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Castorina G, Domergue F, Chiara M, Zilio M, Persico M, Ricciardi V, Horner DS, Consonni G. Drought-Responsive ZmFDL1/MYB94 Regulates Cuticle Biosynthesis and Cuticle-Dependent Leaf Permeability. Plant Physiol 2020; 184:266-282. [PMID: 32665334 PMCID: PMC7479886 DOI: 10.1104/pp.20.00322] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/01/2020] [Indexed: 05/14/2023]
Abstract
In all land plants, the outer surface of aerial parts is covered by the cuticle, a complex lipid layer that constitutes a barrier against damage caused by environmental factors and provides protection against nonstomatal water loss. We show in this study that both cuticle deposition and cuticle-dependent leaf permeability during the juvenile phase of plant development are controlled by the maize (Zea mays) transcription factor ZmFUSED LEAVES 1 (FDL1)/MYB94. Biochemical analysis showed altered cutin and wax biosynthesis and deposition in fdl1-1 mutant seedlings at the coleoptile stage. Among cutin compounds, ω-hydroxy fatty acids and polyhydroxy-fatty acids were specifically affected, while the reduction of epicuticular waxes was mainly observed in primary long chain alcohols and, to a minor extent, in long-chain wax esters. Transcriptome analysis allowed the identification of candidate genes involved in lipid metabolism and the assembly of a proposed pathway for cuticle biosynthesis in maize. Lack of ZmFDL1/MYB94 affects the expression of genes located in different modules of the pathway, and we highlighted the correspondence between gene transcriptional variations and biochemical defects. We observed a decrease in cuticle-dependent leaf permeability in maize seedlings exposed to drought as well as abscisic acid treatment, which implies coordinated changes in the transcript levels of ZmFDL1/MYB94 and associated genes. Overall, our results suggest that the response to water stress implies the activation of wax biosynthesis and the involvement of both ZmFDL1/MYB94 and abscisic acid regulatory pathways.
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Affiliation(s)
- Giulia Castorina
- Department of Agricultural and Environmental Sciences (DiSAA), Università degli Studi di Milano, 20133 Milan, Italy
| | - Frédéric Domergue
- Laboratoire de Biogenèse Membranaire, Université de Bordeaux, UMR5200, F-33000 Bordeaux, France
- Laboratoire de Biogenèse Membranaire, Centre National de la Recherche Scientifique, UMR5200, F-33000 Bordeaux, France
| | - Matteo Chiara
- Department of Bioscience, Università degli Studi di Milano, 20133 Milan, Italy
| | - Massimo Zilio
- Department of Agricultural and Environmental Sciences (DiSAA), Università degli Studi di Milano, 20133 Milan, Italy
| | - Martina Persico
- Department of Agricultural and Environmental Sciences (DiSAA), Università degli Studi di Milano, 20133 Milan, Italy
| | - Valentina Ricciardi
- Department of Agricultural and Environmental Sciences (DiSAA), Università degli Studi di Milano, 20133 Milan, Italy
| | | | - Gabriella Consonni
- Department of Agricultural and Environmental Sciences (DiSAA), Università degli Studi di Milano, 20133 Milan, Italy
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Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). Gigascience 2019; 8:5202456. [PMID: 30496513 PMCID: PMC6324554 DOI: 10.1093/gigascience/giy142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/14/2018] [Indexed: 11/12/2022] Open
Abstract
Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica). Findings As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp. Conclusions This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
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Affiliation(s)
- Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Lucy Poveda
- Functional Genomics Center of Zurich, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | | | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California, 91768, USA
| | - Luca Canova
- Department of Biochemistry, University of Pavia, Via Taramelli 12, Pavia, 27100, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
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3
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Marzano F, Faienza MF, Caratozzolo MF, Brunetti G, Chiara M, Horner DS, Annese A, D'Erchia AM, Consiglio A, Pesole G, Sbisà E, Inzaghi E, Cianfarani S, Tullo A. Pilot study on circulating miRNA signature in children with obesity born small for gestational age and appropriate for gestational age. Pediatr Obes 2018; 13:803-811. [PMID: 30160046 DOI: 10.1111/ijpo.12439] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 02/01/2023]
Abstract
BACKGROUND Children born small for gestational age (SGA) are at increased risk of metabolic dysfunction. Dysregulation of specific microRNAs (miRNAs) contributes to aberrant gene expression patterns underlying metabolic dysfunction. OBJECTIVE We aimed to determine and compare circulating miRNA (c-miRNA) profile of SGA and appropriate for gestational age (AGA) children with obesity and with normal weight, in order to identify biomarkers for early detection of increased risk of developing metabolic dysfunction in SGA and AGA children with obesity. METHODS Small non-coding RNAs from serum of 15 SGA children with obesity (OB-SGA), 10 SGA children with normal weight (NW-SGA), 17 AGA children with obesity (OB-AGA) and 12 AGA children with normal weight (NW-AGA) (mean age 11.2 ± 2.6) have been extracted and sequenced in order to detect and quantify miRNA expression profiles. RESULTS RNA-seq analyses showed 28 miRNAs dysregulated in OB-SGA vs. NW-SGA and 19 miRNAs dysregulated in OB-AGA vs. NW-AGA. Among these, miR-92a-3p, miR-122-5p, miR-423-5p, miR-484, miR-486-3p and miR-532-5p were up regulated, and miR-181b-5p was down regulated in both OB-SGA and OB-AGA compared with normal weight counterparts. Pathway analysis and miRNA target prediction suggested that these miRNAs were particularly involved in insulin signalling, glucose transport, insulin resistance, cholesterol and lipid metabolism. CONCLUSION We identified a specific profile of c-miRNAs in SGA and AGA children with obesity compared with SGA and AGA children with normal weight. These c-miRNAs could represent specific biomarkers for early detection of increased risk of developing metabolic dysfunction in SGA and AGA children with obesity.
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Affiliation(s)
- F Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies-IBIOM, CNR, Bari, Italy
| | - M F Faienza
- Department of Biomedical Sciences and Human Oncology, Section of Pediatrics, University of Bari "A. Moro,", Bari, Italy
| | - M F Caratozzolo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies-IBIOM, CNR, Bari, Italy
| | - G Brunetti
- Department of Basic Medical Sciences, Neuroscience, and Sense Organs, Section of Human Anatomy and Histology, University of Bari "A. Moro", Bari, Italy
| | - M Chiara
- Department of Biosciences, University of Milan, Milan, Italy
| | - D S Horner
- Department of Biosciences, University of Milan, Milan, Italy
| | - A Annese
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies-IBIOM, CNR, Bari, Italy
| | - A M D'Erchia
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies-IBIOM, CNR, Bari, Italy.,Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - A Consiglio
- Institute for Biomedical Technologies of Bari - ITB, National Research Council, Bari, Italy
| | - G Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies-IBIOM, CNR, Bari, Italy
| | - E Sbisà
- Institute for Biomedical Technologies of Bari - ITB, National Research Council, Bari, Italy
| | - E Inzaghi
- Dipartimento Pediatrico Universitario Ospedaliero, "Bambino Gesu`" Children's Hospital - Tor Vergata University, Rome, Italy
| | - S Cianfarani
- Dipartimento Pediatrico Universitario Ospedaliero, "Bambino Gesu`" Children's Hospital - Tor Vergata University, Rome, Italy.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - A Tullo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies-IBIOM, CNR, Bari, Italy
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Chiara M, Gioiosa S, Chillemi G, D'Antonio M, Flati T, Picardi E, Zambelli F, Horner DS, Pesole G, Castrignanò T. CoVaCS: a consensus variant calling system. BMC Genomics 2018; 19:120. [PMID: 29402227 PMCID: PMC5800023 DOI: 10.1186/s12864-018-4508-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
Background The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome resequencing data is progressively increasing underlining the need for accurate and time-effective bioinformatics systems for genotyping - a crucial prerequisite for identification of candidate causal mutations in diagnostic screens. Results Here we present CoVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool. Importantly our system exhibits better sensitivity and higher specificity than equivalent commercial software. Conclusions CoVaCS offers optimized pipelines integrating state of the art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES) and target-gene sequencing (TGS) data. The system is currently hosted at Cineca, and offers the speed of a HPC computing facility, a crucial consideration when large numbers of samples must be analysed. Importantly, all the analyses are performed automatically allowing high reproducibility of the results. As such, we believe that CoVaCS can be a valuable tool for the analysis of human genome resequencing studies. CoVaCS is available at: https://bioinformatics.cineca.it/covacs. Electronic supplementary material The online version of this article (10.1186/s12864-018-4508-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matteo Chiara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Silvia Gioiosa
- SCAI, Cineca, Consorzio Interuniversitario di Supercalcolo, Rome, Italy.,Istituto di Biomembrane Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Giovanni Chillemi
- SCAI, Cineca, Consorzio Interuniversitario di Supercalcolo, Rome, Italy
| | - Mattia D'Antonio
- SCAI, Cineca, Consorzio Interuniversitario di Supercalcolo, Rome, Italy
| | - Tiziano Flati
- SCAI, Cineca, Consorzio Interuniversitario di Supercalcolo, Rome, Italy.,Istituto di Biomembrane Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ernesto Picardi
- Istituto di Biomembrane Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy.,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari "A. Moro", Bari, Italy
| | - Federico Zambelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | | | - Graziano Pesole
- Istituto di Biomembrane Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy. .,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari "A. Moro", Bari, Italy.
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5
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Chiara M, Placido A, Picardi E, Ceci LR, Horner DS, Pesole G. A-GAME: improving the assembly of pooled functional metagenomics sequence data. BMC Genomics 2018; 19:44. [PMID: 29329522 PMCID: PMC5767027 DOI: 10.1186/s12864-017-4369-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/08/2017] [Indexed: 02/06/2023] Open
Abstract
Background Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such “functional metagenomics” experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications. Results Here we present A-GAME (A GAlaxy suite for functional MEtagenomics), a web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. We illustrate the potential of A-GAME workflows using real functional metagenomics data, showing that they outperform alternative metagenomics assemblers. Dedicated tools available in A-GAME allow efficient analysis of pooled libraries and rapid identification of candidate genes, reducing sequencing costs and saving the need for laborious manual annotation. Conclusion In conclusion, we believe A-GAME will constitute a valuable resource for the functional metagenomics community. A-GAME is publicly available at http://beaconlab.it/agame Electronic supplementary material The online version of this article (10.1186/s12864-017-4369-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matteo Chiara
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Antonio Placido
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", via Orabona, 4, 70126, Bari, Italy
| | - Luigi Ruggiero Ceci
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy. .,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy.
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", via Orabona, 4, 70126, Bari, Italy
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6
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Volpicella M, Leoni C, Manzari C, Chiara M, Picardi E, Piancone E, Italiano F, D'Erchia A, Trotta M, Horner DS, Pesole G, Ceci LR. Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq. Sci Rep 2017; 7:8262. [PMID: 28811613 PMCID: PMC5557971 DOI: 10.1038/s41598-017-08934-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/10/2017] [Indexed: 02/06/2023] Open
Abstract
Nickel acts as cofactor for a number of enzymes of many bacteria species. Its homeostasis is ensured by proteins working as ion efflux or accumulation systems. These mechanisms are also generally adopted to counteract life-threatening high extra-cellular Ni2+ concentrations. Little is known regarding nickel tolerance in the genus Sphingobium. We studied the response of the novel Sphingobium sp. ba1 strain, able to adapt to high Ni2+ concentrations. Differential gene expression in cells cultured in 10 mM Ni2+, investigated by RNA-seq analysis, identified 118 differentially expressed genes. Among the 90 up-regulated genes, a cluster including genes coding for nickel and other metal ion efflux systems (similar to either cnrCBA, nccCBA or cznABC) and for a NreB-like permease was found. Comparative analyses among thirty genomes of Sphingobium species show that this cluster is conserved only in two cases, while in the other genomes it is partially present or even absent. The differential expression of genes encoding proteins which could also work as Ni2+-accumulators (HupE/UreJ-like protein, NreA and components of TonB-associated transport and copper-homeostasis systems) was also detected. The identification of Sphingobium sp. ba1 strain adaptive mechanisms to nickel ions, can foster its possible use for biodegradation of poly-aromatic compounds in metal-rich environments.
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Affiliation(s)
- M Volpicella
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - C Leoni
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - C Manzari
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - M Chiara
- Department of Biosciences, University of Milan, Milan, Italy
| | - E Picardi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - E Piancone
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - F Italiano
- IPCF-CNR, Institute for Chemical-Physical Processes, Bari, Italy
| | - A D'Erchia
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - M Trotta
- IPCF-CNR, Institute for Chemical-Physical Processes, Bari, Italy
| | - D S Horner
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy.,Department of Biosciences, University of Milan, Milan, Italy
| | - G Pesole
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - L R Ceci
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy.
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Oliva M, Monno R, D'Addabbo P, Pesole G, Dionisi AM, Scrascia M, Chiara M, Horner DS, Manzari C, Luzzi I, Calia C, D'Erchia AM, Pazzani C. A novel group of IncQ1 plasmids conferring multidrug resistance. Plasmid 2016; 89:22-26. [PMID: 27916622 DOI: 10.1016/j.plasmid.2016.11.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 11/28/2022]
Abstract
The IncQ is a group of non-conjugative but mobilisable plasmids that are found and stably maintained in a wide range of bacteria contributing to the spread of antimicrobial resistance genes and to the insurgence of multidrug resistant bacteria. Here we report the identification, in clinical Salmonella Typhimurium strains, of an IncQ1 plasmid (pNUC) which confers resistance to sulfamethoxazole, streptomycin and tetracycline through the presence of sul2, strAB and tetA genes, respectively. pNUC was detected in five multidrug resistant S. Typhimurium strains collected in Southern Italy from various hospitals and years of isolation. Bioinformatics analyses highlighted the presence of pNUC-like plasmids in pathogenic bacteria of various Enterobacteriaceae genera or species. Taken as a whole, these plasmids constitute a novel group of IncQ1 plasmids that might have originated through recombination events between a tetR-tetA gene cluster (possibly derived from a Tn1721) and a recipient IncQ1 plasmid related to RSF1010. Our findings raise concerns regarding the possible contribution of the newly identified group of IncQ1 plasmids to the spread of tetracycline resistance.
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Affiliation(s)
- M Oliva
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - R Monno
- Department of Basic Medical Sciences Neurosciences and Sense Organs Medical Faculty, University of Bari Piazza G. Cesare Policlinico, 70124 Bari, Italy
| | - P D'Addabbo
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - G Pesole
- Institute of Biomembranes and Bioenergetics, National Research Council, via Amendola 165A, 70125 Bari, Italy; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - A M Dionisi
- Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome 00161, Italy
| | - M Scrascia
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - M Chiara
- Department of Biosciences, University of Milano, via Celoria 26, 20131 Milano, Italy
| | - D S Horner
- Department of Biosciences, University of Milano, via Celoria 26, 20131 Milano, Italy
| | - C Manzari
- Institute of Biomembranes and Bioenergetics, National Research Council, via Amendola 165A, 70125 Bari, Italy
| | - I Luzzi
- Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome 00161, Italy
| | - C Calia
- Department of Basic Medical Sciences Neurosciences and Sense Organs Medical Faculty, University of Bari Piazza G. Cesare Policlinico, 70124 Bari, Italy
| | - A M D'Erchia
- Institute of Biomembranes and Bioenergetics, National Research Council, via Amendola 165A, 70125 Bari, Italy; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - C Pazzani
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy.
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Ariani A, Di Baccio D, Romeo S, Lombardi L, Andreucci A, Lux A, Horner DS, Sebastiani L. RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc. PLoS One 2015; 10:e0117571. [PMID: 25671786 PMCID: PMC4324836 DOI: 10.1371/journal.pone.0117571] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/28/2014] [Indexed: 11/19/2022] Open
Abstract
Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE) genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated) and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO) terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1) probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS) that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees.
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Affiliation(s)
- Andrea Ariani
- BioLabs-Institute of Life Sciences, Scuola Superiore Sant'Anna, I-56127 Pisa, Italy
| | - Daniela Di Baccio
- BioLabs-Institute of Life Sciences, Scuola Superiore Sant'Anna, I-56127 Pisa, Italy
| | - Stefania Romeo
- BioLabs-Institute of Life Sciences, Scuola Superiore Sant'Anna, I-56127 Pisa, Italy
| | - Lara Lombardi
- Department of Biology, Università degli Studi di Pisa, I-56126 Pisa, Italy
| | - Andrea Andreucci
- Department of Biology, Università degli Studi di Pisa, I-56126 Pisa, Italy
| | - Alexander Lux
- Department of Plant Physiology, Faculty of Natural Science, Comenius University in Bratislava, Bratislava, Slovakia
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Luca Sebastiani
- BioLabs-Institute of Life Sciences, Scuola Superiore Sant'Anna, I-56127 Pisa, Italy
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Bertolini E, Verelst W, Horner DS, Gianfranceschi L, Piccolo V, Inzé D, Pè ME, Mica E. Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon. Mol Plant 2013; 6:423-43. [PMID: 23264558 PMCID: PMC3603004 DOI: 10.1093/mp/sss160] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/15/2012] [Indexed: 05/04/2023]
Abstract
Plant responses to drought are regulated by complex genetic and epigenetic networks leading to rapid reprogramming of plant growth. miRNAs have been widely indicated as key players in the regulation of growth and development. The role of miRNAs in drought response was investigated in young leaves of Brachypodium distachyon, a drought-tolerant monocot model species. Adopting an in vivo drought assay, shown to cause a dramatic reduction in leaf size, mostly due to reduced cell expansion, small RNA libraries were produced from proliferating and expanding leaf cells. Next-generation sequencing data were analyzed using an in-house bioinformatics pipeline allowing the identification of 66 annotated miRNA genes and 122 new high confidence predictions greatly expanding the number of known Brachypodium miRNAs. In addition, we identified four TAS3 loci and a large number of siRNA-producing loci that show characteristics suggesting that they may represent young miRNA genes. Most miRNAs showed a high expression level, consistent with their involvement in early leaf development and cell identity. Proliferating and expanding leaf cells respond differently to drought treatment and differential expression analyses suggest novel evidence for an miRNA regulatory network controlling cell division in both normal and stressed conditions and demonstrate that drought triggers a genetic reprogramming of leaf growth in which miRNAs are deeply involved.
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Affiliation(s)
- Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Wim Verelst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - David Stephen Horner
- Department of BioSciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Luca Gianfranceschi
- Department of BioSciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Viviana Piccolo
- Department of BioSciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Erica Mica
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
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Abstract
MOTIVATION Maximum likelihood-based methods to estimate site by site substitution rate variability in aligned homologous protein sequences rely on the formulation of a phylogenetic tree and generally assume that the patterns of relative variability follow a pre-determined distribution. We present a phylogenetic tree-independent method to estimate the relative variability of individual sites within large datasets of homologous protein sequences. It is based upon two simple assumptions. Firstly that substitutions observed between two closely related sequences are likely, in general, to occur at the most variable sites. Secondly that non-conservative amino acid substitutions tend to occur at more variable sites. Our methodology makes no assumptions regarding the underlying pattern of relative variability between sites. RESULTS We have compared, using data simulated under a non-gamma distributed model, the performance of this approach to that of a maximum likelihood method that assumes gamma distributed rates. At low mean rates of evolution our method inferred site by site relative substitution rates more accurately than the maximum likelihood approach in the absence of prior assumptions about the relationships between sequences. Our method does not directly account for the effects of mutational saturation, However, we have incorporated an 'ad-hoc' modification that allows the accurate estimation of relative site variability in fast evolving and saturated datasets.
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Affiliation(s)
- D S Horner
- Dipartimento di Fisiologia e Biochimica Generale, Universita di Milano, 20113 Milano, Italy
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Henze K, Horner DS, Suguri S, Moore DV, Sánchez LB, Müller M, Embley TM. Unique phylogenetic relationships of glucokinase and glucosephosphate isomerase of the amitochondriate eukaryotes Giardia intestinalis, Spironucleus barkhanus and Trichomonas vaginalis. Gene 2001; 281:123-31. [PMID: 11750134 DOI: 10.1016/s0378-1119(01)00773-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Glucokinase (GK) and glucosephosphate isomerase (GPI), the first two enzymes of the glycolytic pathway of the diplomonads Giardia intestinalis and Spironucleus barkhanus, Type I amitochondriate eukaryotes, were sequenced. GPI of the parabasalid Trichomonas vaginalis was also sequenced. The diplomonad GKs belong to a family of specific GKs present in cyanobacteria, in some proteobacteria and also in T. vaginalis, a Type II amitochondriate protist. These enzymes are not part of the hexokinase family, which is broadly distributed among eukaryotes, including the Type I amitochondriate parasite Entamoeba histolytica. G. intestinalis GK expressed in Escherichia coli was specific for glucose and glucosamine, as are its eubacterial homologs. The sequence of diplomonad and trichomonad GPIs formed a monophyletic group more closely related to cyanobacterial and chloroplast sequences than to cytosolic GPIs of other eukaryotes and prokaryotes. The findings show that certain enzymes of the energy metabolism of these amitochondriate protists originated from sources different than those of other eukaryotes. The observation that the two diplomonads and T. vaginalis share the same unusual GK and GPI is consistent with gene trees that suggest a close relationship between diplomonads and parabasalids. The intriguing relationships of these enzymes to cyanobacterial (and chloroplast) enzymes might reflect horizontal gene transfer between the common ancestor of the diplomonad and parabasalid lineages and the ancestor of cyanobacteria.
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Affiliation(s)
- K Henze
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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Horner DS, Embley TM. Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes. Mol Biol Evol 2001; 18:1970-5. [PMID: 11557802 DOI: 10.1093/oxfordjournals.molbev.a003737] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
Hydrogenases, oxygen-sensitive enzymes that can make hydrogen gas, are key to the function of hydrogen-producing organelles (hydrogenosomes), which occur in anaerobic protozoa scattered throughout the eukaryotic tree. Hydrogenases also play a central role in the hydrogen and syntrophic hypotheses for eukaryogenesis. Here, we show that sequences related to iron-only hydrogenases ([Fe] hydrogenases) are more widely distributed among eukaryotes than reports of hydrogen production have suggested. Genes encoding small proteins which contain conserved structural features unique to [Fe] hydrogenases were identified on all well-surveyed aerobic eukaryote genomes. Longer sequences encoding [Fe] hydrogenases also occur in the anaerobic eukaryotes Entamoeba histolytica and Spironucleus barkhanus, both of which lack hydrogenosomes. We also identified a new [Fe] hydrogenase sequence from Trichomonas vaginalis, bringing the total of [Fe] hydrogenases reported for this organism to three, all of which may function within its hydrogenosomes. Phylogenetic analysis and hypothesis testing using likelihood ratio tests and parametric bootstrapping suggest that the [Fe] hydrogenases in anaerobic eukaryotes are not monophyletic. Iron-only hydrogenases from Entamoeba, Spironucleus, and Trichomonas are plausibly monophyletic, consistent with the hypothesis that a gene for [Fe] hydrogenase was already present on the genome of the common, perhaps also anaerobic, ancestor of these phylogenetically distinct eukaryotes. Trees where the [Fe] hydrogenase from the hydrogenosomal ciliate Nyctotherus was constrained to be monophyletic with the other eukaryote sequences were rejected using a likelihood ratio test of monophyly. In most analyses, the Nyctotherus sequence formed a sister group with a [Fe] hydrogenase on the genome of the eubacterium Desulfovibrio vulgaris. Thus, it is possible that Nyctotherus obtained its hydrogenosomal [Fe] hydrogenase from a different source from Trichomonas for its hydrogenosomes. We find no support for the hypothesis that components of the Nyctotherus [Fe] hydrogenase fusion protein derive from the mitochondrial respiratory chain.
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Affiliation(s)
- D S Horner
- Department of Zoology, Natural History Museum, London, England
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Horner DS, Hirt RP, Embley TM. A single eubacterial origin of eukaryotic pyruvate: ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes. Mol Biol Evol 1999; 16:1280-91. [PMID: 10486982 DOI: 10.1093/oxfordjournals.molbev.a026218] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The iron sulfur protein pyruvate: ferredoxin oxidoreductase (PFO) is central to energy metabolism in amitochondriate eukaryotes, including those with hydrogenosomes. Thus, revealing the evolutionary history of PFO is critical to understanding the origin(s) of eukaryote anaerobic energy metabolism. We determined a complete PFO sequence for Spironucleus barkhanus, a large fragment of a PFO sequence from Clostridium pasteurianum, and a fragment of a new PFO from Giardia lamblia. Phylogenetic analyses of eubacterial and eukaryotic PFO genes suggest a complex history for PFO, including possible gene duplications and horizontal transfers among eubacteria. Our analyses favor a common origin for eukaryotic cytosolic and hydrogenosomal PFOs from a single eubacterial source, rather than from separate horizontal transfers as previously suggested. However, with the present sampling of genes and species, we were unable to infer a specific eubacterial sister group for eukaryotic PFO. Thus, we find no direct support for the published hypothesis that the donor of eukaryote PFO was the common alpha-proteobacterial ancestor of mitochondria and hydrogenosomes. We also report that several fungi and protists encode proteins with PFO domains that are likely monophyletic with PFOs from anaerobic protists. In Saccharomyces cerevisiae, PFO domains combine with fragments of other redox proteins to form fusion proteins which participate in methionine biosynthesis. Our results are consistent with the view that PFO, an enzyme previously considered to be specific to energy metabolism in amitochondriate protists, was present in the common ancestor of contemporary eukaryotes and was retained, wholly or in part, during the evolution of oxygen-dependent and mitochondrion-bearing lineages.
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Affiliation(s)
- D S Horner
- Department of Zoology, Natural History Museum, London, England
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Abstract
The three deepest branching eucaryotic lineages in small subunit ribosomal RNA phylogenies are the amitochondriate Microspora, Metamonada and Parabasala. They are followed by either the Euglenozoa (e.g. Euglena and Trypanosoma) or the Percolozoa as the first mitochondria-containing eucaryotes. To investigate the hypothesis of an even earlier timing of the mitochondrion endosymbiosis we have amplified a partial cpn-60 coding region from the parabasalid Trichomonas vaginalis and the first such sequence from a percolozoan, Naegleria fowleri. Analysis of predicted protein sequences reveals a high degree of sequence similarity (> or = 40%) with a selection of published bacterial and mitochondrial cpn-60s for both taxa. Both sequences were recovered within a strongly supported monophyletic group, otherwise defined by mitochondrial sequences, which systematically clustered with alpha-proteobacteria. These results provide compelling evidence that the ancestor of T. vaginalis once contained the endosymbiont which gave rise to mitochondria, and suggest that this symbiosis probably occurred before the Trichomonas lineage diverged from the main eukaryote trunk. It also makes feasible the published hypothesis that the Trichomonas hydrogenosome might represent a biochemically modified mitochondrion. Analysis of the N. fowleri cpn-60 did not support the hypothesis that the mitochondrion-containing Percolozoa represent an earlier branch in the cpn-60 tree than Trichomonas or Trypanosoma.
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Affiliation(s)
- D S Horner
- Department of Zoology, Natural History Museum, London, U.K
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Kaufman RH, Henzl MR, Brown D, Horner DS, Krauss RH, Mehlisch DR, Moore DE, Prentice RL. Comparison of three-day butoconazole treatment with seven-day miconazole treatment for vulvovaginal candidiasis. J Reprod Med 1989; 34:479-83. [PMID: 2671362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In this multicenter, parallel, randomized, investigator-blind trial, we compared the safety and efficacy of a three-day regimen of 2% butoconazole vaginal cream with those of a seven-day regimen of 2% miconazole vaginal cream. Enrolled were 271 nonpregnant women with vulvovaginal candidiasis. Each patient administered her assigned study medication to the posterior vaginal fornix for three or seven consecutive nights. All 271 patients were included in the safety evaluation, and 225 (111 receiving butoconazole and 114 receiving miconazole) were included in the efficacy evaluation. Eight to ten days after treatment completion, 88% of the butoconazole-treated patients and 91% of the miconazole-treated patients were Candida negative; 80% of the butoconazole-treated patients and 82% of the miconazole-treated patients were considered clinically cured. Thirty days after treatment completion, 73% of the butoconazole-treated patients and 69% of the miconazole-treated patients remained Candida negative; 78% of the butoconazole-treated patients and 80% of the miconazole-treated patients remained free of clinical symptoms of vulvovaginitis. None of the differences between the two treatment groups was statistically significant. Six patients (four receiving butoconazole and two receiving miconazole) reported increased symptoms of vulvovaginal irritation, and three of them (two receiving butoconazole and one receiving miconazole) withdrew from the trial. Thus, the efficacy and safety of the three-day butoconazole treatment regimen were equivalent to those of the seven-day miconazole treatment regimen. The advantage of the shorter butoconazole treatment is increased patient compliance with maintenance of high efficacy.
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Affiliation(s)
- R H Kaufman
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas 77025
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