1
|
Fagorzi C, Ilie A, Decorosi F, Cangioli L, Viti C, Mengoni A, diCenzo GC. Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping. Genome Biol Evol 2020; 12:2521-2534. [PMID: 33283865 PMCID: PMC7719227 DOI: 10.1093/gbe/evaa221] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 01/03/2023] Open
Abstract
Rhizobium–legume symbioses serve as paradigmatic examples for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “nonsymbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, the tested strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.
Collapse
Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Alexandru Ilie
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Francesca Decorosi
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Lisa Cangioli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Carlo Viti
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - George C diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.,Department of Biology, Queen's University, Kingston, Ontario, Canada
| |
Collapse
|
2
|
Gallo G, Presta L, Perrin E, Gallo M, Marchetto D, Puglia AM, Fani R, Baldi F. Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages. BMC Microbiol 2018; 18:198. [PMID: 30482178 PMCID: PMC6258164 DOI: 10.1186/s12866-018-1330-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/29/2018] [Indexed: 12/24/2022] Open
Abstract
Background Klebsiella oxytoca DSM 29614 - isolated from acid mine drainages - grows anaerobically using Fe(III)-citrate as sole carbon and energy source, unlike other enterobacteria and K. oxytoca clinical isolates. The DSM 29614 strain is multi metal resistant and produces metal nanoparticles that are embedded in its very peculiar capsular exopolysaccharide. These metal nanoparticles were effective as antimicrobial and anticancer compounds, chemical catalysts and nano-fertilizers. Results The DSM 29614 strain genome was sequenced and analysed by a combination of in silico procedures. Comparative genomics, performed between 85 K. oxytoca representatives and K. oxytoca DSM 29614, revealed that this bacterial group has an open pangenome, characterized by a very small core genome (1009 genes, about 2%), a high fraction of unique (43,808 genes, about 87%) and accessory genes (5559 genes, about 11%). Proteins belonging to COG categories “Carbohydrate transport and metabolism” (G), “Amino acid transport and metabolism” (E), “Coenzyme transport and metabolism” (H), “Inorganic ion transport and metabolism” (P), and “membrane biogenesis-related proteins” (M) are particularly abundant in the predicted proteome of DSM 29614 strain. The results of a protein functional enrichment analysis - based on a previous proteomic analysis – revealed metabolic optimization during Fe(III)-citrate anaerobic utilization. In this growth condition, the observed high levels of Fe(II) may be due to different flavin metal reductases and siderophores as inferred form genome analysis. The presence of genes responsible for the synthesis of exopolysaccharide and for the tolerance to heavy metals was highlighted too. The inferred genomic insights were confirmed by a set of phenotypic tests showing specific metabolic capability in terms of i) Fe2+ and exopolysaccharide production and ii) phosphatase activity involved in precipitation of metal ion-phosphate salts. Conclusion The K. oxytoca DSM 29614 unique capabilities of using Fe(III)-citrate as sole carbon and energy source in anaerobiosis and tolerating diverse metals coincides with the presence at the genomic level of specific genes that can support i) energy metabolism optimization, ii) cell protection by the biosynthesis of a peculiar exopolysaccharide armour entrapping metal ions and iii) general and metal-specific detoxifying activities by different proteins and metabolites. Electronic supplementary material The online version of this article (10.1186/s12866-018-1330-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Giuseppe Gallo
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Viale delle Scienze, ed. 16, 90128, Palermo, Italy.
| | - Luana Presta
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy
| | - Elena Perrin
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy
| | - Michele Gallo
- Dipartimento di Scienze Molecolari e Nanosistemi, University Cà Foscari Venezia, Via Torino 155, 30172, Mestre, Venezia, Italy
| | - Davide Marchetto
- Dipartimento di Scienze Molecolari e Nanosistemi, University Cà Foscari Venezia, Via Torino 155, 30172, Mestre, Venezia, Italy
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy
| | - Franco Baldi
- Dipartimento di Scienze Molecolari e Nanosistemi, University Cà Foscari Venezia, Via Torino 155, 30172, Mestre, Venezia, Italy
| |
Collapse
|
3
|
Perrin E, Fondi M, Bosi E, Mengoni A, Buroni S, Scoffone VC, Valvano M, Fani R. Subfunctionalization influences the expansion of bacterial multidrug antibiotic resistance. BMC Genomics 2017; 18:834. [PMID: 29084524 PMCID: PMC5663151 DOI: 10.1186/s12864-017-4222-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 10/17/2017] [Indexed: 01/09/2023] Open
Abstract
Background Antibiotic resistance is a major problem for human health. Multidrug resistance efflux pumps, especially those of the Resistance-Nodulation-Cell Division (RND) family, are major contributors to high-level antibiotic resistance in Gram-negative bacteria. Most bacterial genomes contain several copies of the different classes of multidrug resistance efflux pumps. Gene duplication and gain of function by the duplicate copies of multidrug resistance efflux pump genes plays a key role in the expansion and diversification of drug-resistance mechanisms. Results We used two members of the Burkholderia RND superfamily as models to understand how duplication events affect the antibiotic resistance of these strains. First, we analyzed the conservation and distribution of these two RND systems and their regulators across the Burkholderia genus. Through genetic manipulations, we identified both the exact substrate range of these transporters and their eventual interchangeability. We also performed a directed evolution experiment, combined with next generation sequencing, to evaluate the role of antibiotics in the activation of the expression of these systems. Together, our results indicate that the first step to diversify the functions of these pumps arises from changes in their regulation (subfunctionalization) instead of functional mutations. Further, these pumps could rewire their regulation to respond to antibiotics, thus maintaining high genomic plasticity. Conclusions Studying the regulatory network that controls the expression of the RND pumps will help understand and eventually control the development and expansion of drug resistance. Electronic supplementary material The online version of this article (10.1186/s12864-017-4222-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Emanuele Bosi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy
| | - Viola Camilla Scoffone
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy
| | - Miguel Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Rd, Belfast, BT9 7BL, UK
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy.
| |
Collapse
|
4
|
New Genome Sequence of an Echinaceapurpurea Endophyte, Arthrobacter sp. Strain EpSL27, Able To Inhibit Human-Opportunistic Pathogens. GENOME ANNOUNCEMENTS 2017. [PMID: 28642378 PMCID: PMC5481584 DOI: 10.1128/genomea.00565-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We announce here the draft genome sequence of Arthrobacter sp. strain EpSL27, isolated from the stem and leaves of the medicinal plant Echinacea purpurea and able to inhibit human-pathogenic bacterial strains. The genome sequencing of this strain may lead to the identification of genes involved in the production of antimicrobial molecules.
Collapse
|
5
|
Phenotypic and genomic characterization of the antimicrobial producer Rheinheimera sp. EpRS3 isolated from the medicinal plant Echinacea purpurea: insights into its biotechnological relevance. Res Microbiol 2016; 168:293-305. [PMID: 27884784 DOI: 10.1016/j.resmic.2016.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 12/23/2022]
Abstract
In recent years, there has been increasing interest in plant microbiota; however, despite medicinal plant relevance, very little is known about their highly complex endophytic communities. In this work, we report on the genomic and phenotypic characterization of the antimicrobial compound producer Rheinheimera sp. EpRS3, a bacterial strain isolated from the rhizospheric soil of the medicinal plant Echinacea purpurea. In particular, EpRS3 is able to inhibit growth of different bacterial pathogens (Bcc, Acinetobacter baumannii, and Klebsiella pneumoniae) which might be related to the presence of gene clusters involved in the biosynthesis of different types of secondary metabolites. The outcomes presented in this work highlight the fact that the strain possesses huge biotechnological potential; indeed, it also shows antimicrobial effects upon well-described multidrug-resistant (MDR) human pathogens, and it affects plant root elongation and morphology, mimicking indole acetic acid (IAA) action.
Collapse
|
6
|
Presta L, Fondi M, Perrin E, Maida I, Miceli E, Chiellini C, Maggini V, Bogani P, Di Pilato V, Rossolini GM, Mengoni A, Fani R. Arthrobacter sp. EpRS66 and Arthrobacter sp. EpRS71: Draft Genome Sequences from Two Bacteria Isolated from Echinacea purpurea Rhizospheric Soil. Front Microbiol 2016; 7:1417. [PMID: 27672382 PMCID: PMC5018518 DOI: 10.3389/fmicb.2016.01417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/26/2016] [Indexed: 11/15/2022] Open
Affiliation(s)
- Luana Presta
- Department of Biology, University of Florence Florence, Italy
| | - Marco Fondi
- Department of Biology, University of Florence Florence, Italy
| | - Elena Perrin
- Department of Biology, University of Florence Florence, Italy
| | - Isabel Maida
- Department of Biology, University of Florence Florence, Italy
| | | | | | | | - Patrizia Bogani
- Department of Biology, University of Florence Florence, Italy
| | - Vincenzo Di Pilato
- Department of Surgery and Translational Medicine, University of Florence Florence, Italy
| | - Gian M Rossolini
- Department of Medical Biotechnologies, University of SienaSiena, Italy; Department of Experimental and Clinical Medicine, University of FlorenceFlorence, Italy; Clinical Microbiology and Virology Unit, Careggi University HospitalFlorence, Italy; Don Carlo Gnocchi FoundationFlorence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence Florence, Italy
| | - Renato Fani
- Department of Biology, University of Florence Florence, Italy
| |
Collapse
|
7
|
Guan X, Yi Y, Huang Y, Hu Y, Li X, Wang X, Fan H, Wang G, Wang D. Revealing potential molecular targets bridging colitis and colorectal cancer based on multidimensional integration strategy. Oncotarget 2015; 6:37600-12. [PMID: 26461477 PMCID: PMC4741951 DOI: 10.18632/oncotarget.6067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 09/24/2015] [Indexed: 02/05/2023] Open
Abstract
Chronic inflammation may play a vital role in the pathogenesis of inflammation-associated tumors. However, the underlying mechanisms bridging ulcerative colitis (UC) and colorectal cancer (CRC) remain unclear. Here, we integrated multidimensional interaction resources, including gene expression profiling, protein-protein interactions (PPIs), transcriptional and post-transcriptional regulation data, and virus-host interactions, to tentatively explore potential molecular targets that functionally link UC and CRC at a systematic level. In this work, by deciphering the overlapping genes, crosstalking genes and pivotal regulators of both UC- and CRC-associated functional module pairs, we revealed a variety of genes (including FOS and DUSP1, etc.), transcription factors (including SMAD3 and ETS1, etc.) and miRNAs (including miR-155 and miR-196b, etc.) that may have the potential to complete the connections between UC and CRC. Interestingly, further analyses of the virus-host interaction network demonstrated that several virus proteins (including EBNA-LP of EBV and protein E7 of HPV) frequently inter-connected to UC- and CRC-associated module pairs with their validated targets significantly enriched in both modules of the host. Together, our results suggested that multidimensional integration strategy provides a novel approach to discover potential molecular targets that bridge the connections between UC and CRC, which could also be extensively applied to studies on other inflammation-related cancers.
Collapse
Affiliation(s)
- Xu Guan
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ying Yi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yan Huang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongfei Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Xishan Wang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huihui Fan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Guiyu Wang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| |
Collapse
|