1
|
Kucho KI, Asukai K, Nguyen TV. NAD + Synthetase is Required for Free-living and Symbiotic Nitrogen Fixation in the Actinobacterium Frankia casuarinae. Microbes Environ 2023; 38. [PMID: 36858533 PMCID: PMC10037102 DOI: 10.1264/jsme2.me22093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Frankia spp. are multicellular actinobacteria that fix atmospheric dinitrogen (N2) not only in the free-living state, but also in root-nodule symbioses with more than 200 plant species, called actinorhizal plants. To identify novel Frankia genes involved in N2 fixation, we previously isolated mutants of Frankia casuarinae that cannot fix N2. One of these genes, mutant N3H4, did not induce nodulation when inoculated into the host plant Casuarina glauca. Cell lineages that regained the ability to fix N2 as free-living cells were isolated from the mutant cell population. These restored strains also regained the ability to stimulate nodulation. A comparative ana-lysis of the genomes of mutant N3H4 and restored strains revealed that the mutant carried a mutation (Thr584Ile) in the glutamine-dependent NAD+ synthetase gene (Francci3_3146), while restored strains carried an additional suppressor mutation (Asp478Asn) in the same gene. Under nitrogen-depleted conditions, the concentration of NAD(H) was markedly lower in the mutant strain than in the wild type, whereas it was higher in restored strains. These results indicate that glutamine-dependent NAD+ synthetase plays critical roles in both free-living and symbiotic N2 fixation in Frankia.
Collapse
Affiliation(s)
- Ken-Ichi Kucho
- Graduate School of Science and Engineering, Kagoshima University
| | - Koya Asukai
- Graduate School of Science and Engineering, Kagoshima University
| | - Thanh Van Nguyen
- Graduate School of Science and Engineering, Kagoshima University
| |
Collapse
|
2
|
Gifford I, Vance S, Nguyen G, Berry AM. A Stable Genetic Transformation System and Implications of the Type IV Restriction System in the Nitrogen-Fixing Plant Endosymbiont Frankia alni ACN14a. Front Microbiol 2019; 10:2230. [PMID: 31608043 PMCID: PMC6769113 DOI: 10.3389/fmicb.2019.02230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 09/11/2019] [Indexed: 12/26/2022] Open
Abstract
Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes that are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. The corresponding endosymbionts, Frankia and the rhizobia, however, are distantly related groups of bacteria, leading to questions about their symbiotic mechanisms and evolutionary history. To date, a stable system of electrotransformation has been lacking in Frankia despite numerous attempts by research groups worldwide. We have identified type IV methyl-directed restriction systems, highly-expressed in a range of actinobacteria, as a likely barrier to Frankia transformation. Here we report the successful electrotransformation of the model strain F. alni ACN14a with an unmethylated, broad host-range replicating plasmid, expressing chloramphenicol-resistance for selection and GFP as a marker of gene expression. This system circumvented the type IV restriction barrier and allowed the stable maintenance of the plasmid. During nitrogen limitation, Frankia differentiates into two cell types: the vegetative hyphae and nitrogen-fixing vesicles. When the expression of egfp under the control of the nif gene cluster promoter was localized using fluorescence imaging, the expression of nitrogen fixation in nitrogen-limited culture was localized in Frankia vesicles but not in hyphae. The ability to separate gene expression patterns between Frankia hyphae and vesicles will enable deeper comparisons of molecular signaling and metabolic exchange between Frankia-actinorhizal and rhizobia-legume symbioses to be made, and may broaden potential applications in agriculture. Further downstream applications are possible, including gene knock-outs and complementation, to open up a range of experiments in Frankia and its symbioses. Additionally, in the transcriptome of F. alni ACN14a, type IV restriction enzymes were highly expressed in nitrogen-replete culture but their expression strongly decreased during symbiosis. The down-regulation of type IV restriction enzymes in symbiosis suggests that horizontal gene transfer may occur more frequently inside the nodule, with possible new implications for the evolution of Frankia.
Collapse
Affiliation(s)
- Isaac Gifford
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | | | | | | |
Collapse
|
3
|
Evolution and Functional Analysis of orf1 Within nif Gene Cluster from Paenibacillus graminis RSA19. Int J Mol Sci 2019; 20:ijms20051145. [PMID: 30845717 PMCID: PMC6429469 DOI: 10.3390/ijms20051145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
Paenibacillus is a genus of Gram-positive, facultative anaerobic and endospore-forming bacteria. Genomic sequence analysis has revealed that a compact nif (nitrogen fixation) gene cluster comprising 9–10 genes nifBHDKENX(orf1)hesAnifV is conserved in diazotrophic Paenibacillus species. The evolution and function of the orf1 gene within the nif gene cluster of Paenibacillus species is unknown. In this study, a careful comparison analysis of the compositions of the nif gene clusters from various diazotrophs revealed that orf1 located downstream of nifENX was identified in anaerobic Clostridium ultunense, the facultative anaerobic Paenibacillus species and aerobic diazotrophs (e.g., Azotobacter vinelandii and Azospirillum brasilense). The predicted amino acid sequences encoded by the orf1 gene, part of the nif gene cluster nifBHDKENXorf1hesAnifV in Paenibacillus graminis RSA19, showed 60–90% identity with those of the orf1 genes located downstream of nifENX from different diazotrophic Paenibacillus species, but shared no significant identity with those of the orf1 genes from different taxa of diazotrophic organisms. Transcriptional analysis showed that the orf1 gene was expressed under nitrogen fixation conditions from the promoter located upstream from nifB. Mutational analysis suggested that the orf1 gene functions in nitrogen fixation in the presence of a high concentration of O2.
Collapse
|
4
|
Bickhart D, Weimer P. Symposium review: Host–rumen microbe interactions may be leveraged to improve the productivity of dairy cows. J Dairy Sci 2018; 101:7680-7689. [DOI: 10.3168/jds.2017-13328] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/31/2017] [Indexed: 11/19/2022]
|
5
|
Ktari A, Gueddou A, Nouioui I, Miotello G, Sarkar I, Ghodhbane-Gtari F, Sen A, Armengaud J, Gtari M. Host Plant Compatibility Shapes the Proteogenome of Frankia coriariae. Front Microbiol 2017; 8:720. [PMID: 28512450 PMCID: PMC5411423 DOI: 10.3389/fmicb.2017.00720] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/06/2017] [Indexed: 01/24/2023] Open
Abstract
Molecular signaling networks in the actinorhizal rhizosphere select host-compatible Frankia strains, trigger the infection process and eventually the genesis of nitrogen-fixing nodules. The molecular triggers involved remain difficult to ascertain. Root exudates (RE) are highly dynamic substrates that play key roles in establishing the rhizosphere microbiome. RE are known to induce the secretion by rhizobia of Nod factors, polysaccharides, and other proteins in the case of legume symbiosis. Next-generation proteomic approach was here used to decipher the key bacterial signals matching the first-step recognition of host plant stimuli upon treatment of Frankia coriariae strain BMG5.1 with RE derived from compatible (Coriaria myrtifolia), incompatible (Alnus glutinosa), and non-actinorhizal (Cucumis melo) host plants. The Frankia proteome dynamics were mainly driven by host compatibility. Both metabolism and signal transduction were the dominant activities for BMG5.1 under the different RE conditions tested. A second set of proteins that were solely induced by C. myrtifolia RE and were mainly linked to cell wall remodeling, signal transduction and host signal processing activities. These proteins may footprint early steps in receptive recognition of host stimuli before subsequent events of symbiotic recruitment.
Collapse
Affiliation(s)
- Amir Ktari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| | - Abdellatif Gueddou
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| | - Imen Nouioui
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| | - Guylaine Miotello
- CEA, DRF, Joliot, Lab Innovative Technologies for Detection and DiagnosticBagnols-sur-Cèze, France
| | - Indrani Sarkar
- Department of Botany, NBU Bioinformatics Facility, University of North BengalSiliguri, India
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| | - Arnab Sen
- Department of Botany, NBU Bioinformatics Facility, University of North BengalSiliguri, India
| | - Jean Armengaud
- CEA, DRF, Joliot, Lab Innovative Technologies for Detection and DiagnosticBagnols-sur-Cèze, France
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| |
Collapse
|
6
|
Furnholm T, Rehan M, Wishart J, Tisa LS. Pb2+ tolerance by Frankia sp. strain EAN1pec involves surface-binding. MICROBIOLOGY-SGM 2017; 163:472-487. [PMID: 28141503 DOI: 10.1099/mic.0.000439] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several Frankia strains have been shown to be lead-resistant. The mechanism of lead resistance was investigated for Frankia sp. strain EAN1pec. Analysis of the cultures by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDAX) and Fourier transforming infrared spectroscopy (FTIR) demonstrated that Frankia sp. strain EAN1pec undergoes surface modifications and binds high quantities of Pb+2. Both labelled and unlabelled shotgun proteomics approaches were used to determine changes in Frankia sp. strain EAN1pec protein expression in response to lead and zinc. Pb2+ specifically induced changes in exopolysaccharides, the stringent response, and the phosphate (pho) regulon. Two metal transporters (a Cu2+-ATPase and cation diffusion facilitator), as well as several hypothetical transporters, were also upregulated and may be involved in metal export. The exported Pb2+ may be precipitated at the cell surface by an upregulated polyphosphate kinase, undecaprenyl diphosphate synthase and inorganic diphosphatase. A variety of metal chaperones for ensuring correct cofactor placement were also upregulated with both Pb+2 and Zn+2 stress. Thus, this Pb+2 resistance mechanism is similar to other characterized systems. The cumulative interplay of these many mechanisms may explain the extraordinary resilience of Frankia sp. strain EAN1pec to Pb+2. A potential transcription factor (DUF156) binding site was identified in association with several proteins identified as upregulated with heavy metals. This site was also discovered, for the first time, in thousands of other organisms across two kingdoms.
Collapse
Affiliation(s)
- Teal Furnholm
- Department of Cellular, Molecular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Medhat Rehan
- Department of Cellular, Molecular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Department of Genetics, College of Agriculture, Kafrelsheikh University, Egypt.,Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Saudi Arabia
| | - Jessica Wishart
- Department of Cellular, Molecular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Louis S Tisa
- Department of Cellular, Molecular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| |
Collapse
|
7
|
An update on research on Frankia and actinorhizal plants on the occasion of the 18th meeting of the Frankia-actinorhizal plants symbiosis. Symbiosis 2016. [DOI: 10.1007/s13199-016-0431-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
8
|
Froussart E, Bonneau J, Franche C, Bogusz D. Recent advances in actinorhizal symbiosis signaling. PLANT MOLECULAR BIOLOGY 2016; 90:613-622. [PMID: 26873697 DOI: 10.1007/s11103-016-0450-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
Nitrogen and phosphorus availability are frequent limiting factors in plant growth and development. Certain bacteria and fungi form root endosymbiotic relationships with plants enabling them to exploit atmospheric nitrogen and soil phosphorus. The relationships between bacteria and plants include nitrogen-fixing Gram-negative proteobacteria called rhizobia that are able to interact with most leguminous plants (Fabaceae) but also with the non-legume Parasponia (Cannabaceae), and actinobacteria Frankia, which are able to interact with about 260 species collectively called actinorhizal plants. Fungi involved in the relationship with plants include Glomeromycota that form an arbuscular mycorrhizal (AM) association intracellularly within the roots of more than 80% of land plants. Increasing numbers of reports suggest that the rhizobial association with legumes has recycled part of the ancestral program used by most plants to interact with AM fungi. This review focuses on the most recent progress made in plant genetic control of root nodulation that occurs in non-legume actinorhizal plant species.
Collapse
Affiliation(s)
- Emilie Froussart
- Equipe Rhizogenèse, UMR DIADE (IRD-UM), Institut de Recherche pour le Développement (IRD), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| | - Jocelyne Bonneau
- Equipe Rhizogenèse, UMR DIADE (IRD-UM), Institut de Recherche pour le Développement (IRD), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| | - Claudine Franche
- Equipe Rhizogenèse, UMR DIADE (IRD-UM), Institut de Recherche pour le Développement (IRD), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France.
| | - Didier Bogusz
- Equipe Rhizogenèse, UMR DIADE (IRD-UM), Institut de Recherche pour le Développement (IRD), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| |
Collapse
|
9
|
Dall'Agnol HPMB, Baraúna RA, de Sá PHCG, Ramos RTJ, Nóbrega F, Nunes CIP, das Graças DA, Carneiro AR, Santos DM, Pimenta AMC, Carepo MSP, Azevedo V, Pellizari VH, Schneider MPC, Silva A. Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation. BMC Genomics 2014; 15:986. [PMID: 25407400 PMCID: PMC4247613 DOI: 10.1186/1471-2164-15-986] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 10/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Exiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica. Although this bacteria has been poorly studied, its genome has already been sequenced. Therefore, it is an appropriate model for the study of thermal adaptation. In the present study, we analyzed the transcriptomes and proteomes of E. antarcticum B7 grown at 0°C and 37°C by SOLiD RNA-Seq, Ion Torrent RNA-Seq and two-dimensional difference gel electrophoresis tandem mass spectrometry (2D-DIGE-MS/MS). RESULTS We found expression of 2,058 transcripts in all replicates from both platforms and differential expression of 564 genes (absolute log2FC≥1, P-value<0.001) comparing the two temperatures by RNA-Seq. A total of 73 spots were differentially expressed between the two temperatures on 2D-DIGE, 25 of which were identified by MS/MS. Some proteins exhibited patterns of dispersion in the gel that are characteristic of post-translational modifications. CONCLUSIONS Our findings suggest that the two sequencing platforms yielded similar results and that different omic approaches may be used to improve the understanding of gene expression. To adapt to low temperatures, E. antarcticum B7 expresses four of the six cold-shock proteins present in its genome. The cold-shock proteins were the most abundant in the bacterial proteome at 0°C. Some of the differentially expressed genes are required to preserve transcription and translation, while others encode proteins that contribute to the maintenance of the intracellular environment and appropriate protein folding. The results denote the complexity intrinsic to the adaptation of psychrotrophic organisms to cold environments and are based on two omic approaches. They also unveil the lifestyle of a bacterial species isolated in Antarctica.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Artur Silva
- Laboratório de Polimorfismo de DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brasil.
| |
Collapse
|
10
|
Ghodhbane-Gtari F, Hezbri K, Ktari A, Sbissi I, Beauchemin N, Gtari M, Tisa LS. Contrasted reactivity to oxygen tensions in Frankia sp. strain CcI3 throughout nitrogen fixation and assimilation. BIOMED RESEARCH INTERNATIONAL 2014; 2014:568549. [PMID: 24987692 PMCID: PMC4058466 DOI: 10.1155/2014/568549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 04/28/2014] [Accepted: 05/15/2014] [Indexed: 11/18/2022]
Abstract
Reconciling the irreconcilable is a primary struggle in aerobic nitrogen-fixing bacteria. Although nitrogenase is oxygen and reactive oxygen species-labile, oxygen tension is required to sustain respiration. In the nitrogen-fixing Frankia, various strategies have been developed through evolution to control the respiration and nitrogen-fixation balance. Here, we assessed the effect of different oxygen tensions on Frankia sp. strain CcI3 growth, vesicle production, and gene expression under different oxygen tensions. Both biomass and vesicle production were correlated with elevated oxygen levels under both nitrogen-replete and nitrogen-deficient conditions. The mRNA levels for the nitrogenase structural genes (nifHDK) were high under hypoxic and hyperoxic conditions compared to oxic conditions. The mRNA level for the hopanoid biosynthesis genes (sqhC and hpnC) was also elevated under hyperoxic conditions suggesting an increase in the vesicle envelope. Under nitrogen-deficient conditions, the hup2 mRNA levels increased with hyperoxic environment, while hup1 mRNA levels remained relatively constant. Taken together, these results indicate that Frankia protects nitrogenase by the use of multiple mechanisms including the vesicle-hopanoid barrier and increased respiratory protection.
Collapse
Affiliation(s)
- Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) and Université Carthage (INSAT), Campus Universitaire, 2092 Tunis, Tunisia
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
| | - Karima Hezbri
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) and Université Carthage (INSAT), Campus Universitaire, 2092 Tunis, Tunisia
| | - Amir Ktari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) and Université Carthage (INSAT), Campus Universitaire, 2092 Tunis, Tunisia
| | - Imed Sbissi
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) and Université Carthage (INSAT), Campus Universitaire, 2092 Tunis, Tunisia
| | - Nicholas Beauchemin
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) and Université Carthage (INSAT), Campus Universitaire, 2092 Tunis, Tunisia
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
| | - Louis S. Tisa
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
| |
Collapse
|
11
|
Lindenstrauss AG, Ehrmann MA, Behr J, Landstorfer R, Haller D, Sartor RB, Vogel RF. Transcriptome analysis of Enterococcus faecalis toward its adaption to surviving in the mouse intestinal tract. Arch Microbiol 2014; 196:423-33. [PMID: 24700373 DOI: 10.1007/s00203-014-0982-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/27/2014] [Accepted: 03/24/2014] [Indexed: 12/15/2022]
Abstract
We have performed a transcriptomic in vivo study with Enterococcus faecalis OG1RF in the intestine of living mice to identify novel latent and adaptive fitness determinants within E. faecalis. From 2,658 genes that are present in E. faecalis strain OG1RF, 124 genes were identified as significantly differentially expressed within the intestinal tract of living mice as compared to exponential growth in BHI broth. The groups of significantly up- or down-regulated genes consisted of 94 and 30 genes, respectively, for which 46 and 18 a clear annotation to a functionally described protein was found. These included genes involved in energy metabolism (e.g., dhaK and glpK pathway), transport and binding mechanisms (e.g., phosphoenolpyruvate carbohydrate PTS) as well as fatty acid metabolism (fab genes). The novel putative fitness determinants found in this work may be helpful for future studies of E. faecalis adaptation to the intestinal tract, which is also a prerequisite for infection in a compromised or inflamed host.
Collapse
Affiliation(s)
- Angela G Lindenstrauss
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350, Freising, Germany
| | | | | | | | | | | | | |
Collapse
|
12
|
Tisa LS, Beauchemin N, Gtari M, Sen A, Wall LG. What stories can the Frankia genomes start to tell us? J Biosci 2013; 38:719-26. [DOI: 10.1007/s12038-013-9364-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
13
|
Alteration of the exopolysaccharide production and the transcriptional profile of free-living Frankia strain CcI3 under nitrogen-fixing conditions. Appl Microbiol Biotechnol 2013; 97:10499-509. [PMID: 24097014 DOI: 10.1007/s00253-013-5277-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
Abstract
We investigated the effect of different nitrogen (N) sources on exopolysaccharide (EPS) production and composition by Frankia strain CcI3, a N2-fixing actinomycete that forms root nodules with Casuarina species. Frankia cells grown in the absence of NH4Cl (i.e., under N2-fixing conditions) produced 1.7-fold more EPS, with lower galactose (45.1 vs. 54.7 mol%) and higher mannose (17.3 vs. 9.7 mol%) contents than those grown in the presence of NH4Cl as a combined N-source. In the absence of the combined N-source, terminally linked and branched residue contents were nearly twice as high with 32.8 vs. 15.1 mol% and 15.1 vs. 8.7 mol%, respectively, than in its presence, while the content of linearly linked residues was lower with 52.1 mol% compared to 76.2 mol%. To find out clues for the altered EPS production at the transcriptional level, we performed whole-gene expression profiling using quantitative reverse transcription PCR and microarray technology. The transcription profiles of Frankia strain CcI3 grown in the absence of NH4Cl revealed up to 2 orders of magnitude higher transcription of nitrogen fixation-related genes compared to those of CcI3 cells grown in the presence of NH4Cl. Unexpectedly, microarray data did not provide evidence for transcriptional regulation as a mechanism for differences in EPS production. These findings indicate effects of nitrogen fixation on the production and composition of EPS in Frankia strain CcI3 and suggest posttranscriptional regulation of enhanced EPS production in the absence of the combined N-source.
Collapse
|
14
|
Abstract
Transposases, enzymes that catalyze the movement of mobile genetic elements, are the most abundant genes in nature. While many bacteria encode an abundance of transposases in their genomes, the current paradigm is that the expression of transposase genes is tightly regulated and generally low due to its severe mutagenic effects. In the current study, we detected the highest number of transposase proteins ever reported in bacteria, in symbionts of the gutless marine worm Olavius algarvensis with metaproteomics. At least 26 different transposases from 12 different families were detected, and genomic and proteomic analyses suggest that many of these are active. This high expression of transposases indicates that the mechanisms for their tight regulation have been disabled or no longer exist.
Collapse
|
15
|
Santi C, Bogusz D, Franche C. Biological nitrogen fixation in non-legume plants. ANNALS OF BOTANY 2013; 111:743-67. [PMID: 23478942 PMCID: PMC3631332 DOI: 10.1093/aob/mct048] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 01/23/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrogen is an essential nutrient in plant growth. The ability of a plant to supply all or part of its requirements from biological nitrogen fixation (BNF) thanks to interactions with endosymbiotic, associative and endophytic symbionts, confers a great competitive advantage over non-nitrogen-fixing plants. SCOPE Because BNF in legumes is well documented, this review focuses on BNF in non-legume plants. Despite the phylogenic and ecological diversity among diazotrophic bacteria and their hosts, tightly regulated communication is always necessary between the microorganisms and the host plant to achieve a successful interaction. Ongoing research efforts to improve knowledge of the molecular mechanisms underlying these original relationships and some common strategies leading to a successful relationship between the nitrogen-fixing microorganisms and their hosts are presented. CONCLUSIONS Understanding the molecular mechanism of BNF outside the legume-rhizobium symbiosis could have important agronomic implications and enable the use of N-fertilizers to be reduced or even avoided. Indeed, in the short term, improved understanding could lead to more sustainable exploitation of the biodiversity of nitrogen-fixing organisms and, in the longer term, to the transfer of endosymbiotic nitrogen-fixation capacities to major non-legume crops.
Collapse
Affiliation(s)
- Carole Santi
- Université de Perpignan, Via Domitia, Avenue Paul Alduy, 66100 Perpignan, France
| | - Didier Bogusz
- Equipe Rhizogenèse, UMR DIADE (IRD/UM2), Institut de Recherche pour le Développement, 911 Avenue Agropolis, BP64501, 34394 Montpellier Cedex 5, France
| | - Claudine Franche
- Equipe Rhizogenèse, UMR DIADE (IRD/UM2), Institut de Recherche pour le Développement, 911 Avenue Agropolis, BP64501, 34394 Montpellier Cedex 5, France
| |
Collapse
|
16
|
Benson DR, Brooks JM, Huang Y, Bickhart DM, Mastronunzio JE. The biology of Frankia sp. strains in the post-genome era. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1310-1316. [PMID: 21848398 DOI: 10.1094/mpmi-06-11-0150] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Progress in understanding symbiotic determinants involved in the N(2)-fixing actinorhizal plant symbioses has been slow but steady. Problems persist with studying the bacterial contributions to the symbiosis using traditional microbiological techniques. However, recent years have seen the emergence of several genomes from Frankia sp. strains and the development of techniques for manipulating plant gene expression. Approaches to understanding the bacterial side of the symbiosis have employed a range of techniques that reveal the proteomes and transcriptomes from both cultured and symbiotic frankiae. The picture beginning to emerge provides some perspective on the heterogeneity of frankial populations in both conditions. In general, frankial populations in root nodules seem to maintain a rather robust metabolism that includes nitrogen fixation and substantial biosynthesis and energy-generating pathways, along with a modified ammonium assimilation program. To date, particular bacterial genes have not been implicated in root nodule formation but some hypotheses are emerging with regard to how the plant and microorganism manage to coexist. In particular, frankiae seem to present a nonpathogenic presence to the plant that may have the effect of minimizing some plant defense responses. Future studies using high-throughput approaches will likely clarify the range of bacterial responses to symbiosis that will need to be understood in light of the more rapidly advancing work on the plant host.
Collapse
Affiliation(s)
- David R Benson
- Department of Molecular and Cell Biology, University of Connecticut, Stors, CT, USA.
| | | | | | | | | |
Collapse
|