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Bettiol A, Urban ML, Emmi G, Galora S, Argento FR, Fini E, Borghi S, Bagni G, Mattioli I, Prisco D, Fiorillo C, Becatti M. SIRT1 and thrombosis. Front Mol Biosci 2024; 10:1325002. [PMID: 38304233 PMCID: PMC10833004 DOI: 10.3389/fmolb.2023.1325002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024] Open
Abstract
Thrombosis is a major cause of morbidity and mortality worldwide, with a complex and multifactorial pathogenesis. Recent studies have shown that SIRT1, a member of the sirtuin family of NAD + -dependent deacetylases, plays a crucial role in regulating thrombosis, modulating key pathways including endothelial activation, platelet aggregation, and coagulation. Furthermore, SIRT1 displays anti-inflammatory activity both in vitro, in vivo and in clinical studies, particularly via the reduction of oxidative stress. On these bases, several studies have investigated the therapeutic potential of targeting SIRT1 for the prevention of thrombosis. This review provides a comprehensive and critical overview of the main preclinical and clinical studies and of the current understanding of the role of SIRT1 in thrombosis.
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Affiliation(s)
- Alessandra Bettiol
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Maria Letizia Urban
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Giacomo Emmi
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Silvia Galora
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze, Italy
| | - Flavia Rita Argento
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze, Italy
| | - Eleonora Fini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze, Italy
| | - Serena Borghi
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze, Italy
| | - Giacomo Bagni
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Irene Mattioli
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Domenico Prisco
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Claudia Fiorillo
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze, Italy
| | - Matteo Becatti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze, Italy
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2
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Eardly B, Meor Osman WA, Ardley J, Zandberg J, Gollagher M, van Berkum P, Elia P, Marinova D, Seshadri R, Reddy TBK, Ivanova N, Pati A, Woyke T, Kyrpides N, Loedolff M, Laird DW, Reeve W. The Genome of the Acid Soil-Adapted Strain Rhizobium favelukesii OR191 Encodes Determinants for Effective Symbiotic Interaction With Both an Inverted Repeat Lacking Clade and a Phaseoloid Legume Host. Front Microbiol 2022; 13:735911. [PMID: 35495676 PMCID: PMC9048898 DOI: 10.3389/fmicb.2022.735911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 02/10/2022] [Indexed: 11/15/2022] Open
Abstract
Although Medicago sativa forms highly effective symbioses with the comparatively acid-sensitive genus Ensifer, its introduction into acid soils appears to have selected for symbiotic interactions with acid-tolerant R. favelukesii strains. Rhizobium favelukesii has the unusual ability of being able to nodulate and fix nitrogen, albeit sub-optimally, not only with M. sativa but also with the promiscuous host Phaseolus vulgaris. Here we describe the genome of R. favelukesii OR191 and genomic features important for the symbiotic interaction with both of these hosts. The OR191 draft genome contained acid adaptation loci, including the highly acid-inducible lpiA/acvB operon and olsC, required for production of lysine- and ornithine-containing membrane lipids, respectively. The olsC gene was also present in other acid-tolerant Rhizobium strains but absent from the more acid-sensitive Ensifer microsymbionts. The OR191 symbiotic genes were in general more closely related to those found in Medicago microsymbionts. OR191 contained the nodA, nodEF, nodHPQ, and nodL genes for synthesis of polyunsaturated, sulfated and acetylated Nod factors that are important for symbiosis with Medicago, but contained a truncated nodG, which may decrease nodulation efficiency with M. sativa. OR191 contained an E. meliloti type BacA, which has been shown to specifically protect Ensifer microsymbionts from Medicago nodule-specific cysteine-rich peptides. The nitrogen fixation genes nifQWZS were present in OR191 and P. vulgaris microsymbionts but absent from E. meliloti-Medicago microsymbionts. The ability of OR191 to nodulate and fix nitrogen symbiotically with P. vulgaris indicates that this host has less stringent requirements for nodulation than M. sativa but may need rhizobial strains that possess nifQWZS for N2-fixation to occur. OR191 possessed the exo genes required for the biosynthesis of succinoglycan, which is required for the Ensifer-Medicago symbiosis. However, 1H-NMR spectra revealed that, in the conditions tested, OR191 exopolysaccharide did not contain a succinyl substituent but instead contained a 3-hydroxybutyrate moiety, which may affect its symbiotic performance with Medicago hosts. These findings provide a foundation for the genetic basis of nodulation requirements and symbiotic effectiveness with different hosts.
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Affiliation(s)
- Bertrand Eardly
- Berks College, Penn State University, Reading, PA, United States
| | - Wan Adnawani Meor Osman
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Julie Ardley
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Jaco Zandberg
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Margaret Gollagher
- Murdoch University Associate, Murdoch, WA, Australia.,Sustainability and Biosecurity, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Peter van Berkum
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD, United States
| | - Patrick Elia
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD, United States
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Rekha Seshadri
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - T B K Reddy
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Natalia Ivanova
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Amrita Pati
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Nikos Kyrpides
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Matthys Loedolff
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Damian W Laird
- Centre for Water Energy and Waste, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Wayne Reeve
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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3
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Goyal RK, Mattoo AK, Schmidt MA. Rhizobial-Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability. Front Microbiol 2021; 12:669404. [PMID: 34177848 PMCID: PMC8226219 DOI: 10.3389/fmicb.2021.669404] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Symbiotic nitrogen fixation (SNF) process makes legume crops self-sufficient in nitrogen (N) in sharp contrast to cereal crops that require an external input by N-fertilizers. Since the latter process in cereal crops results in a huge quantity of greenhouse gas emission, the legume production systems are considered efficient and important for sustainable agriculture and climate preservation. Despite benefits of SNF, and the fact that chemical N-fertilizers cause N-pollution of the ecosystems, the focus on improving SNF efficiency in legumes did not become a breeder’s priority. The size and stability of heritable effects under different environment conditions weigh significantly on any trait useful in breeding strategies. Here we review the challenges and progress made toward decoding the heritable components of SNF, which is considerably more complex than other crop allelic traits since the process involves genetic elements of both the host and the symbiotic rhizobial species. SNF-efficient rhizobial species designed based on the genetics of the host and its symbiotic partner face the test of a unique microbiome for its success and productivity. The progress made thus far in commercial legume crops with relevance to the dynamics of host–rhizobia interaction, environmental impact on rhizobial performance challenges, and what collectively determines the SNF efficiency under field conditions are also reviewed here.
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Affiliation(s)
- Ravinder K Goyal
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Maria Augusta Schmidt
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
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4
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Vandelle E, Colombo T, Regaiolo A, Maurizio V, Libardi T, Puttilli MR, Danzi D, Polverari A. Transcriptional Profiling of Three Pseudomonas syringae pv. actinidiae Biovars Reveals Different Responses to Apoplast-Like Conditions Related to Strain Virulence on the Host. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:376-396. [PMID: 33356409 DOI: 10.1094/mpmi-09-20-0248-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pseudomonas syringae pv. actinidiae is a phytopathogen that causes devastating bacterial canker in kiwifruit. Among five biovars defined by genetic, biochemical, and virulence traits, P. syringae pv. actinidiae biovar 3 (Psa3) is the most aggressive and is responsible for the most recent reported outbreaks; however, the molecular basis of its heightened virulence is unclear. Therefore, we designed the first P. syringae multistrain whole-genome microarray, encompassing biovars Psa1, Psa2, and Psa3 and the well-established model P. syringae pv. tomato, and analyzed early bacterial responses to an apoplast-like minimal medium. Transcriptomic profiling revealed i) the strong activation in Psa3 of all hypersensitive reaction and pathogenicity (hrp) and hrp conserved (hrc) cluster genes, encoding components of the type III secretion system required for bacterial pathogenicity and involved in responses to environmental signals; ii) potential repression of the hrp/hrc cluster in Psa2; and iii) activation of flagellum-dependent cell motility and chemotaxis genes in Psa1. The detailed investigation of three gene families encoding upstream regulatory proteins (histidine kinases, their cognate response regulators, and proteins with diguanylate cyclase or phosphodiesterase domains) indicated that cyclic di-GMP may be a key regulator of virulence in P. syringae pv. actinidiae biovars. The gene expression data were supported by the quantification of biofilm formation. Our findings suggest that diverse early responses to the host apoplast, even among bacteria belonging to the same pathovar, can lead to different virulence strategies and may explain the differing outcomes of infections. Based on our detailed structural analysis of hrp operons, we also propose a revision of hrp cluster organization and operon regulation in P. syringae.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Elodie Vandelle
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Teresa Colombo
- National Research Council of Italy (CNR), Institute of Molecular Biology and Pathology (IBPM) c/o Department of Biochemical Sciences "A. Rossi Fanelli", "Sapienza" University of Rome, Rome, 00185, Italy
| | - Alice Regaiolo
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Vanessa Maurizio
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Tommaso Libardi
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | | | - Davide Danzi
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
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Young JPW, Moeskjær S, Afonin A, Rahi P, Maluk M, James EK, Cavassim MIA, Rashid MHO, Aserse AA, Perry BJ, Wang ET, Velázquez E, Andronov EE, Tampakaki A, Flores Félix JD, Rivas González R, Youseif SH, Lepetit M, Boivin S, Jorrin B, Kenicer GJ, Peix Á, Hynes MF, Ramírez-Bahena MH, Gulati A, Tian CF. Defining the Rhizobium leguminosarum Species Complex. Genes (Basel) 2021; 12:111. [PMID: 33477547 PMCID: PMC7831135 DOI: 10.3390/genes12010111] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a 'natural' unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, "R. indicum" and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
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Affiliation(s)
| | - Sara Moeskjær
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Alexey Afonin
- Laboratory for Genetics of Plant-Microbe Interactions, ARRIAM, Pushkin, 196608 Saint-Petersburg, Russia;
| | - Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India;
| | - Marta Maluk
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; (M.M.); (E.K.J.)
| | - Euan K. James
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; (M.M.); (E.K.J.)
| | - Maria Izabel A. Cavassim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA;
| | - M. Harun-or Rashid
- Biotechnology Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh 2202, Bangladesh;
| | - Aregu Amsalu Aserse
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland;
| | - Benjamin J. Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad De México 11340, Mexico;
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Unidad Asociada Grupo de Interacción planta-microorganismo (Universidad de Salamanca-IRNASA-CSIC), 37007 Salamanca, Spain; (E.V.); (R.R.G.)
| | - Evgeny E. Andronov
- Department of Microbial Monitoring, ARRIAM, Pushkin, 196608 Saint-Petersburg, Russia;
| | - Anastasia Tampakaki
- Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855 Athens, Greece;
| | - José David Flores Félix
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal;
| | - Raúl Rivas González
- Departamento de Microbiología y Genética, Universidad de Salamanca, Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Unidad Asociada Grupo de Interacción planta-microorganismo (Universidad de Salamanca-IRNASA-CSIC), 37007 Salamanca, Spain; (E.V.); (R.R.G.)
| | - Sameh H. Youseif
- Department of Microbial Genetic Resources, National Gene Bank (NGB), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Marc Lepetit
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, 06903 Sophia Antipolis, France;
| | - Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR INRAE-IRD-CIRAD-UM2-SupAgro, Campus International de Baillarguet, TA-A82/J, CEDEX 05, 34398 Montpellier, France;
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK;
| | - Gregory J. Kenicer
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK;
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), 37008 Salamanca, Spain;
| | - Michael F. Hynes
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada;
| | - Martha Helena Ramírez-Bahena
- Departamento de Didáctica de las Matemáticas y de las Ciencias Experimentales. Universidad de Salamanca, 37008 Salamanca, Spain;
| | - Arvind Gulati
- Microbial Prospection, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176 061, India;
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing 100193, China;
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Cao Y, Jiang G, Li M, Fang X, Zhu D, Qiu W, Zhu J, Yu D, Xu Y, Zhong Z, Zhu J. Glutaredoxins Play an Important Role in the Redox Homeostasis and Symbiotic Capacity of Azorhizobium caulinodans ORS571. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1381-1393. [PMID: 32970520 DOI: 10.1094/mpmi-04-20-0098-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Glutaredoxin (GRX) plays an essential role in the control of the cellular redox state and related pathways in many organisms. There is limited information on GRXs from the model nitrogen (N2)-fixing bacterium Azorhizobium caulinodans. In the present work, we identified and performed functional analyses of monothiol and dithiol GRXs in A. caulinodans in the free-living state and during symbiosis with Sesbania rostrata. Our data show that monothiol GRXs may be very important for bacterial growth under normal conditions and in response to oxidative stress due to imbalance of the redox state in grx mutants of A. caulinodans. Functional redundancies were also observed within monothiol and dithiol GRXs in terms of different physiological functions. The changes in catalase activity and iron content in grx mutants were assumed to favor the maintenance of bacterial resistance against oxidants, nodulation, and N2 fixation efficiency in this bacterium. Furthermore, the monothiol GRX12 and dithiol GRX34 play a collective role in symbiotic associations between A. caulinodans and Sesbania rostrata. Our study provided systematic evidence that further investigations are required to understand the importance of glutaredoxins in A. caulinodans and other rhizobia.
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Affiliation(s)
- Yajun Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Gaofei Jiang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Postdoctoral Station of Agricultural Resources and Environment, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Mingxu Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Xingxing Fang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Dan Zhu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Wei Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Juanjuan Zhu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Daogeng Yu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Science, 571737 Danzhou, Hainan, PR China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Postdoctoral Station of Agricultural Resources and Environment, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Zengtao Zhong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Jun Zhu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
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7
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Sorlini C. Microbiology can make a great contribution to the new direction of global politics. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01609-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
Through coevolution with host cells, microorganisms have acquired mechanisms to avoid the detection by the host surveillance system and to use the cell's supplies to establish themselves. Indeed, certain pathogens have evolved proteins that imitate specific eukaryotic cell proteins, allowing them to manipulate host pathways, a phenomenon termed molecular mimicry. Bacterial "eukaryotic-like proteins" are a remarkable example of molecular mimicry. They are defined as proteins that strongly resemble eukaryotic proteins or that carry domains that are predominantly present in eukaryotes and that are generally absent from prokaryotes. The widest diversity of eukaryotic-like proteins known to date can be found in members of the bacterial genus Legionella, some of which cause a severe pneumonia in humans. The characterization of a number of these proteins shed light on their importance during infection. The subsequent identification of eukaryotic-like genes in the genomes of other amoeba-associated bacteria and bacterial symbionts suggested that eukaryotic-like proteins are a common means of bacterial evasion and communication, shaped by the continuous interactions between bacteria and their protozoan hosts. In this review, we discuss the concept of molecular mimicry using Legionella as an example and show that eukaryotic-like proteins effectively manipulate host cell pathways. The study of the function and evolution of such proteins is an exciting field of research that is leading us toward a better understanding of the complex world of bacterium-host interactions. Ultimately, this knowledge will teach us how host pathways are manipulated and how infections may possibly be tackled.
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9
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Ayuso-Calles M, García-Estévez I, Jiménez-Gómez A, Flores-Félix JD, Escribano-Bailón MT, Rivas R. Rhizobium laguerreae Improves Productivity and Phenolic Compound Content of Lettuce ( Lactuca sativa L.) under Saline Stress Conditions. Foods 2020; 9:foods9091166. [PMID: 32847018 PMCID: PMC7555320 DOI: 10.3390/foods9091166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 11/27/2022] Open
Abstract
Lettuce (Lactuca sativa L.) is a widely consumed horticultural species. Its significance lies in a high polyphenolic compound content, including phenolic acids and flavonols. In this work, we have probed the ability of Rhizobium laguerreae HUTR05 to promote lettuce growth, under in vitro and greenhouse conditions (both non-saline and saline conditions). This strain has shown several in vitro plant growth promotion mechanisms, as well as capacity to colonize lettuce seedlings roots. We have analyzed the effect of the rhizobacterium inoculation on mineral and bioactive compounds in lettuce, under greenhouse conditions, and found a rise in the content of certain phenolic acids and flavonoids, such as derivatives of caffeoyl acid and quercetin. The genome analysis of the strain has shown the presence of genes related to plant growth-promoting rhizobacteria (PGPR) mechanisms, defense from saline stress, and phenolic compound metabolism (such as naringenin-chalcone synthase or phenylalanine aminotransferase).
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Affiliation(s)
- Miguel Ayuso-Calles
- Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental de Biología, 37007 Salamanca, Spain; (M.A.-C.); (J.D.F.-F.); (R.R.)
- Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain
| | - Ignacio García-Estévez
- Grupo de Investigación en Polifenoles (GIP), Departamento de Química Analítica, Nutrición y Bromatología, Facultad de Farmacia, Universidad de Salamanca, 37007 Salamanca, Spain; (I.G.-E.); (M.T.E.-B.)
| | - Alejandro Jiménez-Gómez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental de Biología, 37007 Salamanca, Spain; (M.A.-C.); (J.D.F.-F.); (R.R.)
- Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain
- Correspondence: ; Tel.: +34-923294500 (ext. 1919)
| | - José D. Flores-Félix
- Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental de Biología, 37007 Salamanca, Spain; (M.A.-C.); (J.D.F.-F.); (R.R.)
- Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain
| | - M. Teresa Escribano-Bailón
- Grupo de Investigación en Polifenoles (GIP), Departamento de Química Analítica, Nutrición y Bromatología, Facultad de Farmacia, Universidad de Salamanca, 37007 Salamanca, Spain; (I.G.-E.); (M.T.E.-B.)
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental de Biología, 37007 Salamanca, Spain; (M.A.-C.); (J.D.F.-F.); (R.R.)
- Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain
- Associated Unit University of Salamanca CSIC (IRNASA), 37008 Salamanca, Spain
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10
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Klonowska A, Moulin L, Ardley JK, Braun F, Gollagher MM, Zandberg JD, Marinova DV, Huntemann M, Reddy TBK, Varghese NJ, Woyke T, Ivanova N, Seshadri R, Kyrpides N, Reeve WG. Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil. BMC Genomics 2020; 21:214. [PMID: 32143559 PMCID: PMC7060636 DOI: 10.1186/s12864-020-6623-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
Background Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. Results The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance. Conclusions STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
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Affiliation(s)
- Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
| | - Julie Kaye Ardley
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Florence Braun
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398, Montpellier cedex 5, France
| | | | - Jaco Daniel Zandberg
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Dora Vasileva Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, Australia
| | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, USA
| | | | | | | | - Wayne Gerald Reeve
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia.
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11
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Frank AC. Molecular host mimicry and manipulation in bacterial symbionts. FEMS Microbiol Lett 2019; 366:5342066. [PMID: 30877310 DOI: 10.1093/femsle/fnz038] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/18/2019] [Indexed: 12/17/2022] Open
Abstract
It is common among intracellular bacterial pathogens to use eukaryotic-like proteins that mimic and manipulate host cellular processes to promote colonization and intracellular survival. Eukaryotic-like proteins are bacterial proteins with domains that are rare in bacteria, and known to function in the context of a eukaryotic cell. Such proteins can originate through horizontal gene transfer from eukaryotes or, in the case of simple repeat proteins, through convergent evolution. Recent studies of microbiomes associated with several eukaryotic hosts suggest that similar molecular strategies are deployed by cooperative bacteria that interact closely with eukaryotic cells. Some mimics, like ankyrin repeats, leucine rich repeats and tetratricopeptide repeats are shared across diverse symbiotic systems ranging from amoebae to plants, and may have originated early, or evolved independently in multiple systems. Others, like plant-mimicking domains in members of the plant microbiome are likely to be more recent innovations resulting from horizontal gene transfer from the host, or from microbial eukaryotes occupying the same host. Host protein mimics have only been described in a limited set of symbiotic systems, but are likely to be more widespread. Systematic searches for eukaryote-like proteins in symbiont genomes could lead to the discovery of novel mechanisms underlying host-symbiont interactions.
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Affiliation(s)
- A Carolin Frank
- Life and Environmental Sciences, 5200 North Lake Rd, University of California Merced, Merced, CA 95343, USA.,Sierra Nevada Research Institute, School of Natural Sciences, 5200 North Lake Rd, University of California Merced, Merced, CA 95343, USA
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12
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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13
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Levy A, Conway JM, Dangl JL, Woyke T. Elucidating Bacterial Gene Functions in the Plant Microbiome. Cell Host Microbe 2018; 24:475-485. [DOI: 10.1016/j.chom.2018.09.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Cooper B, Campbell KB, Beard HS, Garrett WM, Mowery J, Bauchan GR, Elia P. A Proteomic Network for Symbiotic Nitrogen Fixation Efficiency in Bradyrhizobium elkanii. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:334-343. [PMID: 29117782 DOI: 10.1094/mpmi-10-17-0243-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rhizobia colonize legumes and reduce N2 to NH3 in root nodules. The current model is that symbiotic rhizobia bacteroids avoid assimilating this NH3. Instead, host legume cells form glutamine from NH3, and the nitrogen is returned to the bacteroid as dicarboxylates, peptides, and amino acids. In soybean cells surrounding bacteroids, glutamine also is converted to ureides. One problem for soybean cultivation is inefficiency in symbiotic N2 fixation, the biochemical basis of which is unknown. Here, the proteomes of bacteroids of Bradyrhizobium elkanii USDA76 isolated from N2 fixation-efficient Peking and -inefficient Williams 82 soybean nodules were analyzed by mass spectrometry. Nearly half of the encoded bacterial proteins were quantified. Efficient bacteroids produced greater amounts of enzymes to form Nod factors and had increased amounts of signaling proteins, transporters, and enzymes needed to generate ATP to power nitrogenase and to acquire resources. Parallel investigation of nodule proteins revealed that Peking had no significantly greater accumulation of enzymes needed to assimilate NH3 than Williams 82. Instead, efficient bacteroids had increased amounts of enzymes to produce amino acids, including glutamine, and to form ureide precursors. These results support a model for efficient symbiotic N2 fixation in soybean where the bacteroid assimilates NH3 for itself.
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Affiliation(s)
- Bret Cooper
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | - Kimberly B Campbell
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | - Hunter S Beard
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | | | - Joseph Mowery
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | - Gary R Bauchan
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | - Patrick Elia
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
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15
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Osman WAM, van Berkum P, León-Barrios M, Velázquez E, Elia P, Tian R, Ardley J, Gollagher M, Seshadri R, Reddy TBK, Ivanova N, Woyke T, Pati A, Markowitz V, Baeshen MN, Baeshen NN, Kyrpides N, Reeve W. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. Stand Genomic Sci 2017; 12:58. [PMID: 28975015 PMCID: PMC5613336 DOI: 10.1186/s40793-017-0270-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 09/14/2017] [Indexed: 11/26/2022] Open
Abstract
10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T, 10.1601/nm.1334 A 321T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata-nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.
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Affiliation(s)
| | - Peter van Berkum
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Tenerife, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genetica and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - Patrick Elia
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Amrita Pati
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Mohamed N. Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | | | | | - Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
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16
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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17
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Reeve W, van Berkum P, Ardley J, Tian R, Gollagher M, Marinova D, Elia P, Reddy TBK, Pillay M, Varghese N, Seshadri R, Ivanova N, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N. High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76 T, isolated from Glycine max (L.) Merr. Stand Genomic Sci 2017; 12:26. [PMID: 28270909 PMCID: PMC5336687 DOI: 10.1186/s40793-017-0238-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Glycine max (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, B. elkanii USDA 76T was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria sequencing project. Here the symbiotic abilities of B. elkanii USDA 76T are described, together with its genome sequence information and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2 scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only encoding genes. The B. elkanii USDA 76T genome contains a low GC content region with symbiotic nod and fix genes, indicating the presence of a symbiotic island integration. A comparison of five B. elkanii genomes that formed a clique revealed that 356 of the 9060 protein coding genes of USDA 76T were unique, including 22 genes of an intact resident prophage. A conserved set of 7556 genes were also identified for this species, including genes encoding a general secretion pathway as well as type II, III, IV and VI secretion system proteins. The type III secretion system has previously been characterized as a host determinant for Rj and/or rj soybean cultivars. Here we show that the USDA 76T genome contains genes encoding all the type III secretion system components, including a translocon complex protein NopX required for the introduction of effector proteins into host cells. While many bradyrhizobial strains are unable to nodulate the soybean cultivar Clark (rj1), USDA 76T was able to elicit nodules on Clark (rj1), although in reduced numbers, when plants were grown in Leonard jars containing sand or vermiculite. In these conditions, we postulate that the presence of NopX allows USDA 76T to introduce various effector molecules into this host to enable nodulation.
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Affiliation(s)
- Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Peter van Berkum
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Patrick Elia
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Mohamed N Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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18
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Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T. GENOME ANNOUNCEMENTS 2017; 5:5/4/e01513-16. [PMID: 28126941 PMCID: PMC5270700 DOI: 10.1128/genomea.01513-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rhizobium tibeticum was originally isolated from root nodules of Trigonella archiducis-nicolai grown in Tibet, China. This species is also able to nodulate Medicago sativa and Phaseolus vulgaris The whole-genome sequence of the type strain, R. tibeticum CCBAU85039T, is reported in this study.
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19
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Klonowska A, López-López A, Moulin L, Ardley J, Gollagher M, Marinova D, Tian R, Huntemann M, Reddy T, Varghese N, Woyke T, Markowitz V, Ivanova N, Seshadri R, Baeshen MN, Baeshen NA, Kyrpides N, Reeve W. High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia. Stand Genomic Sci 2017; 12:7. [PMID: 28116041 PMCID: PMC5240323 DOI: 10.1186/s40793-016-0212-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/26/2016] [Indexed: 11/12/2022] Open
Abstract
Rhizobium mesoamericanum STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. The 6,927,906 bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501T. Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.
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Affiliation(s)
- Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | - Aline López-López
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | | | - T.B.K. Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | - Mohamed N. Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nabih A. Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
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20
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Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, Isbandi M, Thomas AD, Ali R, Sharma K, Kyrpides NC, Reddy TBK. Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. Nucleic Acids Res 2017; 45:D446-D456. [PMID: 27794040 PMCID: PMC5210664 DOI: 10.1093/nar/gkw992] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/11/2016] [Accepted: 10/19/2016] [Indexed: 01/28/2023] Open
Abstract
The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects. These are integrated with over 312 metadata fields from which 58 are controlled vocabularies with 2067 terms. The web interface facilitates submission of a diverse range of Sequencing Projects (such as isolate genome, single-cell genome, metagenome, metatranscriptome) and complex Analysis Projects (such as genome from metagenome, or combined assembly from multiple Sequencing Projects). GOLD provides a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes the Genomic Standards Consortium (GSC) Minimum Information standards. This paper describes the data updates and additional features added during the last two years.
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Affiliation(s)
- Supratim Mukherjee
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Dimitri Stamatis
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Jon Bertsch
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Galina Ovchinnikova
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Olena Verezemska
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Michelle Isbandi
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Alex D Thomas
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Rida Ali
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Kaushal Sharma
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Nikos C Kyrpides
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - T B K Reddy
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
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21
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Tian R, Heiden S, Osman WAM, Ardley JK, James EK, Gollagher MM, Tiwari R, Seshadri R, Kyrpides NC, Reeve WG. Evolution of a multi-step phosphorelay signal transduction system in Ensifer: recruitment of the sigma factor RpoN and a novel enhancer-binding protein triggers acid-activated gene expression. Mol Microbiol 2016; 103:829-844. [PMID: 27935141 DOI: 10.1111/mmi.13592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2016] [Indexed: 11/29/2022]
Abstract
Most Ensifer strains are comparatively acid sensitive, compromising their persistence in low pH soils. In the acid-tolerant strain Ensifer medicae WSM419, the acid-activated expression of lpiA is essential for enhancing survival in lethal acidic conditions. Here we characterise a multi-step phosphorelay signal transduction pathway consisting of TcsA, TcrA, FsrR, RpoN and its cognate enhancer-binding protein EbpA, which is required for the induction of lpiA and the downstream acvB gene. The fsrR, tcrA, tcsA and rpoN genes were constitutively expressed, whereas lpiA and acvB were strongly acid-induced. RACE mapping revealed that lpiA/acvB were co-transcribed as an operon from an RpoN promoter. In most Ensifer species, lpiA/acvB is located on the chromosome and the sequence upstream of lpiA lacks an RpoN-binding site. Nearly all Ensifer meliloti strains completely lack ebpA, tcrA, tcsA and fsrR regulatory loci. In contrast, E. medicae strains have lpiA/acvB and ebpA/tcrA/tcsA/fsrR co-located on the pSymA megaplasmid, with lpiA/acvB expression coupled to an RpoN promoter. Here we provide a model for the expression of lpiA/acvB in E. medicae. This unique acid-activated regulatory system provides insights into an evolutionary process which may assist the adaptation of E. medicae to acidic environmental niches.
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Affiliation(s)
- Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Stephan Heiden
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Wan A M Osman
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Julie K Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Margaret M Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Ravi Tiwari
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | | | | | - Wayne G Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
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22
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Lyngwi NA, Nongkhlaw M, Kalita D, Joshi SR. Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach. PLoS One 2016; 11:e0152951. [PMID: 27111883 PMCID: PMC4844137 DOI: 10.1371/journal.pone.0152951] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 02/29/2016] [Indexed: 11/23/2022] Open
Abstract
Bacillus spp. and related genera native to soils of the pristine sacred groves from Meghalaya, India were characterized using biochemical and 16S rRNA gene analysis which revealed dominance of Bacillus, Paenibacillus, Lysinibacillus and Viridibacillus in the groves. Biochemical estimation was carried out for in vitro testing of plant growth promoting traits present in these isolates. PCR screening were performed for plant growth-promoting related genes involved in the biosynthesis of acid phosphatase (AcPho), indolepyruvate decarboxylase (ipdC), 1-aminocyclopropane-1-carboxylate deaminase (accd) and siderophore biosynthesis protein (asbA). 76% of the sacred grove isolates gave an amplified fragment for AcPho. Three of the isolates gave an amplified fragment for IpdC gene. Apart from 2 isolates, all the other isolates including the reference strains were positive for the amplification of the accd gene indicating their potential to produce ACC deaminase enzyme. 42% of the isolates gave an amplified fragment for asbA gene indicating the potential ability of these isolates to produce the catechol type siderophore, petrobactin. Overall findings indicated multiple PGP genetic traits present in these isolates which suggested that these isolates are capable of expressing multiple PGP traits. Phylogenetic and sequence analysis of accd and asbA genes from the isolates revealed that asbA genes from Paenibacillus taichungiensis SG3 and Paenibacillus tylopili SG24 indicated the occurrence of intergeneric horizontal transfer between Paenibacillus and Bacillus.
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Affiliation(s)
- Nathaniel A. Lyngwi
- Microbiology Laboratory, Department of Biotechnology & Bioinformatics, North - Eastern Hill University, Shillong, Meghalaya, India
| | - Macmillan Nongkhlaw
- Microbiology Laboratory, Department of Biotechnology & Bioinformatics, North - Eastern Hill University, Shillong, Meghalaya, India
| | - Debajit Kalita
- Microbiology Laboratory, Department of Biotechnology & Bioinformatics, North - Eastern Hill University, Shillong, Meghalaya, India
| | - Santa Ram Joshi
- Microbiology Laboratory, Department of Biotechnology & Bioinformatics, North - Eastern Hill University, Shillong, Meghalaya, India
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