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Ni H, Hou X, Tian S, Liu C, Zhang G, Peng Y, Chen L, Wang J, Chen Q, Xin D. Insights into the Early Steps of the Symbiotic Interaction between Soybean ( Glycine max) and Sinorhizobium fredii Symbiosis Using Transcriptome, Small RNA, and Degradome Sequencing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17084-17098. [PMID: 39013023 PMCID: PMC11299180 DOI: 10.1021/acs.jafc.4c02312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/18/2024]
Abstract
Symbiotic nitrogen fixation carried out by the soybean-rhizobia symbiosis increases soybean yield and reduces the amount of nitrogen fertilizer that has been applied. MicroRNAs (miRNAs) are crucial in plant growth and development, prompting an investigation into their role in the symbiotic interaction of soybean with partner rhizobia. Through integrated small RNA, transcriptome, and degradome sequencing analysis, 1215 known miRNAs, 314 of them conserved, and 187 novel miRNAs were identified, with 44 differentially expressed miRNAs in soybean roots inoculated with Sinorhizobium fredii HH103 and a ttsI mutant. The study unveiled that the known miRNA gma-MIR398a-p5 was downregulated in the presence of the ttsI mutation, while the target gene of gma-MIR398a-p5, Glyma.06G007500, associated with nitrogen metabolism, was upregulated. The results of this study offer insights for breeding high-efficiency nitrogen-fixing soybean varieties, enhancing crop yield and quality.
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Affiliation(s)
| | | | - Siyi Tian
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Chunyan Liu
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Guoqing Zhang
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Yang Peng
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Lin Chen
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Jinhui Wang
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Qingshan Chen
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Dawei Xin
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
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Karačić S, Palmer B, Gee CT, Bierbaum G. Oxygen-dependent biofilm dynamics in leaf decay: an in vitro analysis. Sci Rep 2024; 14:6728. [PMID: 38509138 PMCID: PMC10955112 DOI: 10.1038/s41598-024-57223-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
Biofilms are important in the natural process of plant tissue degradation. However, fundamental knowledge of biofilm community structure and succession on decaying leaves under different oxygen conditions is limited. Here, we used 16S rRNA and ITS gene amplicon sequencing to investigate the composition, temporal dynamics, and community assembly processes of bacterial and fungal biofilms on decaying leaves in vitro. Leaves harvested from three plant species were immersed in lake water under aerobic and anaerobic conditions in vitro for three weeks. Biofilm-covered leaf samples were collected weekly and investigated by scanning electron microscopy. The results showed that community composition differed significantly between biofilm samples under aerobic and anaerobic conditions, though not among plant species. Over three weeks, a clear compositional shift of the bacterial and fungal biofilm communities was observed. The alpha diversity of prokaryotes increased over time in aerobic assays and decreased under anaerobic conditions. Oxygen availability and incubation time were found to be primary factors influencing the microbial diversity of biofilms on different decaying plant species in vitro. Null models suggest that stochastic processes governed the assembly of biofilm communities of decaying leaves in vitro in the early stages of biofilm formation and were further shaped by niche-associated factors.
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Affiliation(s)
- Sabina Karačić
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
| | - Brianne Palmer
- Bonn Institute of Organismic Biology, Division of Paleontology, University of Bonn, 53115, Bonn, Germany
| | - Carole T Gee
- Bonn Institute of Organismic Biology, Division of Paleontology, University of Bonn, 53115, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
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Nazaret F, Alloing G, Mandon K, Frendo P. MarR Family Transcriptional Regulators and Their Roles in Plant-Interacting Bacteria. Microorganisms 2023; 11:1936. [PMID: 37630496 PMCID: PMC10458429 DOI: 10.3390/microorganisms11081936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
The relationship between plants and associated soil microorganisms plays a major role in ecosystem functioning. Plant-bacteria interactions involve complex signaling pathways regulating various processes required by bacteria to adapt to their fluctuating environment. The establishment and maintenance of these interactions rely on the ability of the bacteria to sense and respond to biotic and abiotic environmental signals. In this context, MarR family transcriptional regulators can use these signals for transcriptional regulation, which is required to establish adapted responses. MarR-like transcriptional regulators are essential for the regulation of the specialized functions involved in plant-bacteria interactions in response to a wide range of molecules associated with the plant host. The conversion of environmental signals into changes in bacterial physiology and behavior allows the bacteria to colonize the plant and ensure a successful interaction. This review focuses on the mechanisms of plant-signal perception by MarR-like regulators, namely how they (i) allow bacteria to cope with the rhizosphere and plant endosphere, (ii) regulate the beneficial functions of Plant-Growth-Promoting Bacteria and (iii) regulate the virulence of phytopathogenic bacteria.
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Affiliation(s)
| | | | | | - Pierre Frendo
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (F.N.); (G.A.); (K.M.)
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Albicoro FJ, Vacca C, Cafiero JH, Draghi WO, Martini MC, Goulian M, Lagares A, Del Papa MF. Comparative Proteomic Analysis Revealing ActJ-Regulated Proteins in Sinorhizobium meliloti. J Proteome Res 2023; 22:1682-1694. [PMID: 37017314 PMCID: PMC10834056 DOI: 10.1021/acs.jproteome.2c00731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
To adapt to different environmental conditions, Sinorhizobium meliloti relies on finely tuned regulatory networks, most of which are unexplored to date. We recently demonstrated that deletion of the two-component system ActJK renders an acid-vulnerable phenotype in S. meliloti and negatively impacts bacteroid development and nodule occupancy as well. To fully understand the role of ActJ in acid tolerance, S. meliloti wild-type and S. meliloti ΔactJ proteomes were compared in the presence or absence of acid stress by nanoflow ultrahigh-performance liquid chromatography coupled to mass spectrometry. The analysis demonstrated that proteins involved in the synthesis of exopolysaccharides (EPSs) were notably enriched in ΔactJ cells in acid pH. Total EPS quantification further revealed that although EPS production was augmented at pH 5.6 in both the ΔactJ and the parental strain, the lack of ActJ significantly enhanced this difference. Moreover, several efflux pumps were found to be downregulated in the ΔactJ strain. Promoter fusion assays suggested that ActJ positively modulated its own expression in an acid medium but not at under neutral conditions. The results presented here identify several ActJ-regulated genes in S. meliloti, highlighting key components associated with ActJK regulation that will contribute to a better understanding of rhizobia adaptation to acid stress.
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Affiliation(s)
- Francisco Javier Albicoro
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Carolina Vacca
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juan Hilario Cafiero
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Walter Omar Draghi
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Carla Martini
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA. USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA. USA
| | - Antonio Lagares
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Florencia Del Papa
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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Chen WF, Meng XF, Jiao YS, Tian CF, Sui XH, Jiao J, Wang ET, Ma SJ. Bacteroid Development, Transcriptome, and Symbiotic Nitrogen-Fixing Comparison of Bradyrhizobium arachidis in Nodules of Peanut (Arachis hypogaea) and Medicinal Legume Sophora flavescens. Microbiol Spectr 2023; 11:e0107922. [PMID: 36656008 PMCID: PMC9927569 DOI: 10.1128/spectrum.01079-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/29/2022] [Indexed: 01/20/2023] Open
Abstract
Bradyrhizobium arachidis strain CCBAU 051107 could differentiate into swollen and nonswollen bacteroids in determinate root nodules of peanut (Arachis hypogaea) and indeterminate nodules of Sophora flavescens, respectively, with different N2 fixation efficiencies. To reveal the mechanism of bacteroid differentiation and symbiosis efficiency in association with different hosts, morphologies, transcriptomes, and nitrogen fixation efficiencies of the root nodules induced by strain CCBAU 051107 on these two plants were compared. Our results indicated that the nitrogenase activity of peanut nodules was 3 times higher than that of S. flavescens nodules, demonstrating the effects of rhizobium-host interaction on symbiotic effectiveness. With transcriptome comparisons, genes involved in biological nitrogen fixation (BNF) and energy metabolism were upregulated, while those involved in DNA replication, bacterial chemotaxis, and flagellar assembly were significantly downregulated in both types of bacteroids compared with those in free-living cells. However, expression levels of genes involved in BNF, the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, hydrogenase synthesis, poly-β-hydroxybutyrate (PHB) degradation, and peptidoglycan biosynthesis were significantly greater in the swollen bacteroids of peanut than those in the nonswollen bacteroids of S. flavescens, while contrasting situations were found in expression of genes involved in urea degradation, PHB synthesis, and nitrogen assimilation. Especially higher expression of ureABEF and aspB genes in bacteroids of S. flavescens might imply that the BNF product and nitrogen transport pathway were different from those in peanut. Our study revealed the first differences in bacteroid differentiation and metabolism of these two hosts and will be helpful for us to explore higher-efficiency symbiosis between rhizobia and legumes. IMPORTANCE Rhizobial differentiation into bacteroids in leguminous nodules attracts scientists to investigate its different aspects. The development of bacteroids in the nodule of the important oil crop peanut was first investigated and compared to the status in the nodule of the extremely promiscuous medicinal legume Sophora flavescens by using just a single rhizobial strain of Bradyrhizobium arachidis, CCBAU 051107. This strain differentiates into swollen bacteroids in peanut nodules and nonswollen bacteroids in S. flavescens nodules. The N2-fixing efficiency of the peanut nodules is three times higher than that of S. flavescens. By comparing the transcriptomes of their bacteroids, we found that they have similar gene expression spectra, such as nitrogen fixation and motivity, but different spectra in terms of urease activity and peptidoglycan biosynthesis. Those altered levels of gene expression might be related to their functions and differentiation in respective nodules. Our studies provided novel insight into the rhizobial differentiation and metabolic alteration in different hosts.
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Affiliation(s)
- Wen Feng Chen
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Xiang Fei Meng
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Yin Shan Jiao
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, México
| | - Sheng Jun Ma
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
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Legumes Regulate Symbiosis with Rhizobia via Their Innate Immune System. Int J Mol Sci 2023; 24:ijms24032800. [PMID: 36769110 PMCID: PMC9917363 DOI: 10.3390/ijms24032800] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Plant roots are constantly exposed to a diverse microbiota of pathogens and mutualistic partners. The host's immune system is an essential component for its survival, enabling it to monitor nearby microbes for potential threats and respond with a defence response when required. Current research suggests that the plant immune system has also been employed in the legume-rhizobia symbiosis as a means of monitoring different rhizobia strains and that successful rhizobia have evolved to overcome this system to infect the roots and initiate nodulation. With clear implications for host-specificity, the immune system has the potential to be an important target for engineering versatile crops for effective nodulation in the field. However, current knowledge of the interacting components governing this pathway is limited, and further research is required to build on what is currently known to improve our understanding. This review provides a general overview of the plant immune system's role in nodulation. With a focus on the cycles of microbe-associated molecular pattern-triggered immunity (MTI) and effector-triggered immunity (ETI), we highlight key molecular players and recent findings while addressing the current knowledge gaps in this area.
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Non-Ionic Osmotic Stress Induces the Biosynthesis of Nodulation Factors and Affects Other Symbiotic Traits in Sinorhizobium fredii HH103. BIOLOGY 2023; 12:biology12020148. [PMID: 36829427 PMCID: PMC9952627 DOI: 10.3390/biology12020148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023]
Abstract
(1) Background: Some rhizobia, such as Rhizobium tropici CIAT 899, activate nodulation genes when grown under osmotic stress. This work aims to determine whether this phenomenon also takes place in Sinorhizobium fredii HH103. (2) Methods: HH103 was grown with and without 400 mM mannitol. β-galactosidase assays, nodulation factor extraction, purification and identification by mass spectrometry, transcriptomics by RNA sequencing, motility assays, analysis of acyl-homoserine lactones, and indole acetic acid quantification were performed. (3) Results: Non-ionic osmotic stress induced the production of nodulation factors. Forty-two different factors were detected, compared to 14 found in the absence of mannitol. Transcriptomics indicated that hundreds of genes were either activated or repressed upon non-ionic osmotic stress. The presence of 400 mM mannitol induced the production of indole acetic acid and acyl homoserine lactones, abolished swimming, and promoted surface motility. (4) Conclusions: In this work, we show that non-ionic stress in S. fredii HH103, caused by growth in the presence of 400 mM mannitol, provokes notable changes not only in gene expression but also in various bacterial traits, including the production of nodulation factors and other symbiotic signals.
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Liu Y, Lin Y, Guan N, Song Y, Li Y, Xie X. A Lipopolysaccharide Synthesis Gene rfaD from Mesorhizobium huakuii Is Involved in Nodule Development and Symbiotic Nitrogen Fixation. Microorganisms 2022; 11:microorganisms11010059. [PMID: 36677351 PMCID: PMC9866225 DOI: 10.3390/microorganisms11010059] [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: 11/28/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Rhizobium lipopolysaccharide (LPS) is an important component of the cell wall of gram-negative bacteria and serves as a signal molecule on the surface of rhizobia, participating in the symbiosis during rhizobia-legume interaction. In this study, we constructed a deletion mutant of ADP-L-glycerol-D-mannoheptosyl-6-exoisomerase (rfaD) of Mesorhizobium huakuii 7653R and a functional complementary strain. The results showed that the deletion of rfaD did not affect the free-living growth rate of 7653R, but that it did affect the LPS synthesis and that it increased sensitivity to abiotic stresses. The rfaD promoter-GUS reporter assay showed that the gene was mainly expressed in the infection zone of the mature nodules. The root nodules formation of the rfaD mutant was delayed during symbiosis with the host plant of Astragalus sinicus. The symbiotic phenotype analyses showed that the nodules of A. sinicus lost symbiotic nitrogen fixation ability, when inoculated with the rfaD mutant strain. In conclusion, our results reveal that the 7653R rfaD gene plays a crucial role in the LPS synthesis involved in the symbiotic interaction between rhizobia and A. sinicus. This study also provides new insights into the molecular mechanisms by which the rhizobia regulate their own gene expression and cell wall components enabling nodulation in legumes.
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Affiliation(s)
- Yuan Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ye Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ning Guan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuting Song
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (Y.L.); (X.X.); Tel.: +86-127-8728-1685 (Y.L.); +86-159-1855-2425 (X.X.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (X.X.); Tel.: +86-127-8728-1685 (Y.L.); +86-159-1855-2425 (X.X.)
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Ratu STN, Amelia L, Okazaki S. Type III effector provides a novel symbiotic pathway in legume-rhizobia symbiosis. Biosci Biotechnol Biochem 2022; 87:28-37. [PMID: 36367542 DOI: 10.1093/bbb/zbac178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022]
Abstract
Rhizobia form nodules on the roots of legumes and fix atmospheric nitrogen into ammonia, thus supplying it to host legumes. In return, plants supply photosynthetic products to maintain rhizobial activities. In most cases, rhizobial Nod factors (NFs) and their leguminous receptors (NFRs) are essential for the establishment of symbiosis. However, recent studies have discovered a novel symbiotic pathway in which rhizobia utilize the type III effectors (T3Es) similar to the pathogenic bacteria to induce nodulation. The T3Es of rhizobia are thought to be evolved from the pathogen, but they have a unique structure distinct from the pathogen, suggesting that it might be customized for symbiotic purposes. This review will focus on the recent findings from the study of rhizobial T3Es, discussing their features on a symbiont and pathogen, and the future perspectives on the role of rhizobial T3Es in symbiosis control technology.
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Affiliation(s)
- Safirah Tasa Nerves Ratu
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Lidia Amelia
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Shin Okazaki
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan.,Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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Ghantasala S, Roy Choudhury S. Nod factor perception: an integrative view of molecular communication during legume symbiosis. PLANT MOLECULAR BIOLOGY 2022; 110:485-509. [PMID: 36040570 DOI: 10.1007/s11103-022-01307-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Compatible interaction between rhizobial Nod factors and host receptors enables initial recognition and signaling events during legume-rhizobia symbiosis. Molecular communication is a new paradigm of information relay, which uses chemical signals or molecules as dialogues for communication and has been witnessed in prokaryotes, plants as well as in animal kingdom. Understanding this fascinating relay of signals between plants and rhizobia during the establishment of a synergistic relationship for biological nitrogen fixation represents one of the hotspots in plant biology research. Predominantly, their interaction is initiated by flavonoids exuding from plant roots, which provokes changes in the expression profile of rhizobial genes. Compatible interactions promote the secretion of Nod factors (NFs) from rhizobia, which are recognised by cognate host receptors. Perception of NFs by host receptors initiates the symbiosis and ultimately leads to the accommodation of rhizobia within root nodules via a series of mutual exchange of signals. This review elucidates the bacterial and plant perspectives during the early stages of symbiosis, explicitly emphasizing the significance of NFs and their cognate NF receptors.
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Affiliation(s)
- Swathi Ghantasala
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India
| | - Swarup Roy Choudhury
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India.
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Sun C. A rhizobial non-coding RNA has an effect on symbiotic nodulation by regulating an ABC transporter. Biochem Biophys Res Commun 2022; 603:82-87. [DOI: 10.1016/j.bbrc.2022.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/03/2022] [Indexed: 11/02/2022]
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12
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Szewczuk-Karpisz K, Bajda T, Tomczyk A, Kuśmierz M, Komaniecka I. Immobilization mechanism of Cd2+/HCrO4-/CrO42- ions and carboxin on montmorillonite modified with Rhizobium leguminosarum bv. trifolii exopolysaccharide. JOURNAL OF HAZARDOUS MATERIALS 2022; 428:128228. [PMID: 35033916 DOI: 10.1016/j.jhazmat.2022.128228] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/27/2021] [Accepted: 01/04/2022] [Indexed: 05/26/2023]
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Identification of an Exopolysaccharide Biosynthesis Gene in Bradyrhizobium diazoefficiens USDA110. Microorganisms 2021; 9:microorganisms9122490. [PMID: 34946092 PMCID: PMC8707904 DOI: 10.3390/microorganisms9122490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/27/2023] Open
Abstract
Exopolysaccharides (EPS) play critical roles in rhizobium-plant interactions. However, the EPS biosynthesis pathway in Bradyrhizobium diazoefficiens USDA110 remains elusive. Here we used transposon (Tn) mutagenesis with the aim to identify genetic elements required for EPS biosynthesis in B. diazoefficiens USDA110. Phenotypic screening of Tn5 insertion mutants grown on agar plates led to the identification of a mutant with a transposon insertion site in the blr2358 gene. This gene is predicted to encode a phosphor-glycosyltransferase that transfers a phosphosugar onto a polyprenol phosphate substrate. The disruption of the blr2358 gene resulted in defective EPS synthesis. Accordingly, the blr2358 mutant showed a reduced capacity to induce nodules and stimulate the growth of soybean plants. Glycosyltransferase genes related to blr2358 were found to be well conserved and widely distributed among strains of the Bradyrhizobium genus. In conclusion, our study resulted in identification of a gene involved in EPS biosynthesis and highlights the importance of EPS in the symbiotic interaction between USDA110 and soybeans.
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Rodríguez-Esperón MC, Eastman G, Sandes L, Garabato F, Eastman I, Iriarte A, Fabiano E, Sotelo-Silveira JR, Platero R. Genomics and transcriptomics insights into luteolin effects on the beta-rhizobial strain Cupriavidus necator UYPR2.512. Environ Microbiol 2021; 24:240-264. [PMID: 34811861 DOI: 10.1111/1462-2920.15845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022]
Abstract
Cupriavidus necator UYPR2.512 is a rhizobial strain that belongs to the Beta-subclass of proteobacteria, able to establish successful symbiosis with Mimosoid legumes. The initial steps of rhizobium-legumes symbioses involve the reciprocal recognition by chemical signals, being luteolin one of the molecules involved. However, there is a lack of information on the effect of luteolin in beta-rhizobia. In this work, we used long-read sequencing to complete the genome of UYPR2.512 providing evidence for the existence of four closed circular replicons. We used an RNA-Seq approach to analyse the response of UYPR2.512 to luteolin. One hundred and forty-five genes were differentially expressed, with similar numbers of downregulated and upregulated genes. Most repressed genes were mapped to the main chromosome, while the upregulated genes were overrepresented among pCne512e, containing the symbiotic genes. Induced genes included the nod operon and genes implicated in exopolysaccharides and flagellar biosynthesis. We identified many genes involved in iron, copper and other heavy metals metabolism. Among repressed genes, we identified genes involved in basal carbon and nitrogen metabolism. Our results suggest that in response to luteolin, C. necator strain UYPR2.512 reshapes its metabolism in order to be prepared for the forthcoming symbiotic interaction.
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Affiliation(s)
- M C Rodríguez-Esperón
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - G Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - L Sandes
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - F Garabato
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - I Eastman
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Montevideo, Uruguay
| | - E Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - J R Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - R Platero
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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15
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Mendoza-Suárez M, Andersen SU, Poole PS, Sánchez-Cañizares C. Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:690567. [PMID: 34489993 PMCID: PMC8416774 DOI: 10.3389/fpls.2021.690567] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.
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Affiliation(s)
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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16
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Krol E, Schäper S, Becker A. Cyclic di-GMP signaling controlling the free-living lifestyle of alpha-proteobacterial rhizobia. Biol Chem 2021; 401:1335-1348. [PMID: 32990642 DOI: 10.1515/hsz-2020-0232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger which has been associated with a motile to sessile lifestyle switch in many bacteria. Here, we review recent insights into c-di-GMP regulated processes related to environmental adaptations in alphaproteobacterial rhizobia, which are diazotrophic bacteria capable of fixing nitrogen in symbiosis with their leguminous host plants. The review centers on Sinorhizobium meliloti, which in the recent years was intensively studied for its c-di-GMP regulatory network.
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Affiliation(s)
- Elizaveta Krol
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Simon Schäper
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
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17
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Acosta-Jurado S, Fuentes-Romero F, Ruiz-Sainz JE, Janczarek M, Vinardell JM. Rhizobial Exopolysaccharides: Genetic Regulation of Their Synthesis and Relevance in Symbiosis with Legumes. Int J Mol Sci 2021; 22:6233. [PMID: 34207734 PMCID: PMC8227245 DOI: 10.3390/ijms22126233] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/03/2021] [Accepted: 06/06/2021] [Indexed: 12/11/2022] Open
Abstract
Rhizobia are soil proteobacteria able to engage in a nitrogen-fixing symbiotic interaction with legumes that involves the rhizobial infection of roots and the bacterial invasion of new organs formed by the plant in response to the presence of appropriate bacterial partners. This interaction relies on a complex molecular dialogue between both symbionts. Bacterial N-acetyl-glucosamine oligomers called Nod factors are indispensable in most cases for early steps of the symbiotic interaction. In addition, different rhizobial surface polysaccharides, such as exopolysaccharides (EPS), may also be symbiotically relevant. EPS are acidic polysaccharides located out of the cell with little or no cell association that carry out important roles both in free-life and in symbiosis. EPS production is very complexly modulated and, frequently, co-regulated with Nod factors, but the type of co-regulation varies depending on the rhizobial strain. Many studies point out a signalling role for EPS-derived oligosaccharides in root infection and nodule invasion but, in certain symbiotic couples, EPS can be dispensable for a successful interaction. In summary, the complex regulation of the production of rhizobial EPS varies in different rhizobia, and the relevance of this polysaccharide in symbiosis with legumes depends on the specific interacting couple.
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Affiliation(s)
- Sebastián Acosta-Jurado
- Department of Microbiology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Seville, Spain; (S.A.-J.); (F.F.-R.); (J.-E.R.-S.)
| | - Francisco Fuentes-Romero
- Department of Microbiology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Seville, Spain; (S.A.-J.); (F.F.-R.); (J.-E.R.-S.)
| | - Jose-Enrique Ruiz-Sainz
- Department of Microbiology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Seville, Spain; (S.A.-J.); (F.F.-R.); (J.-E.R.-S.)
| | - Monika Janczarek
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - José-María Vinardell
- Department of Microbiology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Seville, Spain; (S.A.-J.); (F.F.-R.); (J.-E.R.-S.)
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18
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Antunes VDC, Freitag D, Serrato RV. Differential exopolysaccharide production and composition by Herbaspirillum strains from diverse ecological environments. Arch Microbiol 2021; 203:3883-3892. [PMID: 34009446 DOI: 10.1007/s00203-021-02371-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/22/2021] [Accepted: 05/08/2021] [Indexed: 11/26/2022]
Abstract
Bacteria belonging to the genus Herbaspirillum are found in many different ecological niches. Some species are typically endophytic, while others were reported as free-living organisms that occupy various environments. Also, opportunistic herbaspirilli have been found infecting humans affected by several diseases. We have analyzed the production of exopolysaccharides (EPS) by Herbaspirillum strains isolated from different sources and with distinct ecological characteristics. The monosaccharide composition was determined for the EPS obtained for selected strains including free-living, plant-associated and clinical isolates, and the relationship with the ecological niches occupied by Herbaspirillum spp. is proposed.
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Affiliation(s)
- Valquíria D C Antunes
- Department of Biochemistry and Molecular Biology, Setor de Ciências Biológicas-Centro Politécnico, Universidade Federal do Paraná , R. Francisco H. dos Santos, 100 , PO Box 19046, Curitiba, PR, 81531-980, Brazil
| | - Daniela Freitag
- Department of Biochemistry and Molecular Biology, Setor de Ciências Biológicas-Centro Politécnico, Universidade Federal do Paraná , R. Francisco H. dos Santos, 100 , PO Box 19046, Curitiba, PR, 81531-980, Brazil
| | - Rodrigo V Serrato
- Department of Biochemistry and Molecular Biology, Setor de Ciências Biológicas-Centro Politécnico, Universidade Federal do Paraná , R. Francisco H. dos Santos, 100 , PO Box 19046, Curitiba, PR, 81531-980, Brazil.
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19
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Structure and Development of the Legume-Rhizobial Symbiotic Interface in Infection Threads. Cells 2021; 10:cells10051050. [PMID: 33946779 PMCID: PMC8146911 DOI: 10.3390/cells10051050] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The intracellular infection thread initiated in a root hair cell is a unique structure associated with Rhizobium-legume symbiosis. It is characterized by inverted tip growth of the plant cell wall, resulting in a tunnel that allows invasion of host cells by bacteria during the formation of the nitrogen-fixing root nodule. Regulation of the plant-microbial interface is essential for infection thread growth. This involves targeted deposition of the cell wall and extracellular matrix and tight control of cell wall remodeling. This review describes the potential role of different actors such as transcription factors, receptors, and enzymes in the rearrangement of the plant-microbial interface and control of polar infection thread growth. It also focuses on the composition of the main polymers of the infection thread wall and matrix and the participation of reactive oxygen species (ROS) in the development of the infection thread. Mutant analysis has helped to gain insight into the development of host defense reactions. The available data raise many new questions about the structure, function, and development of infection threads.
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20
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Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins. Curr Genet 2021; 67:769-784. [PMID: 33837815 DOI: 10.1007/s00294-021-01184-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/19/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
A growing body of evidence suggests that Nod Factors molecules are the critical structural components in nitrogen fixation. These molecules have been implicated in plant-microbe signaling. Many enzymes involved in Nod factors biosynthesis; however, the enzymes that decorate (modify) nod factor main structure play a vital role. Here, the computational analysis of GDP-mannose 4,6-dehydratase (NoeL) proteins with great impact in modification of nod factor structure in four genomes of agriculturally important rhizobia (Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium) presented. The NoeL number of amino acids was in the range of 147 (M5AMF5) to 372 (A0A023XWX0, Q89TZ1). The molecular weights were around 41 KDa. The results showed that the strain-specific purification strategy should apply as the pI of the sequences varied significantly (in the range of 5.59 to 9.12). The enzyme sequences and eight 3-dimensional structures predicted with homology modeling and machine learning representing the phylogenetic tree revealed the stability of enzymes in different conditions (Instability and Aliphatic index); however, this stability is also strain-specific. Disulphide bonds were observed in some species; however, the pattern was not detected in all members of the same species. Alpha helix was the dominant secondary structure predicted in all cytoplasmic NoeL. All models were homo-tetramer with acceptable sequence identity, GMEAN and coverage (60, - 1.80, 88, respectively). Additionally, Ramachandran maps showed that more than 94% of residues are in favored regions. We also highlight several key characterizations of NoeL from four rhizobia genomes annotation. These findings provide novel insights into the complexity and diversity of NoeL enzymes among important rhizobia and suggest considering a broader framework of biofilm for future research.
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21
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Castellani LG, Luchetti A, Nilsson JF, Pérez-Giménez J, Wegener C, Schlüter A, Pühler A, Lagares A, Brom S, Pistorio M, Niehaus K, Torres Tejerizo GA. Exopolysaccharide Characterization of Rhizobium favelukesii LPU83 and Its Role in the Symbiosis With Alfalfa. FRONTIERS IN PLANT SCIENCE 2021; 12:642576. [PMID: 33643369 PMCID: PMC7902896 DOI: 10.3389/fpls.2021.642576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/20/2021] [Indexed: 05/03/2023]
Abstract
One of the greatest inputs of available nitrogen into the biosphere occurs through the biological N2-fixation to ammonium as result of the symbiosis between rhizobia and leguminous plants. These interactions allow increased crop yields on nitrogen-poor soils. Exopolysaccharides (EPS) are key components for the establishment of an effective symbiosis between alfalfa and Ensifer meliloti, as bacteria that lack EPS are unable to infect the host plants. Rhizobium favelukesii LPU83 is an acid-tolerant rhizobia strain capable of nodulating alfalfa but inefficient to fix nitrogen. Aiming to identify the molecular determinants that allow R. favelukesii to infect plants, we studied its EPS biosynthesis. LPU83 produces an EPS I identical to the one present in E. meliloti, but the organization of the genes involved in its synthesis is different. The main gene cluster needed for the synthesis of EPS I in E. meliloti, is split into three different sections in R. favelukesii, which probably arose by a recent event of horizontal gene transfer. A R. favelukesii strain devoided of all the genes needed for the synthesis of EPS I is still able to infect and nodulate alfalfa, suggesting that attention should be directed to other molecules involved in the development of the symbiosis.
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Affiliation(s)
- Lucas G. Castellani
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Abril Luchetti
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juliet F. Nilsson
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Julieta Pérez-Giménez
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | | | | | | | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Gonzalo A. Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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22
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Rodríguez S, Correa-Galeote D, Sánchez-Pérez M, Ramírez M, Isidra-Arellano MC, Reyero-Saavedra MDR, Zamorano-Sánchez D, Hernández G, Valdés-López O, Girard L. A Novel OmpR-Type Response Regulator Controls Multiple Stages of the Rhizobium etli - Phaseolus vulgaris N 2-Fixing Symbiosis. Front Microbiol 2021; 11:615775. [PMID: 33384681 PMCID: PMC7769827 DOI: 10.3389/fmicb.2020.615775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/26/2020] [Indexed: 11/22/2022] Open
Abstract
OmpR, is one of the best characterized response regulators families, which includes transcriptional regulators with a variety of physiological roles including the control of symbiotic nitrogen fixation (SNF). The Rhizobium etli CE3 genome encodes 18 OmpR-type regulators; the function of the majority of these regulators during the SNF in common bean, remains elusive. In this work, we demonstrated that a R. etli mutant strain lacking the OmpR-type regulator RetPC57 (ΔRetPC57), formed less nodules when used as inoculum for common bean. Furthermore, we observed reduced expression level of bacterial genes involved in Nod Factors production (nodA and nodB) and of plant early-nodulation genes (NSP2, NIN, NF-YA and ENOD40), in plants inoculated with ΔRetPC57. RetPC57 also contributes to the appropriate expression of genes which products are part of the multidrug efflux pumps family (MDR). Interestingly, nodules elicited by ΔRetPC57 showed increased expression of genes relevant for Carbon/Nitrogen nodule metabolism (PEPC and GOGAT) and ΔRetPC57 bacteroids showed higher nitrogen fixation activity as well as increased expression of key genes directly involved in SNF (hfixL, fixKf, fnrN, fixN, nifA and nifH). Taken together, our data show that the previously uncharacterized regulator RetPC57 is a key player in the development of the R. etli - P. vulgaris symbiosis.
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Affiliation(s)
- Susana Rodríguez
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - David Correa-Galeote
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mishael Sánchez-Pérez
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramírez
- Programa de Genómica Funcional de Eucariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mariel C Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - María Del Rocío Reyero-Saavedra
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - David Zamorano-Sánchez
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Georgina Hernández
- Programa de Genómica Funcional de Eucariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Lourdes Girard
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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23
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Primo E, Bogino P, Cossovich S, Foresto E, Nievas F, Giordano W. Exopolysaccharide II Is Relevant for the Survival of Sinorhizobium meliloti under Water Deficiency and Salinity Stress. Molecules 2020; 25:E4876. [PMID: 33105680 PMCID: PMC7659973 DOI: 10.3390/molecules25214876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
Sinorhizobium meliloti is a soil bacterium of great agricultural importance because of its ability to fix atmospheric nitrogen in symbiotic association with alfalfa (Medicago sativa) roots. We looked into the involvement of exopolysaccharides (EPS) in its survival when exposed to different environmental stressors, as well as in bacteria-bacteria and bacteria-substrate interactions. The strains used were wild-type Rm8530 and two strains that are defective in the biosynthesis of EPS II: wild-type Rm1021, which has a non-functional expR locus, and mutant Rm8530 expA. Under stress by water deficiency, Rm8530 remained viable and increased in number, whereas Rm1021 and Rm8530 expA did not. These differences could be due to Rm8530's ability to produce EPS II. Survival experiments under saline stress showed that viability was reduced for Rm1021 but not for Rm8530 or Rm8530 expA, which suggests the existence of some regulating mechanism dependent on a functional expR that is absent in Rm1021. The results of salinity-induced stress assays regarding biofilm-forming capacity (BFC) and autoaggregation indicated the protective role of EPS II. As a whole, our observations demonstrate that EPS play major roles in rhizobacterial survival.
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Affiliation(s)
| | | | | | | | | | - Walter Giordano
- Instituto de Biotecnología Ambiental y Salud (INBIAS), CONICET, Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto (UNRC), Río Cuarto X5804BYA, Córdoba, Argentina; (E.P.); (P.B.); (S.C.); (E.F.); (F.N.)
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24
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Liu J, Yu X, Qin Q, Dinkins RD, Zhu H. The Impacts of Domestication and Breeding on Nitrogen Fixation Symbiosis in Legumes. Front Genet 2020; 11:00973. [PMID: 33014021 PMCID: PMC7461779 DOI: 10.3389/fgene.2020.00973] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/31/2020] [Indexed: 01/12/2023] Open
Abstract
Legumes are the second most important family of crop plants. One defining feature of legumes is their unique ability to establish a nitrogen-fixing root nodule symbiosis with soil bacteria known as rhizobia. Since domestication from their wild relatives, crop legumes have been under intensive breeding to improve yield and other agronomic traits but with little attention paid to the belowground symbiosis traits. Theoretical models predict that domestication and breeding processes, coupled with high−input agricultural practices, might have reduced the capacity of crop legumes to achieve their full potential of nitrogen fixation symbiosis. Testing this prediction requires characterizing symbiosis traits in wild and breeding populations under both natural and cultivated environments using genetic, genomic, and ecological approaches. However, very few experimental studies have been dedicated to this area of research. Here, we review how legumes regulate their interactions with soil rhizobia and how domestication, breeding and agricultural practices might have affected nodulation capacity, nitrogen fixation efficiency, and the composition and function of rhizobial community. We also provide a perspective on how to improve legume-rhizobial symbiosis in sustainable agricultural systems.
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Affiliation(s)
- Jinge Liu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Xiaocheng Yu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Qiulin Qin
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Randy D Dinkins
- Forage-Animal Production Research Unit, United States Department of Agriculture-Agricultural Research Service, Lexington, KY, United States
| | - Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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25
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Breusing C, Schultz DT, Sudek S, Worden AZ, Young CR. High‐contiguity genome assembly of the chemosynthetic gammaproteobacterial endosymbiont of the cold seep tubeworm
Lamellibrachia barhami. Mol Ecol Resour 2020. [PMCID: PMC7540712 DOI: 10.1111/1755-0998.13220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Symbiotic relationships between vestimentiferan tubeworms and chemosynthetic Gammaproteobacteria build the foundations of many hydrothermal vent and hydrocarbon seep ecosystems in the deep sea. The association between the vent tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has become a model system for symbiosis research in deep‐sea vestimentiferans, while markedly fewer studies have investigated symbiotic relationships in other tubeworm species, especially at cold seeps. Here we sequenced the endosymbiont genome of the tubeworm Lamellibrachia barhami from a cold seep in the Gulf of California, using short‐ and long‐read sequencing technologies in combination with Hi‐C and Dovetail Chicago libraries. Our final assembly had a size of ~4.17 MB, a GC content of 54.54%, 137X coverage, 4153 coding sequences, and a checkm completeness score of 97.19%. A single scaffold contained 99.51% of the genome. Comparative genomic analyses indicated that the L. barhami symbiont shares a set of core genes and many metabolic pathways with other vestimentiferan symbionts, while containing 433 unique gene clusters that comprised a variety of transposases, defence‐related genes and a lineage‐specific CRISPR/Cas3 system. This assembly represents the most contiguous tubeworm symbiont genome resource to date and will be particularly valuable for future comparative genomic studies investigating structural genome evolution, physiological adaptations and host‐symbiont communication in chemosynthetic animal‐microbe symbioses.
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Affiliation(s)
- Corinna Breusing
- Monterey Bay Aquarium Research Institute Moss Landing CA USA
- National Oceanography Centre Southampton UK
| | - Darrin T. Schultz
- Monterey Bay Aquarium Research Institute Moss Landing CA USA
- Department of Biomolecular Engineering and Bioinformatics University of California Santa Cruz Santa Cruz CA USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute Moss Landing CA USA
| | - Alexandra Z. Worden
- Monterey Bay Aquarium Research Institute Moss Landing CA USA
- GEOMAR Helmholtz Centre for Ocean Research Kiel Germany
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26
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Liu Y, Bellich B, Hug S, Eberl L, Cescutti P, Pessi G. The Exopolysaccharide Cepacian Plays a Role in the Establishment of the Paraburkholderia phymatum - Phaseolus vulgaris Symbiosis. Front Microbiol 2020; 11:1600. [PMID: 32765457 PMCID: PMC7378592 DOI: 10.3389/fmicb.2020.01600] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
Paraburkholderia phymatum is a rhizobial strain that belongs to the beta-proteobacteria, a group known to form efficient nitrogen-fixing symbioses within root nodules of several legumes, including the agriculturally important common bean. The establishment of the symbiosis requires the exchange of rhizobial and plant signals such as lipochitooligosaccharides (Nod factors), polysaccharides, and flavonoids. Inspection of the genome of the competitive rhizobium P. phymatum revealed the presence of several polysaccharide biosynthetic gene clusters. In this study, we demonstrate that bceN, a gene encoding a GDP-D-mannose 4,6-dehydratase, which is involved in the production of the exopolysaccharide cepacian, an important component of biofilms produced by closely related opportunistic pathogens of the Burkholderia cepacia complex (Bcc), is required for efficient plant colonization. Wild-type P. phymatum was shown to produce cepacian while a bceN mutant did not. Additionally, the bceN mutant produced a significantly lower amount of biofilm and formed less root nodules compared to the wild-type strain with Phaseolus vulgaris as host plant. Finally, expression of the operon containing bceN was induced by the presence of germinated P. vulgaris seeds under nitrogen limiting conditions suggesting a role of this polysaccharide in the establishment of this ecologically important symbiosis.
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Affiliation(s)
- Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Barbara Bellich
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Sebastian Hug
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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27
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Younginger BS, Friesen ML. Connecting signals and benefits through partner choice in plant-microbe interactions. FEMS Microbiol Lett 2020; 366:5626345. [PMID: 31730203 DOI: 10.1093/femsle/fnz217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 10/17/2019] [Indexed: 12/20/2022] Open
Abstract
Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.
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Affiliation(s)
- Brett S Younginger
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA.,Department of Crop and Soil Sciences, Washington State University, PO Box 646420, 115 Johnson Hall, Pullman, WA 99164, USA
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28
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Tewari S, Sharma S. Rhizobial-metabolite based biocontrol of fusarium wilt in pigeon pea. Microb Pathog 2020; 147:104278. [PMID: 32473389 DOI: 10.1016/j.micpath.2020.104278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/15/2020] [Accepted: 05/25/2020] [Indexed: 11/24/2022]
Abstract
The application of rhizobial cells for improving pigeon pea fitness has been practiced for ages. As cell-based approaches have limitations, the focus is on the usage of cell-free formulations. In the present study exopolysaccharide (EPS) producing, plant health promoting Bradyrhizobium sp. IC-4059 was monitored for its biocontrol potential against Fusarium udum. Strain IC-4059, its EPS, and supernatant antagonized F.udum by 52.6%, 20.5%, and 48.1%, respectively in comparison to control. Diverse formulations prepared using EPS, supernatant, and cells of strain IC-4059 were: EPS based, supernatant based, IC-4059 liquid culture (rhizobia based), dual combination (IC-4059 cells + supernatant; IC-4059 cells + EPS; EPS + supernatant), and triple combination (IC-4059 cells + supernatant + EPS). The potency of these bioformulations was observed under in planta tubes followed by in vivo pot study, both in F.udum infested and non-infested sets taking pigeon pea cultivar UPAS-120 as a model crop. The study highlighted that seeds receiving triple combination exhibited significantly higher plant growth attributes, nodule enhancing, and disease suppressing activity in comparison to individual application of Bradyrhizobium. Antifungal compounds were analyzed by a metabolomic approach using UPLC-MS. Thus, the study disseminates the tripartite role of triple formulation as a plant growth stimulator, nodule enhancer, and disease suppressor, both under in vitro and in vivo conditions in the presence of phytopathogen F. udum.
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Affiliation(s)
- Sakshi Tewari
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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29
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Doin de Moura GG, Remigi P, Masson-Boivin C, Capela D. Experimental Evolution of Legume Symbionts: What Have We Learnt? Genes (Basel) 2020; 11:E339. [PMID: 32210028 PMCID: PMC7141107 DOI: 10.3390/genes11030339] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/17/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022] Open
Abstract
Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. They likely emerged and diversified through independent horizontal transfers of key symbiotic genes. To replay the evolution of a new rhizobium genus under laboratory conditions, the symbiotic plasmid of Cupriavidus taiwanensis was introduced in the plant pathogen Ralstonia solanacearum, and the generated proto-rhizobium was submitted to repeated inoculations to the C. taiwanensis host, Mimosa pudica L.. This experiment validated a two-step evolutionary scenario of key symbiotic gene acquisition followed by genome remodeling under plant selection. Nodulation and nodule cell infection were obtained and optimized mainly via the rewiring of regulatory circuits of the recipient bacterium. Symbiotic adaptation was shown to be accelerated by the activity of a mutagenesis cassette conserved in most rhizobia. Investigating mutated genes led us to identify new components of R. solanacearum virulence and C. taiwanensis symbiosis. Nitrogen fixation was not acquired in our short experiment. However, we showed that post-infection sanctions allowed the increase in frequency of nitrogen-fixing variants among a non-fixing population in the M. pudica-C. taiwanensis system and likely allowed the spread of this trait in natura. Experimental evolution thus provided new insights into rhizobium biology and evolution.
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Affiliation(s)
| | | | | | - Delphine Capela
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31320, France; (G.G.D.d.M.); (P.R.); (C.M.-B.)
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30
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Spribille T, Tagirdzhanova G, Goyette S, Tuovinen V, Case R, Zandberg WF. 3D biofilms: in search of the polysaccharides holding together lichen symbioses. FEMS Microbiol Lett 2020; 367:fnaa023. [PMID: 32037451 PMCID: PMC7164778 DOI: 10.1093/femsle/fnaa023] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
Stable, long-term interactions between fungi and algae or cyanobacteria, collectively known as lichens, have repeatedly evolved complex architectures with little resemblance to their component parts. Lacking any central scaffold, the shapes they assume are casts of secreted polymers that cement cells into place, determine the angle of phototropic exposure and regulate water relations. A growing body of evidence suggests that many lichen extracellular polymer matrices harbor unicellular, non-photosynthesizing organisms (UNPOs) not traditionally recognized as lichen symbionts. Understanding organismal input and uptake in this layer is key to interpreting the role UNPOs play in lichen biology. Here, we review both polysaccharide composition determined from whole, pulverized lichens and UNPOs reported from lichens to date. Most reported polysaccharides are thought to be structural cell wall components. The composition of the extracellular matrix is not definitively known. Several lines of evidence suggest some acidic polysaccharides have evaded detection in routine analysis of neutral sugars and may be involved in the extracellular matrix. UNPOs reported from lichens include diverse bacteria and yeasts for which secreted polysaccharides play important biological roles. We conclude by proposing testable hypotheses on the role that symbiont give-and-take in this layer could play in determining or modifying lichen symbiotic outcomes.
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Affiliation(s)
- Toby Spribille
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Spencer Goyette
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Veera Tuovinen
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Rebecca Case
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Wesley F Zandberg
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3427 University Way, Kelowna, BC V1V 1V7, Canada
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Deciphering the Symbiotic Significance of Quorum Sensing Systems of Sinorhizobium fredii HH103. Microorganisms 2020; 8:microorganisms8010068. [PMID: 31906451 PMCID: PMC7022240 DOI: 10.3390/microorganisms8010068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/26/2019] [Accepted: 12/31/2019] [Indexed: 01/21/2023] Open
Abstract
Quorum sensing (QS) is a bacterial cell-to-cell signaling mechanism that collectively regulates and synchronizes behaviors by means of small diffusible chemical molecules. In rhizobia, QS systems usually relies on the synthesis and detection of N-acyl-homoserine lactones (AHLs). In the model bacterium Sinorhizobium meliloti functions regulated by the QS systems TraI-TraR and SinI-SinR(-ExpR) include plasmid transfer, production of surface polysaccharides, motility, growth rate and nodulation. These systems are also present in other bacteria of the Sinorhizobium genus, with variations at the species and strain level. In Sinorhizobium fredii NGR234 phenotypes regulated by QS are plasmid transfer, growth rate, sedimentation, motility, biofilm formation, EPS production and copy number of the symbiotic plasmid (pSym). The analysis of the S. fredii HH103 genomes reveal also the presence of both QS systems. In this manuscript we characterized the QS systems of S. fredii HH103, determining that both TraI and SinI AHL-synthases proteins are responsible of the production of short- and long-chain AHLs, respectively, at very low and not physiological concentrations. Interestingly, the main HH103 luxR-type genes, expR and traR, are split into two ORFs, suggesting that in S. fredii HH103 the corresponding carboxy-terminal proteins, which contain the DNA-binding motives, may control target genes in an AHL-independent manner. The presence of a split traR gene is common in other S. fredii strains.
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32
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Abstract
We describe the synthesis of the unusual bicyclic sugar bradyrhizose in 14 steps and a 6% overall yield from d-glucose. The synthesis involves the elaboration of a trans-fused carbocyclic ring onto the preexisting glucopyranose framework followed by adjustment of the oxidation levels. Key steps include radical extension of the glucopyranose side chain, ring closing metathesis, allylic oxidation, Luche reduction, hydroxy-directed epoxidation, and acid-catalyzed epoxide opening at the more substituted position.
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Affiliation(s)
- Philemon Ngoje
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States.,Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States.,Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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33
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Xiang Q, Wang J, Qin P, Adil B, Xu K, Gu Y, Yu X, Zhao K, Zhang X, Ma M, Chen Q, Chen X, Yan Y. Effect of common bean seed exudates on growth, lipopolysaccharide production, and lipopolysaccharide transport gene expression of Rhizobium anhuiense. Can J Microbiol 2019; 66:186-193. [PMID: 31751146 DOI: 10.1139/cjm-2019-0413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lipopolysaccharide (LPS) is essential for successful nodulation during the symbiosis of rhizobia and legumes. However, the detailed mechanism of the LPS in this process has not yet been clearly elucidated. In this study, the effects of common bean seed exudates on the growth, lipopolysaccharide production, and lipopolysaccharide transport genes expression (lpt) of Rhizobium anhuiense were investigated. Rhizobium anhuiense exposed to exudates showed changes in LPS electrophoretic profiles and content, whereby the LPS band was wider and the LPS content was higher in R. anhuiense treated with seed exudates. Exudates enhanced cell growth of R. anhuiense in a concentration-dependent manner; R. anhuiense exposed to higher doses of the exudate showed faster growth. Seven lpt genes of R. anhuiense were amplified and sequenced. Sequences of six lpt genes, except for lptE, were the same as those found in previously analyzed R. anhuiense strains, while lptE shared low sequence similarity with other strains. Exposure to the exudates strongly stimulated the expression of all lpt genes. Approximately 6.7- (lptG) to 301-fold (lptE) increases in the transcriptional levels were observed after only 15 min of exposure to exudates. These results indicate that seed exudates affect the LPS by making the cell wall structure more conducive to symbiotic nodulation.
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Affiliation(s)
- Quanju Xiang
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Jie Wang
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Peng Qin
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Bilal Adil
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Kaiwei Xu
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Yunfu Gu
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Xiumei Yu
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Ke Zhao
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Xiaoping Zhang
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Menggen Ma
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Qiang Chen
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Xiaoqiong Chen
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Yanhong Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
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34
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Kosolapova AO, Belousov MV, Sulatskaya AI, Belousova ME, Sulatsky MI, Antonets KS, Volkov KV, Lykholay AN, Shtark OY, Vasileva EN, Zhukov VA, Ivanova AN, Zykin PA, Kuznetsova IM, Turoverov KK, Tikhonovich IA, Nizhnikov AA. Two Novel Amyloid Proteins, RopA and RopB, from the Root Nodule Bacterium Rhizobium leguminosarum. Biomolecules 2019; 9:biom9110694. [PMID: 31690032 PMCID: PMC6920782 DOI: 10.3390/biom9110694] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
Amyloids represent protein fibrils with a highly ordered spatial structure, which not only cause dozens of incurable human and animal diseases but also play vital biological roles in Archaea, Bacteria, and Eukarya. Despite the fact that association of bacterial amyloids with microbial pathogenesis and infectious diseases is well known, there is a lack of information concerning the amyloids of symbiotic bacteria. In this study, using the previously developed proteomic method for screening and identification of amyloids (PSIA), we identified amyloidogenic proteins in the proteome of the root nodule bacterium Rhizobium leguminosarum. Among 54 proteins identified, we selected two proteins, RopA and RopB, which are predicted to have β-barrel structure and are likely to be involved in the control of plant-microbial symbiosis. We demonstrated that the full-length RopA and RopB form bona fide amyloid fibrils in vitro. In particular, these fibrils are β-sheet-rich, bind Thioflavin T (ThT), exhibit green birefringence upon staining with Congo Red (CR), and resist treatment with ionic detergents and proteases. The heterologously expressed RopA and RopB intracellularly aggregate in yeast and assemble into amyloid fibrils at the surface of Escherichia coli. The capsules of the R. leguminosarum cells bind CR, exhibit green birefringence, and contain fibrils of RopA and RopB in vivo.
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Affiliation(s)
- Anastasiia O Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Mikhail V Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Maria E Belousova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Kirill S Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Kirill V Volkov
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Anna N Lykholay
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Oksana Y Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Ekaterina N Vasileva
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Vladimir A Zhukov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Alexandra N Ivanova
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Komarov Botanical Institute RAS, 197376 Komarov Botanical Institute RAS, Russia.
| | - Pavel A Zykin
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
- Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia.
| | - Igor A Tikhonovich
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Anton A Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
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Primo ED, Cossovich S, Nievas F, Bogino P, Humm EA, Hirsch AM, Giordano W. Exopolysaccharide production in Ensifer meliloti laboratory and native strains and their effects on alfalfa inoculation. Arch Microbiol 2019; 202:391-398. [PMID: 31680188 DOI: 10.1007/s00203-019-01756-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/07/2019] [Accepted: 10/22/2019] [Indexed: 01/22/2023]
Abstract
Bacterial surface molecules have an important role in the rhizobia-legume symbiosis. Ensifer meliloti (previously, Sinorhizobium meliloti), a symbiotic Gram-negative rhizobacterium, produces two different exopolysaccharides (EPSs), termed EPS I (succinoglycan) and EPS II (galactoglucan), with different functions in the symbiotic process. Accordingly, we undertook a study comparing the potential differences in alfalfa nodulation by E. meliloti strains with differences in their EPSs production. Strains recommended for inoculation as well as laboratory strains and native strains isolated from alfalfa fields were investigated. This study concentrated on EPS-II production, which results in mucoid colonies that are dependent on the presence of an intact expR gene. The results revealed that although the studied strains exhibited different phenotypes, the differences did not affect alfalfa nodulation itself. However, subtle changes in timing and efficacy to the effects of inoculation with the different strains may result because of other as-yet unknown factors. Thus, additional research is needed to determine the most effective inoculant strains and the best conditions for improving alfalfa production under agricultural conditions.
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Affiliation(s)
- Emiliano D Primo
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Sacha Cossovich
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Fiorela Nievas
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Pablo Bogino
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Ethan A Humm
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, Los Angeles, USA
| | - Ann M Hirsch
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, Los Angeles, USA.,Molecular Biology Institute, University of California-Los Angeles, Los Angeles, USA
| | - Walter Giordano
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.
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Naranjo E, Merfa MV, Ferreira V, Jain M, Davis MJ, Bahar O, Gabriel DW, De La Fuente L. Liberibacter crescens biofilm formation in vitro: establishment of a model system for pathogenic 'Candidatus Liberibacter spp.'. Sci Rep 2019; 9:5150. [PMID: 30914689 PMCID: PMC6435755 DOI: 10.1038/s41598-019-41495-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/11/2019] [Indexed: 11/23/2022] Open
Abstract
The Liberibacter genus comprises insect endosymbiont bacterial species that cause destructive plant diseases, including Huanglongbing in citrus and zebra chip in potato. To date, pathogenic 'Candidatus Liberibacter spp.' (CLs) remain uncultured, therefore the plant-associated Liberibacter crescens (Lcr), only cultured species of the genus, has been used as a biological model for in vitro studies. Biofilm formation by CLs has been observed on the outer midgut surface of insect vectors, but not in planta. However, the role of biofilm formation in the life cycle of these pathogens remains unclear. Here, a model system for studying CLs biofilms was developed using Lcr. By culture media modifications, bovine serum albumin (BSA) was identified as blocking initial cell-surface adhesion. Removal of BSA allowed for the first time observation of Lcr biofilms. After media optimization for biofilm formation, we demonstrated that Lcr attaches to surfaces, and form cell aggregates embedded in a polysaccharide matrix both in batch cultures and under flow conditions in microfluidic chambers. Biofilm structures may represent excellent adaptive advantages for CLs during insect vector colonization helping with host retention, immune system evasion, and transmission. Future studies using the Lcr model established here will help in the understanding of the biology of CLs.
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Affiliation(s)
- Eber Naranjo
- Department of Entomology and Plant Pathology, Auburn University, Auburn, USA
| | - Marcus V Merfa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, USA
| | - Virginia Ferreira
- Bioscience Department, College of Chemistry, University of the Republic, Montevideo, Uruguay
| | - Mukesh Jain
- Department of Plant Pathology, University of Florida, Gainesville, USA
| | - Michael J Davis
- Citrus Research and Education Center, University of Florida, Gainesville, USA
| | - Ofir Bahar
- Department of Plant Pathology and Weed Research, ARO - Volcani Center, Bet-Dagan, Israel
| | - Dean W Gabriel
- Department of Plant Pathology, University of Florida, Gainesville, USA
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Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae. ISME JOURNAL 2019; 13:1831-1844. [PMID: 30877285 DOI: 10.1038/s41396-019-0398-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics, revealing a potential role in complementing the host's arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of transmission in this symbiosis which, together with a large effective population size explains the cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the candidate mechanisms enabling a permanent association in the phyllosphere.
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Wang D, Couderc F, Tian CF, Gu W, Liu LX, Poinsot V. Conserved Composition of Nod Factors and Exopolysaccharides Produced by Different Phylogenetic Lineage Sinorhizobium Strains Nodulating Soybean. Front Microbiol 2018; 9:2852. [PMID: 30534119 PMCID: PMC6275314 DOI: 10.3389/fmicb.2018.02852] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/06/2018] [Indexed: 12/31/2022] Open
Abstract
The structural variation of symbiotic signals released by rhizobia determines the specificity of their interaction with legume plants. Previous studies showed that Sinorhizobium strains from different phylogenetic lineages had different symbiotic performance on certain cultivated soybeans. Whether they released similar or different symbiotic signals remained unclear. In this study, we compared their nod and exo gene clusters and made a detailed structural analysis of Nod factors and EPS by ESI-MS/MS and two dimensions NMR. Even if there are some differences among nod or exo gene clusters; they produced much conserved Nod factor and EPS compositions. The Nod factors consist of a cocktail of β-(1, 4)-linked tri-, tetra-, and pentamers of N-acetyl-D-glucosamine (GlcNAc). The C2 position on the non-reducing terminal end is modified by a lipid chain that contains 16 or 18 atoms of carbon–with or without unsaturations-, and the C6 position on the reducing residue is decorated by a fucose or a 2-O-methylfucose. Their EPS are composed of glucose, galactose, glucuronic acid, pyruvic acid in the ratios 5:1:2:1 or 6:1:2:1. These findings indicate that soybean cultivar compatibility of Sinorhizobium strains does not result from Nod factor or EPS structure variations. The structure comparison of the soybean microbionts with other Sinorhizobium strains showed that Nod factor structures of soybean microbionts are much conserved, although there are no specific genes shared by the soybean microsymbionts. EPS produced by Sinorhizobium strains are different from those of Bradyrhizobium. All above is consistent with the previous deduction that Nod factor structures are related to host range, while those of EPS are connected with phylogeny.
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Affiliation(s)
- Dan Wang
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangzhou, China.,Laboratoire des IMRCP, UMR5623 Université Paul Sabatier, CNRS, Toulouse, France.,State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - François Couderc
- Laboratoire des IMRCP, UMR5623 Université Paul Sabatier, CNRS, Toulouse, France
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenjie Gu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangzhou, China
| | - Li Xue Liu
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Verena Poinsot
- Laboratoire des IMRCP, UMR5623 Université Paul Sabatier, CNRS, Toulouse, France
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Libault M. Transcriptional Reprogramming of Legume Genomes: Perspective and Challenges Associated With Single-Cell and Single Cell-Type Approaches During Nodule Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1600. [PMID: 30467509 PMCID: PMC6237103 DOI: 10.3389/fpls.2018.01600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/17/2018] [Indexed: 05/11/2023]
Abstract
Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through functional genomic studies, plant transcriptomes have been used by scientists to reveal plant genes potentially controlling nodulation. However, it is important to acknowledge that the physiology, transcriptomic programs, and biochemical properties of the plant cells involved in nodulation are continuously regulated. They also differ between the different cell-types composing the nodules. To generate a more accurate picture of the transcriptome, epigenome, proteome, and metabolome of the cells infected by rhizobia and cells composing the nodule, there is a need to implement plant single-cell and single cell-types strategies and methods. Accessing such information would allow a better understanding of the infection of plant cells by rhizobia and will help understanding the complex interactions existing between rhizobia and the plant cells. In this mini-review, we are reporting the current knowledge on legume nodulation gained by plant scientists at the level of single cell-types, and provide perspectives on single cell/single cell-type approaches when applied to legume nodulation.
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Affiliation(s)
- Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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40
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Osińska-Jaroszuk M, Jaszek M, Starosielec M, Sulej J, Matuszewska A, Janczarek M, Bancerz R, Wydrych J, Wiater A, Jarosz-Wilkołazka A. Bacterial exopolysaccharides as a modern biotechnological tool for modification of fungal laccase properties and metal ion binding. Bioprocess Biosyst Eng 2018; 41:973-989. [PMID: 29582151 PMCID: PMC6013525 DOI: 10.1007/s00449-018-1928-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/22/2018] [Indexed: 11/29/2022]
Abstract
Four bacterial EPSs extracted from Rhizobium leguminosarum bv. trifolii Rt24.2, Sinorhizobium meliloti Rm1021, Bradyrhizobium japonicum USDA110, and Bradyrhizobium elkanii USDA76 were determined towards their metal ion adsorption properties and possible modification of Cerrena unicolor laccase properties. The highest magnesium and iron ion-sorption capacity (~ 42 and ~ 14.5%, respectively) was observed for EPS isolated from B. japonicum USDA110. An evident influence of EPSs on the stability of laccase compared to the control values (without EPSs) was shown after 30-day incubation at 25 °C. The residual activity of laccases was obtained in the presence of Rh76EPS and Rh1021EPS, i.e., 49.5 and 41.5% of the initial catalytic activity, respectively. This result was confirmed by native PAGE electrophoresis. The EPS effect on laccase stability at different pH (from 3.8 to 7.0) was also estimated. The most significant changes at the optimum pH value (pH 5.8) was observed in samples of laccase stabilized by Rh76EPS and Rh1021EPS. Cyclic voltamperometry was used for analysis of electrochemical parameters of laccase stabilized by bacterial EPS and immobilized on single-walled carbon nanotubes (SWCNTs) with aryl residues. Laccases with Rh76EPS and Rh1021EPS had an evident shift of the value of the redox potential compared to the control without EPS addition. In conclusion, the results obtained in this work present a new potential use of bacterial EPSs as a metal-binding component and a modulator of laccase properties especially stability of enzyme activity, which can be a very effective tool in biotechnology and industrial applications.
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Affiliation(s)
- Monika Osińska-Jaroszuk
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland.
| | - Magdalena Jaszek
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Magdalena Starosielec
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Justyna Sulej
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Anna Matuszewska
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Monika Janczarek
- Department of Genetics and Microbiology, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Renata Bancerz
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Jerzy Wydrych
- Department of Comparative Anatomy and Anthropology, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Adrian Wiater
- Department of Industrial Microbiology, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Anna Jarosz-Wilkołazka
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
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41
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Liu W, Sun Y, Shen R, Dang X, Liu X, Sui F, Li Y, Zhang Z, Alexandre G, Elmerich C, Xie Z. A Chemotaxis-Like Pathway of Azorhizobium caulinodans Controls Flagella-Driven Motility, Which Regulates Biofilm Formation, Exopolysaccharide Biosynthesis, and Competitive Nodulation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:737-749. [PMID: 29424664 DOI: 10.1094/mpmi-12-17-0290-r] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The genome of the Azorhizobium caulinodans ORS571 contains a unique chemotaxis gene cluster (che) including five chemotaxis genes: cheA, cheW, cheY1, cheB, and cheR. Analysis of the role of the chemotaxis cluster of A. caulinodans using deletion mutant strains revealed that CheA or the Che signaling pathway controls chemotaxis behavior and flagella-driven motility and plays important roles in formation of biofilms and production of extracellular polysaccharides (EPS). Furthermore, the deletion mutants (ΔcheA and ΔcheA-R) were defective in competitive adsorption and colonization on the root surface of host plants. In addition, a functional CheA or Che pathway promoted competitive nodulation on roots and stems. Interestingly, a nonflagellated mutant, ΔfliM, displayed a phenotype highly similar to that of the ΔcheA or ΔcheA-R mutant strains. These findings suggest that through controlling flagella-driven motility behavior, the chemotaxis signaling pathway in A. caulinodans coordinates biofilm formation, EPS, and competitive colonization and nodulation.
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Affiliation(s)
- Wei Liu
- 1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Yu Sun
- 1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Rimin Shen
- 1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- 2 Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xiaoxiao Dang
- 1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xiaolin Liu
- 1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Fu Sui
- 1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Yan Li
- 1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhenpeng Zhang
- 1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Gladys Alexandre
- 3 Biochemistry, Cellular and Molecular Biology Department, University of Tennessee, Knoxville, U.S.A.; and
| | | | - Zhihong Xie
- 1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
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42
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Chagas FO, Pessotti RDC, Caraballo-Rodríguez AM, Pupo MT. Chemical signaling involved in plant-microbe interactions. Chem Soc Rev 2018; 47:1652-1704. [PMID: 29218336 DOI: 10.1039/c7cs00343a] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.
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Affiliation(s)
- Fernanda Oliveira Chagas
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (FCFRP-USP), Avenida do Café, s/n, 14040-903, Ribeirão Preto-SP, Brazil.
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43
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Klonowska A, Melkonian R, Miché L, Tisseyre P, Moulin L. Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history. BMC Genomics 2018; 19:105. [PMID: 29378510 PMCID: PMC5789663 DOI: 10.1186/s12864-018-4487-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called "alpha" and "beta"-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adaptation toward symbiotic nitrogen fixation in beta-rhizobia compared to alpha-rhizobia. In a previous study (Melkonian et al., Environ Microbiol 16:2099-111, 2014) we described the symbiotic competitiveness of M. pudica symbionts belonging to Burkholderia, Cupriavidus and Rhizobium species. RESULTS In this article we present a comparative analysis of the transcriptomes (by RNAseq) of B. phymatum STM815 (BP), C. taiwanensis LMG19424 (CT) and R. mesoamericanum STM3625 (RM) in conditions mimicking the early steps of symbiosis (i.e. perception of root exudates). BP exhibited the strongest transcriptome shift both quantitatively and qualitatively, which mirrors its high competitiveness in the early steps of symbiosis and its ancient evolutionary history as a symbiont, while CT had a minimal response which correlates with its status as a younger symbiont (probably via acquisition of symbiotic genes from a Burkholderia ancestor) and RM had a typical response of Alphaproteobacterial rhizospheric bacteria. Interestingly, the upregulation of nodulation genes was the only common response among the three strains; the exception was an up-regulated gene encoding a putative fatty acid hydroxylase, which appears to be a novel symbiotic gene specific to Mimosa symbionts. CONCLUSION The transcriptional response to root exudates was correlated to each strain nodulation competitiveness, with Burkholderia phymatum appearing as the best specialised symbiont of Mimosa pudica.
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Affiliation(s)
| | - Rémy Melkonian
- IRD, UMR LSTM, Campus de Baillarguet, Montpellier, France
| | - Lucie Miché
- IRD, UMR LSTM, Campus de Baillarguet, Montpellier, France.,Present address: Aix Marseille University, University of Avignon, CNRS, IRD, IMBE, Marseille, France
| | | | - Lionel Moulin
- IRD, Cirad, University of Montpellier, IPME, Montpellier, France.
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44
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Kelly S, Sullivan JT, Kawaharada Y, Radutoiu S, Ronson CW, Stougaard J. Regulation of Nod factor biosynthesis by alternative NodD proteins at distinct stages of symbiosis provides additional compatibility scrutiny. Environ Microbiol 2018; 20:97-110. [PMID: 29194913 DOI: 10.1111/1462-2920.14006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/07/2017] [Accepted: 11/14/2017] [Indexed: 01/18/2023]
Abstract
The Lotus japonicus symbiont Mesorhizobium loti R7A encodes two copies of nodD and here we identify striking differences in Nod factor biosynthesis gene induction by NodD1 and NodD2 both in vitro and in planta. We demonstrate that induction of Nod factor biosynthesis genes is preferentially controlled by NodD1 and NodD2 at specific stages of symbiotic infection. NodD2 is primarily responsible for induction in the rhizosphere and within nodules, while NodD1 is primarily responsible for induction within root hair infection threads. nodD1 and nodD2 mutants showed significant symbiotic phenotypes and competition studies establish that nodD1 and nodD2 mutants were severely outcompeted by wild-type R7A, indicating that both proteins are required for proficient symbiotic infection. These results suggest preferential activation of NodD1 and NodD2 by different inducing compounds produced at defined stages of symbiotic infection. We identified Lotus chalcone isomerase CHI4 as a root hair induced candidate involved in the biosynthesis of an inducer compound that may be preferentially recognized by NodD1 within root hair infection threads. We propose an alternative explanation for the function of multiple copies of nodD that provides the host plant with another level of compatibility scrutiny at the stage of infection thread development.
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Affiliation(s)
- Simon Kelly
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Aarhus 8000 C, Denmark
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Yasuyuki Kawaharada
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Aarhus 8000 C, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Aarhus 8000 C, Denmark
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Aarhus 8000 C, Denmark
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45
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Wang Q, Liu J, Zhu H. Genetic and Molecular Mechanisms Underlying Symbiotic Specificity in Legume-Rhizobium Interactions. FRONTIERS IN PLANT SCIENCE 2018; 9:313. [PMID: 29593768 PMCID: PMC5854654 DOI: 10.3389/fpls.2018.00313] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/23/2018] [Indexed: 05/20/2023]
Abstract
Legumes are able to form a symbiotic relationship with nitrogen-fixing soil bacteria called rhizobia. The result of this symbiosis is to form nodules on the plant root, within which the bacteria can convert atmospheric nitrogen into ammonia that can be used by the plant. Establishment of a successful symbiosis requires the two symbiotic partners to be compatible with each other throughout the process of symbiotic development. However, incompatibility frequently occurs, such that a bacterial strain is unable to nodulate a particular host plant or forms nodules that are incapable of fixing nitrogen. Genetic and molecular mechanisms that regulate symbiotic specificity are diverse, involving a wide range of host and bacterial genes/signals with various modes of action. In this review, we will provide an update on our current knowledge of how the recognition specificity has evolved in the context of symbiosis signaling and plant immunity.
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46
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Marczak M, Mazur A, Koper P, Żebracki K, Skorupska A. Synthesis of Rhizobial Exopolysaccharides and Their Importance for Symbiosis with Legume Plants. Genes (Basel) 2017; 8:E360. [PMID: 29194398 PMCID: PMC5748678 DOI: 10.3390/genes8120360] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/26/2017] [Accepted: 11/29/2017] [Indexed: 12/25/2022] Open
Abstract
Rhizobia dwell and multiply in the soil and represent a unique group of bacteria able to enter into a symbiotic interaction with plants from the Fabaceae family and fix atmospheric nitrogen inside de novo created plant organs, called nodules. One of the key determinants of the successful interaction between these bacteria and plants are exopolysaccharides, which represent species-specific homo- and heteropolymers of different carbohydrate units frequently decorated by non-carbohydrate substituents. Exopolysaccharides are typically built from repeat units assembled by the Wzx/Wzy-dependent pathway, where individual subunits are synthesized in conjunction with the lipid anchor undecaprenylphosphate (und-PP), due to the activity of glycosyltransferases. Complete oligosaccharide repeat units are transferred to the periplasmic space by the activity of the Wzx flippase, and, while still being anchored in the membrane, they are joined by the polymerase Wzy. Here we have focused on the genetic control over the process of exopolysaccharides (EPS) biosynthesis in rhizobia, with emphasis put on the recent advancements in understanding the mode of action of the key proteins operating in the pathway. A role played by exopolysaccharide in Rhizobium-legume symbiosis, including recent data confirming the signaling function of EPS, is also discussed.
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Affiliation(s)
- Małgorzata Marczak
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Andrzej Mazur
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Piotr Koper
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Kamil Żebracki
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Anna Skorupska
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland.
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47
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Capela D, Marchetti M, Clérissi C, Perrier A, Guetta D, Gris C, Valls M, Jauneau A, Cruveiller S, Rocha EPC, Masson-Boivin C. Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont. Mol Biol Evol 2017; 34:2503-2521. [PMID: 28535261 DOI: 10.1093/molbev/msx165] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ecological transitions between different lifestyles, such as pathogenicity, mutualism and saprophytism, have been very frequent in the course of microbial evolution, and often driven by horizontal gene transfer. Yet, how genomes achieve the ecological transition initiated by the transfer of complex biological traits remains poorly known. Here, we used experimental evolution, genomics, transcriptomics and high-resolution phenotyping to analyze the evolution of the plant pathogen Ralstonia solanacearum into legume symbionts, following the transfer of a natural plasmid encoding the essential mutualistic genes. We show that a regulatory pathway of the recipient R. solanacearum genome involved in extracellular infection of natural hosts was reused to improve intracellular symbiosis with the Mimosa pudica legume. Optimization of intracellular infection capacity was gained through mutations affecting two components of a new regulatory pathway, the transcriptional regulator efpR and a region upstream from the RSc0965-0967 genes of unknown functions. Adaptive mutations caused the downregulation of efpR and the over-expression of a downstream regulatory module, the three unknown genes RSc3146-3148, two of which encoding proteins likely associated to the membrane. This over-expression led to important metabolic and transcriptomic changes and a drastic qualitative and quantitative improvement of nodule intracellular infection. In addition, these adaptive mutations decreased the virulence of the original pathogen. The complete efpR/RSc3146-3148 pathway could only be identified in the genomes of the pathogenic R. solanacearum species complex. Our findings illustrate how the rewiring of a genetic network regulating virulence allows a radically different type of symbiotic interaction and contributes to ecological transitions and trade-offs.
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Affiliation(s)
- Delphine Capela
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Marta Marchetti
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Camille Clérissi
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.,Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
| | - Anthony Perrier
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Dorian Guetta
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Carine Gris
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Marc Valls
- Department of Genetics, University of Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, Spain
| | - Alain Jauneau
- Fédération de Recherches Agrobiosciences, Interactions, Biodiversity, Plateforme d'Imagerie TRI, CNRS, UPS, Castanet-Tolosan, France
| | - Stéphane Cruveiller
- CNRS-UMR8030 and Commissariat à l'Energie Atomique et aux Energies Alternatives CEA/DRF/IG/GEN LABGeM, Evry, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
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48
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Trattnig N, Farcet JB, Gritsch P, Christler A, Pantophlet R, Kosma P. Synthesis of a Pentasaccharide Fragment Related to the Inner Core Region of Rhizobial and Agrobacterial Lipopolysaccharides. J Org Chem 2017; 82:12346-12358. [PMID: 29028168 PMCID: PMC5715290 DOI: 10.1021/acs.joc.7b02172] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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The
pentasaccharide fragment α-d-Man-(1 →
5)-[α-d-Kdo-(2 → 4)-]α-d-Kdo-(2
→ 6)-β-d-GlcNAc-(1 → 6)-α-d-GlcNAc equipped with a 3-aminopropyl spacer moiety was prepared
by a sequential assembly of monosaccharide building blocks. The glucosamine
disaccharide—as a backbone surrogate of the bacterial lipid
A region—was synthesized using an 1,3-oxazoline donor, which
was followed by coupling with an isopropylidene-protected Kdo-fluoride
donor to afford a protected tetrasaccharide intermediate. Eventually,
an orthogonally protected manno-configured trichloroacetimidate
donor was used to achieve the sterically demanding glycosylation of
the 5-OH group of Kdo in good yield. The resulting pentasaccharide
is suitably protected for further chain elongation at positions 3,
4, and 6 of the terminal mannose. Global deprotection afforded the
target pentasaccharide to be used for the conversion into neoglycoconjugates
and “clickable” ligands.
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Affiliation(s)
- Nino Trattnig
- Department of Chemistry, University of Natural Resources and Life Sciences , A-1190 Vienna, Austria
| | - Jean-Baptiste Farcet
- Department of Chemistry, University of Natural Resources and Life Sciences , A-1190 Vienna, Austria
| | - Philipp Gritsch
- Department of Chemistry, University of Natural Resources and Life Sciences , A-1190 Vienna, Austria
| | - Anna Christler
- Department of Chemistry, University of Natural Resources and Life Sciences , A-1190 Vienna, Austria
| | - Ralph Pantophlet
- Faculty of Health Sciences and Department of Molecular Biology and Biochemistry, Simon Fraser University , Burnaby, British Columbia V5A1S6, Canada
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences , A-1190 Vienna, Austria
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49
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Kelly S, Radutoiu S, Stougaard J. Legume LysM receptors mediate symbiotic and pathogenic signalling. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:152-158. [PMID: 28787662 DOI: 10.1016/j.pbi.2017.06.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/14/2017] [Accepted: 06/16/2017] [Indexed: 05/13/2023]
Abstract
Legume-rhizobia symbiosis is coordinated through the production and perception of signal molecules by both partners with legume LysM receptor kinases performing a central role in this process. Receptor complex formation and signalling outputs derived from these are regulated through ligand binding and further modulated by a diverse variety of interactors. The challenge now is to understand the molecular mechanisms of these reported interactors. Recently attributed roles of LysM receptors in the perception of rhizobial exopolysaccharide, distinguishing between pathogens and symbionts, and assembly of root and rhizosphere communities expand on the importance of these receptors. These studies also highlight challenges, such as identification of cognate ligands, formation of responsive receptor complexes and separation of downstream signal transduction pathways.
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Affiliation(s)
- Simon Kelly
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK - 8000 Aarhus, Denmark
| | - Simona Radutoiu
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK - 8000 Aarhus, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK - 8000 Aarhus, Denmark.
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50
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Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens. PLoS Pathog 2017; 13:e1006525. [PMID: 28742161 PMCID: PMC5542703 DOI: 10.1371/journal.ppat.1006525] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/03/2017] [Accepted: 07/12/2017] [Indexed: 02/06/2023] Open
Abstract
Extracellular capsules constitute the outermost layer of many bacteria, are major virulence factors, and affect antimicrobial therapies. They have been used as epidemiological markers and recently became vaccination targets. Despite the efforts to biochemically serotype capsules in a few model pathogens, little is known of their taxonomic and environmental distribution. We developed, validated, and made available a computational tool, CapsuleFinder, to identify capsules in genomes. The analysis of over 2500 prokaryotic genomes, accessible in a database, revealed that ca. 50% of them—including Archaea—encode a capsule. The Wzx/Wzy-dependent capsular group was by far the most abundant. Surprisingly, a fifth of the genomes encode more than one capsule system—often from different groups—and their non-random co-occurrence suggests the existence of negative and positive epistatic interactions. To understand the role of multiple capsules, we queried more than 6700 metagenomes for the presence of species encoding capsules and showed that their distribution varied between environmental categories and, within the human microbiome, between body locations. Species encoding capsules, and especially those encoding multiple capsules, had larger environmental breadths than the other species. Accordingly, capsules were more frequent in environmental bacteria than in pathogens and, within the latter, they were more frequent among facultative pathogens. Nevertheless, capsules were frequent in clinical samples, and were usually associated with fast-growing bacteria with high infectious doses. Our results suggest that capsules increase the environmental range of bacteria and make them more resilient to environmental perturbations. Capsules might allow opportunistic pathogens to profit from empty ecological niches or environmental perturbations, such as those resulting from antibiotic therapy, to colonize the host. Capsule-associated virulence might thus be a by-product of environmental adaptation. Understanding the role of capsules in natural environments might enlighten their function in pathogenesis. Extracellular capsules protect bacterial cells from external aggressions such as antibiotics or desiccation, but can also be targeted by vaccines. Since little was known about their frequency across Prokaryotes, we created and made freely available a computational tool, CapsuleFinder, to identify them from genomic data. Surprisingly, its use showed that many bacterial strains, especially those with the largest genomes, encode several capsules. The frequencies of the different combinations of capsule groups depended strongly on the phyla and the groups themselves, suggesting the existence of epistatic interactions between capsules. Bacteria encoding capsule systems were found in many natural environments, and were frequent in the human microbiome. In contrast to their frequent association with virulence, we found many more capsules in non-pathogens or facultative pathogens than among obligatory pathogens. We suggest that capsules increase the environmental breadth of bacteria thereby facilitating host colonization by opportunistic pathogens.
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