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Blanco P, Hipólito A, García-Pastor L, Trigo da Roza F, Toribio-Celestino L, Ortega A, Vergara E, San Millán Á, Escudero J. Identification of promoter activity in gene-less cassettes from Vibrionaceae superintegrons. Nucleic Acids Res 2024; 52:2961-2976. [PMID: 38214222 PMCID: PMC11014356 DOI: 10.1093/nar/gkad1252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
Integrons are genetic platforms that acquire new genes encoded in integron cassettes (ICs), building arrays of adaptive functions. ICs generally encode promoterless genes, whose expression relies on the platform-associated Pc promoter, with the cassette array functioning as an operon-like structure regulated by the distance to the Pc. This is relevant in large sedentary chromosomal integrons (SCIs) carrying hundreds of ICs, like those in Vibrio species. We selected 29 gene-less cassettes in four Vibrio SCIs, and explored whether their function could be related to the transcription regulation of adjacent ICs. We show that most gene-less cassettes have promoter activity on the sense strand, enhancing the expression of downstream cassettes. Additionally, we identified the transcription start sites of gene-less ICs through 5'-RACE. Accordingly, we found that most of the superintegron in Vibrio cholerae is not silent. These promoter cassettes can trigger the expression of a silent dfrB9 cassette downstream, increasing trimethoprim resistance >512-fold in V. cholerae and Escherichia coli. Furthermore, one cassette with an antisense promoter can reduce trimethoprim resistance when cloned downstream. Our findings highlight the regulatory role of gene-less cassettes in the expression of adjacent cassettes, emphasizing their significance in SCIs and their clinical importance if captured by mobile integrons.
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Affiliation(s)
- Paula Blanco
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Alberto Hipólito
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Lucía García-Pastor
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Filipa Trigo da Roza
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid 28049, Spain
| | - Alba Cristina Ortega
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Ester Vergara
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro San Millán
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid 28049, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid 28222, Spain
| | - José Antonio Escudero
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
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Gnanagobal H, Cao T, Hossain A, Vasquez I, Chakraborty S, Chukwu-Osazuwa J, Boyce D, Espinoza MJ, García-Angulo VA, Santander J. Role of riboflavin biosynthesis gene duplication and transporter in Aeromonas salmonicida virulence in marine teleost fish. Virulence 2023; 14:2187025. [PMID: 36895132 PMCID: PMC10012899 DOI: 10.1080/21505594.2023.2187025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Active flavins derived from riboflavin (vitamin B2) are essential for life. Bacteria biosynthesize riboflavin or scavenge it through uptake systems, and both mechanisms may be present. Because of riboflavin's critical importance, the redundancy of riboflavin biosynthetic pathway (RBP) genes might be present. Aeromonas salmonicida, the aetiological agent of furunculosis, is a pathogen of freshwater and marine fish, and its riboflavin pathways have not been studied. This study characterized the A. salmonicida riboflavin provision pathways. Homology search and transcriptional orchestration analysis showed that A. salmonicida has a main riboflavin biosynthetic operon that includes ribD, ribE1, ribBA, and ribH genes. Outside the main operon, putative duplicated genes ribA, ribB and ribE, and a ribN riboflavin importer encoding gene, were found. Monocistronic mRNA ribA, ribB and ribE2 encode for their corresponding functional riboflavin biosynthetic enzyme. While the product of ribBA conserved the RibB function, it lacked the RibA function. Likewise, ribN encodes a functional riboflavin importer. Transcriptomics analysis indicated that external riboflavin affected the expression of a relatively small number of genes, including a few involved in iron metabolism. ribB was downregulated in response to external riboflavin, suggesting negative feedback. Deletion of ribA, ribB and ribE1 showed that these genes are required for A. salmonicida riboflavin biosynthesis and virulence in Atlantic lumpfish (Cyclopterus lumpus). A. salmonicida riboflavin auxotrophic attenuated mutants conferred low protection to lumpfish against virulent A. salmonicida. Overall, A. salmonicida has multiple riboflavin endowment forms, and duplicated riboflavin provision genes are critical for A. salmonicida infection.
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Affiliation(s)
- Hajarooba Gnanagobal
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Trung Cao
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Ahmed Hossain
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Ignacio Vasquez
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Setu Chakraborty
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Joy Chukwu-Osazuwa
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Danny Boyce
- The Dr. Joe Brown Aquatic Research Building (JBARB), Ocean Sciences Centre, Memorial University of Newfoundland, St John's, Canada
| | - María Jesus Espinoza
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Víctor Antonio García-Angulo
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
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Yang R, Shi Q, Huang T, Yan Y, Li S, Fang Y, Li Y, Liu L, Liu L, Wang X, Peng Y, Fan J, Zou L, Lin S, Chen G. The natural pyrazolotriazine pseudoiodinine from Pseudomonas mosselii 923 inhibits plant bacterial and fungal pathogens. Nat Commun 2023; 14:734. [PMID: 36759518 PMCID: PMC9911603 DOI: 10.1038/s41467-023-36433-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Natural products largely produced by Pseudomonads-like soil-dwelling microorganisms are a consistent source of antimicrobial metabolites and pesticides. Herein we report the isolation of Pseudomonas mosselii strain 923 from rice rhizosphere soils of paddy fields, which specifically inhibit the growth of plant bacterial pathogens Xanthomonas species and the fungal pathogen Magnaporthe oryzae. The antimicrobial compound is purified and identified as pseudoiodinine using high-resolution mass spectra, nuclear magnetic resonance and single-crystal X-ray diffraction. Genome-wide random mutagenesis, transcriptome analysis and biochemical assays define the pseudoiodinine biosynthetic cluster as psdABCDEFG. Pseudoiodinine biosynthesis is proposed to initiate from guanosine triphosphate and 1,6-didesmethyltoxoflavin is a biosynthetic intermediate. Transposon mutagenesis indicate that GacA is the global regulator. Furthermore, two noncoding small RNAs, rsmY and rsmZ, positively regulate pseudoiodinine transcription, and the carbon storage regulators CsrA2 and CsrA3, which negatively regulate the expression of psdA. A 22.4-fold increase in pseudoiodinine production is achieved by optimizing the media used for fermentation, overexpressing the biosynthetic operon, and removing the CsrA binding sites. Both of the strain 923 and purified pseudoiodinine in planta inhibit the pathogens without affecting the rice host, suggesting that pseudoiodinine can be used to control plant diseases.
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Affiliation(s)
- Ruihuan Yang
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qing Shi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yichao Yan
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shengzhang Li
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuan Fang
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying Li
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linlin Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Longyu Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yongzheng Peng
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiangbo Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lifang Zou
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Gongyou Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Hernández-Fernández G, Galán B, Carmona M, Castro L, García JL. Transcriptional response of the xerotolerant Arthrobacter sp. Helios strain to PEG-induced drought stress. Front Microbiol 2022; 13:1009068. [PMID: 36312951 PMCID: PMC9608346 DOI: 10.3389/fmicb.2022.1009068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
A new bacterial strain has been isolated from the microbiome of solar panels and classified as Arthrobacter sp. Helios according to its 16S rDNA, positioning it in the “Arthrobacter citreus group.” The isolated strain is highly tolerant to desiccation, UV radiation and to the presence of metals and metalloids, while it is motile and capable of growing in a variety of carbon sources. These characteristics, together with observation that Arthrobacter sp. Helios seems to be permanently prepared to handle the desiccation stress, make it very versatile and give it a great potential to use it as a biotechnological chassis. The new strain genome has been sequenced and its analysis revealed that it is extremely well poised to respond to environmental stresses. We have analyzed the transcriptional response of this strain to PEG6000-mediated arid stress to investigate the desiccation resistance mechanism. Most of the induced genes participate in cellular homeostasis such as ion and osmolyte transport and iron scavenging. Moreover, the greatest induction has been found in a gene cluster responsible for biogenic amine catabolism, suggesting their involvement in the desiccation resistance mechanism in this bacterium.
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Affiliation(s)
- Gabriel Hernández-Fernández
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - Manuel Carmona
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - Laura Castro
- Department of Chemical and Materials Engineering, Complutense University of Madrid, Madrid, Spain
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
- *Correspondence: José Luis García,
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Hong M, Jang I, Son Y, Yi C, Park W. Agricultural by-products and oyster shell as alternative nutrient sources for microbial sealing of early age cracks in mortar. AMB Express 2021; 11:11. [PMID: 33409575 PMCID: PMC7788133 DOI: 10.1186/s13568-020-01166-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/11/2020] [Indexed: 12/19/2022] Open
Abstract
Bio-concrete using bacterially produced calcium carbonate can repair microcracks but is still relatively expensive due to the addition of bacteria, nutrients, and calcium sources. Agricultural by-products and oyster shells were used to produce economical bio-concrete. Sesame meal was the optimal agricultural by-product for low-cost spore production of the alkaliphilic Bacillus miscanthi strain AK13. Transcriptomic dataset was utilized to compare the gene expressions of AK13 strain under neutral and alkaline conditions, which suggested that NaCl and riboflavin could be chosen as growth-promoting factors at alkaline pH. The optimal levels of sesame meal, NaCl, and riboflavin were induced with the central composite design to create an economical medium, in which AK13 strain formed more spores with less price than in commercial sporulation medium. Calcium nitrate obtained from nitric acid treatment of oyster shell powder increased the initial compressive strength of cement mortar. Non-ureolytic calcium carbonate precipitation by AK13 using oyster shell-derived calcium ions was verified by energy-dispersive X-ray spectroscopy and X-ray diffraction analysis. Stereomicroscope and field emission scanning electron microscopy confirmed that oyster shell-derived calcium ions, along with soybean meal-solution, increased the bacterial survival and calcium carbonate precipitation inside mortar cracks. These data suggest the possibility of commercializing bacterial self-healing concrete with economical substitutes for culture medium, growth nutrient, and calcium sources.
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IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae. Genes (Basel) 2020; 11:genes11101184. [PMID: 33053678 PMCID: PMC7600106 DOI: 10.3390/genes11101184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
The pathogen Vibrio cholerae has multiple iron acquisition systems which allow bacteria to exploit a variety of iron sources across the different environments on which it thrives. The expression of such iron uptake systems is highly regulated, mainly by the master iron homeostasis regulator Fur but also by other mechanisms. Recently, we documented that the expression of many of the iron-responsive genes is also modulated by riboflavin. Among them, the open reading frame VCA0231, repressed both by riboflavin and iron, encodes a putative transcriptional regulator of the AraC/XylS family. Nonetheless, the genes or functions affected by this factor are unknown. In the present study, a series of in silico analyses was performed in order to identify the putative functions associated with the product of VCA0231. The STRING database predicted many iron uptake genes as functional partners for the product of VCA0231. In addition, a genomic neighborhood analysis with the Enzyme Function Initiative tools detected many Pfam families involved in iron homeostasis genetically associated with VCA0231. Moreover, a phylogenetic tree showed that other AraC/XylS members known to regulate siderophore utilization in bacteria clustered together and the product of VCA0231 localized in this cluster. This suggested that the product of VCA0231, here named IurV, is involved in the regulation of iron uptake processes. RNAseq was performed to determine the transcriptional effects of a deletion in VCA0231. A total of 52 genes were overexpressed and 21 genes were downregulated in response to the iurV deletion. Among these, several iron uptake genes and other iron homeostasis-related genes were found. Six gene ontology (GO) functional terms were enriched in the upregulated genes, of which five were related to iron metabolism. The regulatory pattern observed in the transcriptomics of a subset of genes was independently confirmed by quantitative real time PCR analysis. The results indicate that IurV is a novel regulator of the AraC/XylS family involved in the repression of iron uptake genes. Whether this effect is direct or indirect remains to be determined.
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7
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Lozano Aguirre LF, Salazar JC, Vásquez JI, García-Angulo VA. Interdependency of regulatory effects of iron and riboflavin in the foodborne pathogen Shigella flexneri determined by integral transcriptomics. PeerJ 2020; 8:e9553. [PMID: 32983629 PMCID: PMC7500357 DOI: 10.7717/peerj.9553] [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] [Received: 09/26/2019] [Accepted: 06/24/2020] [Indexed: 11/24/2022] Open
Abstract
Shigella flexneri is the causative agent of dysentery. For pathogens, iron is a critical micronutrient as its bioavailability is usually low in bacterial niches. This metal is involved in critical physiological processes mainly as a component of important metabolic molecules involved in redox reactions. Usually bacteria respond to fluctuations in iron availability to regulate iron acquisition and other iron-related functions. Recently the close metabolic feedback between iron and riboflavin, another pivotal biological redox agent, began to draw attention in bacteria. This is a widespread biological phenomenon, partly characterized by the coordination of regulatory responses to iron and riboflavin, probably owed to the involvement of these cofactors in common processes. Nonetheless, no systematic analyses to determine the extent of this regulatory effect have been performed in any species. Here, the transcriptomics responses to iron, riboflavin, iron in the presence of riboflavin and riboflavin in the presence of iron were assessed and compared in S. flexneri. The riboflavin regulon had a 43% overlap with the iron regulon. Notably, the presence of riboflavin highly increased the number of iron-responsive genes. Reciprocally, iron drastically changed the pool of riboflavin-responsive genes. Gene ontology (GO) functional terms enrichment analysis showed that biological processes were distinctively enriched for each subgroup of responsive genes. Among the biological processes regulated by iron and riboflavin were iron uptake, amino acids metabolism and electron transfer for ATP synthesis. Thus, iron and riboflavin highly affect the transcriptomics responses induced by each other in S. flexneri. GO terms analysis suggests that iron and riboflavin coordinately regulate specific physiological functions involving redox metabolism.
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Affiliation(s)
- Luis Fernando Lozano Aguirre
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Juan Carlos Salazar
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - José Ignacio Vásquez
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John, Canada
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Levade I, Saber MM, Midani FS, Chowdhury F, Khan AI, Begum YA, Ryan ET, David LA, Calderwood SB, Harris JB, LaRocque RC, Qadri F, Shapiro BJ, Weil AA. Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study. J Infect Dis 2020; 223:342-351. [PMID: 32610345 PMCID: PMC7857355 DOI: 10.1093/infdis/jiaa358] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Susceptibility to Vibrio cholerae infection is affected by blood group, age, and preexisting immunity, but these factors only partially explain who becomes infected. A recent study used 16S ribosomal RNA amplicon sequencing to quantify the composition of the gut microbiome and identify predictive biomarkers of infection with limited taxonomic resolution. METHODS To achieve increased resolution of gut microbial factors associated with V. cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera. RESULTS Using machine learning, we resolved species, strains, gene families, and cellular pathways in the microbiome at the time of exposure to V. cholerae to identify markers that predict infection and symptoms. Use of metagenomic features improved the precision and accuracy of prediction relative to 16S sequencing. We also predicted disease severity, although with greater uncertainty than our infection prediction. Species within the genera Prevotella and Bifidobacterium predicted protection from infection, and genes involved in iron metabolism were also correlated with protection. CONCLUSION Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera.
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Affiliation(s)
- Inès Levade
- Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Morteza M Saber
- Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Firas S Midani
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, USA,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Fahima Chowdhury
- Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ashraful I Khan
- Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Yasmin A Begum
- Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lawrence A David
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, USA,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA,Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Stephen B Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Firdausi Qadri
- Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - B Jesse Shapiro
- Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada,Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada,McGill Genome Centre, Montreal, Quebec, Canada,Correspondence: B. Jesse Shapiro, McGill University, Montreal, Quebec, Canada ()
| | - Ana A Weil
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
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Lipidomics of human adipose tissue reveals diversity between body areas. PLoS One 2020; 15:e0228521. [PMID: 32544198 PMCID: PMC7297320 DOI: 10.1371/journal.pone.0228521] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background and aims Adipose tissue plays a pivotal role in storing excess fat and its composition reflects the history of person’s lifestyle and metabolic health. Broad profiling of lipids with mass spectrometry has potential for uncovering new knowledge on the pathology of obesity, metabolic syndrome, diabetes and other related conditions. Here, we developed a lipidomic method for analyzing human subcutaneous adipose biopsies. We applied the method to four body areas to understand the differences in lipid composition between these areas. Materials and methods Adipose tissue biopsies from 10 participants were analyzed using ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. The sample preparation optimization included the optimization of the lipid extraction, the sample amount and the sample dilution factor to detect lipids in an appropriate concentration range. Lipidomic analyses were performed for adipose tissue collected from the abdomen, breast, thigh and lower back. Differences in lipid levels between tissues were visualized with heatmaps. Results Lipidomic analysis on human adipose biopsies lead to the identification of 186lipids in 2 mg of sample. Technical variation of the lipid-class specific internal standards were below 5%, thus indicating acceptable repeatability. Triacylglycerols were highly represented in the adipose tissue samples, and lipids from 13 lipid classes were identified. Long polyunsaturated triacylglycerols in higher levels in thigh (q<0.05), when compared with the abdomen, breast and lower back, indicating that the lipidome was area-specific. Conclusion The method presented here is suitable for the analysis of lipid profiles in 2 mg of adipose tissue. The amount of fat across the body is important for health but we argue that also the distribution and the particular profile of the lipidome may be relevant for metabolic outcomes. We suggest that the method presented in this paper could be useful for detecting such aberrations.
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Wang J, Lonergan ZR, Gonzalez-Gutierrez G, Nairn BL, Maxwell CN, Zhang Y, Andreini C, Karty JA, Chazin WJ, Trinidad JC, Skaar EP, Giedroc DP. Multi-metal Restriction by Calprotectin Impacts De Novo Flavin Biosynthesis in Acinetobacter baumannii. Cell Chem Biol 2019; 26:745-755.e7. [PMID: 30905682 PMCID: PMC6525019 DOI: 10.1016/j.chembiol.2019.02.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/20/2019] [Accepted: 02/18/2019] [Indexed: 02/07/2023]
Abstract
Calprotectin (CP) inhibits bacterial viability through extracellular chelation of transition metals. However, how CP influences general metabolism remains largely unexplored. We show here that CP restricts bioavailable Zn and Fe to the pathogen Acinetobacter baumannii, inducing an extensive multi-metal perturbation of cellular physiology. Proteomics reveals severe metal starvation, and a strain lacking the candidate ZnII metallochaperone ZigA possesses altered cellular abundance of multiple essential Zn-dependent enzymes and enzymes in de novo flavin biosynthesis. The ΔzigA strain exhibits decreased cellular flavin levels during metal starvation. Flavin mononucleotide provides regulation of this biosynthesis pathway, via a 3,4-dihydroxy-2-butanone 4-phosphate synthase (RibB) fusion protein, RibBX, and authentic RibB. We propose that RibBX ensures flavin sufficiency under CP-induced Fe limitation, allowing flavodoxins to substitute for Fe-ferredoxins as cell reductants. These studies elucidate adaptation to nutritional immunity and define an intersection between metallostasis and cellular metabolism in A. baumannii.
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Affiliation(s)
- Jiefei Wang
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Zachery R Lonergan
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Brittany L Nairn
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christina N Maxwell
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Yixiang Zhang
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Claudia Andreini
- Magnetic Resonance Centre (CERM), University of Florence, Florence, 50019 Sesto Fiorentino, Italy
| | - Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Walter J Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
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11
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Zhang Y, Blaby-Haas CE, Steimle S, Verissimo AF, Garcia-Angulo VA, Koch HG, Daldal F, Khalfaoui-Hassani B. Cu Transport by the Extended Family of CcoA-like Transporters (CalT) in Proteobacteria. Sci Rep 2019; 9:1208. [PMID: 30718766 PMCID: PMC6362234 DOI: 10.1038/s41598-018-37988-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/11/2018] [Indexed: 01/01/2023] Open
Abstract
Comparative genomic studies of the bacterial MFS-type copper importer CcoA, required for cbb3-type cytochrome c oxidase (cbb3-Cox) biogenesis, revealed a widespread CcoA-like transporters (CalT) family, containing the conserved CcoA Cu-binding MxxxM and HxxxM motifs. Surprisingly, this family also included the RfnT-like proteins, earlier suggested to transport riboflavin. However, presence of the Cu-binding motifs in these proteins raised the possibility that they might be Cu transporters. To test this hypothesis, the genomic context of the corresponding genes was examined, and three of such genes from Ochrobactrum anthropi, Rhodopseudomonas palustris and Agrobacterium tumefaciens were expressed in Escherichia coli (ΔribB) and Rhodobacter capsulatus (ΔccoA) mutants. Copper and riboflavin uptake abilities of these strains were compared with those expressing R. capsulatus CcoA and Rhizobium leguminosarum RibN as bona fide copper and riboflavin importers, respectively. Overall data demonstrated that the "RfnT-like" CalT proteins are unable to efficiently transport riboflavin, but they import copper like CcoA. Nevertheless, even though expressed and membrane-localized in a R. capsulatus mutant lacking CcoA, these transporters were unable to accumulate Cu or complement for cbb3-Cox defect. This lack of functional exchangeability between the different subfamilies of CalT homologs suggests that MFS-type bacterial copper importers might be species-specific.
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Affiliation(s)
- Yang Zhang
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- School of Life Science, Xiamen University, Xiamen, 361102, China
| | | | - Stefan Steimle
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andreia F Verissimo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- bioMT-Institute for Biomolecular Targeting, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Victor A Garcia-Angulo
- Microbiology and Mycology Department, Insituto de Ciencias Biomédicas, University of Chile, Santiago, Chile
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Stefan-Meier-Strasse 17, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Bahia Khalfaoui-Hassani
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- IPREM, UMR CNRS 5254, and Université de Pau et des Pays de l'Adour, BP1155, Pau, France
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12
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Sepúlveda Cisternas I, Salazar JC, García-Angulo VA. Overview on the Bacterial Iron-Riboflavin Metabolic Axis. Front Microbiol 2018; 9:1478. [PMID: 30026736 PMCID: PMC6041382 DOI: 10.3389/fmicb.2018.01478] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/13/2018] [Indexed: 01/10/2023] Open
Abstract
Redox reactions are ubiquitous in biological processes. Enzymes involved in redox metabolism often use cofactors in order to facilitate electron-transfer reactions. Common redox cofactors include micronutrients such as vitamins and metals. By far, while iron is the main metal cofactor, riboflavin is the most important organic cofactor. Notably, the metabolism of iron and riboflavin seem to be intrinsically related across life kingdoms. In bacteria, iron availability influences expression of riboflavin biosynthetic genes. There is documented evidence for riboflavin involvement in surpassing iron-restrictive conditions in some species. This is probably achieved through increase in iron bioavailability by reduction of extracellular iron, improvement of iron uptake pathways and boosting hemolytic activity. In some cases, riboflavin may also work as replacement of iron as enzyme cofactor. In addition, riboflavin is involved in dissimilatory iron reduction during extracellular respiration by some species. The main direct metabolic relationships between riboflavin and iron in bacterial physiology are reviewed here.
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Affiliation(s)
- Ignacio Sepúlveda Cisternas
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Juan C Salazar
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Víctor A García-Angulo
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
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13
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Jiménez-Munguía I, Calderón-Santiago M, Rodríguez-Franco A, Priego-Capote F, Rodríguez-Ortega MJ. Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4. PeerJ 2018; 6:e4966. [PMID: 29915696 PMCID: PMC6004102 DOI: 10.7717/peerj.4966] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/23/2018] [Indexed: 11/20/2022] Open
Abstract
We applied multi-omics approaches (transcriptomics, proteomics and metabolomics) to study the effect of iron starvation on the Gram-positive human pathogen Streptococcus pneumoniae to elucidate global changes in the bacterium in a condition similar to what can be found in the host during an infectious episode. We treated the reference strain TIGR4 with the iron chelator deferoxamine mesylate. DNA microarrays revealed changes in the expression of operons involved in multiple biological processes, with a prevalence of genes coding for ion binding proteins. We also studied the changes in protein abundance by 2-DE followed by MALDI-TOF/TOF analysis of total cell extracts and secretome fractions. The main proteomic changes were found in proteins related to the primary and amino sugar metabolism, especially in enzymes with divalent cations as cofactors. Finally, the metabolomic analysis of intracellular metabolites showed altered levels of amino sugars involved in the cell wall peptidoglycan metabolism. This work shows the utility of multi-perspective studies that can provide complementary results for the comprehension of how a given condition can influence global physiological changes in microorganisms.
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Affiliation(s)
- Irene Jiménez-Munguía
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
| | - Mónica Calderón-Santiago
- Departamento de Química Analítica, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
| | - Antonio Rodríguez-Franco
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
| | - Feliciano Priego-Capote
- Departamento de Química Analítica, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
| | - Manuel J Rodríguez-Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
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