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Tan W, Nian H, Tran LSP, Jin J, Lian T. Small peptides: novel targets for modulating plant-rhizosphere microbe interactions. Trends Microbiol 2024:S0966-842X(24)00085-4. [PMID: 38670883 DOI: 10.1016/j.tim.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The crucial role of rhizosphere microbes in plant growth and their resilience to environmental stresses underscores the intricate communication between microbes and plants. Plants are equipped with a diverse set of signaling molecules that facilitate communication across different biological kingdoms, although our comprehension of these mechanisms is still evolving. Small peptides produced by plants (SPPs) and microbes (SPMs) play a pivotal role in intracellular signaling and are essential in orchestrating various plant development stages. In this review, we posit that SPPs and SPMs serve as crucial signaling agents for the bidirectional cross-kingdom communication between plants and rhizosphere microbes. We explore several potential mechanistic pathways through which this communication occurs. Additionally, we propose that leveraging small peptides, inspired by plant-rhizosphere microbe interactions, represents an innovative approach in the field of holobiont engineering.
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Affiliation(s)
- Weiyi Tan
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
| | - Jing Jin
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
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Bashyal S, Gautam CK, Müller LM. CLAVATA signaling in plant-environment interactions. PLANT PHYSIOLOGY 2024; 194:1336-1357. [PMID: 37930810 PMCID: PMC10904329 DOI: 10.1093/plphys/kiad591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Plants must rapidly and dynamically adapt to changes in their environment. Upon sensing environmental signals, plants convert them into cellular signals, which elicit physiological or developmental changes that allow them to respond to various abiotic and biotic cues. Because plants can be simultaneously exposed to multiple environmental cues, signal integration between plant cells, tissues, and organs is necessary to induce specific responses. Recently, CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides and their cognate CLAVATA-type receptors received increased attention for their roles in plant-environment interactions. CLE peptides are mobile signaling molecules, many of which are induced by a variety of biotic and abiotic stimuli. Secreted CLE peptides are perceived by receptor complexes on the surface of their target cells, which often include the leucine-rich repeat receptor-like kinase CLAVATA1. Receptor activation then results in cell-type and/or environment-specific responses. This review summarizes our current understanding of the diverse roles of environment-regulated CLE peptides in modulating plant responses to environmental cues. We highlight how CLE signals regulate plant physiology by fine-tuning plant-microbe interactions, nutrient homeostasis, and carbon allocation. Finally, we describe the role of CLAVATA receptors in the perception of environment-induced CLE signals and discuss how diverse CLE-CLAVATA signaling modules may integrate environmental signals with plant physiology and development.
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Affiliation(s)
- Sagar Bashyal
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | | | - Lena Maria Müller
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
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Thomas J, Frugoli J. Mutation of BAM2 rescues the sunn hypernodulation phenotype in Medicago truncatula, suggesting that a signaling pathway like CLV1/BAM in Arabidopsis affects nodule number. FRONTIERS IN PLANT SCIENCE 2024; 14:1334190. [PMID: 38273950 PMCID: PMC10808729 DOI: 10.3389/fpls.2023.1334190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
The unique evolutionary adaptation of legumes for nitrogen-fixing symbiosis leading to nodulation is tightly regulated by the host plant. The autoregulation of nodulation (AON) pathway negatively regulates the number of nodules formed in response to the carbon/nitrogen metabolic status of the shoot and root by long-distance signaling to and from the shoot and root. Central to AON signaling in the shoots of Medicago truncatula is SUNN, a leucine-rich repeat receptor-like kinase with high sequence similarity with CLAVATA1 (CLV1), part of a class of receptors in Arabidopsis involved in regulating stem cell populations in the root and shoot. This class of receptors in Arabidopsis includes the BARELY ANY MERISTEM family, which, like CLV1, binds to CLE peptides and interacts with CLV1 to regulate meristem development. M. truncatula contains five members of the BAM family, but only MtBAM1 and MtBAM2 are highly expressed in the nodules 48 hours after inoculation. Plants carry mutations in individual MtBAMs, and several double BAM mutant combinations all displayed wild-type nodule number phenotypes. However, Mtbam2 suppressed the sunn-5 hypernodulation phenotype and partially rescued the short root length phenotype of sunn-5 when present in a sunn-5 background. Grafting determined that bam2 suppresses supernodulation from the roots, regardless of the SUNN status of the root. Overexpression of MtBAM2 in wild-type plants increases nodule numbers, while overexpression of MtBAM2 in some sunn mutants rescues the hypernodulation phenotype, but not the hypernodulation phenotypes of AON mutant rdn1-2 or crn. Relative expression measurements of the nodule transcription factor MtWOX5 downstream of the putative bam2 sunn-5 complex revealed disruption of meristem signaling; while both bam2 and bam2 sunn-5 influence MtWOX5 expression, the expression changes are in different directions. We propose a genetic model wherein the specific root interactions of BAM2/SUNN are critical for signaling in nodule meristem cell homeostasis in M. truncatula.
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Affiliation(s)
| | - Julia Frugoli
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
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Chaulagain D, Schnabel E, Lin EX, Garcia RR, Noorai RE, Müller LM, Frugoli JA. TML1 AND TML2 SYNERGISTICALLY REGULATE NODULATION BUT NOT ARBUSCULAR MYCORRHIZA IN MEDICAGO TRUNCATULA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570674. [PMID: 38106087 PMCID: PMC10723381 DOI: 10.1101/2023.12.07.570674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Two symbiotic processes, nodulation and arbuscular mycorrhiza, are primarily controlled by the plant's need for nitrogen (N) and phosphorus (P), respectively. Autoregulation of Nodulation (AON) and Autoregulation of Mycorrhization (AOM) share multiple components - plants that make too many nodules usually have higher arbuscule density. The protein TML (TOO MUCH LOVE) was shown to function in roots to maintain susceptibly to rhizobial infection under low N conditions and control nodule number through AON in Lotus japonicus. M. truncatula has two sequence homologs: MtTML1 and MtTML2. We report the generation of stable single and double mutants harboring multiple allelic variations in MtTML1 and MtTML2 using CRISPR-Cas9 targeted mutagenesis and screening of a transposon mutagenesis library. Plants containing single mutations in either gene produced twice the nodules of wild type plants whereas plants containing mutations in both genes displayed a synergistic effect, forming 20x more nodules and short roots compared to wild type plants. The synergistic effect on nodulation was maintained in the presence of 10mM nitrogen, but not observed in root length phenotypes. Examination of expression and heterozygote effects suggest genetic compensation may play a role in the observed synergy. However, plants with mutations in both TMLs had no detectable change in arbuscular mycorrhizal associations, suggesting that MtTMLs are specific to nodulation and nitrate signaling. The mutants created will be useful tools to dissect the mechanism of synergistic action of MtTML1 and MtTML2 in M. truncatula nodulation as well as the separation of AON from AOM.
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Zhang RY, Massey B, Mathesius U, Clarke VC. Photosynthetic Gains in Super-Nodulating Mutants of Medicago truncatula under Elevated Atmospheric CO 2 Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:441. [PMID: 36771529 PMCID: PMC9920600 DOI: 10.3390/plants12030441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Legumes are generally considered to be more responsive to elevated CO2 (eCO2) conditions due to the benefits provided by symbiotic nitrogen fixation. In response to high carbohydrate demand from nodules, legumes display autoregulation of nodulation (AON) to restrict nodules to the minimum number necessary to sustain nitrogen supply under current photosynthetic levels. AON mutants super-nodulate and typically grow smaller than wild-type plants under ambient CO2. Here, we show that AON super-nodulating mutants have substantially higher biomass under eCO2 conditions, which is sustained through increased photosynthetic investment. We examined photosynthetic and physiological traits across super-nodulating rdn1-1 (Root Determined Nodulation) and sunn4 (Super Numeric Nodules) and non-nodulating nfp1 (Nod Factor Perception) Medicago truncatula mutants. Under eCO2 conditions, super-nodulating plants exhibited increased rates of carboxylation (Vcmax) and electron transport (J) relative to wild-type and non-nodulating counterparts. The substantially higher rate of CO2 assimilation in eCO2-grown sunn4 super-nodulating plants was sustained through increased production of key photosynthetic enzymes, including Rieske FeS. We hypothesize that AON mutants are carbon-limited and can perform better at eCO2 through improved photosynthesis. Nodulating legumes, especially those with higher nitrogen fixation capability, are likely to out-perform non-nodulating plants under future CO2 conditions and will be important tools for understanding carbon and nitrogen partitioning under eCO2 conditions and future crop improvements.
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Affiliation(s)
- Rose Y. Zhang
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Baxter Massey
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Ulrike Mathesius
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Victoria C. Clarke
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, TAS 7005, Australia
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Pereira WJ, Knaack S, Chakraborty S, Conde D, Folk RA, Triozzi PM, Balmant KM, Dervinis C, Schmidt HW, Ané J, Roy S, Kirst M. Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade. THE NEW PHYTOLOGIST 2022; 234:634-649. [PMID: 35092309 PMCID: PMC9302667 DOI: 10.1111/nph.18006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen-fixing bacteria in the root nodule. This root-nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggesting a critical, but undetermined, evolutionary event at the base of this clade. To identify putative regulatory sequences implicated in the evolution of RNS, we evaluated the genomes of 25 species capable of nodulation and identified 3091 conserved noncoding sequences (CNS) in the nitrogen-fixing clade (NFC). We show that the chromatin accessibility of 452 CNS correlates significantly with the regulation of genes responding to lipochitooligosaccharides in Medicago truncatula. These included 38 CNS in proximity to 19 known genes involved in RNS. Five such regions are upstream of MtCRE1, Cytokinin Response Element 1, required to activate a suite of downstream transcription factors necessary for nodulation in M. truncatula. Genetic complementation of an Mtcre1 mutant showed a significant decrease of nodulation in the absence of the five CNS, when they are driving the expression of a functional copy of MtCRE1. CNS identified in the NFC may harbor elements required for the regulation of genes controlling RNS in M. truncatula.
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Affiliation(s)
- Wendell J. Pereira
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Sara Knaack
- Wisconsin Institute for DiscoveryUniversity of Wisconsin‐MadisonMadisonWI53715USA
| | | | - Daniel Conde
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityStarkvilleMS39762USA
| | - Paolo M. Triozzi
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Kelly M. Balmant
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Christopher Dervinis
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Henry W. Schmidt
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Jean‐Michel Ané
- Department of BacteriologyUniversity of Wisconsin‐MadisonMadisonWI53706USA
- Department of AgronomyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Sushmita Roy
- Wisconsin Institute for DiscoveryUniversity of Wisconsin‐MadisonMadisonWI53715USA
- Department of Biostatistics and Medical InformaticsUniversity of Wisconsin‐MadisonMadisonWI53715USA
| | - Matias Kirst
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFL32611USA
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Concha C, Doerner P. The impact of the rhizobia-legume symbiosis on host root system architecture. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3902-3921. [PMID: 32337556 PMCID: PMC7316968 DOI: 10.1093/jxb/eraa198] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/22/2020] [Indexed: 05/20/2023]
Abstract
Legumes form symbioses with rhizobia to fix N2 in root nodules to supplement their nitrogen (N) requirements. Many studies have shown how symbioses affect the shoot, but far less is understood about how they modify root development and root system architecture (RSA). RSA is the distribution of roots in space and over time. RSA reflects host resource allocation into below-ground organs and patterns of host resource foraging underpinning its resource acquisition capacity. Recent studies have revealed a more comprehensive relationship between hosts and symbionts: the latter can affect host resource acquisition for phosphate and iron, and the symbiont's production of plant growth regulators can enhance host resource flux and abundance. We review the current understanding of the effects of rhizobia-legume symbioses on legume root systems. We focus on resource acquisition and allocation within the host to conceptualize the effect of symbioses on RSA, and highlight opportunities for new directions of research.
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Affiliation(s)
- Cristobal Concha
- Institute for Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Peter Doerner
- Institute for Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Roy S, Liu W, Nandety RS, Crook A, Mysore KS, Pislariu CI, Frugoli J, Dickstein R, Udvardi MK. Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation. THE PLANT CELL 2020; 32:15-41. [PMID: 31649123 PMCID: PMC6961631 DOI: 10.1105/tpc.19.00279] [Citation(s) in RCA: 320] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 09/17/2019] [Accepted: 10/24/2019] [Indexed: 05/13/2023]
Abstract
Since 1999, various forward- and reverse-genetic approaches have uncovered nearly 200 genes required for symbiotic nitrogen fixation (SNF) in legumes. These discoveries advanced our understanding of the evolution of SNF in plants and its relationship to other beneficial endosymbioses, signaling between plants and microbes, the control of microbial infection of plant cells, the control of plant cell division leading to nodule development, autoregulation of nodulation, intracellular accommodation of bacteria, nodule oxygen homeostasis, the control of bacteroid differentiation, metabolism and transport supporting symbiosis, and the control of nodule senescence. This review catalogs and contextualizes all of the plant genes currently known to be required for SNF in two model legume species, Medicago truncatula and Lotus japonicus, and two crop species, Glycine max (soybean) and Phaseolus vulgaris (common bean). We also briefly consider the future of SNF genetics in the era of pan-genomics and genome editing.
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Affiliation(s)
- Sonali Roy
- Noble Research Institute, Ardmore, Oklahoma 73401
| | - Wei Liu
- Noble Research Institute, Ardmore, Oklahoma 73401
| | | | - Ashley Crook
- College of Science, Clemson University, Clemson, South Carolina 29634
| | | | | | - Julia Frugoli
- College of Science, Clemson University, Clemson, South Carolina 29634
| | - Rebecca Dickstein
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton Texas 76203
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