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Zheng L, Han Z, Wang S, Gao A, Liu L, Pan H, Zhang H. Transcriptomic analysis and knockout experiments reveal the role of suhB in the biocontrol effects of Pantoea jilinensis D25 on Botrytis cinerea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170771. [PMID: 38336045 DOI: 10.1016/j.scitotenv.2024.170771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Tomato gray mold, caused by Botrytis cinerea, is an important disease in tomato. Pantoea jilinensis D25, isolated form tomato rhizosphere soil, can prevent B. cinerea infection in tomato. To determine the underlying biocontrol mechanism, the transcriptome of P. jilinensis D25 was assessed. Differential expression analysis revealed that 941 genes were upregulated and 997 genes were downregulated. Through transcriptome analysis, the suhB gene was knocked out. ΔPj-suhB exhibited lower swimming motility and colonization abilities than strain D25. After 4 days of co-cultivation, ΔPj-suhB could reduce the colony diameter, mycelial weight, and spore production of B. cinerea with the inhibitory rates of 31.72 %, 39.62 %, and 47.42 %, respectively, compared with control. However, the inhibitory rates of strain D25 were 52.91 %, 60.09 %, and 76.85 %, respectively, compared with control. Strain D25 could significantly downregulate pathogenesis-related genes in B. cinerea, whereas the expression level of these genes in B. cinerea was higher after treatment with ΔPj-suhB than after that with strain D25. In vitro experiments revealed that the lesion area and disease control efficacy were 1.520 and 0.038 cm2 and 68.7 % and 99.0 %, respectively, after ΔPj-suhB and strain D25 treatments. Pot experiments revealed that ΔPj-suhB and strain D25 could prevent tomato plants from B. cinerea infection with the disease reduction rate of 37.5 % and 75.0 %, respectively. Though the activities of defense-related enzymes and expression level of defense related genes in tomato plants were increased under ΔPj-suhB treatment, these effects were higher after strain D25 treatment. Thus, these results demonstrated that suhB was the key gene in strain D25 underlying its biocontrol effect and mobility.
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Affiliation(s)
- Lining Zheng
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, PR China
| | - Zhe Han
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, PR China
| | - Shengyi Wang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, PR China
| | - Ao Gao
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, PR China
| | - Ling Liu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, PR China
| | - Hongyu Pan
- College of Plant Sciences, Jilin University, Changchun 130062, PR China
| | - Hao Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, PR China.
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Ruest MK, Supina BSI, Dennis JJ. Bacteriophage steering of Burkholderia cenocepacia toward reduced virulence and increased antibiotic sensitivity. J Bacteriol 2023; 205:e0019623. [PMID: 37791751 PMCID: PMC10601696 DOI: 10.1128/jb.00196-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/06/2023] [Indexed: 10/05/2023] Open
Abstract
Antibiotic resistance in bacteria is a growing global concern and has spurred increasing efforts to find alternative therapeutics, such as the use of bacterial viruses, or bacteriophages. One promising approach is to use phages that not only kill pathogenic bacteria but also select phage-resistant survivors that are newly sensitized to traditional antibiotics, in a process called "phage steering." Members of the bacterial genus Burkholderia, which includes various human pathogens, are highly resistant to most antimicrobial agents, including serum immune components, antimicrobial peptides, and polymixin-class antibiotics. However, the application of phages in combination with certain antibiotics can produce synergistic effects that more effectively kill pathogenic bacteria. Herein, we demonstrate that Burkholderia cenocepacia serum resistance is due to intact lipopolysaccharide (LPS) and membranes, and phage-induced resistance altering LPS structure can enhance bacterial sensitivity not only to immune components in serum but also to membrane-associated antibiotics such as colistin. IMPORTANCE Bacteria frequently encounter selection pressure from both antibiotics and lytic phages, but little is known about the interactions between antibiotics and phages. This study provides new insights into the evolutionary trade-offs between phage resistance and antibiotic sensitivity. The creation of phage resistance through changes in membrane structure or lipopolysaccharide composition can simultaneously be a major cause of antibiotic sensitivity. Our results provide evidence of synergistic therapeutic efficacy in phage-antibiotic interactions and have implications for the future clinical use of phage steering in phage therapy applications.
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Affiliation(s)
- Marta K. Ruest
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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3
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Dillard LR, Glass EM, Lewis AL, Thomas-White K, Papin JA. Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment. mSystems 2023; 8:e0068922. [PMID: 36511689 PMCID: PMC9948698 DOI: 10.1128/msystems.00689-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/13/2022] [Indexed: 12/15/2022] Open
Abstract
Gardnerella is the primary pathogenic bacterial genus present in the polymicrobial condition known as bacterial vaginosis (BV). Despite BV's high prevalence and associated chronic and acute women's health impacts, the Gardnerella pangenome is largely uncharacterized at both the genetic and functional metabolic levels. Here, we used genome-scale metabolic models to characterize in silico the Gardnerella pangenome metabolic content. We also assessed the metabolic functional capacity in a BV-positive cervicovaginal fluid context. The metabolic capacity varied widely across the pangenome, with 38.15% of all reactions being core to the genus, compared to 49.60% of reactions identified as being unique to a smaller subset of species. We identified 57 essential genes across the pangenome via in silico gene essentiality screens within two simulated vaginal metabolic environments. Four genes, gpsA, fas, suhB, and psd, were identified as core essential genes critical for the metabolic function of all analyzed bacterial species of the Gardnerella genus. Further understanding these core essential metabolic functions could inform novel therapeutic strategies to treat BV. Machine learning applied to simulated metabolic network flux distributions showed limited clustering based on the sample isolation source, which further supports the presence of extensive core metabolic functionality across this genus. These data represent the first metabolic modeling of the Gardnerella pangenome and illustrate strain-specific interactions with the vaginal metabolic environment across the pangenome. IMPORTANCE Bacterial vaginosis (BV) is the most common vaginal infection among reproductive-age women. Despite its prevalence and associated chronic and acute women's health impacts, the diverse bacteria involved in BV infection remain poorly characterized. Gardnerella is the genus of bacteria most commonly and most abundantly represented during BV. In this paper, we use metabolic models, which are a computational representation of the possible functional metabolism of an organism, to investigate metabolic conservation, gene essentiality, and pathway utilization across 110 Gardnerella strains. These models allow us to investigate in silico how strains may differ with respect to their metabolic interactions with the vaginal-host environment.
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Affiliation(s)
- Lillian R. Dillard
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Emma M. Glass
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Amanda L. Lewis
- Department of Obstetrics and Gynecology, University of California—San Diego, La Jolla, California, USA
| | | | - Jason A. Papin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
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4
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Flores-Vega VR, Lara-Zavala BA, Jarillo-Quijada MD, Fernández-Vázquez JL, Alcántar-Curiel MD, Vargas-Roldán SY, Ares MA, de la Cruz MA, Morfín-Otero R, Rodríguez-Noriega E, Santos-Preciado JI, Rosales-Reyes R. Burkholderia vietnamiensis causing infections in noncystic fibrosis patients in a tertiary care hospital in Mexico. Diagn Microbiol Infect Dis 2023; 105:115866. [PMID: 36525921 DOI: 10.1016/j.diagmicrobio.2022.115866] [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: 08/01/2022] [Revised: 10/31/2022] [Accepted: 11/19/2022] [Indexed: 11/26/2022]
Abstract
Burkholderia cepacia complex (Bcc) species are opportunistic pathogens widely distributed in the environment and often infect people with cystic fibrosis (CF). This study aims to determine which genomovars of the Bcc can cause infections in non-CF patients from a tertiary care hospital in Mexico and if they carry virulence factors that could increase their pathogenicity. We identified 23 clinical isolates that carry the recA gene. Twenty-two of them belongs to the genomovar V (B. vietnamiensis) and one to the genomovar II (B. multivorans). Thirteen pulsotypes were identified among 22 B. vietnamiensis isolates. All clinical isolates produced biofilm were motile and cytotoxic on murine macrophage-like RAW264.7 and in A549 human lung epithelial cells. In conclusion, B. vietnamiensis causes infections in non-CF patients in a tertiary care hospital in Mexico, rapid identification of this pathogen can help physicians to establish a better antimicrobial treatment.
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Affiliation(s)
- Verónica Roxana Flores-Vega
- Facultad de Medicina, Unidad de Medicina Experimental, Universidad Nacional Autónoma de México, Mexico City, Mexico; Escuela de Ciencias de la Salud, Universidad del Valle de México, Campus Coyoacán, Mexico City, Mexico
| | - Berenice Alejandra Lara-Zavala
- Facultad de Medicina, Unidad de Medicina Experimental, Universidad Nacional Autónoma de México, Mexico City, Mexico; Escuela de Ciencias de la Salud, Universidad del Valle de México, Campus Coyoacán, Mexico City, Mexico
| | - Ma Dolores Jarillo-Quijada
- Facultad de Medicina, Unidad de Medicina Experimental, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - José Luis Fernández-Vázquez
- Facultad de Medicina, Unidad de Medicina Experimental, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Silvia Yalid Vargas-Roldán
- Facultad de Medicina, Unidad de Medicina Experimental, Universidad Nacional Autónoma de México, Mexico City, Mexico; Laboratorio de Microbiología, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional Siglo XXI, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Miguel A de la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional Siglo XXI, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rayo Morfín-Otero
- Hospital Civil de Guadalajara Fray Antonio Alcalde, Instituto de Patología Infecciosa y Experimental, Guadalajara, Jalisco, Mexico
| | - Eduardo Rodríguez-Noriega
- Hospital Civil de Guadalajara Fray Antonio Alcalde, Instituto de Patología Infecciosa y Experimental, Guadalajara, Jalisco, Mexico
| | - José Ignacio Santos-Preciado
- Facultad de Medicina, Unidad de Medicina Experimental, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Facultad de Medicina, Unidad de Medicina Experimental, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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Multifunctional Amyloids in the Biology of Gram-Positive Bacteria. Microorganisms 2020; 8:microorganisms8122020. [PMID: 33348645 PMCID: PMC7766987 DOI: 10.3390/microorganisms8122020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/18/2023] Open
Abstract
Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.
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Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach. Int J Mol Sci 2019; 20:ijms20143451. [PMID: 31337077 PMCID: PMC6679007 DOI: 10.3390/ijms20143451] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 02/08/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii strains cause life-threatening infections due to the lack of therapeutic options. Although the main mechanisms underlying antibiotic-resistance have been extensively studied, the general response to maintain bacterial viability under antibiotic exposure deserves to be fully investigated. Since the periplasmic space contains several proteins with crucial cellular functions, besides carbapenemases, we decided to study the periplasmic proteome of the multidrug-resistant (MDR) A. baumannii AB5075 strain, grown in the absence and presence of imipenem (IMP). Through the proteomic approach, 65 unique periplasmic proteins common in both growth conditions were identified: eight proteins involved in protein fate, response to oxidative stress, energy metabolism, antibiotic-resistance, were differentially expressed. Among them, ABUW_1746 and ABUW_2363 gene products presented the tetratricopeptide repeat motif, mediating protein-protein interactions. The expression switch of these proteins might determine specific protein interactions to better adapt to changing environmental conditions. ABUW_2868, encoding a heat shock protein likely involved in protection against oxidative stress, was upregulated in IMP-exposed bacteria. Accordingly, the addition of periplasmic proteins from A. baumannii cultured with IMP increased bacterial viability in an antioxidant activity assay. Overall, this study provides the first insights about the composition of the periplasmic proteins of a MDR A. baumannii strain, its biological response to IMP and suggests possible new targets to develop alternative antibiotic drugs.
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Molecular mechanisms of polymyxin resistance and detection of mcr genes. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2018; 163:28-38. [PMID: 30439931 DOI: 10.5507/bp.2018.070] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is an ever-increasing global problem. Major commercial antibiotics often fail to fight common bacteria, and some pathogens have become multi-resistant. Polymyxins are potent bactericidal antibiotics against gram-negative bacteria. Known resistance to polymyxin includes intrinsic, mutational and adaptive mechanisms, with the recently described horizontally acquired resistance mechanisms. In this review, we present several strategies for bacteria to develop enhanced resistance to polymyxins, focusing on changes in the outer membrane, efflux and other resistance determinants. Better understanding of the genes involved in polymyxin resistance may pave the way for the development of new and effective antimicrobial agents. We also report novel in silico tested primers for PCR assay that may be able distinguish colistin-resistant isolates carrying the plasmid-encoded mcr genes and will assist in combating the spread of colistin resistance in bacteria.
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8
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Polese V, de Paula Soares C, da Silva PRA, Simões-Araújo JL, Baldani JI, Vidal MS. Selection and validation of reference genes for RT-qPCR indicates that juice of sugarcane varieties modulate the expression of C metabolism genes in the endophytic diazotrophic Herbaspirillum rubrisubalbicans strain HCC103. Antonie Van Leeuwenhoek 2017; 110:1555-1568. [DOI: 10.1007/s10482-017-0906-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/28/2017] [Indexed: 12/24/2022]
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9
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Puigvert M, Guarischi-Sousa R, Zuluaga P, Coll NS, Macho AP, Setubal JC, Valls M. Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii. FRONTIERS IN PLANT SCIENCE 2017; 8:370. [PMID: 28373879 PMCID: PMC5357869 DOI: 10.3389/fpls.2017.00370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/02/2017] [Indexed: 05/03/2023]
Abstract
Bacterial wilt of potatoes-also called brown rot-is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by sequencing transcripts from infected tissue avoiding prokaryotic RNA enrichment.
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Affiliation(s)
- Marina Puigvert
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | | | - Paola Zuluaga
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | - Núria S. Coll
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | - Alberto P. Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences (CAS)Shanghai, China
| | - João C. Setubal
- Department of Biochemistry, University of São PauloSão Paulo, Brazil
| | - Marc Valls
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
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Terakawa A, Natsume A, Okada A, Nishihata S, Kuse J, Tanaka K, Takenaka S, Ishikawa S, Yoshida KI. Bacillus subtilis 5'-nucleotidases with various functions and substrate specificities. BMC Microbiol 2016; 16:249. [PMID: 27784292 PMCID: PMC5080769 DOI: 10.1186/s12866-016-0866-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Escherichia coli, nagD, yrfG, yjjG, yieH, yigL, surE, and yfbR encode 5'-nucleotidases that hydrolyze the phosphate group of 5'-nucleotides. In Bacillus subtilis, genes encoding 5'-nucleotidase have remained to be identified. RESULTS We found that B. subtilis ycsE, araL, yutF, ysaA, and yqeG show suggestive similarities to nagD. Here, we expressed them in E. coli to purify the respective His6-tagged proteins. YcsE exhibited significant 5'-nucleotidase activity with a broader specificity, whereas the other four enzymes had rather weak but suggestive activities with various capacities and substrate specificities. In contrast, B. subtilis yktC shares high similarity with E. coli suhB encoding an inositol monophosphatase. YktC exhibited inositol monophosphatase activity as well as 5'-nucleotidase activity preferential for GMP and IMP. The ycsE, yktC, and yqeG genes are induced by oxidative stress and were dispensable, although yqeG was required to maintain normal growth on solid medium. In the presence of diamide, only mutants lacking yktC exhibited enhanced growth defects, whereas the other mutants without ycsE or yqeG did not. CONCLUSIONS Accordingly, in B. subtilis, at least YcsE and YktC acted as major 5'-nucleotidases and the four minor enzymes might function when the intracellular concentrations of substrates are sufficiently high. In addition, YktC is involved in resistance to oxidative stress caused by diamide, while YqeG is necessary for normal colony formation on solid medium.
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Affiliation(s)
- Ayako Terakawa
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Ayane Natsume
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Atsushi Okada
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Shogo Nishihata
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Junko Kuse
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kosei Tanaka
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Shinji Takenaka
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan.,Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Ken-Ichi Yoshida
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan. .,Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan.
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11
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Macroscopic amyloid fiber formation by staphylococcal biofilm associated SuhB protein. Biophys Chem 2016; 217:32-41. [DOI: 10.1016/j.bpc.2016.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/04/2016] [Accepted: 07/27/2016] [Indexed: 11/22/2022]
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12
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Abstract
UNLABELLED A complex of highly conserved proteins consisting of NusB, NusE, NusA, and NusG is required for robust expression of rRNA in Escherichia coli. This complex is proposed to prevent Rho-dependent transcription termination by a process known as "antitermination." The mechanism of this antitermination in rRNA is poorly understood but requires association of NusB and NusE with a specific RNA sequence in rRNA known as BoxA. Here, we identify a novel member of the rRNA antitermination machinery: the inositol monophosphatase SuhB. We show that SuhB associates with elongating RNA polymerase (RNAP) at rRNA in a NusB-dependent manner. Although we show that SuhB is required for BoxA-mediated antitermination in a reporter system, our data indicate that the major function of the NusB/E/A/G/SuhB complex is not to prevent Rho-dependent termination of rRNA but rather to promote correct rRNA maturation. This occurs through formation of a SuhB-mediated loop between NusB/E/BoxA and RNAP/NusA/G. Thus, we have reassigned the function of these proteins at rRNA and identified another key player in this complex. IMPORTANCE As RNA polymerase transcribes the rRNA operons in E. coli, it complexes with a set of proteins called Nus that confer enhanced rates of transcription elongation, correct folding of rRNA, and rRNA assembly with ribosomal proteins to generate a fully functional ribosome. Four Nus proteins were previously known, NusA, NusB, NusE, and NusG; here, we discover and describe a fifth, SuhB, that is an essential component of this complex. We demonstrate that the main function of this SuhB-containing complex is not to prevent premature transcription termination within the rRNA operon, as had been long claimed, but to enable rRNA maturation and a functional ribosome fully competent for translation.
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Rosales-Reyes R, Alcántar-Curiel MD, Jarillo-Quijada MD, Gayosso-Vázquez C, Morfin-Otero MDR, Rodríguez-Noriega E, Santos-Preciado JI. Biofilm Formation and Susceptibility to Polymyxin B by a Highly Prevalent Clone of Multidrug-Resistant Acinetobacter baumannii from a Mexican Tertiary Care Hospital. Chemotherapy 2015; 61:8-14. [PMID: 26536333 DOI: 10.1159/000440605] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 08/24/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Acinetobacter baumannii has emerged as a major cause of hospital-associated infections with increased morbidity and mortality among those affected. METHODS A total of 85 isolates of a highly prevalent multidrug-resistant clone, identified during the period 2007-2011, were analyzed for biofilm formation on a polystyrene surface. The minimal inhibitory concentration was determined by the Sensititre System, the agar disk diffusion method and then read by means of the BIOMIC system and serial dilutions on Müller-Hinton agar. RESULTS In this study, covering a period of 5 years (2007-2011), we demonstrate that a particular clone emerged as the most prevalent, with an associated lethality of 28.2%. We demonstrate that 92.9% of strains corresponding to this clone are biofilm producers. Our results also demonstrate that all isolates were 100% susceptible to polymyxin B. CONCLUSION Our study suggests that the high prevalence and lethality of this multidrug-resistant clone of A. baumannii and its persistence over close to 5 years in a Mexican tertiary hospital environment can be explained in part by the ability of these clinical isolates of A. baumannii to form biofilms.
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Shi J, Jin Y, Bian T, Li K, Sun Z, Cheng Z, Jin S, Wu W. SuhB is a novel ribosome associated protein that regulates expression of MexXY by modulating ribosome stalling inPseudomonas aeruginosa. Mol Microbiol 2015; 98:370-83. [DOI: 10.1111/mmi.13126] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Jing Shi
- State Key Laboratory of Medicinal Chemical Biology; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education; Department of Microbiology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education; Department of Microbiology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Ting Bian
- State Key Laboratory of Medicinal Chemical Biology; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education; Department of Microbiology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Kewei Li
- State Key Laboratory of Medicinal Chemical Biology; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education; Department of Microbiology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Ziyu Sun
- State Key Laboratory of Medicinal Chemical Biology; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education; Department of Microbiology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education; Department of Microbiology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education; Department of Microbiology; College of Life Sciences; Nankai University; Tianjin 300071 China
- Department of Molecular Genetics and Microbiology; College of Medicine; University of Florida; Gainesville FL 32610 USA
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education; Department of Microbiology; College of Life Sciences; Nankai University; Tianjin 300071 China
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Gluconacetobacter diazotrophicus PAL5 possesses an active quorum sensing regulatory system. Antonie van Leeuwenhoek 2014; 106:497-506. [PMID: 24974195 DOI: 10.1007/s10482-014-0218-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/13/2014] [Indexed: 10/25/2022]
Abstract
The endophytic bacterium Gluconacetobacter diazotrophicus colonizes a broad range of host plants. Its plant growth-promoting capability is related to the capacity to perform biological nitrogen fixation, the biosynthesis of siderophores, antimicrobial substances and the solubilization of mineral nutrients. Colonization of and survival in these endophytic niche requires a complex regulatory network. Among these, quorum sensing systems (QS) are signaling mechanisms involved in the control of several genes related to microbial interactions, host colonization and stress survival. G. diazotrophicus PAL5 possesses a QS composed of a luxR and a luxI homolog, and produces eight molecules from the AHL family as QS signals. In this report data are provided showing that glucose concentration modifies the relative levels of these signal molecules. The activity of G. diazotrophicus PAL5 QS is also altered in presence of other carbon sources and under saline stress conditions. Inactivation of the QS system of G. diazotrophicus PAL5 by means of a quorum quenching strategy allowed the identification of extracellular and intracellular proteins under the control of this regulatory mechanism.
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16
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Common duckweed (Lemna minor) is a versatile high-throughput infection model for the Burkholderia cepacia complex and other pathogenic bacteria. PLoS One 2013; 8:e80102. [PMID: 24223216 PMCID: PMC3819297 DOI: 10.1371/journal.pone.0080102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 10/07/2013] [Indexed: 01/05/2023] Open
Abstract
Members of the Burkholderia cepacia complex (Bcc) have emerged in recent decades as problematic pulmonary pathogens of cystic fibrosis (CF) patients, with severe infections progressing to acute necrotizing pneumonia and sepsis. This study presents evidence that Lemna minor (Common duckweed) is useful as a plant model for the Bcc infectious process, and has potential as a model system for bacterial pathogenesis in general. To investigate the relationship between Bcc virulence in duckweed and Galleria mellonella (Greater wax moth) larvae, a previously established Bcc infection model, a duckweed survival assay was developed and used to determine LD50 values. A strong correlation (R2 = 0.81) was found between the strains’ virulence ranks in the two infection models, suggesting conserved pathways in these vastly different hosts. To broaden the application of the duckweed model, enteropathogenic Escherichia coli (EPEC) and five isogenic mutants with previously established LD50 values in the larval model were tested against duckweed, and a strong correlation (R2 = 0.93) was found between their raw LD50 values. Potential virulence factors in B. cenocepacia K56-2 were identified using a high-throughput screen against single duckweed plants. In addition to the previously characterized antifungal compound (AFC) cluster genes, several uncharacterized genes were discovered including a novel lysR regulator, a histidine biosynthesis gene hisG, and a gene located near the gene encoding the recently characterized virulence factor SuhBBc. Finally, to demonstrate the utility of this model in therapeutic applications, duckweed was rescued from Bcc infection by treating with bacteriophage at 6-h intervals. It was observed that phage application became ineffective at a timepoint that coincided with a sharp increase in bacterial invasion of plant tissue. These results indicate that common duckweed can serve as an effective infection model for the investigation of bacterial virulence factors and therapeutic strategies to combat them.
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SuhB is a regulator of multiple virulence genes and essential for pathogenesis of Pseudomonas aeruginosa. mBio 2013; 4:e00419-13. [PMID: 24169572 PMCID: PMC3809559 DOI: 10.1128/mbio.00419-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
During initial colonization and chronic infection, pathogenic bacteria encounter distinct host environments. Adjusting gene expression accordingly is essential for the pathogenesis. Pseudomonas aeruginosa has evolved complicated regulatory networks to regulate different sets of virulence factors to facilitate colonization and persistence. The type III secretion system (T3SS) and motility are associated with acute infections, while biofilm formation and the type VI secretion system (T6SS) are associated with chronic persistence. To identify novel regulatory genes required for pathogenesis, we screened a P. aeruginosa transposon (Tn) insertion library and found suhB to be an essential gene for the T3SS gene expression. The expression of suhB was upregulated in a mouse acute lung infection model, and loss of suhB resulted in avirulence. Suppression of T3SS gene expression in the suhB mutant is linked to a defective translation of the T3SS master regulator, ExsA. Further studies demonstrated that suhB mutation led to the upregulation of GacA and its downstream small RNAs, RsmY and RsmZ, triggering T6SS expression and biofilm formation while inhibiting the T3SS. Our results demonstrate that an in vivo-inducible gene, suhB, reciprocally regulates genes associated with acute and chronic infections and plays an essential role in the pathogenesis of P. aeruginosa. A variety of bacterial pathogens, such as Pseudomonas aeruginosa, cause acute and chronic infections in humans. During infections, pathogens produce different sets of virulence genes for colonization, tissue damage, and dissemination and for countering host immune responses. Complex regulatory networks control the delicate tuning of gene expression in response to host environments to enable the survival and growth of invading pathogens. Here we identified suhB as a critical gene for the regulation of virulence factors in P. aeruginosa. The expression of suhB was upregulated during acute infection in an animal model, and mutation of suhB rendered P. aeruginosa avirulent. Moreover, we demonstrate that SuhB is required for the activation of virulence factors associated with acute infections while suppressing virulence factors associated with chronic infections. Our report provides new insights into the multilayered regulatory network of virulence genes in P. aeruginosa.
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18
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Chemical communication of antibiotic resistance by a highly resistant subpopulation of bacterial cells. PLoS One 2013; 8:e68874. [PMID: 23844246 PMCID: PMC3700957 DOI: 10.1371/journal.pone.0068874] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/03/2013] [Indexed: 01/05/2023] Open
Abstract
The overall antibiotic resistance of a bacterial population results from the combination of a wide range of susceptibilities displayed by subsets of bacterial cells. Bacterial heteroresistance to antibiotics has been documented for several opportunistic Gram-negative bacteria, but the mechanism of heteroresistance is unclear. We use Burkholderia cenocepacia as a model opportunistic bacterium to investigate the implications of heterogeneity in the response to the antimicrobial peptide polymyxin B (PmB) and also other bactericidal antibiotics. Here, we report that B. cenocepacia is heteroresistant to PmB. Population analysis profiling also identified B. cenocepacia subpopulations arising from a seemingly homogenous culture that are resistant to higher levels of polymyxin B than the rest of the cells in the culture, and can protect the more sensitive cells from killing, as well as sensitive bacteria from other species, such as Pseudomonas aeruginosa and Escherichia coli. Communication of resistance depended on upregulation of putrescine synthesis and YceI, a widely conserved low-molecular weight secreted protein. Deletion of genes for the synthesis of putrescine and YceI abrogate protection, while pharmacologic inhibition of putrescine synthesis reduced resistance to polymyxin B. Polyamines and YceI were also required for heteroresistance of B. cenocepacia to various bactericidal antibiotics. We propose that putrescine and YceI resemble "danger" infochemicals whose increased production by a bacterial subpopulation, becoming more resistant to bactericidal antibiotics, communicates higher level of resistance to more sensitive members of the population of the same or different species.
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Lima TB, Pinto MFS, Ribeiro SM, de Lima LA, Viana JC, Gomes Júnior N, Cândido EDS, Dias SC, Franco OL. Bacterial resistance mechanism: what proteomics can elucidate. FASEB J 2013; 27:1291-303. [PMID: 23349550 DOI: 10.1096/fj.12-221127] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antibiotics are important therapeutic agents commonly used for the control of bacterial infectious diseases; however, resistance to antibiotics has become a global public health problem. Therefore, effective therapy in the treatment of resistant bacteria is necessary and, to achieve this, a detailed understanding of mechanisms that underlie drug resistance must be sought. To fill the multiple gaps that remain in understanding bacterial resistance, proteomic tools have been used to study bacterial physiology in response to antibiotic stress. In general, the global analysis of changes in the protein composition of bacterial cells in response to treatment with antibiotic agents has made it possible to construct a database of proteins involved in the process of resistance to drugs with similar mechanisms of action. In the past few years, progress in using proteomic tools has provided the most realistic picture of the infective process, since these tools detect the end products of gene biosynthetic pathways, which may eventually determine a biological phenotype. In most bacterial species, alterations occur in energy and nitrogen metabolism regulation; glucan biosynthesis is up-regulated; amino acid, protein, and nucleotide synthesis is affected; and various proteins show a stress response after exposing these microorganisms to antibiotics. These issues have been useful in identifying targets for the development of novel antibiotics and also in understanding, at the molecular level, how bacteria resist antibiotics.
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Affiliation(s)
- Thais Bergamin Lima
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, Brazil
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