [Indexed: 01/10/2023] Open
Abstract
Aspirin has provided clear benefits to human health. But salicylic acid (SAL) -the main aspirin biometabolite- exerts several effects on eukaryote and prokaryote cells. SAL can affect, for instance, the expression of Staphylococcus aureus virulence factors. SAL can also form complexes with iron cations and it has been shown that different iron chelating molecules diminished the formation of S. aureus biofilm. The aim of this study was to elucidate whether the iron content limitation caused by SAL can modify the S. aureus metabolism and/or metabolic regulators thus changing the expression of the main polysaccharides involved in biofilm formation. The exposure of biofilm to 2 mM SAL induced a 27% reduction in the intracellular free Fe2+ concentration compared with the controls. In addition, SAL depleted 23% of the available free Fe2+ cation in culture media. These moderate iron-limited conditions promoted an intensification of biofilms formed by strain Newman and by S. aureus clinical isolates related to the USA300 and USA100 clones. The slight decrease in iron bioavailability generated by SAL was enough to induce the increase of PIA expression in biofilms formed by methicillin-resistant as well as methicillin-sensitive S. aureus strains. S. aureus did not produce capsular polysaccharide (CP) when it was forming biofilms under any of the experimental conditions tested. Furthermore, SAL diminished aconitase activity and stimulated the lactic fermentation pathway in bacteria forming biofilms. The polysaccharide composition of S. aureus biofilms was examined and FTIR spectroscopic analysis revealed a clear impact of SAL in a codY-dependent manner. Moreover, SAL negatively affected codY transcription in mature biofilms thus relieving the CodY repression of the ica operon. Treatment of mice with SAL induced a significant increase of S aureus colonization. It is suggested that the elevated PIA expression induced by SAL might be responsible for the high nasal colonization observed in mice. SAL-induced biofilms may contribute to S. aureus infection persistence in vegetarian individuals as well as in patients that frequently consume aspirin.
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Affiliation(s)
- Cristian Dotto
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
| | - Andrea Lombarte Serrat
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
| | - Natalia Cattelan
- Facultad de Ciencias Exactas, Centro de Investigación y Desarrollo de Fermentaciones Industriales (CINDEFI), Centro Científico Technológico Consejo Nacional de Investigaciones Científicas y Tócnicas (CTT CONICET La Plata), Universidad Nacional de La Plata La Plata, Argentina
| | - María S Barbagelata
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
| | - Osvaldo M Yantorno
- Facultad de Ciencias Exactas, Centro de Investigación y Desarrollo de Fermentaciones Industriales (CINDEFI), Centro Científico Technológico Consejo Nacional de Investigaciones Científicas y Tócnicas (CTT CONICET La Plata), Universidad Nacional de La Plata La Plata, Argentina
| | - Daniel O Sordelli
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
| | - Monika Ehling-Schulz
- Functional Microbiology, Institute for Microbiology, University of Veterinary Medicine Vienna, Austria
| | - Tom Grunert
- Functional Microbiology, Institute for Microbiology, University of Veterinary Medicine Vienna, Austria
| | - Fernanda R Buzzola
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
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Versatility of Biofilm Matrix Molecules in Staphylococcus epidermidis Clinical Isolates and Importance of Polysaccharide Intercellular Adhesin Expression during High Shear Stress. mSphere 2016; 1:mSphere00165-16. [PMID: 27747298 PMCID: PMC5064449 DOI: 10.1128/msphere.00165-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/20/2016] [Indexed: 01/13/2023] Open
Abstract
Staphylococcus epidermidis is a leading cause of infections related to biomaterials, mostly due to their ability to form biofilm. Biofilm accumulation mechanisms vary, including those that are dependent on specific proteins, environmental DNA (eDNA), or polysaccharide intercellular adhesin (PIA). We found that those isolates obtained from high-shear environments, such as the lumen of a catheter, are more likely to produce PIA-mediated biofilms than those isolates obtained from a low-shear biomaterial-related infection. This suggests that PIA functions as a mechanism that is protective against shear flow. Finally, we performed selection experiments documenting the heterogeneity of biofilm accumulation molecules that function in the absence of PIA, further documenting the biofilm-forming potential of S. epidermidis. Staphylococcus epidermidis is a leading cause of hospital-associated infections, including those of intravascular catheters, cerebrospinal fluid shunts, and orthopedic implants. Multiple biofilm matrix molecules with heterogeneous characteristics have been identified, including proteinaceous, polysaccharide, and nucleic acid factors. Two of the best-studied components in S. epidermidis include accumulation-associated protein (Aap) and polysaccharide intercellular adhesin (PIA), produced by the enzymatic products of the icaADBC operon. Biofilm composition varies by strain as well as environmental conditions, and strains producing PIA-mediated biofilms are more robust. Clinically, biofilm-mediated infections occur in a variety of anatomical sites with diverse physiological properties. To test the hypothesis that matrix composition exhibits niche specificity, biofilm-related genetic and physical properties were compared between S. epidermidis strains isolated from high-shear and low-shear environments. Among a collection of 105 clinical strains, significantly more isolates from high-shear environments carried the icaADBC operon than did those from low-shear settings (43.9% versus 22.9%, P < 0.05), while there was no significant difference in the presence of aap (77.2% versus 75.0%, P > 0.05). Additionally, a significantly greater number of high-shear isolates were capable of forming biofilm in vitro in a microtiter assay (82.5% versus 45.8%, P < 0.0001). However, even among high-shear clinical isolates, less than half contained the icaADBC locus; therefore, we selected for ica-negative variants with increased attachment to abiotic surfaces to examine PIA-independent biofilm mechanisms. Sequencing of selected variants identified substitutions capable of enhancing biofilm formation in multiple genes, further highlighting the heterogeneity of S. epidermidis biofilm molecules and mechanisms. IMPORTANCEStaphylococcus epidermidis is a leading cause of infections related to biomaterials, mostly due to their ability to form biofilm. Biofilm accumulation mechanisms vary, including those that are dependent on specific proteins, environmental DNA (eDNA), or polysaccharide intercellular adhesin (PIA). We found that those isolates obtained from high-shear environments, such as the lumen of a catheter, are more likely to produce PIA-mediated biofilms than those isolates obtained from a low-shear biomaterial-related infection. This suggests that PIA functions as a mechanism that is protective against shear flow. Finally, we performed selection experiments documenting the heterogeneity of biofilm accumulation molecules that function in the absence of PIA, further documenting the biofilm-forming potential of S. epidermidis.
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Abstract
Pathogenic bacteria must contend with immune systems that actively restrict the availability of nutrients and cofactors, and create a hostile growth environment. To deal with these hostile environments, pathogenic bacteria have evolved or acquired virulence determinants that aid in the acquisition of nutrients. This connection between pathogenesis and nutrition may explain why regulators of metabolism in nonpathogenic bacteria are used by pathogenic bacteria to regulate both metabolism and virulence. Such coordinated regulation is presumably advantageous because it conserves carbon and energy by aligning synthesis of virulence determinants with the nutritional environment. In Gram-positive bacterial pathogens, at least three metabolite-responsive global regulators, CcpA, CodY, and Rex, have been shown to coordinate the expression of metabolism and virulence genes. In this chapter, we discuss how environmental challenges alter metabolism, the regulators that respond to this altered metabolism, and how these regulators influence the host-pathogen interaction.
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Abstract
Virulence gene expression serves two main functions, growth in/on the host, and the acquisition of nutrients. Therefore, it is obvious that nutrient availability is important to control expression of virulence genes. In any cell, enzymes are the components that are best informed about the availability of their respective substrates and products. It is thus not surprising that bacteria have evolved a variety of strategies to employ this information in the control of gene expression. Enzymes that have a second (so-called moonlighting) function in the regulation of gene expression are collectively referred to as trigger enzymes. Trigger enzymes may have a second activity as a direct regulatory protein that can bind specific DNA or RNA targets under particular conditions or they may affect the activity of transcription factors by covalent modification or direct protein-protein interaction. In this chapter, we provide an overview on these mechanisms and discuss the relevance of trigger enzymes for virulence gene expression in bacterial pathogens.
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Kleinschmidt S, Huygens F, Faoagali J, Rathnayake IU, Hafner LM. Staphylococcus epidermidis as a cause of bacteremia. Future Microbiol 2015; 10:1859-79. [DOI: 10.2217/fmb.15.98] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus epidermidis is a biofilm-producing commensal organism found ubiquitously on human skin and mucous membranes, as well as on animals and in the environment. Biofilm formation enables this organism to evade the host immune system. Colonization of percutaneous devices or implanted medical devices allows bacteria access to the bloodstream. Isolation of this organism from blood cultures may represent either contamination during the blood collection procedure or true bacteremia. S. epidermidis bloodstream infections may be indolent compared with other bacteria. Isolation of S. epidermidis from a blood culture may present a management quandary for clinicians. Over-treatment may lead to patient harm and increases in healthcare costs. There are numerous reports indicating the difficulty of predicting clinical infection in patients with positive blood cultures with this organism. No reliable phenotypic or genotypic algorithms currently exist to predict the pathogenicity of a S. epidermidis bloodstream infection. This review will discuss the latest advances in identification methods, global population structure, pathogenicity, biofilm formation, antimicrobial resistance and clinical significance of the detection of S. epidermidis in blood cultures. Previous studies that have attempted to discriminate between invasive and contaminating strains of S. epidermidis in blood cultures will be analyzed.
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Affiliation(s)
- Sharon Kleinschmidt
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Microbiology Department, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Flavia Huygens
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Joan Faoagali
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Louise M Hafner
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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Takahashi N, Shinjoh M, Tomita H, Fujino A, Sugita K, Katohno Y, Kuroda T, Kikuchi K. Catheter-related blood stream infection caused by Dermacoccus barathri, representing the first case of Dermacoccus infection in humans. J Infect Chemother 2015; 21:613-6. [PMID: 26044303 DOI: 10.1016/j.jiac.2015.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 11/18/2022]
Abstract
A 7-year-old boy undergoing home parenteral nutrition with totally implantable central venous access device for chronic intestinal pseudo-obstruction experienced repeated episodes of fever with a temperature above 39.0 °C despite the antibiotic treatment. The fever was considered to be catheter-related blood stream infections, as no other etiology could be justified. Repeated blood culture tests revealed negative after 1-week incubation, whereas some samples of blood collected from the central venous catheter yielded positive and gram-positive rods were detected. These bacteria were detected repeatedly, then the central venous access device was removed with consideration for the possibility of this bacteria being a pathogen. Thereafter, the fever did not recur and the blood culture tests were negative. The causative agent was identified as Dermacoccus barathri based on the 16S rRNA gene sequence and phylogenetic analysis of 6118-bp concatenated sequences of 4 housekeeping genes. Genus Dermacoccus are one form of Actinomycetes isolated from human skin and water, but human infection with Dermacoccus spp. has not been previously reported and the pathogenicity of the bacteria remains unclear. To our knowledge, this is the first reported case of Dermacoccus infection in humans.
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Affiliation(s)
- Nobuhiro Takahashi
- Department of Pediatric Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masayoshi Shinjoh
- Department of Pediatrics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Hirofumi Tomita
- Department of Pediatric Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Akihiro Fujino
- Department of Pediatric Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kayoko Sugita
- Center for Infectious Diseases and Infection Control, Keio University Hospital, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yasuhiro Katohno
- Central Clinical Laboratory, Keio University Hospital, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Tatsuo Kuroda
- Department of Pediatric Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Ken Kikuchi
- Department of Infection Control Science, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; Department of Infectious Diseases, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
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36
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Sousa C, França A, Cerca N. Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms. Biotechniques 2014; 57:295-301. [PMID: 25495729 DOI: 10.2144/000114238] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/08/2014] [Indexed: 11/23/2022] Open
Abstract
Gene expression quantification can be a useful tool in studying the properties of bacterial biofilms. Unfortunately, techniques such as RNA extraction, cDNA synthesis, and quantitative PCR (qPCR) can introduce variability into mRNA transcript measurements, obscuring biologically relevant results. Here we sought to identify the steps that impair accurate gene expression quantification from Staphylococcus epidermidis biofilm samples. We devised an experimental setup that could be used to determine the contribution of each experimental step to the variability of mRNA transcript measurement. Among factors tested, biofilm growth contributed the most bias to gene expression quantification. Additional experiments demonstrated that pooling biofilms together reduced this variability, resulting in more accurate gene expression analysis results. We therefore recommend pooling in order to reduce the variability associated with gene expression quantification from biofilm samples.
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Affiliation(s)
- Cármen Sousa
- CEB-Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Angela França
- CEB-Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Nuno Cerca
- CEB-Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
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37
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Islam N, Kim Y, Ross JM, Marten MR. Proteomic analysis of Staphylococcus aureus biofilm cells grown under physiologically relevant fluid shear stress conditions. Proteome Sci 2014; 12:21. [PMID: 24855455 PMCID: PMC4013085 DOI: 10.1186/1477-5956-12-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 04/17/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The biofilm forming bacterium Staphylococcus aureus is responsible for maladies ranging from severe skin infection to major diseases such as bacteremia, endocarditis and osteomyelitis. A flow displacement system was used to grow S. aureus biofilms in four physiologically relevant fluid shear rates (50, 100, 500 and 1000 s(-1)) to identify proteins that are associated with biofilm. RESULTS Global protein expressions from the membrane and cytosolic fractions of S. aureus biofilm cells grown under the above shear rate conditions are reported. Sixteen proteins in the membrane-enriched fraction and eight proteins in the cytosolic fraction showed significantly altered expression (p < 0.05) under increasing fluid shear. These 24 proteins were identified using nano-LC-ESI-MS/MS. They were found to be associated with various metabolic functions such as glycolysis / TCA pathways, protein synthesis and stress tolerance. Increased fluid shear stress did not influence the expression of two important surface binding proteins: fibronectin-binding and collagen-binding proteins. CONCLUSIONS The reported data suggest that while the general metabolic function of the sessile bacteria is minimal under high fluid shear stress conditions, they seem to retain the binding capacity to initiate new infections.
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Affiliation(s)
- Nazrul Islam
- Current address: Department of Plant Sciences, University of Maryland, College Park, MD 20742, USA
| | - Yonghyun Kim
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Julia M Ross
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Mark R Marten
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
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Influence of iron and aeration on Staphylococcus aureus growth, metabolism, and transcription. J Bacteriol 2014; 196:2178-89. [PMID: 24706736 DOI: 10.1128/jb.01475-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a prominent nosocomial pathogen and a major cause of biomaterial-associated infections. The success of S. aureus as a pathogen is due in part to its ability to adapt to stressful environments. As an example, the transition from residing in the nares to residing in the blood or deeper tissues is accompanied by changes in the availability of nutrients and elements such as oxygen and iron. As such, nutrients, oxygen, and iron are important determinants of virulence factor synthesis in S. aureus. In addition to influencing virulence factor synthesis, oxygen and iron are critical cofactors in enzymatic and electron transfer reactions; thus, a change in iron or oxygen availability alters the bacterial metabolome. Changes in metabolism create intracellular signals that alter the activity of metabolite-responsive regulators such as CodY, RpiRc, and CcpA. To assess the extent of metabolomic changes associated with oxygen and iron limitation, S. aureus cells were cultivated in iron-limited medium and/or with decreasing aeration, and the metabolomes were examined by nuclear magnetic resonance (NMR) spectroscopy. As expected, oxygen and iron limitation dramatically decreased tricarboxylic acid (TCA) cycle activity, creating a metabolic block and significantly altering the metabolome. These changes were most prominent during post-exponential-phase growth, when TCA cycle activity was maximal. Importantly, many of the effects of iron limitation were obscured by aeration limitation. Aeration limitation not only obscured the metabolic effects of iron limitation but also overrode the transcription of iron-regulated genes. Finally, in contrast to previous speculation, we confirmed that acidification of the culture medium occurs independent of the availability of iron.
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Somerville GA, Powers R. Growth and preparation of Staphylococcus epidermidis for NMR metabolomic analysis. Methods Mol Biol 2014; 1106:71-91. [PMID: 24222456 DOI: 10.1007/978-1-62703-736-5_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The "omics" era began with transcriptomics and this progressed into proteomics. While useful, these approaches provide only circumstantial information about carbon flow, metabolic status, redox poise, etc. To more directly address these metabolic concerns, researchers have turned to the emerging field of metabolomics. In our laboratories, we frequently use NMR metabolomics to acquire a snapshot of bacterial metabolomes during stressful or transition events. Irrespective of the "omics" method of choice, the experimental outcome depends on the proper cultivation and preparation of bacterial samples. In addition, the integration of these large datasets requires that these cultivation conditions be clearly defined.
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Affiliation(s)
- Greg A Somerville
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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Halouska S, Zhang B, Gaupp R, Lei S, Snell E, Fenton RJ, Barletta RG, Somerville GA, Powers R. Revisiting Protocols for the NMR Analysis of Bacterial Metabolomes. JOURNAL OF INTEGRATED OMICS 2013; 3:120-137. [PMID: 26078915 PMCID: PMC4465129 DOI: 10.5584/jiomics.v3i2.139] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past decade, metabolomics has emerged as an important technique for systems biology. Measuring all the metabolites in a biological system provides an invaluable source of information to explore various cellular processes, and to investigate the impact of environmental factors and genetic modifications. Nuclear magnetic resonance (NMR) spectroscopy is an important method routinely employed in metabolomics. NMR provides comprehensive structural and quantitative information useful for metabolomics fingerprinting, chemometric analysis, metabolite identification and metabolic pathway construction. A successful metabolomics study relies on proper experimental protocols for the collection, handling, processing and analysis of metabolomics data. Critically, these protocols should eliminate or avoid biologically-irrelevant changes to the metabolome. We provide a comprehensive description of our NMR-based metabolomics procedures optimized for the analysis of bacterial metabolomes. The technical details described within this manuscript should provide a useful guide to reliably apply our NMR-based metabolomics methodology to systems biology studies.
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Affiliation(s)
- Steven Halouska
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Bo Zhang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Rosmarie Gaupp
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905
| | - Shulei Lei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Emily Snell
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Robert J. Fenton
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905
| | - Raul G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905
| | - Greg A. Somerville
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
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Troxell B, Hassan HM. Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria. Front Cell Infect Microbiol 2013; 3:59. [PMID: 24106689 PMCID: PMC3788343 DOI: 10.3389/fcimb.2013.00059] [Citation(s) in RCA: 290] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/18/2013] [Indexed: 12/16/2022] Open
Abstract
In the ancient anaerobic environment, ferrous iron (Fe2+) was one of the first metal cofactors. Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe3+) and later to defend against reactive oxygen species (ROS) generated by the Fenton chemistry. To acquire Fe3+, bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for Fe3+. However, during infection the host restricts iron from pathogens by producing iron- and siderophore-chelating proteins, by exporting iron from intracellular pathogen-containing compartments, and by limiting absorption of dietary iron. Ferric Uptake Regulator (Fur) is a transcription factor which utilizes Fe2+ as a corepressor and represses siderophore synthesis in pathogens. Fur, directly or indirectly, controls expression of enzymes that protect against ROS damage. Thus, the challenges of iron homeostasis and defense against ROS are addressed via Fur. Although the role of Fur as a repressor is well-documented, emerging evidence demonstrates that Fur can function as an activator. Fur activation can occur through three distinct mechanisms (1) indirectly via small RNAs, (2) binding at cis regulatory elements that enhance recruitment of the RNA polymerase holoenzyme (RNAP), and (3) functioning as an antirepressor by removing or blocking DNA binding of a repressor of transcription. In addition, Fur homologs control defense against peroxide stress (PerR) and control uptake of other metals such as zinc (Zur) and manganese (Mur) in pathogenic bacteria. Fur family members are important for virulence within bacterial pathogens since mutants of fur, perR, or zur exhibit reduced virulence within numerous animal and plant models of infection. This review focuses on the breadth of Fur regulation in pathogenic bacteria.
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Affiliation(s)
- Bryan Troxell
- Department of Immunology and Microbiology, Indiana University School of Medicine Indianapolis, IN, USA
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A dysfunctional tricarboxylic acid cycle enhances fitness of Staphylococcus epidermidis during β-lactam stress. mBio 2013; 4:mBio.00437-13. [PMID: 23963176 PMCID: PMC3747581 DOI: 10.1128/mbio.00437-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A recent controversial hypothesis suggested that the bactericidal action of antibiotics is due to the generation of endogenous reactive oxygen species (ROS), a process requiring the citric acid cycle (tricarboxylic acid [TCA] cycle). To test this hypothesis, we assessed the ability of oxacillin to induce ROS production and cell death in Staphylococcus epidermidis strain 1457 and an isogenic citric acid cycle mutant. Our results confirm a contributory role for TCA-dependent ROS in enhancing susceptibility of S. epidermidis toward β-lactam antibiotics and also revealed a propensity for clinical isolates to accumulate TCA cycle dysfunctions presumably as a way to tolerate these antibiotics. The increased protection from β-lactam antibiotics could result from pleiotropic effects of a dysfunctional TCA cycle, including increased resistance to oxidative stress, reduced susceptibility to autolysis, and a more positively charged cell surface. Staphylococcus epidermidis, a normal inhabitant of the human skin microflora, is the most common cause of indwelling medical device infections. In the present study, we analyzed 126 clinical S. epidermidis isolates and discovered that tricarboxylic acid (TCA) cycle dysfunctions are relatively common in the clinical environment. We determined that a dysfunctional TCA cycle enables S. epidermidis to resist oxidative stress and alter its cell surface properties, making it less susceptible to β-lactam antibiotics.
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Inactivation of the Pta-AckA pathway causes cell death in Staphylococcus aureus. J Bacteriol 2013; 195:3035-44. [PMID: 23625849 DOI: 10.1128/jb.00042-13] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
During growth under conditions of glucose and oxygen excess, Staphylococcus aureus predominantly accumulates acetate in the culture medium, suggesting that the phosphotransacetylase-acetate kinase (Pta-AckA) pathway plays a crucial role in bacterial fitness. Previous studies demonstrated that these conditions also induce the S. aureus CidR regulon involved in the control of cell death. Interestingly, the CidR regulon is comprised of only two operons, both encoding pyruvate catabolic enzymes, suggesting an intimate relationship between pyruvate metabolism and cell death. To examine this relationship, we introduced ackA and pta mutations in S. aureus and tested their effects on bacterial growth, carbon and energy metabolism, cid expression, and cell death. Inactivation of the Pta-AckA pathway showed a drastic inhibitory effect on growth and caused accumulation of dead cells in both pta and ackA mutants. Surprisingly, inactivation of the Pta-AckA pathway did not lead to a decrease in the energy status of bacteria, as the intracellular concentrations of ATP, NAD(+), and NADH were higher in the mutants. However, inactivation of this pathway increased the rate of glucose consumption, led to a metabolic block at the pyruvate node, and enhanced carbon flux through both glycolysis and the tricarboxylic acid (TCA) cycle. Intriguingly, disruption of the Pta-AckA pathway also induced the CidR regulon, suggesting that activation of alternative pyruvate catabolic pathways could be an important survival strategy for the mutants. Collectively, the results of this study demonstrate the indispensable role of the Pta-AckA pathway in S. aureus for maintaining energy and metabolic homeostasis during overflow metabolism.
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Prasad UV, Vasu D, Kumar YN, Kumar PS, Yeswanth S, Swarupa V, Phaneendra BV, Chaudhary A, Sarma PVGK. Cloning, expression and characterization of NADP-dependent isocitrate dehydrogenase from Staphylococcus aureus. Appl Biochem Biotechnol 2013; 169:862-9. [PMID: 23288593 DOI: 10.1007/s12010-012-0027-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 12/10/2012] [Indexed: 12/01/2022]
Abstract
The Krebs cycle dictates oxidative and reductive conditions in Staphylococcus aureus and is mainly regulated by isocitrate dehydrogenase (IDH) which plays pivotal role in the growth and pathogenesis of the bacteria. In the present study, IDH gene from S. aureus ATCC12600 was cloned in the Sma I site of pQE 30 vector; the resultant clone was named as UVIDH1. The insert in the clone was sequenced (accession number HM067707), and the sequence showed complete homology with IDH sequence of other S. aureus strains reported in the database indicating presence of single enzyme in S. aureus, and considerable sequence homology with other bacteria was observed; however, only 24% homology was found with NADP-dependent human IDH. Phylogenetically, the S. aureus IDH showed close identity with Bacillus subtilis and high degree of variability with other bacteria and human IDH. The expression of IDH in the clone UVIDH1 was induced with 1 mM IPTG, and the recombinant IDH was purified by passing through nickel metal chelate column; the purified recombinant IDH showed a single band in SDS-PAGE with a molecular weight of 40 kDa; K(m) and V(max) for isocitrate are 8.2 ± 0.28 and 525 ± 25 μM NADPH/mg/min, respectively, and for cofactor NADP 67.5 ± 2.82 μM and V(max) 50.5 ± 2.12 μM NADPH/mg/min.
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Affiliation(s)
- U Venkateswara Prasad
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, India
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Nuxoll AS, Halouska SM, Sadykov MR, Hanke ML, Bayles KW, Kielian T, Powers R, Fey PD. CcpA regulates arginine biosynthesis in Staphylococcus aureus through repression of proline catabolism. PLoS Pathog 2012; 8:e1003033. [PMID: 23209408 PMCID: PMC3510247 DOI: 10.1371/journal.ppat.1003033] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 10/01/2012] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus aureus is a leading cause of community-associated and nosocomial infections. Imperative to the success of S. aureus is the ability to adapt and utilize nutrients that are readily available. Genomic sequencing suggests that S. aureus has the genes required for synthesis of all twenty amino acids. However, in vitro experimentation demonstrates that staphylococci have multiple amino acid auxotrophies, including arginine. Although S. aureus possesses the highly conserved anabolic pathway that synthesizes arginine via glutamate, we demonstrate here that inactivation of ccpA facilitates the synthesis of arginine via the urea cycle utilizing proline as a substrate. Mutations within putA, rocD, arcB1, argG and argH abolished the ability of S. aureus JE2 ccpA::tetL to grow in the absence of arginine, whereas an interruption in argJBCF, arcB2, or proC had no effect. Furthermore, nuclear magnetic resonance demonstrated that JE2 ccpA::ermB produced 13C5 labeled arginine when grown with 13C5 proline. Taken together, these data support the conclusion that S. aureus synthesizes arginine from proline during growth on secondary carbon sources. Furthermore, although highly conserved in all sequenced S. aureus genomes, the arginine anabolic pathway (ArgJBCDFGH) is not functional under in vitro growth conditions. Finally, a mutation in argH attenuated virulence in a mouse kidney abscess model in comparison to wild type JE2 demonstrating the importance of arginine biosynthesis in vivo via the urea cycle. However, mutations in argB, argF, and putA did not attenuate virulence suggesting both the glutamate and proline pathways are active and they, or their pathway intermediates, can complement each other in vivo. Although Staphylococcus aureus encodes the highly conserved arginine biosynthesis pathway via glutamate, arginine is an essential amino acid. We found that a mutation in ccpA, a gene encoding a protein facilitating carbon catabolite repression, mediates arginine biosynthesis under in vitro growth conditions. However, both genetic and biochemical evidence suggested that a S. aureus ccpA mutant synthesizes arginine via proline and the urea cycle, a pathway not demonstrated in bacteria before. Furthermore, an animal model of S. aureus infection demonstrated the importance of arginine biosynthesis in vivo. This new pathway sheds light on important host-pathogen interactions and suggests S. aureus has evolved to address arginine depletion in the host by synthesizing arginine from a readily available substrate such as proline.
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Affiliation(s)
- Austin S. Nuxoll
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Steven M. Halouska
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Marat R. Sadykov
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Mark L. Hanke
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kenneth W. Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Tammy Kielian
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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Zhang BB, Chen L, Cheung PCK. Proteomic insights into the stimulatory effect of Tween 80 on mycelial growth and exopolysaccharide production of an edible mushroom Pleurotus tuber-regium. Biotechnol Lett 2012; 34:1863-7. [PMID: 22714275 DOI: 10.1007/s10529-012-0975-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 05/25/2012] [Indexed: 10/28/2022]
Abstract
Proteomic analysis was applied to investigate the mechanism of the stimulatory effect of Tween 80 on the mycelial growth and exopolysaccharide production by an edible mushroom Pleurotus tuber-regium. 32 differentially expressed proteins were identified by one-dimension gel electrophoresis. Combined with our previous findings, the up-regulation of heat shock proteins might help to maintain cellular viability under environmental stress. The up-regulation of ATP:citrate lyase isoform 2 could suppress the activity of tricarboxylic acid cycle and, consequently, stimulate exopolysaccharide production. The present results provide important insight to the mechanism by which stimulatory agents (Tween 80) can increase the production of useful fungal metabolites and also fill the gap of our knowledge on the under-developed mushroom proteomics.
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Affiliation(s)
- Bo-Bo Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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47
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Abstract
Infectious diseases can be difficult to cure, especially if the pathogen forms a biofilm. After decades of extensive research into the morphology, physiology and genomics of biofilm formation, attention has recently been directed toward the analysis of the cellular metabolome in order to understand the transformation of a planktonic cell to a biofilm. Metabolomics can play an invaluable role in enhancing our understanding of the underlying biological processes related to the structure, formation and antibiotic resistance of biofilms. A systematic view of metabolic pathways or processes responsible for regulating this 'social structure' of microorganisms may provide critical insights into biofilm-related drug resistance and lead to novel treatments. This review will discuss the development of NMR-based metabolomics as a technology to study medically relevant biofilms. Recent advancements from case studies reviewed in this manuscript have shown the potential of metabolomics to shed light on numerous biological problems related to biofilms.
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Affiliation(s)
- Bo Zhang
- Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304, USA
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Pozzi C, Waters EM, Rudkin JK, Schaeffer CR, Lohan AJ, Tong P, Loftus BJ, Pier GB, Fey PD, Massey RC, O'Gara JP. Methicillin resistance alters the biofilm phenotype and attenuates virulence in Staphylococcus aureus device-associated infections. PLoS Pathog 2012; 8:e1002626. [PMID: 22496652 PMCID: PMC3320603 DOI: 10.1371/journal.ppat.1002626] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 02/23/2012] [Indexed: 01/15/2023] Open
Abstract
Clinical isolates of Staphylococcus aureus can express biofilm phenotypes promoted by the major cell wall autolysin and the fibronectin-binding proteins or the icaADBC-encoded polysaccharide intercellular adhesin/poly-N-acetylglucosamine (PIA/PNAG). Biofilm production in methicillin-susceptible S. aureus (MSSA) strains is typically dependent on PIA/PNAG whereas methicillin-resistant isolates express an Atl/FnBP-mediated biofilm phenotype suggesting a relationship between susceptibility to β-lactam antibiotics and biofilm. By introducing the methicillin resistance gene mecA into the PNAG-producing laboratory strain 8325-4 we generated a heterogeneously resistant (HeR) strain, from which a homogeneous, high-level resistant (HoR) derivative was isolated following exposure to oxacillin. The HoR phenotype was associated with a R602H substitution in the DHHA1 domain of GdpP, a recently identified c-di-AMP phosphodiesterase with roles in resistance/tolerance to β-lactam antibiotics and cell envelope stress. Transcription of icaADBC and PNAG production were impaired in the 8325-4 HoR derivative, which instead produced a proteinaceous biofilm that was significantly inhibited by antibodies against the mecA-encoded penicillin binding protein 2a (PBP2a). Conversely excision of the SCCmec element in the MRSA strain BH1CC resulted in oxacillin susceptibility and reduced biofilm production, both of which were complemented by mecA alone. Transcriptional activity of the accessory gene regulator locus was also repressed in the 8325-4 HoR strain, which in turn was accompanied by reduced protease production and significantly reduced virulence in a mouse model of device infection. Thus, homogeneous methicillin resistance has the potential to affect agr- and icaADBC-mediated phenotypes, including altered biofilm expression and virulence, which together are consistent with the adaptation of healthcare-associated MRSA strains to the antibiotic-rich hospital environment in which they are frequently responsible for device-related infections in immuno-compromised patients. The acquisition of mecA, which encodes penicillin binding protein 2a (PBP2a) and methicillin resistance, by Staphylococcus aureus has added to an already impressive array of virulence mechanisms including enzyme and toxin production, biofilm forming capacity and immune evasion. And yet clinical data does not indicate that healthcare-associated methicillin resistant S. aureus (MRSA) strains are more virulent than their methicillin-susceptible counterparts. Here our findings suggest that MRSA sacrifices virulence potential for antibiotic resistance and that expression of methicillin resistance alters the biofilm phenotype but does not interfere with the colonization of implanted medical devices in vivo. High level expression of PBP2a, which was associated with a mutation in the c-di-AMP phosphodiesterase gene gdpP, resulted in these pleiotrophic effects by blocking icaADBC-dependent polysaccharide type biofilm development and promoting an alternative PBP2a-mediated biofilm, repressing the accessory gene regulator and extracellular protease production, and attenuating virulence in a mouse device-infection model. Thus the adaptation of MRSA to the hospital environment has apparently focused on the acquisition of antibiotic resistance and retention of biofilm forming capacity, which are likely to be more advantageous than metabolically-expensive enzyme and toxin production in immunocompromised patients with implanted medical devices offering a route to infection.
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Affiliation(s)
- Clarissa Pozzi
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Elaine M. Waters
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Justine K. Rudkin
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Carolyn R. Schaeffer
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Amanda J. Lohan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Pin Tong
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Brendan J. Loftus
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Gerald B. Pier
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Ruth C. Massey
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - James P. O'Gara
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- * E-mail:
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49
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Cue D, Lei MG, Lee CY. Genetic regulation of the intercellular adhesion locus in staphylococci. Front Cell Infect Microbiol 2012; 2:38. [PMID: 23061050 PMCID: PMC3459252 DOI: 10.3389/fcimb.2012.00038] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/05/2012] [Indexed: 01/29/2023] Open
Abstract
The formation of biofilms by Staphylococcus aureus and Staphylococcus epidermidis is an important aspect of many staphylococcal infections, most notably endocarditis, osteomyelitis and infections associated with indwelling medical devices. The major constituents of staphylococcal biofilms are polysaccharides, such as poly N-acetyl glucosamine (PIA/PNAG), cell surface and secreted bacterial proteins, and extracellular DNA. The exact composition of biofilms often varies considerably between different strains of staphylococci and between different sites of infection by the same strain. PIA/PNAG is synthesized by the products of four genes, icaADBC, that are encoded in a single operon. A fifth gene, icaR, is a negative regulator of icaADBC. Expression of icaADBC is tightly regulated, but can often be induced in vitro by growing staphylococci in the presence of high salt, high glucose, or ethanol. Regulation of icaADBC is complex and numerous regulatory factors have been implicated in control of icaADBC. Many of these are well known global transcriptional regulatory factors like SarA and sigmaB, whereas other regulators, such as IcaR, seem to affect expression of relatively few genes. Here, we will summarize how various regulatory factors affect the production of PIA/PNAG in staphylococci.
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Affiliation(s)
- David Cue
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock AR, USA
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50
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Sadykov MR, Hartmann T, Mattes TA, Hiatt M, Jann NJ, Zhu Y, Ledala N, Landmann R, Herrmann M, Rohde H, Bischoff M, Somerville GA. CcpA coordinates central metabolism and biofilm formation in Staphylococcus epidermidis. MICROBIOLOGY-SGM 2011; 157:3458-3468. [PMID: 21964732 DOI: 10.1099/mic.0.051243-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Staphylococcus epidermidis is an opportunistic bacterium whose infections often involve the formation of a biofilm on implanted biomaterials. In S. epidermidis, the exopolysaccharide facilitating bacterial adherence in a biofilm is polysaccharide intercellular adhesin (PIA), whose synthesis requires the enzymes encoded within the intercellular adhesin operon (icaADBC). In vitro, the formation of S. epidermidis biofilms is enhanced by conditions that repress tricarboxylic acid (TCA) cycle activity, such as growth in a medium containing glucose. In many Gram-positive bacteria, repression of TCA cycle genes in response to glucose is accomplished by catabolite control protein A (CcpA). CcpA is a member of the GalR-LacI repressor family that mediates carbon catabolite repression, leading us to hypothesize that catabolite control of S. epidermidis biofilm formation is indirectly regulated by CcpA-dependent repression of the TCA cycle. To test this hypothesis, ccpA deletion mutants were constructed in strain 1457 and 1457-acnA and the effects on TCA cycle activity, biofilm formation and virulence were assessed. As anticipated, deletion of ccpA derepressed TCA cycle activity and inhibited biofilm formation; however, ccpA deletion had only a modest effect on icaADBC transcription. Surprisingly, deletion of ccpA in strain 1457-acnA, a strain whose TCA cycle is inactive and where icaADBC transcription is derepressed, strongly inhibited icaADBC transcription. These observations demonstrate that CcpA is a positive effector of biofilm formation and icaADBC transcription and a repressor of TCA cycle activity.
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Affiliation(s)
- Marat R Sadykov
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, USA
| | - Torsten Hartmann
- Institute of Medical Microbiology and Hygiene, University of Saarland Hospital, Homburg/Saar, Germany
| | - Theodoric A Mattes
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, USA
| | - Megan Hiatt
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, USA
| | - Naja J Jann
- Division of Infection Biology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Yefei Zhu
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, USA
| | - Nagender Ledala
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, USA
| | - Regine Landmann
- Division of Infection Biology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, University of Saarland Hospital, Homburg/Saar, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, University of Saarland Hospital, Homburg/Saar, Germany
| | - Greg A Somerville
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, USA
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