1
|
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.
Collapse
|
2
|
Sharma A, Sinharoy S, Bisht NC. The mysterious non-arbuscular mycorrhizal status of Brassicaceae species. Environ Microbiol 2023; 25:917-930. [PMID: 36655756 DOI: 10.1111/1462-2920.16339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023]
Abstract
The Brassicaceae family is unique in not fostering functional symbiosis with arbuscular mycorrhiza (AM). The family is also special in possessing glucosinolates, a class of secondary metabolites predominantly functioning for plant defence. We have reviewed what effect the glucosinolates of this non-symbiotic host have on AM or vice versa. Isothiocyanates, the toxic degradation product of the glucosinolates, particularly the indolic and benzenic glucosinolates, are known to be involved in the inhibition of AM. Interestingly, AM colonization enhances glucosinolate production in two AM-host in the Brassicales family- Moringa oleifera and Tropaeolum spp. PHOSPHATE STARVATION RESPONSE 1 (PHR1), a central transcription factor that controls phosphate starvation response also activates the glucosinolate biosynthesis in AM non-host Arabidopsis thaliana. Recently, the advances in whole-genome sequencing, enabling extensive ecological microbiome studies have helped unravel the Brassicaceae microbiome, identifying new mutualists that compensate for the loss of AM symbiosis, and reporting cues for some influence of glucosinolates on the microbiome structure. We advocate that glucosinolate is an important candidate in determining the mycorrhizal status of Brassicaceae and has played a major role in its symbiosis-defence trade-off. We also identify key open questions in this area that remain to be addressed in the future.
Collapse
Affiliation(s)
- Aprajita Sharma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Naveen C Bisht
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| |
Collapse
|
3
|
Khatri R, Pant SR, Sharma K, Niraula PM, Lawaju BR, Lawrence KS, Alkharouf NW, Klink VP. Glycine max Homologs of DOESN'T MAKE INFECTIONS 1, 2, and 3 Function to Impair Heterodera glycines Parasitism While Also Regulating Mitogen Activated Protein Kinase Expression. FRONTIERS IN PLANT SCIENCE 2022; 13:842597. [PMID: 35599880 PMCID: PMC9114929 DOI: 10.3389/fpls.2022.842597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
Glycine max root cells developing into syncytia through the parasitic activities of the pathogenic nematode Heterodera glycines underwent isolation by laser microdissection (LM). Microarray analyses have identified the expression of a G. max DOESN'T MAKE INFECTIONS3 (DMI3) homolog in syncytia undergoing parasitism but during a defense response. DMI3 encodes part of the common symbiosis pathway (CSP) involving DMI1, DMI2, and other CSP genes. The identified DMI gene expression, and symbiosis role, suggests the possible existence of commonalities between symbiosis and defense. G. max has 3 DMI1, 12 DMI2, and 2 DMI3 paralogs. LM-assisted gene expression experiments of isolated syncytia under further examination here show G. max DMI1-3, DMI2-7, and DMI3-2 expression occurring during the defense response in the H. glycines-resistant genotypes G.max [Peking/PI548402] and G.max [PI88788] indicating a broad and consistent level of expression of the genes. Transgenic overexpression (OE) of G. max DMI1-3, DMI2-7, and DMI3-2 impairs H. glycines parasitism. RNA interference (RNAi) of G. max DMI1-3, DMI2-7, and DMI3-2 increases H. glycines parasitism. The combined opposite outcomes reveal a defense function for these genes. Prior functional transgenic analyses of the 32-member G. max mitogen activated protein kinase (MAPK) gene family has determined that 9 of them act in the defense response to H. glycines parasitism, referred to as defense MAPKs. RNA-seq analyses of root RNA isolated from the 9 G. max defense MAPKs undergoing OE or RNAi reveal they alter the relative transcript abundances (RTAs) of specific DMI1, DMI2, and DMI3 paralogs. In contrast, transgenically-manipulated DMI1-3, DMI2-7, and DMI3-2 expression influences MAPK3-1 and MAPK3-2 RTAs under certain circumstances. The results show G. max homologs of the CSP, and defense pathway are linked, apparently involving co-regulated gene expression.
Collapse
Affiliation(s)
- Rishi Khatri
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Shankar R. Pant
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Keshav Sharma
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Prakash M. Niraula
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Bisho R. Lawaju
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - Kathy S. Lawrence
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - Nadim W. Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD, United States
| | - Vincent P. Klink
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States
- USDA ARS NEA BARC Molecular Plant Pathology Laboratory, Beltsville, MD, United States
- Center for Computational Sciences High Performance Computing Collaboratory, Mississippi State University, Starkville, MS, United States
| |
Collapse
|
4
|
Rutten L, Miyata K, Roswanjaya YP, Huisman R, Bu F, Hartog M, Linders S, van Velzen R, van Zeijl A, Bisseling T, Kohlen W, Geurts R. Duplication of Symbiotic Lysin Motif Receptors Predates the Evolution of Nitrogen-Fixing Nodule Symbiosis. PLANT PHYSIOLOGY 2020; 184:1004-1023. [PMID: 32669419 PMCID: PMC7536700 DOI: 10.1104/pp.19.01420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/07/2020] [Indexed: 05/02/2023]
Abstract
Rhizobium nitrogen-fixing nodule symbiosis occurs in two taxonomic lineages: legumes (Fabaceae) and the genus Parasponia (Cannabaceae). Both symbioses are initiated upon the perception of rhizobium-secreted lipochitooligosaccharides (LCOs), called Nod factors. Studies in the model legumes Lotus japonicus and Medicago truncatula showed that rhizobium LCOs are perceived by a heteromeric receptor complex of distinct Lys motif (LysM)-type transmembrane receptors named NOD FACTOR RECEPTOR1 (LjNFR1) and LjNFR5 (L. japonicus) and LYSM DOMAIN CONTAINING RECEPTOR KINASE3 (MtLYK3)-NOD FACTOR PERCEPTION (MtNFP; M. truncatula). Recent phylogenomic comparative analyses indicated that the nodulation traits of legumes, Parasponia spp., as well as so-called actinorhizal plants that establish a symbiosis with diazotrophic Frankia spp. bacteria share an evolutionary origin about 110 million years ago. However, the evolutionary trajectory of LysM-type LCO receptors remains elusive. By conducting phylogenetic analysis, transcomplementation studies, and CRISPR-Cas9 mutagenesis in Parasponia andersonii, we obtained insight into the origin of LCO receptors essential for nodulation. We identified four LysM-type receptors controlling nodulation in P. andersonii: PanLYK1, PanLYK3, PanNFP1, and PanNFP2 These genes evolved from ancient duplication events predating and coinciding with the origin of nodulation. Phylogenetic and functional analyses associated the occurrence of a functional NFP2-orthologous receptor to LCO-driven nodulation. Legumes and Parasponia spp. use orthologous LysM-type receptors to perceive rhizobium LCOs, suggesting a shared evolutionary origin of LCO-driven nodulation. Furthermore, we found that both PanLYK1 and PanLYK3 are essential for intracellular arbuscule formation of mutualistic endomycorrhizal fungi. PanLYK3 also acts as a chitin oligomer receptor essential for innate immune signaling, demonstrating functional analogy to CHITIN ELECITOR RECEPTOR KINASE-type receptors.
Collapse
Affiliation(s)
- Luuk Rutten
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Kana Miyata
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Yuda Purwana Roswanjaya
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
- Centre of Technology for Agricultural Production, Agency for the Assessment and Application of Technology, 10340 Jakarta, Indonesia
| | - Rik Huisman
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Fengjiao Bu
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Marijke Hartog
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Sidney Linders
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Arjan van Zeijl
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
5
|
Tokumoto Y, Hashimoto K, Soyano T, Aoki S, Iwasaki W, Fukuhara M, Nakagawa T, Saeki K, Yokoyama J, Fujita H, Kawaguchi M. Assessment of Polygala paniculata (Polygalaceae) characteristics for evolutionary studies of legume-rhizobia symbiosis. JOURNAL OF PLANT RESEARCH 2020; 133:109-122. [PMID: 31828682 PMCID: PMC8057963 DOI: 10.1007/s10265-019-01159-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/02/2019] [Indexed: 06/10/2023]
Abstract
Root nodule (RN) symbiosis is a mutualistic interaction observed between nitrogen-fixing soil bacteria and nodulating plants, which are scattered in only four orders of angiosperms called nitrogen-fixing clade. Most of legumes engage in RN symbiosis with rhizobia. Molecular genetic analyses with legumes and non-leguminous nodulating plants revealed that RN symbiosis utilizes early signalling components that are required for symbiosis with arbuscular mycorrhizal (AM) fungi. However detailed evolutionary processes are still largely unknown. Comparative analyses with non-nodulating species phylogenetically related to legumes could be better strategies to study the evolution of RN symbiosis in legumes. Polygala paniculata is a non-leguminous species that belongs to a family different from legumes but that is classified into the same order, Fabales. It has appropriate characteristics for cultivation in laboratories: small body size, high fertility and short lifecycles. Therefore, we further assessed whether this species is suitable as a model species for comparative studies with legumes. We first validated that the plant we obtained in Palau was truly P. paniculata by molecular phylogenetic analysis using rbcL sequences. The estimated genome size of this species was less than those of two model legumes, Lotus japonicus and Medicago truncatula. We determined conditions for cultivation in vitro and for hairy root formation from P. paniculata seedlings. It would facilitate to investigate gene functions in this species. The ability of P. paniculata to interact with AM fungi was confirmed by inoculation with Rhizophagus irregularis, suggesting the presence of early signalling factors that might be involved in RN symbiosis. Unexpectedly, branching of root hairs was observed when inoculated with Mesorhizobium loti broad host range strain NZP2037, indicating that P. paniculata has the biological potential to respond to rhizobia. We propose that P. paniculata is used as a model plant for the evolutionary study of RN symbiosis.
Collapse
Grants
- 16H01248 Ministry of Education, Culture, Sports, Science and Technology
- 16H06279 Ministry of Education, Culture, Sports, Science and Technology
- 16K08149 Ministry of Education, Culture, Sports, Science and Technology
- 17K07509 Ministry of Education, Culture, Sports, Science and Technology
Collapse
Affiliation(s)
- Yuji Tokumoto
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444 8585, Japan
| | - Kayo Hashimoto
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444 8585, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444 8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444 8585, Japan
| | - Seishiro Aoki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113 0032, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113 0032, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564, Japan
| | - Mai Fukuhara
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444 8585, Japan
| | - Tomomi Nakagawa
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464 8602, Japan
| | - Kazuhiko Saeki
- Department of Biological Sciences and Kyousei Science Center for Life and Nature, Nara Women's University, Nara, 630 8506, Japan
| | - Jun Yokoyama
- Faculty of Science, Yamagata University, Yamagata, 990 8560, Japan
| | - Hironori Fujita
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444 8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444 8585, Japan
- Astrobiology Center, Mitaka, Tokyo, 181 8588, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444 8585, Japan.
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444 8585, Japan.
| |
Collapse
|
6
|
He J, Zhang C, Dai H, Liu H, Zhang X, Yang J, Chen X, Zhu Y, Wang D, Qi X, Li W, Wang Z, An G, Yu N, He Z, Wang YF, Xiao Y, Zhang P, Wang E. A LysM Receptor Heteromer Mediates Perception of Arbuscular Mycorrhizal Symbiotic Signal in Rice. MOLECULAR PLANT 2019; 12:1561-1576. [PMID: 31706032 DOI: 10.1016/j.molp.2019.10.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
Symbiotic microorganisms improve nutrient uptake by plants. To initiate mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, plants perceive Myc factors, including lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (CO4/CO5), secreted by AM fungi. However, the molecular mechanism of Myc factor perception remains elusive. In this study, we identified a heteromer of LysM receptor-like kinases consisting of OsMYR1/OsLYK2 and OsCERK1 that mediates the perception of AM fungi in rice. CO4 directly binds to OsMYR1, promoting the dimerization and phosphorylation of this receptor complex. Compared with control plants, Osmyr1 and Oscerk1 mutant rice plants are less sensitive to Myc factors and show decreased AM colonization. We engineered transgenic rice by expressing chimeric receptors that respectively replaced the ectodomains of OsMYR1 and OsCERK1 with those from the homologous Nod factor receptors MtNFP and MtLYK3 of Medicago truncatula. Transgenic plants displayed increased calcium oscillations in response to Nod factors compared with control rice. Our study provides significant mechanistic insights into AM symbiotic signal perception in rice. Expression of chimeric Nod/Myc receptors achieves a potentially important step toward generating cereals that host nitrogen-fixing bacteria.
Collapse
Affiliation(s)
- Jiangman He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chi Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huiling Dai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Huan Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xi Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yayun Zhu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Dapeng Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Xiaofeng Qi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Weichao Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhihui Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Guoyong An
- Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Nan Yu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yong-Fei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Youli Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| |
Collapse
|
7
|
Kumar J, Choudhary AK, Gupta DS, Kumar S. Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses. Int J Mol Sci 2019; 20:E2971. [PMID: 31216660 PMCID: PMC6627977 DOI: 10.3390/ijms20122971] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/18/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.
Collapse
Affiliation(s)
- Jitendra Kumar
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | | | - Debjyoti Sen Gupta
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 6299, Rabat-Institute, Rabat, Morocco.
| |
Collapse
|
8
|
Das DR, Horváth B, Kundu A, Kaló P, DasGupta M. Functional conservation of CYCLOPS in crack entry legume Arachis hypogaea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:232-241. [PMID: 30824056 DOI: 10.1016/j.plantsci.2018.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
Root nodule symbiosis in legumes is established following interaction of compatible rhizobia that activates an array of genes, commonly known as symbiotic-pathway, resulting in nodule development. In model legumes, bacterial entry mainly occurs through infection thread involving the expression of transcription factor CYCLOPS/IPD3. Here we show the functional analysis of AhCYCLOPS in Arachis hypogaea where bacteria invade roots through epidermal cracks. Exploiting significant cross-species domain conservation, trans-complementation experiments involving ectopic expression of AhCYCLOPS in transgenic hairy-roots of Medicago truncatula ipd3 mutants resulted in functional complementation of Medicago nodules. Moreover, native promoter of AhCYCLOPS was sufficient for this cross-species complementation irrespective of the different modes of infection of roots by rhizobia and nodule ontology. To unravel the role of AhCYCLOPS during 'crack-entry' nodulation in A. hypogaea, RNAi of AhCYCLOPS was performed which resulted in delayed nodule inception followed by drastic reduction in nodule number on transgenic hairy-roots. The infection zone of a significant number of RNAi nodules showed presence of infected cells with enlarged nucleus and rod shaped undifferentiated bacteria. Expression analysis showed downregulation of several nodulation responsible effectors endorsing the compromised condition of RNAi roots. Together, the results indicated that AhCYCLOPS plays an important role in A. hypogaea nodule development.
Collapse
Affiliation(s)
- Debapriya Rajlakshmi Das
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Beatrix Horváth
- Agricultural Biotechnology Institute, NARIC, Szent-Györgyi Albert u. 4, Gödöllő, Hungary
| | - Anindya Kundu
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Péter Kaló
- Agricultural Biotechnology Institute, NARIC, Szent-Györgyi Albert u. 4, Gödöllő, Hungary
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| |
Collapse
|
9
|
Kafle A, Garcia K, Wang X, Pfeffer PE, Strahan GD, Bücking H. Nutrient demand and fungal access to resources control the carbon allocation to the symbiotic partners in tripartite interactions of Medicago truncatula. PLANT, CELL & ENVIRONMENT 2019; 42:270-284. [PMID: 29859016 DOI: 10.1111/pce.13359] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 05/04/2023]
Abstract
Legumes form tripartite interactions with arbuscular mycorrhizal fungi and rhizobia, and both root symbionts exchange nutrients against carbon from their host. The carbon costs of these interactions are substantial, but our current understanding of how the host controls its carbon allocation to individual root symbionts is limited. We examined nutrient uptake and carbon allocation in tripartite interactions of Medicago truncatula under different nutrient supply conditions, and when the fungal partner had access to nitrogen, and followed the gene expression of several plant transporters of the Sucrose Uptake Transporter (SUT) and Sugars Will Eventually be Exported Transporter (SWEET) family. Tripartite interactions led to synergistic growth responses and stimulated the phosphate and nitrogen uptake of the plant. Plant nutrient demand but also fungal access to nutrients played an important role for the carbon transport to different root symbionts, and the plant allocated more carbon to rhizobia under nitrogen demand, but more carbon to the fungal partner when nitrogen was available. These changes in carbon allocation were consistent with changes in the SUT and SWEET expression. Our study provides important insights into how the host plant controls its carbon allocation under different nutrient supply conditions and changes its carbon allocation to different root symbionts to maximize its symbiotic benefits.
Collapse
Affiliation(s)
- Arjun Kafle
- South Dakota State University, Biology and Microbiology Department, Brookings, South Dakota
| | - Kevin Garcia
- South Dakota State University, Biology and Microbiology Department, Brookings, South Dakota
| | - Xiurong Wang
- South Dakota State University, Biology and Microbiology Department, Brookings, South Dakota
- South China Agricultural University, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Root Biology Center, Guangzhou, China
| | - Philip E Pfeffer
- Eastern Regional Research Center, USDA, Agricultural Research Service, Wyndmoor, Pennslyvania
| | - Gary D Strahan
- Eastern Regional Research Center, USDA, Agricultural Research Service, Wyndmoor, Pennslyvania
| | - Heike Bücking
- South Dakota State University, Biology and Microbiology Department, Brookings, South Dakota
| |
Collapse
|
10
|
Miura C, Yamaguchi K, Miyahara R, Yamamoto T, Fuji M, Yagame T, Imaizumi-Anraku H, Yamato M, Shigenobu S, Kaminaka H. The Mycoheterotrophic Symbiosis Between Orchids and Mycorrhizal Fungi Possesses Major Components Shared with Mutualistic Plant-Mycorrhizal Symbioses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1032-1047. [PMID: 29649962 DOI: 10.1094/mpmi-01-18-0029-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Achlorophylous and early developmental stages of chorolophylous orchids are highly dependent on carbon and other nutrients provided by mycorrhizal fungi, in a nutritional mode termed mycoheterotrophy. Previous findings have implied that some common properties at least partially underlie the mycorrhizal symbioses of mycoheterotrophic orchids and that of autotrophic arbuscular mycorrhizal (AM) plants; however, information about the molecular mechanisms of the relationship between orchids and their mycorrhizal fungi is limited. In this study, we characterized the molecular basis of an orchid-mycorrhizal (OM) symbiosis by analyzing the transcriptome of Bletilla striata at an early developmental stage associated with the mycorrhizal fungus Tulasnella sp. The essential components required for the establishment of mutual symbioses with AM fungi or rhizobia in most terrestrial plants were identified from the B. striata gene set. A cross-species gene complementation analysis showed one of the component genes, calcium and calmodulin-dependent protein kinase gene CCaMK in B. striata, retains functional characteristics of that in AM plants. The expression analysis revealed the activation of homologs of AM-related genes during the OM symbiosis. Our results suggest that orchids possess, at least partly, the molecular mechanisms common to AM plants.
Collapse
Affiliation(s)
- Chihiro Miura
- 1 Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Katsushi Yamaguchi
- 2 Functional Genomics Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Ryohei Miyahara
- 1 Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Tatsuki Yamamoto
- 3 Graduate School of Agriculture, Tottori University, Tottori, Japan
| | - Masako Fuji
- 1 Faculty of Agriculture, Tottori University, Tottori, Japan
| | | | - Haruko Imaizumi-Anraku
- 5 Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan; and
| | | | - Shuji Shigenobu
- 2 Functional Genomics Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | | |
Collapse
|
11
|
Chen A, Gu M, Wang S, Chen J, Xu G. Transport properties and regulatory roles of nitrogen in arbuscular mycorrhizal symbiosis. Semin Cell Dev Biol 2018. [DOI: 10.1016/j.semcdb.2017.06.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
12
|
Leppyanen IV, Shakhnazarova VY, Shtark OY, Vishnevskaya NA, Tikhonovich IA, Dolgikh EA. Receptor-Like Kinase LYK9 in Pisum sativum L. Is the CERK1-Like Receptor that Controls Both Plant Immunity and AM Symbiosis Development. Int J Mol Sci 2017; 19:E8. [PMID: 29267197 PMCID: PMC5795960 DOI: 10.3390/ijms19010008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 01/24/2023] Open
Abstract
Plants are able to discriminate and respond to structurally related chitooligosaccharide (CO) signals from pathogenic and symbiotic fungi. In model plants Arabidopsis thaliana and Oryza sativa LysM-receptor like kinases (LysM-RLK) AtCERK1 and OsCERK1 (chitin elicitor receptor kinase 1) were shown to be involved in response to CO signals. Based on phylogenetic analysis, the pea Pisum sativum L. LysM-RLK PsLYK9 was chosen as a possible candidate given its role on the CERK1-like receptor. The knockdown regulation of the PsLyk9 gene by RNA interference led to increased susceptibility to fungal pathogen Fusarium culmorum. Transcript levels of PsPAL2, PsPR10 defense-response genes were significantly reduced in PsLyk9 RNAi roots. PsLYK9's involvement in recognizing short-chain COs as most numerous signals of arbuscular mycorrhizal (AM) fungi, was also evaluated. In transgenic roots with PsLyk9 knockdown treated with short-chain CO5, downregulation of AM symbiosis marker genes (PsDELLA3, PsNSP2, PsDWARF27) was observed. These results clearly indicate that PsLYK9 appears to be involved in the perception of COs and subsequent signal transduction in pea roots. It allows us to conclude that PsLYK9 is the most likely CERK1-like receptor in pea to be involved in the control of plant immunity and AM symbiosis formation.
Collapse
Affiliation(s)
- Irina V Leppyanen
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Vlada Y Shakhnazarova
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Oksana Y Shtark
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Nadezhda A Vishnevskaya
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Igor A Tikhonovich
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Elena A Dolgikh
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| |
Collapse
|
13
|
Konishi N, Okubo T, Yamaya T, Hayakawa T, Minamisawa K. Nitrate Supply-Dependent Shifts in Communities of Root-Associated Bacteria in Arabidopsis. Microbes Environ 2017; 32:314-323. [PMID: 29187692 PMCID: PMC5745015 DOI: 10.1264/jsme2.me17031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application. The relative abundance of operational taxonomic units of 25.8% was significantly changed by the amount of nitrate supplied. Moreover, at the family level, the relative abundance of several major root-associated bacteria including Burkholderiaceae, Paenibacillaceae, Bradyrhizobiaceae, and Rhizobiaceae markedly fluctuated with the application of nitrate. These results suggest that the application of nitrate strongly affects root-associated bacterial ecosystems in Arabidopsis. Bulk soil bacterial communities were also affected by the application of nitrate; however, these changes were markedly different from those in root-associated bacteria. These results also suggest that nitrate-dependent alterations in root-associated bacterial communities are mainly affected by plant-derived factors in Arabidopsis. T-DNA insertion plant lines of the genes for two transcription factors involved in nitrate signaling in Arabidopsis roots, NLP7 and TCP20, showed similar nitrate-dependent shifts in root-associated bacterial communities from the wild-type, whereas minor differences were observed in root-associated bacteria. Thus, these results indicate that NLP7 and TCP20 are not major regulators of nitrate-dependent bacterial communities in Arabidopsis roots.
Collapse
Affiliation(s)
- Noriyuki Konishi
- Graduate School of Agricultural Science, Tohoku University.,Division for Interdisciplinary Advanced Research and Education, Tohoku University
| | - Takashi Okubo
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization
| | - Tomoyuki Yamaya
- Division for Interdisciplinary Advanced Research and Education, Tohoku University
| | | | | |
Collapse
|
14
|
Rhizobium as a Crop Enhancer and Biofertilizer for Increased Non-legume Production. SOIL BIOLOGY 2017. [DOI: 10.1007/978-3-319-64982-5_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
15
|
Miyata K, Hayafune M, Kobae Y, Kaku H, Nishizawa Y, Masuda Y, Shibuya N, Nakagawa T. Evaluation of the Role of the LysM Receptor-Like Kinase, OsNFR5/OsRLK2 for AM Symbiosis in Rice. PLANT & CELL PHYSIOLOGY 2016; 57:2283-2290. [PMID: 27519312 DOI: 10.1093/pcp/pcw144] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 08/05/2016] [Indexed: 05/19/2023]
Abstract
In legume-specific rhizobial symbiosis, host plants perceive rhizobial signal molecules, Nod factors, by a pair of LysM receptor-like kinases, NFR1/LYK3 and NFR5/NFP, and activate symbiotic responses through the downstream signaling components also required for arbuscular mycorrhizal (AM) symbiosis. Recently, the rice NFR1/LYK3 ortholog, OsCERK1, was shown to play crucial roles for AM symbiosis. On the other hand, the roles of the NFR5/NFP ortholog in rice have not been elucidated, while it has been shown that NFR5/NFP orthologs, Parasponia PaNFR5 and tomato SlRLK10, engage in AM symbiosis. OsCERK1 also triggers immune responses in combination with a receptor partner, OsCEBiP, against fungal or bacterial infection, thus regulating opposite responses against symbiotic and pathogenic microbes. However, it has not been elucidated how OsCERK1 switches these opposite functions. Here, we analyzed the function of the rice NFR5/NFP ortholog, OsNFR5/OsRLK2, as a possible candidate of the OsCERK1 partner for symbiotic signaling. Inoculation of AM fungi induced the expression of OsNFR5 in the rice root, and the chimeric receptor consisting of the extracellular domain of LjNFR5 and the intracellular domain of OsNFR5 complemented the Ljnfr5 mutant for rhizobial symbiosis, indicating that the intracellular kinase domain of OsNFR5 could activate symbiotic signaling in Lotus japonicus. Although these data suggested the possible involvement of OsNFR5 in AM symbiosis, osnfr5 knockout mutants were colonized by AM fungi similar to the wild-type rice. These observations suggested several possibilities including the presence of functionally redundant genes other than OsNFR5 or involvement of novel ligands, which do not require OsNFR5 for recognition.
Collapse
Affiliation(s)
- Kana Miyata
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Masahiro Hayafune
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Yoshihiro Kobae
- National Agriculture and Food Research Organization (NARO), Hokkaido Agricultural Research Center, Agro-environmental Research Division 1, Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555 Japan
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Yoko Nishizawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8602 Japan
| | - Yoshiki Masuda
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Tomomi Nakagawa
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585 Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602 Japan
| |
Collapse
|
16
|
Li Y, Jackson SA. Crowdsourcing the nodulation gene network discovery environment. BMC Bioinformatics 2016; 17:223. [PMID: 27230384 PMCID: PMC4880984 DOI: 10.1186/s12859-016-1089-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 05/21/2016] [Indexed: 11/16/2022] Open
Abstract
Background The Legumes (Fabaceae) are an economically and ecologically important group of plant species with the conspicuous capacity for symbiotic nitrogen fixation in root nodules, specialized plant organs containing symbiotic microbes. With the aim of understanding the underlying molecular mechanisms leading to nodulation, many efforts are underway to identify nodulation-related genes and determine how these genes interact with each other. In order to accurately and efficiently reconstruct nodulation gene network, a crowdsourcing platform, CrowdNodNet, was created. Results The platform implements the jQuery and vis.js JavaScript libraries, so that users are able to interactively visualize and edit the gene network, and easily access the information about the network, e.g. gene lists, gene interactions and gene functional annotations. In addition, all the gene information is written on MediaWiki pages, enabling users to edit and contribute to the network curation. Conclusions Utilizing the continuously updated, collaboratively written, and community-reviewed Wikipedia model, the platform could, in a short time, become a comprehensive knowledge base of nodulation-related pathways. The platform could also be used for other biological processes, and thus has great potential for integrating and advancing our understanding of the functional genomics and systems biology of any process for any species. The platform is available at http://crowd.bioops.info/, and the source code can be openly accessed at https://github.com/bioops/crowdnodnet under MIT License.
Collapse
Affiliation(s)
- Yupeng Li
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, 30602, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, 30602, GA, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, 30602, GA, USA. .,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, 30602, GA, USA.
| |
Collapse
|
17
|
Gu Y, Xing S, He C. Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution. Genome Biol Evol 2016; 8:635-48. [PMID: 26868598 PMCID: PMC4824202 DOI: 10.1093/gbe/evw021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2016] [Indexed: 02/07/2023] Open
Abstract
Gene loss is the driving force for changes in genome and morphology; however, this particular evolutionary event has been poorly investigated in leguminous plants. Legumes (Fabaceae) have some lineage-specific and diagnostic characteristics that are distinct from other angiosperms. To understand the potential role of gene loss in the evolution of legumes, we compared six genome-sequenced legume species of Papilionoideae, the largest representative clade of Fabaceae, such as Glycine max, with 34 nonlegume plant species, such as Arabidopsis thaliana. The results showed that the putative orthologs of the 34 Arabidopsis genes belonging to 29 gene families were absent in these legume species but these were conserved in the sequenced nonlegume angiosperm lineages. Further evolutionary analyses indicated that the orthologs of these genes were almost completely lost in the Papillionoideae ancestors, thus designated as the legume lost genes (LLGs), and these underwent purifying selection in nonlegume plants. Most LLGs were functionally unknown. In Arabidopsis, two LLGs were well-known genes that played a role in plant immunity such as HARMLESS TO OZONE LAYER 1 and HOPZ-ACTIVATED RESISTANCE 1, and 16 additional LLGs were predicted to participate in plant-pathogen interactions in in silico expression and protein-protein interaction network analyses. Most of these LLGs' orthologs in various plants were also found to be associated with biotic stress response, indicating the conserved role of these genes in plant defense. The evolutionary implication of LLGs during the development of the ability of symbiotic nitrogen fixation involving plant and bacterial interactions, which is a well-known characteristic of most legumes, is also discussed. Our work sheds light on the evolutionary implication of gene loss events in Papilionoideae evolution, as well as provides new insights into crop design to improve nitrogen fixation capacity.
Collapse
Affiliation(s)
- Yongzhe Gu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China Graduate University, Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Shilai Xing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China Graduate University, Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China
| |
Collapse
|
18
|
Qiao Z, Pingault L, Nourbakhsh-Rey M, Libault M. Comprehensive Comparative Genomic and Transcriptomic Analyses of the Legume Genes Controlling the Nodulation Process. FRONTIERS IN PLANT SCIENCE 2016; 7:34. [PMID: 26858743 PMCID: PMC4732000 DOI: 10.3389/fpls.2016.00034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/10/2016] [Indexed: 06/05/2023]
Abstract
Nitrogen is one of the most essential plant nutrients and one of the major factors limiting crop productivity. Having the goal to perform a more sustainable agriculture, there is a need to maximize biological nitrogen fixation, a feature of legumes. To enhance our understanding of the molecular mechanisms controlling the interaction between legumes and rhizobia, the symbiotic partner fixing and assimilating the atmospheric nitrogen for the plant, researchers took advantage of genetic and genomic resources developed across different legume models (e.g., Medicago truncatula, Lotus japonicus, Glycine max, and Phaseolus vulgaris) to identify key regulatory protein coding genes of the nodulation process. In this study, we are presenting the results of a comprehensive comparative genomic analysis to highlight orthologous and paralogous relationships between the legume genes controlling nodulation. Mining large transcriptomic datasets, we also identified several orthologous and paralogous genes characterized by the induction of their expression during nodulation across legume plant species. This comprehensive study prompts new insights into the evolution of the nodulation process in legume plant and will benefit the scientific community interested in the transfer of functional genomic information between species.
Collapse
|
19
|
Nakagawa T, Imaizumi-Anraku H. Rice arbuscular mycorrhiza as a tool to study the molecular mechanisms of fungal symbiosis and a potential target to increase productivity. RICE (NEW YORK, N.Y.) 2015; 8:32. [PMID: 26516078 PMCID: PMC4626465 DOI: 10.1186/s12284-015-0067-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 10/22/2015] [Indexed: 05/08/2023]
Abstract
Rice (Oryza sativa L.) is a monocot model crop for cereal molecular biology. Following the emergence of molecular genetics of arbuscular mycorrhizal (AM) symbiosis in model legumes in the 1990s, studies on rice genetic resources have considerably contributed to our understanding of the molecular mechanisms and evolution of root intracellular symbioses.In this review, we trace the history of these studies and suggest the potential utility of AM symbiosis for improvement in rice productivity.
Collapse
Affiliation(s)
- Tomomi Nakagawa
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Haruko Imaizumi-Anraku
- Division of Plant Sicences, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki, 305-8602, Japan.
| |
Collapse
|
20
|
Watts-Williams SJ, Cavagnaro TR. Using mycorrhiza-defective mutant genotypes of non-legume plant species to study the formation and functioning of arbuscular mycorrhiza: a review. MYCORRHIZA 2015; 25:587-97. [PMID: 25862569 DOI: 10.1007/s00572-015-0639-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/18/2015] [Indexed: 05/03/2023]
Abstract
A significant challenge facing the study of arbuscular mycorrhiza is the establishment of suitable non-mycorrhizal treatments that can be compared with mycorrhizal treatments. A number of options are available, including soil disinfection or sterilisation, comparison of constitutively mycorrhizal and non-mycorrhizal plant species, comparison of plants grown in soils with different inoculum potential and the comparison of mycorrhiza-defective mutant genotypes with their mycorrhizal wild-type progenitors. Each option has its inherent advantages and limitations. Here, the potential to use mycorrhiza-defective mutant and wild-type genotype plant pairs as tools to study the functioning of mycorrhiza is reviewed. The emphasis of this review is placed on non-legume plant species, as mycorrhiza-defective plant genotypes in legumes have recently been extensively reviewed. It is concluded that non-legume mycorrhiza-defective mutant and wild-type pairs are useful tools in the study of mycorrhiza. However, the mutant genotypes should be well characterised and, ideally, meet a number of key criteria. The generation of more mycorrhiza-defective mutant genotypes in agronomically important plant species would be of benefit, as would be more research using these genotype pairs, especially under field conditions.
Collapse
Affiliation(s)
- Stephanie J Watts-Williams
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia.
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA.
| | - Timothy R Cavagnaro
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| |
Collapse
|
21
|
Chen X, Miché L, Sachs S, Wang Q, Buschart A, Yang H, Vera Cruz CM, Hurek T, Reinhold-Hurek B. Rice responds to endophytic colonization which is independent of the common symbiotic signaling pathway. THE NEW PHYTOLOGIST 2015; 208:531-43. [PMID: 26009800 DOI: 10.1111/nph.13458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/13/2015] [Indexed: 05/11/2023]
Abstract
As molecular interactions of plants with N2 -fixing endophytes are largely uncharacterized, we investigated whether the common signaling pathway (CSP) shared by root nodule symbioses (RNS) and arbuscular mycorrhizal (AM) symbioses may have been recruited for the endophytic Azoarcus sp.-rice (Oryza sativa) interaction, and combined this investigation with global approaches to characterize rice root responses to endophytic colonization. Putative homologs of genes required for the CSP were analyzed for their putative role in endophytic colonization. Proteomic and suppressive subtractive hybridization (SSH) approaches were also applied, and a comparison of defense-related processes was carried out by setting up a pathosystem for flooded roots with Xanthomonas oryzae pv. oryzae strain PXO99 (Xoo). All tested genes were expressed in rice roots seedlings but not induced upon Azoarcus sp. inoculation, and the oscyclops and oscastor mutants were not impaired in endophytic colonization. Global approaches highlighted changes in rice metabolic activity and Ca(2+) -dependent signaling in roots colonized by endophytes, including some stress proteins. Marker genes for defense responses were induced to a lesser extent by the endophytes than by the pathogen, indicating a more compatible interaction. Our results thus suggest that rice roots respond to endophytic colonization by inducing metabolic shifts and signaling events, for which the CSP is not essential.
Collapse
Affiliation(s)
- Xi Chen
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Lucie Miché
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Sabrina Sachs
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Qi Wang
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Anna Buschart
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Haiyuan Yang
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Casiana M Vera Cruz
- The International Rice Research Institute, MCPC Box 3727, 1271, Makati, Philippines
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| |
Collapse
|
22
|
Indrasumunar A, Wilde J, Hayashi S, Li D, Gresshoff PM. Functional analysis of duplicated Symbiosis Receptor Kinase (SymRK) genes during nodulation and mycorrhizal infection in soybean (Glycine max). JOURNAL OF PLANT PHYSIOLOGY 2015; 176:157-68. [PMID: 25617765 DOI: 10.1016/j.jplph.2015.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/23/2014] [Accepted: 01/02/2015] [Indexed: 06/04/2023]
Abstract
Association between legumes and rhizobia results in the formation of root nodules, where symbiotic nitrogen fixation occurs. The early stages of this association involve a complex of signalling events between the host and microsymbiont. Several genes dealing with early signal transduction have been cloned, and one of them encodes the leucine-rich repeat (LRR) receptor kinase (SymRK; also termed NORK). The Symbiosis Receptor Kinase gene is required by legumes to establish a root endosymbiosis with Rhizobium bacteria as well as mycorrhizal fungi. Using degenerate primer and BAC sequencing, we cloned duplicated SymRK homeologues in soybean called GmSymRKα and GmSymRKβ. These duplicated genes have high similarity of nucleotide (96%) and amino acid sequence (95%). Sequence analysis predicted a malectin-like domain within the extracellular domain of both genes. Several putative cis-acting elements were found in promoter regions of GmSymRKα and GmSymRKβ, suggesting a participation in lateral root development, cell division and peribacteroid membrane formation. The mutant of SymRK genes is not available in soybean; therefore, to know the functions of these genes, RNA interference (RNAi) of these duplicated genes was performed. For this purpose, RNAi construct of each gene was generated and introduced into the soybean genome by Agrobacterium rhizogenes-mediated hairy root transformation. RNAi of GmSymRKβ gene resulted in an increased reduction of nodulation and mycorrhizal infection than RNAi of GmSymRKα, suggesting it has the major activity of the duplicated gene pair. The results from the important crop legume soybean confirm the joint phenotypic action of GmSymRK genes in both mycorrhizal and rhizobial infection seen in model legumes.
Collapse
Affiliation(s)
- Arief Indrasumunar
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Julia Wilde
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Satomi Hayashi
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Dongxue Li
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Peter M Gresshoff
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia.
| |
Collapse
|
23
|
Wang JP, Munyampundu JP, Xu YP, Cai XZ. Phylogeny of Plant Calcium and Calmodulin-Dependent Protein Kinases (CCaMKs) and Functional Analyses of Tomato CCaMK in Disease Resistance. FRONTIERS IN PLANT SCIENCE 2015; 6:1075. [PMID: 26697034 PMCID: PMC4672059 DOI: 10.3389/fpls.2015.01075] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/17/2015] [Indexed: 05/14/2023]
Abstract
Calcium and calmodulin-dependent protein kinase (CCaMK) is a member of calcium/calmodulin-dependent protein kinase superfamily and is essential to microbe- plant symbiosis. To date, the distribution of CCaMK gene in plants has not yet been completely understood, and its function in plant disease resistance remains unclear. In this study, we systemically identified the CCaMK genes in genomes of 44 plant species in Phytozome and analyzed the function of tomato CCaMK (SlCCaMK) in resistance to various pathogens. CCaMKs in 18 additional plant species were identified, yet the absence of CCaMK gene in green algae and cruciferous species was confirmed. Sequence analysis of full-length CCaMK proteins from 44 plant species demonstrated that plant CCaMKs are highly conserved across all domains. Most of the important regulatory amino acids are conserved throughout all sequences, with the only notable exception being observed in N-terminal autophosphorylation site corresponding to Ser 9 in the Medicago truncatula CCaMK. CCaMK gene structures are similar, mostly containing six introns with a phase profile of 200200 and the exception was only noticed at the first exons. Phylogenetic analysis demonstrated that CCaMK lineage is likely to have diverged early from a calcium-dependent protein kinase (CDPK) gene in the ancestor of all nonvascular plant species. The SlCCaMK gene was widely and differently responsive to diverse pathogenic stimuli. Furthermore, knock-down of SlCCaMK reduced tomato resistance to Sclerotinia sclerotiorum and Pseudomonas syringae pv. tomato (Pst) DC3000 and decreased H2O2 accumulation in response to Pst DC3000 inoculation. Our results reveal that SlCCaMK positively regulates disease resistance in tomato via promoting H2O2 accumulation. SlCCaMK is the first CCaMK gene proved to function in plant disease resistance.
Collapse
Affiliation(s)
- Ji-Peng Wang
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Jean-Pierre Munyampundu
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - You-Ping Xu
- Centre of Analysis and Measurement, Zhejiang UniversityHangzhou, China
| | - Xin-Zhong Cai
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
- State Key Laboratory of Rice Biology, Zhejiang UniversityHangzhou, China
- *Correspondence: Xin-Zhong Cai
| |
Collapse
|
24
|
Miyata K, Kozaki T, Kouzai Y, Ozawa K, Ishii K, Asamizu E, Okabe Y, Umehara Y, Miyamoto A, Kobae Y, Akiyama K, Kaku H, Nishizawa Y, Shibuya N, Nakagawa T. The bifunctional plant receptor, OsCERK1, regulates both chitin-triggered immunity and arbuscular mycorrhizal symbiosis in rice. PLANT & CELL PHYSIOLOGY 2014; 55:1864-72. [PMID: 25231970 DOI: 10.1093/pcp/pcu129] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plants are constantly exposed to threats from pathogenic microbes and thus developed an innate immune system to protect themselves. On the other hand, many plants also have the ability to establish endosymbiosis with beneficial microbes such as arbuscular mycorrhizal (AM) fungi or rhizobial bacteria, which improves the growth of host plants. How plants evolved these systems managing such opposite plant-microbe interactions is unclear. We show here that knockout (KO) mutants of OsCERK1, a rice receptor kinase essential for chitin signaling, were impaired not only for chitin-triggered defense responses but also for AM symbiosis, indicating the bifunctionality of OsCERK1 in defense and symbiosis. On the other hand, a KO mutant of OsCEBiP, which forms a receptor complex with OsCERK1 and is essential for chitin-triggered immunity, established mycorrhizal symbiosis normally. Therefore, OsCERK1 but not chitin-triggered immunity is required for AM symbiosis. Furthermore, experiments with chimeric receptors showed that the kinase domains of OsCERK1 and homologs from non-leguminous, mycorrhizal plants could trigger nodulation signaling in legume-rhizobium interactions as the kinase domain of Nod factor receptor1 (NFR1), which is essential for triggering the nodulation program in leguminous plants, did. Because leguminous plants are believed to have developed the rhizobial symbiosis on the basis of AM symbiosis, our results suggest that the symbiotic function of ancestral CERK1 in AM symbiosis enabled the molecular evolution to leguminous NFR1 and resulted in the establishment of legume-rhizobia symbiosis. These results also suggest that OsCERK1 and homologs serve as a molecular switch that activates defense or symbiotic responses depending on the infecting microbes.
Collapse
Affiliation(s)
- Kana Miyata
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan These authors contributed equally to this work
| | - Toshinori Kozaki
- Tokyo University of Agriculture & Technology, Fuchu, Tokyo, 183-8509 Japan These authors contributed equally to this work
| | - Yusuke Kouzai
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Kenjirou Ozawa
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Kazuo Ishii
- Tokyo University of Agriculture & Technology, Fuchu, Tokyo, 183-8509 Japan
| | - Erika Asamizu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572 Japan
| | - Yoshihiro Okabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572 Japan
| | - Yosuke Umehara
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Ayano Miyamoto
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Yoshihiro Kobae
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Kohki Akiyama
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531 Japan
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Yoko Nishizawa
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Tomomi Nakagawa
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| |
Collapse
|
25
|
Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution. PLoS Genet 2014; 10:e1004487. [PMID: 25032823 PMCID: PMC4102449 DOI: 10.1371/journal.pgen.1004487] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 05/20/2014] [Indexed: 02/06/2023] Open
Abstract
Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant–microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages. Symbiotic associations between eukaryotes and microbes play essential roles in the nutrition, health and behavior of both partners. It is well accepted that hosts control and shape their associated microbiome. In this study, we provide evidence that symbiotic microbes also participate in the evolution of host genomes. In particular, we show that the independent loss of a symbiosis in several plant lineages results in a convergent modification of non-host genomes. Interestingly, a significant fraction of genes lost in non-hosts play an important role in this symbiosis, supporting the use of comparative genomics as a powerful approach to identify undiscovered gene networks.
Collapse
|
26
|
Delaux PM, Varala K, Edger PP, Coruzzi GM, Pires JC, Ané JM. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution. PLoS Genet 2014. [PMID: 25032823 DOI: 10.1371/journal.pgen.100448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant-microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.
Collapse
Affiliation(s)
- Pierre-Marc Delaux
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kranthi Varala
- Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Patrick P Edger
- Bond Life Sciences Center, Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - J Chris Pires
- Bond Life Sciences Center, Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
27
|
De Mita S, Streng A, Bisseling T, Geurts R. Evolution of a symbiotic receptor through gene duplications in the legume-rhizobium mutualism. THE NEW PHYTOLOGIST 2014; 201:961-972. [PMID: 24400903 DOI: 10.1111/nph.12549] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/16/2013] [Indexed: 05/11/2023]
Abstract
The symbiosis between legumes and nitrogen-fixing rhizobia co-opted pre-existing endomycorrhizal features. In particular, both symbionts release lipo-chitooligosaccharides (LCOs) that are recognized by LysM-type receptor kinases. We investigated the evolutionary history of rhizobial LCO receptor genes MtLYK3-LjNFR1 to gain insight into the evolutionary origin of the rhizobial symbiosis. We performed a phylogenetic analysis integrating gene copies from nonlegumes and legumes, including the non-nodulating, phylogenetically basal legume Cercis chinensis. Signatures of differentiation between copies were investigated through patterns of molecular evolution. We show that two rounds of duplication preceded the evolution of the rhizobial symbiosis in legumes. Molecular evolution patterns indicate that the resulting three paralogous gene copies experienced different selective constraints. In particular, one copy maintained the ancestral function, and another specialized into perception of rhizobial LCOs. It has been suggested that legume LCO receptors evolved from a putative ancestral defense-related chitin receptor through the acquisition of two kinase motifs. However, the phylogenetic analysis shows that these domains are actually ancestral, suggesting that this scenario is unlikely. Our study underlines the evolutionary significance of gene duplication and subsequent neofunctionalization in MtLYK3-LjNFR1 genes. We hypothesize that their ancestor was more likely a mycorrhizal LCO receptor, than a defense-related receptor kinase.
Collapse
Affiliation(s)
- Stéphane De Mita
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
- INRA Nancy-Lorraine, UMR Interactions Arbres/Micro-organismes, 54380, Champenoux, France
| | - Arend Streng
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - René Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| |
Collapse
|
28
|
Chen C, Zhu H. Are common symbiosis genes required for endophytic rice-rhizobial interactions? PLANT SIGNALING & BEHAVIOR 2013; 8:25453. [PMID: 23838959 PMCID: PMC4002627 DOI: 10.4161/psb.25453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Legume plants are able to establish root nodule symbioses with nitrogen-fixing bacteria, called rhizobia. Recent studies revealed that the root nodule symbiosis has co-opted the signaling pathway that mediates the ancestral mycorrhizal symbiosis that occurs in most land plants. Despite being unable to induce nodulation, rhizobia have been shown to be able to infect and colonize the roots of non-legumes such as rice. One fascinating question is whether establishment of such associations requires the common symbiosis (Sym) genes that are essential for infection of plant cells by mycorrhizal fungi and rhizobia in legumes. Here, we demonstrated that the common Sym genes are not required for endophytic colonization of rice roots by nitrogen-fixing rhizobia.
Collapse
Affiliation(s)
- Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences; Changsha, PR China
| | - Hongyan Zhu
- Department of Plant and Soil Sciences; University of Kentucky; Lexington, KY, USA
- Correspondence to: Hongyan Zhu,
| |
Collapse
|
29
|
Barros de Carvalho GA, Batista JSS, Marcelino-Guimarães FC, Costa do Nascimento L, Hungria M. Transcriptional analysis of genes involved in nodulation in soybean roots inoculated with Bradyrhizobium japonicum strain CPAC 15. BMC Genomics 2013; 14:153. [PMID: 23497193 PMCID: PMC3608089 DOI: 10.1186/1471-2164-14-153] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 02/28/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Biological nitrogen fixation in root nodules is a process of great importance to crops of soybean [Glycine max (L.) Merr.], as it may provide the bulk of the plant's needs for nitrogen. Legume nodulation involves several complex steps and, although studied for many decades, much remains to be understood. RESULTS This research aimed at analyzing the global expression of genes in soybean roots of a Brazilian cultivar (Conquista) inoculated with Bradyrhizobium japonicum CPAC 15, a strain broadly used in commercial inoculants in Brazil. To achieve this, we used the suppressive subtractive hybridization (SSH) technique combined with Illumina sequencing. The subtractive library (non-inoculated x inoculated) of soybean roots resulted in 3,210 differentially expressed transcripts at 10 days after inoculation were studied. The data were grouped according to the ontologies of the molecular functions and biological processes. Several classes of genes were confirmed as related to N2 fixation and others were reported for the first time. CONCLUSIONS During nodule formation, a higher percentage of genes were related to primary metabolism, cell-wall modifications and the antioxidant defense system. Putative symbiotic functions were attributed to some of these genes for the first time.
Collapse
Affiliation(s)
- Gesiele Almeida Barros de Carvalho
- Empresa Brasileira de Pesquisa Agropecuária, CNPSo, PO Box 231, Londrina, Paraná 86001-970, Brazil
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, PO Box 6001, Londrina, Paraná 86051-990, Brazil
| | | | | | - Leandro Costa do Nascimento
- Laboratório de Genômica e Expressão, Institute of Biology, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo 13083-862, Brazil
| | - Mariangela Hungria
- Empresa Brasileira de Pesquisa Agropecuária, CNPSo, PO Box 231, Londrina, Paraná 86001-970, Brazil
| |
Collapse
|
30
|
|
31
|
Mao D, Chen C. Colinearity and similar expression pattern of rice DREB1s reveal their functional conservation in the cold-responsive pathway. PLoS One 2012; 7:e47275. [PMID: 23077584 PMCID: PMC3473061 DOI: 10.1371/journal.pone.0047275] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/10/2012] [Indexed: 01/11/2023] Open
Abstract
The clustered genes C-repeat (CRT) binding factor (CBF)1/dehydration-responsive element binding protein (DREB)1B, CBF2/DREB1C, and CBF3/DREB1A play a central role in cold acclimation and facilitate plant resistance to freezing in Arabidopsis thaliana. Rice (Oryza sativa L.) is very sensitive to low temperatures; enhancing the cold stress tolerance of rice is a key challenge to increasing its yield. In this study, we demonstrate chilling acclimation, a phenomenon similar to Arabidopsis cold acclimation, in rice. To determine whether rice CBF/DREB1 genes participate in this cold-responsive pathway, all putative homologs of Arabidopsis DREB1 genes were filtered from the complete rice genome through a BLASTP search, followed by phylogenetic, colinearity and expression analysis. We thereby identified 10 rice genes as putative DREB1 homologs: nine of these were located in rice genomic regions with some colinearity to the Arabidopsis CBF1–CBF4 region. Expression profiling revealed that six of these genes (Os01g73770, Os02g45450, Os04g48350, Os06g03670, Os09g35010, and Os09g35030) were similarly expressed in response to chilling acclimation and cold stress and were co-expressed with genes involved in cold signalling, suggesting that these DREB1 homologs may be involved in the cold response in rice. The results presented here serve as a prelude towards understanding the function of rice homologs of DREB1 genes in cold-sensitive crops.
Collapse
Affiliation(s)
- Donghai Mao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- * E-mail:
| |
Collapse
|
32
|
Hayward A, Vighnesh G, Delay C, Samian MR, Manoli S, Stiller J, McKenzie M, Edwards D, Batley J. Second-generation sequencing for gene discovery in the Brassicaceae. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:750-759. [PMID: 22765874 DOI: 10.1111/j.1467-7652.2012.00719.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The Brassicaceae contains the most diverse collection of agriculturally important crop species of all plant families. Yet, this is one of the few families that do not form functional symbiotic associations with mycorrhizal fungi in the soil for improved nutrient acquisition. The genes involved in this symbiosis were more recently recruited by legumes for symbiotic association with nitrogen-fixing rhizobia bacteria. This study applied second-generation sequencing (SGS) and analysis tools to discover that two such genes, NSP1 (Nodulation Signalling Pathway 1) and NSP2, remain conserved in diverse members of the Brassicaceae despite the absence of these symbioses. We demonstrate the utility of SGS data for the discovery of putative gene homologs and their analysis in complex polyploid crop genomes with little prior sequence information. Furthermore, we show how this data can be applied to enhance downstream reverse genetics analyses. We hypothesize that Brassica NSP genes may function in the root in other plant-microbe interaction pathways that were recruited for mycorrhizal and rhizobial symbioses during evolution.
Collapse
Affiliation(s)
- Alice Hayward
- ARC Centre of Excellence for Integrative Legume Research, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Gust AA, Willmann R, Desaki Y, Grabherr HM, Nürnberger T. Plant LysM proteins: modules mediating symbiosis and immunity. TRENDS IN PLANT SCIENCE 2012; 17:495-502. [PMID: 22578284 DOI: 10.1016/j.tplants.2012.04.003] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/05/2012] [Accepted: 04/11/2012] [Indexed: 05/18/2023]
Abstract
Microbial glycans, such as bacterial peptidoglycans, fungal chitin or rhizobacterial Nod factors (NFs), are important signatures for plant immune activation or for the establishment of beneficial symbioses. Plant lysin motif (LysM) domain proteins serve as modules mediating recognition of these different N-acetylglucosamine (GlcNAc)-containing ligands, suggesting that this class of proteins evolved from an ancient sensor for GlcNAc. During early plant evolution, these glycans probably served as immunogenic patterns activating LysM protein receptor-mediated plant immunity and stopping microbial infection. The biochemical potential of plant LysM proteins for sensing microbial GlcNAc-containing glycans has probably since favored the evolution of receptors facilitating microbial infection and symbiosis.
Collapse
Affiliation(s)
- Andrea A Gust
- Department of Plant Biochemistry, ZMBP, University of Tübingen, 72076 Tübingen, Germany.
| | | | | | | | | |
Collapse
|
34
|
Waters MT, Brewer PB, Bussell JD, Smith SM, Beveridge CA. The Arabidopsis ortholog of rice DWARF27 acts upstream of MAX1 in the control of plant development by strigolactones. PLANT PHYSIOLOGY 2012; 159:1073-85. [PMID: 22623516 PMCID: PMC3387695 DOI: 10.1104/pp.112.196253] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/17/2012] [Indexed: 05/18/2023]
Abstract
Strigolactones (SLs) are carotenoid-derived plant hormones that regulate shoot branching, secondary growth, root development, and responses to soil phosphate. In Arabidopsis (Arabidopsis thaliana), SL biosynthesis requires the sequential action of two carotenoid cleavage dioxygenases, MORE AXILLARY GROWTH3 (MAX3) and MAX4, followed by a cytochrome P450, MAX1. In rice (Oryza sativa), the plastid-localized protein DWARF27 (OsD27) is also necessary for SL biosynthesis, but the equivalent gene in Arabidopsis has not been identified. Here, we use phylogenetic analysis of D27-like sequences from photosynthetic organisms to identify AtD27, the likely Arabidopsis ortholog of OsD27. Using reverse genetics, we show that AtD27 is required for the inhibition of secondary bud outgrowth and that exogenous application of the synthetic SL GR24 can rescue the increased branching phenotype of an Atd27 mutant. Furthermore, we use grafting to demonstrate that AtD27 operates on a nonmobile precursor upstream of MAX1 in the SL biosynthesis pathway. Consistent with the plastid localization of OsD27, we also show that AtD27 possesses a functional plastid transit peptide. We demonstrate that AtD27 transcripts are subject to both local feedback and auxin-dependent signals, albeit to a lesser extent than MAX3 and MAX4, suggesting that early steps in SL biosynthesis are coregulated at the transcriptional level. By identifying an additional component of the canonical SL biosynthesis pathway in Arabidopsis, we provide a new tool to investigate the regulation of shoot branching and other SL-dependent developmental processes.
Collapse
|
35
|
Willmann R, Nürnberger T. How plant lysin motif receptors get activated: lessons learned from structural biology. Sci Signal 2012; 5:pe28. [PMID: 22740685 DOI: 10.1126/scisignal.2003274] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lysin motif (LysM) receptor kinases are unique to plants and serve important functions in plant-microbe interactions. These proteins recognize microbe-derived N-acetylglucosamine (NAG)-containing ligands, but the molecular mode of ligand perception and of receptor activation has remained unknown. The three-dimensional structure of the LysM receptor kinase CERK1 (chitin elicitor receptor kinase 1) from Arabidopsis thaliana has been reported. CERK1 binds NAG oligomers derived from chitin-the major constituent of fungal cell walls-and mediates immunity to fungal infection. The crystal structure of CERK1 complexed with a NAG pentamer revealed that three NAG moieties attach tightly to one of three lysin motifs within the CERK1 ectodomain. Receptor activation and immune signaling requires, however, ligand-induced CERK1 homodimerization. By acting as bivalent ligands, NAG octamers stabilize CERK1 dimers, providing a structural explanation for why the immunogenic activity of NAG oligomers is restricted to fragments larger than those required for receptor binding. Because CERK1 might serve as a paradigm for the functionality of a whole class of plant LysM proteins, insight into its mode of action will direct future research on these receptors.
Collapse
Affiliation(s)
- Roland Willmann
- University of Tübingen, Center for Plant Molecular Biology-Plant Biochemistry, Germany.
| | | |
Collapse
|
36
|
Venkateshwaran M, Cosme A, Han L, Banba M, Satyshur KA, Schleiff E, Parniske M, Imaizumi-Anraku H, Ané JM. The recent evolution of a symbiotic ion channel in the legume family altered ion conductance and improved functionality in calcium signaling. THE PLANT CELL 2012; 24:2528-45. [PMID: 22706284 PMCID: PMC3406897 DOI: 10.1105/tpc.112.098475] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Arbuscular mycorrhiza and the rhizobia-legume symbiosis are two major root endosymbioses that facilitate plant nutrition. In Lotus japonicus, two symbiotic cation channels, CASTOR and POLLUX, are indispensable for the induction of nuclear calcium spiking, one of the earliest plant responses to symbiotic partner recognition. During recent evolution, a single amino acid substitution in DOES NOT MAKE INFECTIONS1 (DMI1), the POLLUX putative ortholog in the closely related Medicago truncatula, rendered the channel solo sufficient for symbiosis; castor, pollux, and castor pollux double mutants of L. japonicus were rescued by DMI1 alone, while both Lj-CASTOR and Lj-POLLUX were required for rescuing a dmi1 mutant of M. truncatula. Experimental replacement of the critical serine by an alanine in the selectivity filter of Lj-POLLUX conferred a symbiotic performance indistinguishable from DMI1. Electrophysiological characterization of DMI1 and Lj-CASTOR (wild-type and mutants) by planar lipid bilayer experiments combined with calcium imaging in Human Embryonic Kidney-293 cells expressing DMI1 (the wild type and mutants) suggest that the serine-to-alanine substitution conferred reduced conductance with a long open state to DMI1 and improved its efficiency in mediating calcium oscillations. We propose that this single amino acid replacement in the selectivity filter made DMI1 solo sufficient for symbiosis, thus explaining the selective advantage of this allele at the mechanistic level.
Collapse
Affiliation(s)
| | - Ana Cosme
- Ludwig-Maximilians-Universität München, Faculty of Biology, Genetics, 82152 Martinsried, Germany
| | - Lu Han
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Mari Banba
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Kenneth A. Satyshur
- University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705
| | | | - Martin Parniske
- Ludwig-Maximilians-Universität München, Faculty of Biology, Genetics, 82152 Martinsried, Germany
| | - Haruko Imaizumi-Anraku
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
- Address correspondence to
| |
Collapse
|
37
|
Ivanov S, Fedorova EE, Limpens E, De Mita S, Genre A, Bonfante P, Bisseling T. Rhizobium-legume symbiosis shares an exocytotic pathway required for arbuscule formation. Proc Natl Acad Sci U S A 2012. [PMID: 22566631 DOI: 10.1073/pnas.1200407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Endosymbiotic interactions are characterized by the formation of specialized membrane compartments, by the host in which the microbes are hosted, in an intracellular manner. Two well-studied examples, which are of major agricultural and ecological importance, are the widespread arbuscular mycorrhizal symbiosis and the Rhizobium-legume symbiosis. In both symbioses, the specialized host membrane that surrounds the microbes forms a symbiotic interface, which facilitates the exchange of, for example, nutrients in a controlled manner and, therefore, forms the heart of endosymbiosis. Despite their key importance, the molecular and cellular mechanisms underlying the formation of these membrane interfaces are largely unknown. Recent studies strongly suggest that the Rhizobium-legume symbiosis coopted a signaling pathway, including receptor, from the more ancient arbuscular mycorrhizal symbiosis to form a symbiotic interface. Here, we show that two highly homologous exocytotic vesicle-associated membrane proteins (VAMPs) are required for formation of the symbiotic membrane interface in both interactions. Silencing of these Medicago VAMP72 genes has a minor effect on nonsymbiotic plant development and nodule formation. However, it blocks symbiosome as well as arbuscule formation, whereas root colonization by the microbes is not affected. Identification of these VAMP72s as common symbiotic regulators in exocytotic vesicle trafficking suggests that the ancient exocytotic pathway forming the periarbuscular membrane compartment has also been coopted in the Rhizobium-legume symbiosis.
Collapse
Affiliation(s)
- Sergey Ivanov
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
38
|
Ivanov S, Fedorova EE, Limpens E, De Mita S, Genre A, Bonfante P, Bisseling T. Rhizobium-legume symbiosis shares an exocytotic pathway required for arbuscule formation. Proc Natl Acad Sci U S A 2012; 109:8316-21. [PMID: 22566631 PMCID: PMC3361388 DOI: 10.1073/pnas.1200407109] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Endosymbiotic interactions are characterized by the formation of specialized membrane compartments, by the host in which the microbes are hosted, in an intracellular manner. Two well-studied examples, which are of major agricultural and ecological importance, are the widespread arbuscular mycorrhizal symbiosis and the Rhizobium-legume symbiosis. In both symbioses, the specialized host membrane that surrounds the microbes forms a symbiotic interface, which facilitates the exchange of, for example, nutrients in a controlled manner and, therefore, forms the heart of endosymbiosis. Despite their key importance, the molecular and cellular mechanisms underlying the formation of these membrane interfaces are largely unknown. Recent studies strongly suggest that the Rhizobium-legume symbiosis coopted a signaling pathway, including receptor, from the more ancient arbuscular mycorrhizal symbiosis to form a symbiotic interface. Here, we show that two highly homologous exocytotic vesicle-associated membrane proteins (VAMPs) are required for formation of the symbiotic membrane interface in both interactions. Silencing of these Medicago VAMP72 genes has a minor effect on nonsymbiotic plant development and nodule formation. However, it blocks symbiosome as well as arbuscule formation, whereas root colonization by the microbes is not affected. Identification of these VAMP72s as common symbiotic regulators in exocytotic vesicle trafficking suggests that the ancient exocytotic pathway forming the periarbuscular membrane compartment has also been coopted in the Rhizobium-legume symbiosis.
Collapse
Affiliation(s)
- Sergey Ivanov
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Elena E. Fedorova
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Erik Limpens
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Stephane De Mita
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Andrea Genre
- Dipartimento di Biologia Vegetale, Universita’ di Torino, 10125 Turin, Italy; and
| | - Paola Bonfante
- Dipartimento di Biologia Vegetale, Universita’ di Torino, 10125 Turin, Italy; and
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
39
|
Abstract
Legume plants are able to engage in root nodule symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia. This mutualistic association is highly specific, such that each rhizobial species/strain interacts with only a specific group of legumes, and vice versa. Symbiosis specificity can occur at multiple phases of the interaction, ranging from initial bacterial attachment and infection to late nodule development associated with nitrogen fixation. Genetic control of symbiosis specificity is complex, involving fine-tuned signal communication between the symbiotic partners. Here we review our current understanding of the mechanisms used by the host and bacteria to choose their symbiotic partners, with a special focus on the role that the host immunity plays in controlling the specificity of the legume - rhizobial symbiosis.
Collapse
Affiliation(s)
- Dong Wang
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.
| | | | | | | |
Collapse
|
40
|
Antolín-Llovera M, Ried MK, Binder A, Parniske M. Receptor kinase signaling pathways in plant-microbe interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:451-73. [PMID: 22920561 DOI: 10.1146/annurev-phyto-081211-173002] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant receptor-like kinases (RLKs) function in diverse signaling pathways, including the responses to microbial signals in symbiosis and defense. This versatility is achieved with a common overall structure: an extracytoplasmic domain (ectodomain) and an intracellular protein kinase domain involved in downstream signal transduction. Various surfaces of the leucine-rich repeat (LRR) ectodomain superstructure are utilized for interaction with the cognate ligand in both plant and animal receptors. RLKs with lysin-motif (LysM) ectodomains confer recognitional specificity toward N-acetylglucosamine-containing signaling molecules, such as chitin, peptidoglycan (PGN), and rhizobial nodulation factor (NF), that induce immune or symbiotic responses. Signaling downstream of RLKs does not follow a single pattern; instead, the detailed analysis of brassinosteroid (BR) signaling, innate immunity, and symbiosis revealed at least three largely nonoverlapping pathways. In this review, we focus on RLKs involved in plant-microbe interactions and contrast the signaling pathways leading to symbiosis and defense.
Collapse
|
41
|
Liu W, Kohlen W, Lillo A, Op den Camp R, Ivanov S, Hartog M, Limpens E, Jamil M, Smaczniak C, Kaufmann K, Yang WC, Hooiveld GJ, Charnikhova T, Bouwmeester HJ, Bisseling T, Geurts R. Strigolactone biosynthesis in Medicago truncatula and rice requires the symbiotic GRAS-type transcription factors NSP1 and NSP2. THE PLANT CELL 2011; 23:3853-65. [PMID: 22039214 PMCID: PMC3229154 DOI: 10.1105/tpc.111.089771] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 08/31/2011] [Accepted: 10/09/2011] [Indexed: 05/18/2023]
Abstract
Legume GRAS (GAI, RGA, SCR)-type transcription factors NODULATION SIGNALING PATHWAY1 (NSP1) and NSP2 are essential for rhizobium Nod factor-induced nodulation. Both proteins are considered to be Nod factor response factors regulating gene expression after symbiotic signaling. However, legume NSP1 and NSP2 can be functionally replaced by nonlegume orthologs, including rice (Oryza sativa) NSP1 and NSP2, indicating that both proteins are functionally conserved in higher plants. Here, we show that NSP1 and NSP2 are indispensable for strigolactone (SL) biosynthesis in the legume Medicago truncatula and in rice. Mutant nsp1 plants do not produce SLs, whereas in M. truncatula, NSP2 is essential for conversion of orobanchol into didehydro-orobanchol, which is the main SL produced by this species. The disturbed SL biosynthesis in nsp1 nsp2 mutant backgrounds correlates with reduced expression of DWARF27, a gene essential for SL biosynthesis. Rice and M. truncatula represent distinct phylogenetic lineages that split approximately 150 million years ago. Therefore, we conclude that regulation of SL biosynthesis by NSP1 and NSP2 is an ancestral function conserved in higher plants. NSP1 and NSP2 are single-copy genes in legumes, which implies that both proteins fulfill dual regulatory functions to control downstream targets after rhizobium-induced signaling as well as SL biosynthesis in nonsymbiotic conditions.
Collapse
Affiliation(s)
- Wei Liu
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wouter Kohlen
- Department of Plant Science, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Alessandra Lillo
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Rik Op den Camp
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Sergey Ivanov
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Marijke Hartog
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Erik Limpens
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Muhammad Jamil
- Department of Plant Science, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Cezary Smaczniak
- Plant Research International–Bioscience, Laboratory of Molecular Biology, 6708 PB Wageningen, The Netherlands
| | - Kerstin Kaufmann
- Plant Research International–Bioscience, Laboratory of Molecular Biology, 6708 PB Wageningen, The Netherlands
| | - Wei-Cai Yang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guido J.E.J. Hooiveld
- Division of Human Nutrition, Wageningen University, 6703 HD Wageningen, The Netherlands
| | - Tatsiana Charnikhova
- Department of Plant Science, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Harro J. Bouwmeester
- Department of Plant Science, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Centre for BioSystems Genomics, 6708 PB Wageningen, The Netherlands
| | - Ton Bisseling
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
- College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - René Geurts
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Address correspondence to
| |
Collapse
|
42
|
Streng A, op den Camp R, Bisseling T, Geurts R. Evolutionary origin of rhizobium Nod factor signaling. PLANT SIGNALING & BEHAVIOR 2011; 6:1510-4. [PMID: 21904113 PMCID: PMC3256379 DOI: 10.4161/psb.6.10.17444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 07/22/2011] [Indexed: 05/09/2023]
Abstract
For over two decades now, it is known that the nodule symbiosis between legume plants and nitrogen fixing rhizobium bacteria is set in motion by the bacterial signal molecule named nodulation (Nod) factor. Upon Nod factor perception a signaling cascade is activated that is also essential for endomycorrhizal symbiosis (Fig. 1). This suggests that rhizobium co-opted the evolutionary far more ancient mycorrhizal signaling pathway in order to establish an endosymbiotic interaction with legumes. As arbuscular mycorrhizal fungi of the Glomeromycota phylum can establish a symbiosis with the fast majority of land plants, it is most probable that this signaling cascade is wide spread in plant kingdom. However, Nod factor perception generally is considered to be unique to legumes. Two recent breakthroughs on the evolutionary origin of Rhizobium Nod factor signaling demonstrate that this is not the case. The purification of Nod factor-like molecules excreted by the mycorrhizal fungus Glomus intraradices and the role of the LysM-type Nod factor receptor PaNFP in the non-legume Parasponia andersonii provide novel understanding on the evolution of rhizobial Nod factor signaling.
Collapse
Affiliation(s)
- Arend Streng
- Department of Plant Sciences; Laboratory of Molecular Biology; Wageningen University; Wageningen, The Netherlands
| | - Rik op den Camp
- Department of Plant Sciences; Laboratory of Molecular Biology; Wageningen University; Wageningen, The Netherlands
| | - Ton Bisseling
- Department of Plant Sciences; Laboratory of Molecular Biology; Wageningen University; Wageningen, The Netherlands
- College of Science; King Saud University; Riyadh, Saudi Arabia
| | - René Geurts
- Department of Plant Sciences; Laboratory of Molecular Biology; Wageningen University; Wageningen, The Netherlands
| |
Collapse
|
43
|
Gough C, Cullimore J. Lipo-chitooligosaccharide signaling in endosymbiotic plant-microbe interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:867-78. [PMID: 21469937 DOI: 10.1094/mpmi-01-11-0019] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The arbuscular mycorrhizal (AM) and the rhizobia-legume (RL) root endosymbioses are established as a result of signal exchange in which there is mutual recognition of diffusible signals produced by plant and microbial partners. It was discovered 20 years ago that the key symbiotic signals produced by rhizobial bacteria are lipo-chitooligosaccharides (LCO), called Nod factors. These LCO are perceived via lysin-motif (LysM) receptors and activate a signaling pathway called the common symbiotic pathway (CSP), which controls both the RL and the AM symbioses. Recent work has established that an AM fungus, Glomus intraradices, also produces LCO that activate the CSP, leading to induction of gene expression and root branching in Medicago truncatula. These Myc-LCO also stimulate mycorrhization in diverse plants. In addition, work on the nonlegume Parasponia andersonii has shown that a LysM receptor is required for both successful mycorrhization and nodulation. Together these studies show that structurally related signals and the LysM receptor family are key components of both nodulation and mycorrhization. LysM receptors are also involved in the perception of chitooligosaccharides (CO), which are derived from fungal cell walls and elicit defense responses and resistance to pathogens in diverse plants. The discovery of Myc-LCO and a LysM receptor required for the AM symbiosis, therefore, not only raises questions of how legume plants discriminate fungal and bacterial endosymbionts but also, more generally, of how plants discriminate endosymbionts from pathogenic microorganisms using structurally related LCO and CO signals and of how these perception mechanisms have evolved.
Collapse
Affiliation(s)
- Clare Gough
- Laboratory of Plant-Microbe Interactions, UMR CNRS-INRA 2594-441, Castanet-Tolosan Cedex, France.
| | | |
Collapse
|
44
|
Bordat A, Savois V, Nicolas M, Salse J, Chauveau A, Bourgeois M, Potier J, Houtin H, Rond C, Murat F, Marget P, Aubert G, Burstin J. Translational Genomics in Legumes Allowed Placing In Silico 5460 Unigenes on the Pea Functional Map and Identified Candidate Genes in Pisum sativum L. G3 (BETHESDA, MD.) 2011; 1:93-103. [PMID: 22384322 PMCID: PMC3276132 DOI: 10.1534/g3.111.000349] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 05/06/2011] [Indexed: 12/31/2022]
Abstract
To identify genes involved in phenotypic traits, translational genomics from highly characterized model plants to poorly characterized crop plants provides a valuable source of markers to saturate a zone of interest as well as functionally characterized candidate genes. In this paper, an integrated view of the pea genetic map was developed. A series of gene markers were mapped and their best reciprocal homologs were identified on M. truncatula, L. japonicus, soybean, and poplar pseudomolecules. Based on the syntenic relationships uncovered between pea and M. truncatula, 5460 pea Unigenes were tentatively placed on the consensus map. A new bioinformatics tool, http://www.thelegumeportal.net/pea_mtr_translational_toolkit, was developed that allows, for any gene sequence, to search its putative position on the pea consensus map and hence to search for candidate genes among neighboring Unigenes. As an example, a promising candidate gene for the hypernodulation mutation nod3 in pea was proposed based on the map position of the likely homolog of Pub1, a M. truncatula gene involved in nodulation regulation. A broader view of pea genome evolution was obtained by revealing syntenic relationships between pea and sequenced genomes. Blocks of synteny were identified which gave new insights into the evolution of chromosome structure in Papillionoids and Eudicots. The power of the translational genomics approach was underlined.
Collapse
|
45
|
The genotype of the calcium/calmodulin-dependent protein kinase gene (CCaMK) determines bacterial community diversity in rice roots under paddy and upland field conditions. Appl Environ Microbiol 2011; 77:4399-405. [PMID: 21551283 DOI: 10.1128/aem.00315-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of the Oryza sativa calcium/calmodulin-dependent protein kinase OsCCaMK genotype (dominant homozygous [D], heterozygous [H], recessive homozygous [R]) on rice root-associated bacteria, including endophytes and epiphytes, were examined by using a Tos17 rice mutant line under paddy and upland field conditions. Roots were sampled at the flowering stage and were subjected to clone library analyses. The relative abundance of Alphaproteobacteria was noticeably decreased in R plants under both paddy and upland conditions (0.8% and 3.0%, respectively) relative to those in D plants (10.3% and 17.4%, respectively). Population shifts of the Sphingomonadales and Rhizobiales were mainly responsible for this low abundance in R plants. The abundance of Anaerolineae (Chloroflexi) and Clostridia (Firmicutes) was increased in R plants under paddy conditions. The abundance of a subpopulation of Actinobacteria (Saccharothrix spp. and unclassified Actinosynnemataceae) was increased in R plants under upland conditions. Principal coordinate analysis revealed unidirectional community shifts in relation to OsCCaMK gene dosage under both conditions. In addition, shoot length, tiller number, and plant weight decreased as the OsCCaMK gene dosage decreased under upland conditions. These results suggest significant impacts of OsCCaMK on both the diversity of root-associated bacteria and rice plant growth under both paddy and upland field conditions.
Collapse
|
46
|
Kohlen W, Charnikhova T, Liu Q, Bours R, Domagalska MA, Beguerie S, Verstappen F, Leyser O, Bouwmeester H, Ruyter-Spira C. Strigolactones are transported through the xylem and play a key role in shoot architectural response to phosphate deficiency in nonarbuscular mycorrhizal host Arabidopsis. PLANT PHYSIOLOGY 2011; 155:974-87. [PMID: 21119045 PMCID: PMC3032481 DOI: 10.1104/pp.110.164640] [Citation(s) in RCA: 288] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Accepted: 11/23/2010] [Indexed: 05/18/2023]
Abstract
The biosynthesis of the recently identified novel class of plant hormones, strigolactones, is up-regulated upon phosphate deficiency in many plant species. It is generally accepted that the evolutionary origin of strigolactone up-regulation is their function as a rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi. In this work, we demonstrate that this induction is conserved in Arabidopsis (Arabidopsis thaliana), although Arabidopsis is not a host for arbuscular mycorrhizal fungi. We demonstrate that the increase in strigolactone production contributes to the changes in shoot architecture observed in response to phosphate deficiency. Using high-performance liquid chromatography, column chromatography, and multiple reaction monitoring-liquid chromatography-tandem mass spectrometry analysis, we identified two strigolactones (orobanchol and orobanchyl acetate) in Arabidopsis and have evidence of the presence of a third (5-deoxystrigol). We show that at least one of them (orobanchol) is strongly reduced in the putative strigolactone biosynthetic mutants more axillary growth1 (max1) and max4 but not in the signal transduction mutant max2. Orobanchol was also detected in xylem sap and up-regulated under phosphate deficiency, which is consistent with the idea that root-derived strigolactones are transported to the shoot, where they regulate branching. Moreover, two additional putative strigolactone-like compounds were detected in xylem sap, one of which was not detected in root exudates. Together, these results show that xylem-transported strigolactones contribute to the regulation of shoot architectural response to phosphate-limiting conditions.
Collapse
|
47
|
Chabaud M, Genre A, Sieberer BJ, Faccio A, Fournier J, Novero M, Barker DG, Bonfante P. Arbuscular mycorrhizal hyphopodia and germinated spore exudates trigger Ca2+ spiking in the legume and nonlegume root epidermis. THE NEW PHYTOLOGIST 2011; 189:347-55. [PMID: 20880223 DOI: 10.1111/j.1469-8137.2010.03464.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
• The aim of this study was to investigate Ca(2+) responses to endosymbiotic arbuscular mycorrhizal (AM) fungi in the host root epidermis following pre-infection hyphopodium formation in both legumes and nonlegumes, and to determine to what extent these responses could be mimicked by germinated fungal spore exudate. • Root organ cultures of both Medicago truncatula and Daucus carota, expressing the nuclear-localized cameleon reporter NupYC2.1, were used to monitor AM-elicited Ca(2+) responses in host root tissues. • Ca(2+) spiking was observed in cells contacted by AM hyphopodia for both hosts, with highest frequencies correlating with the epidermal nucleus positioned facing the fungal contact site. Treatment with AM spore exudate also elicited Ca(2+) spiking within the AM-responsive zone of the root and, in both cases, spiking was dependent on the M. truncatula common SYM genes DMI1/2, but not on the rhizobial Nod factor perception gene NFP. • These findings support the conclusion that AM fungal root penetration is preceded by a SYM pathway-dependent oscillatory Ca(2+) response, whose evolutionary origin predates the divergence between asterid and rosid clades. Our results further show that fungal symbiotic signals are already generated during spore germination, and that cameleon-expressing root organ cultures represent a novel AM-specific bio-assay for such signals.
Collapse
Affiliation(s)
- Mireille Chabaud
- Laboratory of Plant-Microbe Interactions, UMR CNRS-INRA 2594/441, Castanet-Tolosan, France
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Nakagawa T, Kaku H, Shimoda Y, Sugiyama A, Shimamura M, Takanashi K, Yazaki K, Aoki T, Shibuya N, Kouchi H. From defense to symbiosis: limited alterations in the kinase domain of LysM receptor-like kinases are crucial for evolution of legume-Rhizobium symbiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:169-80. [PMID: 21223383 DOI: 10.1111/j.1365-313x.2010.04411.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nitrogen-fixing symbiosis between legumes and rhizobia is initiated by the recognition of rhizobial Nod factors (NFs) by host plants. NFs are diversely modified derivatives of chitin oligosaccharide, a fungal elicitor that induces defense responses in plants. Recent evidence has shown that both NFs and chitin elicitors are recognized by structurally related LysM receptor kinases. Transcriptome analyses of Lotus japonicus roots indicated that NFs not only activate symbiosis genes but also transiently activate defense-related genes through NF receptors. Conversely, chitin oligosaccharides were able to activate symbiosis genes independently of NF receptors. Analyses using chimeric genes consisting of the LysM receptor domain of a Lotus japonicus NF receptor, NFR1, and the kinase domain of an Arabidopsis chitin receptor, CERK1, demonstrated that substitution of a portion of the αEF helix in CERK1 with the amino acid sequence YAQ from the corresponding region of NFR1 enables L. japonicus nfr1 mutants to establish symbiosis with Mesorhizobium loti. We also showed that the kinase domains of two Lotus japonicus LysM receptor kinases, Lys6 and Lys7, which also possess the YAQ sequence, suppress the symbiotic defect of nfr1. These results strongly suggest that, in addition to adaptation of extracellular LysM domains to NFs, limited alterations in the kinase domain of chitin receptors have played a crucial role in shifting the intracellular signaling to symbiosis from defense responses, thus constituting one of the key genetic events in the evolution of root nodule symbiosis in legume plants.
Collapse
Affiliation(s)
- Tomomi Nakagawa
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Op den Camp R, Streng A, De Mita S, Cao Q, Polone E, Liu W, Ammiraju JSS, Kudrna D, Wing R, Untergasser A, Bisseling T, Geurts R. LysM-Type Mycorrhizal Receptor Recruited for Rhizobium Symbiosis in Nonlegume Parasponia. Science 2010; 331:909-12. [DOI: 10.1126/science.1198181] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
50
|
Kouchi H, Imaizumi-Anraku H, Hayashi M, Hakoyama T, Nakagawa T, Umehara Y, Suganuma N, Kawaguchi M. How many peas in a pod? Legume genes responsible for mutualistic symbioses underground. PLANT & CELL PHYSIOLOGY 2010; 51:1381-97. [PMID: 20660226 PMCID: PMC2938637 DOI: 10.1093/pcp/pcq107] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The nitrogen-fixing symbiosis between legume plants and Rhizobium bacteria is the most prominent plant-microbe endosymbiotic system and, together with mycorrhizal fungi, has critical importance in agriculture. The introduction of two model legume species, Lotus japonicus and Medicago truncatula, has enabled us to identify a number of host legume genes required for symbiosis. A total of 26 genes have so far been cloned from various symbiotic mutants of these model legumes, which are involved in recognition of rhizobial nodulation signals, early symbiotic signaling cascades, infection and nodulation processes, and regulation of nitrogen fixation. These accomplishments during the past decade provide important clues to understanding not only the molecular mechanisms underlying plant-microbe endosymbiotic associations but also the evolutionary aspects of nitrogen-fixing symbiosis between legume plants and Rhizobium bacteria. In this review we survey recent progress in molecular genetic studies using these model legumes.
Collapse
Affiliation(s)
- Hiroshi Kouchi
- Department of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
| | | | | | | | | | | | | | | |
Collapse
|