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Ambreetha S, Zincke D, Balachandar D, Mathee K. Genomic and metabolic versatility of Pseudomonas aeruginosa contributes to its inter-kingdom transmission and survival. J Med Microbiol 2024; 73. [PMID: 38362900 DOI: 10.1099/jmm.0.001791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
Pseudomonas aeruginosa is one of the most versatile bacteria with renowned pathogenicity and extensive drug resistance. The diverse habitats of this bacterium include fresh, saline and drainage waters, soil, moist surfaces, taps, showerheads, pipelines, medical implants, nematodes, insects, plants, animals, birds and humans. The arsenal of virulence factors produced by P. aeruginosa includes pyocyanin, rhamnolipids, siderophores, lytic enzymes, toxins and polysaccharides. All these virulent elements coupled with intrinsic, adaptive and acquired antibiotic resistance facilitate persistent colonization and lethal infections in different hosts. To date, treating pulmonary diseases remains complicated due to the chronic secondary infections triggered by hospital-acquired P. aeruginosa. On the contrary, this bacterium can improve plant growth by suppressing phytopathogens and insects. Notably, P. aeruginosa is one of the very few bacteria capable of trans-kingdom transmission and infection. Transfer of P. aeruginosa strains from plant materials to hospital wards, animals to humans, and humans to their pets occurs relatively often. Recently, we have identified that plant-associated P. aeruginosa strains could be pathologically similar to clinical isolates. In this review, we have highlighted the genomic and metabolic factors that facilitate the dominance of P. aeruginosa across different biological kingdoms and the varying roles of this bacterium in plant and human health.
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Affiliation(s)
- Sakthivel Ambreetha
- Developmental Biology and Genetics, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Diansy Zincke
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
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2
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Gul M, Khan RS, Islam ZU, Khan S, Shumaila A, Umar S, Khan S, Brekhna, Zahoor M, Ditta A. Nanoparticles in plant resistance against bacterial pathogens: current status and future prospects. Mol Biol Rep 2024; 51:92. [PMID: 38194006 DOI: 10.1007/s11033-023-08914-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/14/2023] [Indexed: 01/10/2024]
Abstract
Nanoparticles (NPs) serve immense roles in various fields of science. They have vastly upgraded conventional methods in the fields of agriculture and food sciences to eliminate growing threats of crop damage and disease, caused by various phytopathogens including bacteria, fungi, viruses, and some insects. Bacterial diseases resulted in mass damage of crops by adopting antibacterial resistance, which has proved to be a major threat leading to food scarcity. Therefore, numerous NPs with antibacterial potentials have been formulated to overcome the problem of antibiotic resistance alongside an increase in crop yield and boosting plant immunity. NPs synthesized through green synthesis techniques have proved to be more effective and environment-friendly than those synthesized via chemical methods. NPs exhibit great roles in plants ranging from enhanced crop yield to disease suppression, to targeted drug and pesticide deliveries inside the plants and acting as biosensors for pathogen detection. NPs serves major roles in disruption of cellular membranes, ROS production, altering of DNA and protein entities and changing energy transductions. This review focuses on the antibacterial effect of NPs on several plant bacterial pathogens, mostly, against Pseudomonas syringe, Ralstonia solanacearum, Xanthomonas axonopodis, Clavibacter michiganensisand Pantoea ananatis both in vivo and ex vivo, thereby minimizing their antibacterial resistance and enhancing the plants acquired immunity. Therefore, NPs present a safer and more reliable bactericidal activity against various disease-causing bacteria in plants.
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Affiliation(s)
- Maria Gul
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Raham Sher Khan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan.
| | - Zia Ul Islam
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sumayya Khan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Amina Shumaila
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sidra Umar
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sajad Khan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Brekhna
- Department of Physics, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Zahoor
- Department of Biochemistry, University of Malakand, Chakdara, 18800, Pakistan
| | - Allah Ditta
- Department of Environmental Sciences, Shaheed Benazir Bhutto University, Upper Dir, 18000, Sheringal, Khyber Pakhtunkhwa, Pakistan
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
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3
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Genetic and Environmental Investigation of a Novel Phenylamino Acetamide Inhibitor of the Pseudomonas aeruginosa Type III Secretion System. Appl Environ Microbiol 2023; 89:e0175222. [PMID: 36519869 PMCID: PMC9888221 DOI: 10.1128/aem.01752-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Traditional antibiotics target essential cellular components or metabolic pathways conserved in both pathogenic and nonpathogenic bacteria. Unfortunately, long-term antibiotic use often leads to antibiotic resistance and disruption of the overall microbiota. In this work, we identified a phenylamino acetamide compound, named 187R, that strongly inhibited the expression of the type III secretion system (T3SS) encoding genes and the secretion of the T3SS effector proteins in Pseudomonas aeruginosa. T3SS is an important virulence factor, as T3SS-deficient strains of P. aeruginosa are greatly attenuated in virulence. We further showed that 187R had no effect on bacterial growth, implying a reduced selective pressure for the development of resistance. 187R-mediated repression of T3SS was dependent on ExsA, the master regulator of T3SS in P. aeruginosa. The impact of 187R on the host-associated microbial community was also tested using the Arabidopsis thaliana phyllosphere as a model. Both culture-independent (Illumina sequencing) and culture-dependent (Biolog) methods showed that the application of 187R had little impact on the composition and function of microbial community compared to the antibiotic streptomycin. Together, these results suggested that compounds that target virulence factors could serve as an alternative strategy for disease management caused by bacterial pathogens. IMPORTANCE New antimicrobial therapies are urgently needed, since antibiotic resistance in human pathogens has become one of the world's most urgent public health problems. Antivirulence therapy has been considered a promising alternative for the management of infectious diseases, as antivirulence compounds target only the virulence factors instead of the growth of bacteria, and they are therefore unlikely to affect commensal microorganisms. However, the impacts of antivirulence compounds on the host microbiota are not well understood. We report a potent synthetic inhibitor of the P. aeruginosa T3SS, 187R, and its effect on the host microbiota of Arabidopsis. Both culture-independent (Illumina sequencing) and culture-dependent (Biolog) methods showed that the impacts of the antivirulence compound on the composition and function of host microbiota were limited. These results suggest that antivirulence compounds can be a potential alternative method to antibiotics.
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Hodgson RJ, Liddicoat C, Cando‐Dumancela C, Blyth C, Watson CD, Breed MF. Local and non‐local soil microbiota impede germination of the endangered
Acacia whibleyana. AUSTRAL ECOL 2023. [DOI: 10.1111/aec.13275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Riley J. Hodgson
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
| | - Craig Liddicoat
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
- School of Public Health University of Adelaide Adelaide South Australia Australia
| | | | - Colette Blyth
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Carl D. Watson
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
| | - Martin F. Breed
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
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5
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Kong F, Yang L. Pathogen-triggered changes in plant development: Virulence strategies or host defense mechanism? Front Microbiol 2023; 14:1122947. [PMID: 36876088 PMCID: PMC9975269 DOI: 10.3389/fmicb.2023.1122947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/25/2023] [Indexed: 02/17/2023] Open
Abstract
Plants, as sessile organisms, are constantly exposed to pathogens in nature. Plants rely on physical barriers, constitutive chemical defenses, and sophisticated inducible immunity to fight against pathogens. The output of these defense strategies is highly associated with host development and morphology. Successful pathogens utilize various virulence strategies to colonize, retrieve nutrients, and cause disease. In addition to the overall defense-growth balance, the host-pathogen interactions often lead to changes in the development of specific tissues/organs. In this review, we focus on recent advances in understanding the molecular mechanisms of pathogen-induced changes in plants' development. We discuss that changes in host development could be a target of pathogen virulence strategies or an active defense strategy of plants. Current and ongoing research about how pathogens shape plant development to increase their virulence and causes diseases could give us novel views on plant disease control.
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Affiliation(s)
- Feng Kong
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Li Yang
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
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6
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Potential of nanobiosensor in sustainable agriculture: the state-of-art. Heliyon 2022; 8:e12207. [PMID: 36578430 PMCID: PMC9791828 DOI: 10.1016/j.heliyon.2022.e12207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/28/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
A rapid surge in world population leads to an increase in worldwide demand for agricultural products. Nanotechnology and its applications in agriculture have appeared as a boon to civilization with enormous potential in transforming conventional farming practices into redefined farming activities. Low-cost portable nanobiosensors are the most effective diagnostic tool for the rapid on-site assessment of plant and soil health including plant biotic and abiotic stress level, nutritional status, presence of hazardous chemicals in soil, etc. to maintain proper farming and crop productivity. Nanobiosensors detect physiological signals and convert them into standardized detectable signals. In order to achieve a reliable sensing analysis, nanoparticles can aid in signal amplification and sensor sensitivity by lowering the detection limit. The high selectivity and sensitivity of nanobiosensors enable early detection and management of targeted abnormalities. This study identifies the types of nanobiosensors according to the target application in agriculture sector.
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Li C, Dong S, Beckles DM, Miao H, Sun J, Liu X, Wang W, Zhang S, Gu X. The qLTG1.1 candidate gene CsGAI regulates low temperature seed germination in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2593-2607. [PMID: 35764690 DOI: 10.1007/s00122-022-04097-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
The CsGAI gene, identified by map-based, was involved in regulating seed germination in low temperature via the GA and ABA signaling pathways. Low temperature reduces the percentage of seeds germinating and delays seed germinating time, thus posing a threat to cucumber production. However, the molecular mechanism regulating low temperature germination in cucumber is unknown. We here dissected a major quantitative trait locus qLTG1.1 that controls seed germination at low temperature in cucumber. First, we fine-mapped qLTG1.1 to a 46.3-kb interval, containing three candidate genes. Sequence alignment and gene expression analysis identified Csa1G408720 as the gene of interest that was highly expressed in seeds, and encoded a highly conserved, low temperature-regulated DELLA family protein CsGAI. GUS expression analysis indicated that higher promoter activity underscored higher transcriptional expression of the CsGAI gene. Consistent with the known roles of GAI in ABA and GA signaling during germination, genes involved in the GA (CsGA2ox, CsGA3ox) and ABA biosynthetic pathways (CsABA1, CsABA2, CsAAO3 and CsNCED) were found to be differently regulated in the tolerant and sensitive genotypes under low temperatures, and this was reflected in differences in their ratio of GA-to-ABA. Based on these data, we proposed a working model explaining how CsGAI integrates the GA and ABA signaling pathways, to regulate cucumber seed germination at low temperature, thus providing new insights into this mechanism.
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Affiliation(s)
- Caixia Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shaoyun Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Diane M Beckles
- Department of Plant Sciences, University of California, One Shield Avenue, Dav is Davis, CA, 95616, USA
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaqiang Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoping Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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8
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Solis-Ortiz CS, Gonzalez-Bernal J, Kido-Díaz HA, Peña-Uribe CA, López-Bucio JS, López-Bucio J, Guevara-García ÁA, García-Pineda E, Villegas J, Campos-García J, Reyes de La Cruz H. Bacterial cyclodipeptides elicit Arabidopsis thaliana immune responses reducing the pathogenic effects of Pseudomonas aeruginosa PAO1 strains on plant development. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153738. [PMID: 35690030 DOI: 10.1016/j.jplph.2022.153738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Plants being sessile organisms are exposed to various biotic and abiotic factors, thus causing stress. The Pseudomonas aeruginosa bacterium is an opportunistic pathogen for animals, insects, and plants. Direct exposure of Arabidopsis thaliana to the P. aeruginosa PAO1 strain induces plant death by producing a wide variety of virulence factors, which are regulated mainly by quorum sensing systems. Besides virulence factors, P. aeruginosa PAO1 also produces cyclodipeptides (CDPs), which possess auxin-like activity and promote plant growth through activation of the target of the rapamycin (AtTOR) pathway. On the other hand, plant defense mechanisms are regulated through the production of phytohormones, such as salicylic acid (SA) and jasmonic acid (JA), which are induced in response to pathogen-associated molecular patterns (PAMPs), activating defense genes associated with SA and JA such as PATHOGENESIS-RELATED-1 (PR-1) and LIPOXYGENASE2 (LOX2), respectively. PR proteins are suggested to play critical roles in coordinating the Systemic Acquired Resistance (SAR). In contrast, LOX proteins (LOX2, LOX3, and LOX4) have been associated with the production of JA by producing its precursors, oxylipins. The activation of defense mechanisms involves signaling cascades such as Mitogen-Activated Protein Kinases (MAPKs) or the TOR pathway as a switch for re-directing energy towards defense or growth. In this work, we challenged A. thaliana (wild type, mpk6 or mpk3 mutants, and overexpressing TOR) seedlings with P. aeruginosa PAO1 strains to identify the role of bacterial CDPs in the plant immune response. Results showed that the pre-exposure of these Arabidopsis seedlings to CDPs significantly reduced plant infection of the pathogenic P. aeruginosa PAO1 strains, indicating that plants that over-express AtTOR or lack MPK3/MPK6 protein-kinases are more susceptible to the pathogenic effects. In addition, CDPs induced the GUS activity only in the LOX2::GUS plants, indicative of JA-signaling activation. Our findings indicate that the CDPs are molecules that trigger SA-independent and JA-dependent defense responses in A. thaliana; hence, bacterial CDPs may be considered elicitors of the Arabidopsis immune response to pathogens.
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Affiliation(s)
- Cristhian Said Solis-Ortiz
- Laboratorio de Biotecnología Molecular de Plantas, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | - Javier Gonzalez-Bernal
- Laboratorio de Biotecnología Molecular de Plantas, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | - Héctor Antonio Kido-Díaz
- Laboratorio de Biotecnología Molecular de Plantas, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | - Cesar Artuto Peña-Uribe
- Laboratorio de Biotecnología Molecular de Plantas, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | - Jesús Salvador López-Bucio
- Laboratorio de Biotecnología Molecular de Plantas, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | - José López-Bucio
- Laboratorio de Biología del Desarrollo Vegetal, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | | | - Ernesto García-Pineda
- Laboratorio de Bioquímica y Biología Molecular de Plantas, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | - Javier Villegas
- Laboratorio de Interacción Suelo Planta Microorganismo, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | - Jesús Campos-García
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico.
| | - Homero Reyes de La Cruz
- Laboratorio de Biotecnología Molecular de Plantas, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico.
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9
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Patteson JB, Fortinez CM, Putz AT, Rodriguez-Rivas J, Bryant LH, Adhikari K, Weigt M, Schmeing TM, Li B. Structure and Function of a Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis. J Am Chem Soc 2022; 144:14057-14070. [PMID: 35895935 DOI: 10.1021/jacs.1c13404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehydroamino acids are important structural motifs and biosynthetic intermediates for natural products. Many bioactive natural products of nonribosomal origin contain dehydroamino acids; however, the biosynthesis of dehydroamino acids in most nonribosomal peptides is not well understood. Here, we provide biochemical and bioinformatic evidence in support of the role of a unique class of condensation domains in dehydration (CmodAA). We also obtain the crystal structure of a CmodAA domain, which is part of the nonribosomal peptide synthetase AmbE in the biosynthesis of the antibiotic methoxyvinylglycine. Biochemical analysis reveals that AmbE-CmodAA modifies a peptide substrate that is attached to the donor carrier protein. Mutational studies of AmbE-CmodAA identify several key residues for activity, including four residues that are mostly conserved in the CmodAA subfamily. Alanine mutation of these conserved residues either significantly increases or decreases AmbE activity. AmbE exhibits a dimeric conformation, which is uncommon and could enable transfer of an intermediate between different protomers. Our discovery highlights a central dehydrating function for CmodAA domains that unifies dehydroamino acid biosynthesis in diverse nonribosomal peptide pathways. Our work also begins to shed light on the mechanism of CmodAA domains. Understanding CmodAA domain function may facilitate identification of new natural products that contain dehydroamino acids and enable engineering of dehydroamino acids into nonribosomal peptides.
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Affiliation(s)
- Jon B Patteson
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Camille Marie Fortinez
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Andrew T Putz
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Juan Rodriguez-Rivas
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - L Henry Bryant
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kamal Adhikari
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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10
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Almeida RND, Greenberg M, Bundalovic-Torma C, Martel A, Wang PW, Middleton MA, Chatterton S, Desveaux D, Guttman DS. Predictive modeling of Pseudomonas syringae virulence on bean using gradient boosted decision trees. PLoS Pathog 2022; 18:e1010716. [PMID: 35877772 PMCID: PMC9352200 DOI: 10.1371/journal.ppat.1010716] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 08/04/2022] [Accepted: 06/30/2022] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas syringae is a genetically diverse bacterial species complex responsible for numerous agronomically important crop diseases. Individual P. syringae isolates are assigned pathovar designations based on their host of isolation and the associated disease symptoms, and these pathovar designations are often assumed to reflect host specificity although this assumption has rarely been rigorously tested. Here we developed a rapid seed infection assay to measure the virulence of 121 diverse P. syringae isolates on common bean (Phaseolus vulgaris). This collection includes P. syringae phylogroup 2 (PG2) bean isolates (pathovar syringae) that cause bacterial spot disease and P. syringae phylogroup 3 (PG3) bean isolates (pathovar phaseolicola) that cause the more serious halo blight disease. We found that bean isolates in general were significantly more virulent on bean than non-bean isolates and observed no significant virulence difference between the PG2 and PG3 bean isolates. However, when we compared virulence within PGs we found that PG3 bean isolates were significantly more virulent than PG3 non-bean isolates, while there was no significant difference in virulence between PG2 bean and non-bean isolates. These results indicate that PG3 strains have a higher level of host specificity than PG2 strains. We then used gradient boosting machine learning to predict each strain’s virulence on bean based on whole genome k-mers, type III secreted effector k-mers, and the presence/absence of type III effectors and phytotoxins. Our model performed best using whole genome data and was able to predict virulence with high accuracy (mean absolute error = 0.05). Finally, we functionally validated the model by predicting virulence for 16 strains and found that 15 (94%) had virulence levels within the bounds of estimated predictions. This study strengthens the hypothesis that P. syringae PG2 strains have evolved a different lifestyle than other P. syringae strains as reflected in their lower level of host specificity. It also acts as a proof-of-principle to demonstrate the power of machine learning for predicting host specific adaptation. Pseudomonas syringae is a genetically diverse Gammaproteobacterial species complex responsible for numerous agronomically important crop diseases. Strains in the P. syringae species complex are frequently categorized into pathovars depending on pathogenic characteristics such as host of isolation and disease symptoms. Common bean pathogens from P. syringae are known to cause two major diseases: (1) pathovar phaseolicola strains from phylogroup 3 cause halo blight disease, characterized by large necrotic lesions surrounded by a chlorotic zone or halo of yellow tissue; and (2) pathovar syringae strains from phylogroup 2 causes bacterial spot disease, characterized by brown leaf spots. While halo blight can cause serious crop losses, bacterial spot disease is generally of minor agronomic concern. Recently, statistical genetic and machine learning approaches have been applied to genomic data to identify genes underlying traits of interest or predict the outcome of host-microbe interactions. Here, we apply machine learning to P. syringae genomic data to predict virulence on bean. We first characterized the virulence of P. syringae isolates on common bean using a seed infection assay and then applied machine learning to the genomic data from the same strains to generate a predictive model for virulence on bean. We found that machine learning models built with k-mers from either full genome data or virulence factors could predict bean virulence with high accuracy. We also confirmed prior work showing that phylogroup 3 halo blight pathogens display a stronger degree of phylogenetic clustering and host specificity compared to phylogroup 2 brown spot pathogens. This works serves as a proof-of-principle for the power of machine learning for predicting host specificity and may find utility in agricultural diagnostic microbiology.
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Affiliation(s)
- Renan N. D. Almeida
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Michael Greenberg
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | | | - Alexandre Martel
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Pauline W. Wang
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
| | - Maggie A. Middleton
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
| | - Syama Chatterton
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - David S. Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
- * E-mail:
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11
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Mo Doped WO3 Nanoparticles as Nanopriming Agent for Promoting the Seed Germination and their Effects on Bacterial Growth. J CLUST SCI 2021. [DOI: 10.1007/s10876-021-02206-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Ahmad S, Strunk CH, Schott-Verdugo SN, Jaeger KE, Kovacic F, Gohlke H. Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity. J Chem Inf Model 2021; 61:5626-5643. [PMID: 34748335 DOI: 10.1021/acs.jcim.1c00973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates have remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free-energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid (FA) products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by FA-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.
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Affiliation(s)
- Sabahuddin Ahmad
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christoph Heinrich Strunk
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan N Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Centro de Bioinformática y Simulación Molecular (CBSM), Faculty of Engineering, University of Talca, 3460000 Talca, Chile.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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13
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Michalet S, Allard PM, Commun C, Ngoc VTN, Nouwade K, Gioia B, Dijoux-Franca MG, Wolfender JL, Doléans-Jordheim A. Alkyl-Quinolones derivatives as potential biomarkers for Pseudomonas aeruginosa infection chronicity in Cystic Fibrosis. Sci Rep 2021; 11:20722. [PMID: 34671079 PMCID: PMC8528811 DOI: 10.1038/s41598-021-99467-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 09/17/2021] [Indexed: 01/20/2023] Open
Abstract
In Cystic Fibrosis (CF), a rapid and standardized definition of chronic infection would allow a better management of Pseudomonas aeruginosa (Pa) infections, as well as a quick grouping of patients during clinical trials allowing better comparisons between studies. With this purpose, we compared the metabolic profiles of 44 in vitro cultures of Pa strains isolated from CF patients at different stages of infection in order to identify metabolites differentially synthetized according to these clinical stages. Compounds produced and secreted by each strain in the supernatant of a liquid culture were analysed by metabolomic approaches (UHPLC-DAD-ESI/QTOF, UV and UPLC-Orbitrap, MS). Multivariate analyses showed that first colonization strains could be differentiated from chronic colonization ones, by producing notably more Alkyl-Quinolones (AQs) derivatives. Especially, five AQs were discriminant: HQC5, HQNOC7, HQNOC7:1, db-PQS C9 and HQNOC9:1. However, the production of HHQ was equivalent between strain types. The HHQ/HQNOC9:1 ratio was then found to be significantly different between chronic and primo-colonising strains by using both UV (p = 0.003) and HRMS data (p = 1.5 × 10-5). Our study suggests that some AQ derivatives can be used as biomarkers for an improved management of CF patients as well as a better definition of the clinical stages of Pa infection.
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Affiliation(s)
- Serge Michalet
- grid.25697.3f0000 0001 2172 4233Université de Lyon, Lyon, France ,grid.7849.20000 0001 2150 7757Université Claude Bernard Lyon 1, Lyon, France ,grid.7849.20000 0001 2150 7757Research Group on Environmental Multiresistance and Bacterial Efflux, UMR CNRS 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, ISPB, Villeurbanne, France
| | - Pierre-Marie Allard
- grid.8591.50000 0001 2322 4988School of Pharmaceutical Sciences and Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneve 4, Switzerland
| | - Carine Commun
- grid.25697.3f0000 0001 2172 4233Université de Lyon, Lyon, France ,grid.7849.20000 0001 2150 7757Université Claude Bernard Lyon 1, Lyon, France ,grid.7849.20000 0001 2150 7757Research Group on Bacterial Opportunistic Pathogens and Environment, UMR CNRS 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, ISPB, Villeurbanne, France
| | - Van Thanh Nguyen Ngoc
- grid.25697.3f0000 0001 2172 4233Université de Lyon, Lyon, France ,grid.7849.20000 0001 2150 7757Université Claude Bernard Lyon 1, Lyon, France ,grid.7849.20000 0001 2150 7757Research Group on Environmental Multiresistance and Bacterial Efflux, UMR CNRS 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, ISPB, Villeurbanne, France
| | - Kodjo Nouwade
- grid.25697.3f0000 0001 2172 4233Université de Lyon, Lyon, France ,grid.7849.20000 0001 2150 7757Université Claude Bernard Lyon 1, Lyon, France ,grid.7849.20000 0001 2150 7757Research Group on Environmental Multiresistance and Bacterial Efflux, UMR CNRS 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, ISPB, Villeurbanne, France
| | - Bruna Gioia
- grid.25697.3f0000 0001 2172 4233Université de Lyon, Lyon, France ,grid.7849.20000 0001 2150 7757Université Claude Bernard Lyon 1, Lyon, France ,EA 4446, Molécules bioactives et chimie médicinale (B2MC), ISPB-Faculté de Pharmacie, Lyon, France
| | - Marie-Geneviève Dijoux-Franca
- grid.25697.3f0000 0001 2172 4233Université de Lyon, Lyon, France ,grid.7849.20000 0001 2150 7757Université Claude Bernard Lyon 1, Lyon, France ,grid.7849.20000 0001 2150 7757Research Group on Environmental Multiresistance and Bacterial Efflux, UMR CNRS 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, ISPB, Villeurbanne, France
| | - Jean-Luc Wolfender
- grid.8591.50000 0001 2322 4988School of Pharmaceutical Sciences and Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneve 4, Switzerland
| | - Anne Doléans-Jordheim
- grid.25697.3f0000 0001 2172 4233Université de Lyon, Lyon, France ,grid.7849.20000 0001 2150 7757Université Claude Bernard Lyon 1, Lyon, France ,grid.7849.20000 0001 2150 7757Research Group on Bacterial Opportunistic Pathogens and Environment, UMR CNRS 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, ISPB, Villeurbanne, France ,grid.413852.90000 0001 2163 3825Laboratoire de Bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
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14
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Ambreetha S, Marimuthu P, Mathee K, Balachandar D. Rhizospheric and endophytic Pseudomonas aeruginosa in edible vegetable plants share molecular and metabolic traits with clinical isolates. J Appl Microbiol 2021; 132:3226-3248. [PMID: 34608722 DOI: 10.1111/jam.15317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/28/2021] [Accepted: 09/21/2021] [Indexed: 01/02/2023]
Abstract
AIM Pseudomonas aeruginosa, a leading opportunistic pathogen causing hospital-acquired infections, is also commonly found in agricultural settings. However, there are minimal attempts to examine the molecular and functional attributes shared by agricultural and clinical strains of P. aeruginosa. This study investigates the presence of P. aeruginosa in edible vegetable plants (including salad vegetables) and analyses the evolutionary and metabolic relatedness of the agricultural and clinical strains. METHODS AND RESULTS Eighteen rhizospheric and endophytic P. aeruginosa strains were isolated from cucumber, tomato, eggplant, and chili directly from the farms. The identity of these strains was confirmed using biochemical and molecular assays. The genetic and metabolic traits of these plant-associated P. aeruginosa isolates were compared with clinical strains. DNA fingerprinting and 16S rDNA-based phylogenetic analyses revealed that the plant- and human-associated strains are evolutionarily related. Both agricultural and clinical isolates possessed plant-beneficial properties, including mineral solubilization to release essential nutrients (phosphorous, potassium, and zinc), ammonification, and the ability to release extracellular pyocyanin, siderophore, and indole-3 acetic acid. CONCLUSION These findings suggest that rhizospheric and endophytic P. aeruginosa strains are genetically and functionally analogous to the clinical isolates. In addition, the genotypic and phenotypic traits do not correlate with plant sources or ecosystems. SIGNIFICANCE AND IMPACT OF THE STUDY This study reconfirms that edible plants are the potential source for human and animal transmission of P. aeruginosa.
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Affiliation(s)
- Sakthivel Ambreetha
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.,Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
| | - Ponnusamy Marimuthu
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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15
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Abstract
The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa. IMPORTANCE Seed microbiota can have a crucial role for crop installation by modulating dormancy, germination, seedling development, and recruitment of plant symbionts. Little knowledge is available on the fraction of the plant microbiota that is acquired through seeds. We characterize the encounter between seed and soil communities and how they colonize the seedling together. Transmission success and seedling community assemblage can be influenced by the variation of initial microbial pools, i.e., plant genotype and cropping year for seeds and diversity level for soils. Despite a supposed resident advantage of the seed microbiota, we show that transmission success is in favor of the soil microbiota. Our results also suggest that successful plant-microbiome engineering based on native seed or soil microbiota must include rare taxa.
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16
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Fei X, Lina W, Jiayang C, Meng F, Guodong W, Yaping Y, Langjun C. Variations of microbial community in Aconitum carmichaeli Debx. rhizosphere soilin a short-term continuous cropping system. J Microbiol 2021; 59:481-490. [PMID: 33779961 DOI: 10.1007/s12275-021-0515-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Aconitum carmichaeli Debx. (Ranunculaceae) is a potential source of an important herbal drug named "Fuzi", which is derived from the lateral root of the plant. Increased therapeutic usage resulted in the great demand for artificial cultivation of A. carmichaeli, however, the obstacles caused by continuous cropping is a serious problem. Continuous cropping has shown to affect the soil biological and non-biological factors. The current study attempted to discover the variations of microbial communities and soil properties in short-term continuous cropping of A. carmichaeli. An experimental procedure with A. carmichaeli planted two years continuously was established. The variation of the soil microbial community, disease incidence, soil properties, and the correlation between soil microbe and disease incidence were investigated. The disease incidence increased during the continuous cropping of A. carmichaeli. The PCoA and LefSe results indicated that fungal communities in rhizosphere soil were altered during the short-term continuous croppingand the bacterial community was disturbed by the cultivation of A. carmichaeli, however, in the following two years of continuous cropping period, the soil bacterial community has not changed obviously. Proportions of some fungal and bacterial genera were varied significantly (p < 0.05), and some genera of microflora showed a significant correlation with adisease incidence of A. carmichaeli. Microorganisms contributing to community composition discrepancy were also elucidated. Continuous cropping of A. carmichaeli disturbed the rhizosphere soil microbial community and altered the soil chemical parameters and soil pH. These variations in soil may be related to the occurrence of plant diseases. The current study will not only provide theoretical and experimental evidence for the A. carmichaeli continuous cropping obstacles but will also contribute to A. carmichaeli agricultural production and soil improvement.
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Affiliation(s)
- Xia Fei
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'An, 710021, China
| | - Wang Lina
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Chen Jiayang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Fu Meng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Wang Guodong
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Yan Yaping
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Cui Langjun
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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17
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A Raf-like kinase is required for smoke-induced seed dormancy in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2021; 118:2020636118. [PMID: 33795513 DOI: 10.1073/pnas.2020636118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plants sense and integrate diverse stimuli to determine the timing for germination. A smoke compound, 3,4,5-trimethylfuran-2(5H)-one (trimethylbutenolide, TMB), has been identified to inhibit the seed germination of higher plants. To understand the mode of action, we examined various physiological and molecular aspects of the TMB-dependent inhibition of seed germination in Arabidopsis thaliana The results indicated that the effect of TMB is due to the enhanced physiological dormancy, which is modulated by other dormancy regulatory cues such as after-ripening, stratification, and ABA/GA signaling. In addition, gene expression profiling showed that TMB caused genome-wide transcriptional changes, altering the expression of a series of dormancy-related genes. Based on the TMB-responsive physiological contexts in Arabidopsis, we performed mutant screening to isolate genetic components that underpin the TMB-induced seed dormancy. As a result, the TMB-RESISTANT1 (TES1) gene in Arabidopsis, encoding a B2 group Raf-like kinase, was identified. Phenotypic analysis of the tes1 mutant implicated that TES1 has a critical role in the TMB-responsive gene expression and the inhibition of seed germination. Taken together, we propose that plants have been equipped with a TMB sensory pathway through which the TMB induces the seed dormancy in a TES1-dependent way.
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18
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Berrios L, Ely B. Genes related to redox and cell curvature facilitate interactions between Caulobacter strains and Arabidopsis. PLoS One 2021; 16:e0249227. [PMID: 33793620 PMCID: PMC8016251 DOI: 10.1371/journal.pone.0249227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/12/2021] [Indexed: 12/28/2022] Open
Abstract
Bacteria play an integral role in shaping plant growth and development. However, the genetic factors that facilitate plant-bacteria interactions remain largely unknown. Here, we demonstrated the importance of two bacterial genetic factors that facilitate the interactions between plant-growth-promoting (PGP) bacteria in the genus Caulobacter and the host plant Arabidopsis. Using homologous recombination, we disrupted the cytochrome ubiquinol oxidase (cyo) operon in both C. vibrioides CB13 and C. segnis TK0059 by knocking out the expression of cyoB (critical subunit of the cyo operon) and showed that the mutant strains were unable to enhance the growth of Arabidopsis. In addition, disruption of the cyo operon, metabolomic reconstructions, and pH measurements suggested that both elevated cyoB expression and acid production by strain CB13 contribute to the previously observed inhibition of Arabidopsis seed germination. We also showed that the crescent shape of the PGP bacterial strain C. crescentus CB15 contributes to its ability to enhance plant growth. Thus, we have identified specific genetic factors that explain how select Caulobacter strains interact with Arabidopsis plants.
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Affiliation(s)
- Louis Berrios
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United State of America
- * E-mail:
| | - Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United State of America
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19
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Cook J, Douglas GM, Zhang J, Glick BR, Langille MGI, Liu KH, Cheng Z. Transcriptomic profiling of Brassica napus responses to Pseudomonas aeruginosa. Innate Immun 2020; 27:143-157. [PMID: 33353474 PMCID: PMC7882811 DOI: 10.1177/1753425920980512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen of plants. Unlike the well-characterized plant defense responses to highly adapted bacterial phytopathogens, little is known about plant response to P. aeruginosa infection. In this study, we examined the Brassica napus (canola) tissue-specific response to P. aeruginosa infection using RNA sequencing. Transcriptomic analysis of canola seedlings over a 5 day P. aeruginosa infection revealed that many molecular processes involved in plant innate immunity were up-regulated, whereas photosynthesis was down-regulated. Phytohormones control many vital biological processes within plants, including growth and development, senescence, seed setting, fruit ripening, and innate immunity. The three main phytohormones involved in plant innate immunity are salicylic acid (SA), jasmonic acid (JA), and ethylene (ET). Many bacterial pathogens have evolved multiple strategies to manipulate these hormone responses in order to infect plants successfully. Interestingly, gene expression within all three phytohormone (SA, JA, and ET) signaling pathways was up-regulated in response to P. aeruginosa infection. This study identified a unique plant hormone response to the opportunistic bacterial pathogen P. aeruginosa infection.
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Affiliation(s)
- Jamie Cook
- Department of Microbiology and Immunology, Dalhousie University, Canada
| | - Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Canada
| | - Janie Zhang
- Department of Microbiology and Immunology, Dalhousie University, Canada
| | | | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Canada.,Department of Pharmacology, Dalhousie University, Canada.,Integrated Microbiome Resource (IMR), Dalhousie University, Canada
| | - Kun-Hsiang Liu
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, USA.,Department of Genetics, Harvard Medical School, USA.,State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwestern Agriculture and Forestry University, People's Republic of China
| | - Zhenyu Cheng
- Department of Microbiology and Immunology, Dalhousie University, Canada
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20
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Berlanga-Clavero MV, Molina-Santiago C, de Vicente A, Romero D. More than words: the chemistry behind the interactions in the plant holobiont. Environ Microbiol 2020; 22:4532-4544. [PMID: 32794337 DOI: 10.1111/1462-2920.15197] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 02/04/2023]
Abstract
Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant-associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant-microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant-microbe and microbe-microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe-microbe and microbe-plant communication pathways during plant development and on different plant organs.
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Affiliation(s)
- María Victoria Berlanga-Clavero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
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21
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Carrera-Castaño G, Calleja-Cabrera J, Pernas M, Gómez L, Oñate-Sánchez L. An Updated Overview on the Regulation of Seed Germination. PLANTS 2020; 9:plants9060703. [PMID: 32492790 PMCID: PMC7356954 DOI: 10.3390/plants9060703] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.
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22
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Transcriptome Profiling Analysis Reveals Co-regulation of Hormone Pathways in Foxtail Millet during Sclerospora graminicola Infection. Int J Mol Sci 2020; 21:ijms21041226. [PMID: 32059399 PMCID: PMC7072888 DOI: 10.3390/ijms21041226] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/24/2020] [Accepted: 01/25/2020] [Indexed: 11/16/2022] Open
Abstract
Sclerospora graminicola (Sacc.) Schroeter is a biotrophic pathogen of foxtail millet (Setaria italica) and increasingly impacts crop production. We explored the main factors for symptoms such as dwarfing of diseased plants and the “hedgehog panicle” by determining panicle characteristics of varieties infected with S. graminicola and analyzing the endogenous hormone-related genes in leaves of Jingu 21. Results indicated that different varieties infected by S. graminicola exhibited various symptoms. Transcriptome analysis revealed that the ent-copalyl diphosphate synthetase (CPS) encoded by Seita.2G144900 and ent-kaurene synthase (KS) encoded by Seita.2G144400 were up-regulated 4.7-fold and 2.8-fold, respectively. Results showed that the biosynthesis of gibberellin might be increased, but the gibberellin signal transduction pathway might be blocked. The abscisic acid (ABA) 8′-hydroxylase encoded by Seita.6G181300 was continuously up-regulated by 4.2-fold, 2.7-fold, 14.3-fold, and 12.9-fold from TG1 to TG4 stage, respectively. Seita.2G144900 and Seita.2G144400 increased 79-fold and 51-fold, respectively, at the panicle development stage, promoting the formation of a “hedgehog panicle”. Jasmonic acid-related synthesis enzymes LOX2s, AOS, and AOC were up-regulated at the early stage of infection, indicating that jasmonic acid played an essential role in early response to S. graminicola infection. The expression of YUC-related genes of the auxin synthesis was lower than that of the control at TG3 and TG4 stages, but the amidase encoded by Seita.2G313400 was up-regulated by more than 30-fold, indicating that the main biosynthesis pathway of auxin had changed. The results suggest that there was co-regulation of the hormone pathways during the infection of foxtail millet by S. graminicola.
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Cornelis P. Putting an end to the Pseudomonas aeruginosa IQS controversy. Microbiologyopen 2019; 9:e962. [PMID: 31667921 PMCID: PMC7002111 DOI: 10.1002/mbo3.962] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/10/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Despite published evidence that IQS (2-(2-hydroxylphenyl)-thiazole-4-carbaldehyde) is in fact aeruginaldehyde, a by-product of the siderophore pyochelin biosynthesis or degradation and that the ambABCDE genes are not responsible for IQS synthesis, several authors, including in top review journals, perpetuate the wrong information. I hope that this short comment will clarify the situation once and for all.
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Affiliation(s)
- Pierre Cornelis
- Department of Bioengineering Sciences, Laboratory of Microbiology, Vrije Universiteit Brussel, Brussels, Belgium.,Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, Évreux, France
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Hu Y, Han X, Yang M, Zhang M, Pan J, Yu D. The Transcription Factor INDUCER OF CBF EXPRESSION1 Interacts with ABSCISIC ACID INSENSITIVE5 and DELLA Proteins to Fine-Tune Abscisic Acid Signaling during Seed Germination in Arabidopsis. THE PLANT CELL 2019; 31:1520-1538. [PMID: 31123050 PMCID: PMC6635857 DOI: 10.1105/tpc.18.00825] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/19/2019] [Accepted: 05/06/2019] [Indexed: 05/04/2023]
Abstract
ABSCISIC ACID INSENSITIVE5 (ABI5) is a crucial regulator of abscisic acid (ABA) signaling pathways involved in repressing seed germination and postgerminative growth in Arabidopsis (Arabidopsis thaliana). ABI5 is precisely modulated at the posttranslational level; however, the transcriptional regulatory mechanisms underlying ABI5 and its interacting transcription factors remain largely unknown. Here, we found that INDUCER OF CBF EXPRESSION1 (ICE1) physically associates with ABI5. ICE1 negatively regulates ABA responses during seed germination and directly suppresses ABA-responsive LATE EMBRYOGENESIS ABUNDANT6 (EM6) and EM1 expression. Genetic analysis demonstrated that the ABA-hypersensitive phenotype of the ice1 mutant requires ABI5. ICE1 interferes with the transcriptional activity of ABI5 to mediate downstream regulons. Importantly, ICE1 also interacts with DELLA proteins, which stimulate ABI5 during ABA signaling. Disruption of ICE1 partially restored the ABA-hyposensitive phenotype of the della mutant, gai-t6 rga-t2 rgl1-1 rgl2-1, indicating that ICE1 functions antagonistically with DELLA in ABA signaling. Consistently, DELLA proteins repress ICE1's transcriptional function and the antagonistic effect of ICE1 on ABI5. Collectively, our study demonstrates that ICE1 antagonizes ABI5 and DELLA activity to maintain the appropriate level of ABA signaling during seed germination, providing a mechanistic understanding of how ABA signaling is fine-tuned by a transcriptional complex involving ABI5 and its interacting partners.
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Affiliation(s)
- Yanru Hu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xiao Han
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Milian Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghui Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinjing Pan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Diqiu Yu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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The Root Cap Cuticle: A Cell Wall Structure for Seedling Establishment and Lateral Root Formation. Cell 2019; 176:1367-1378.e8. [PMID: 30773319 DOI: 10.1016/j.cell.2019.01.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 11/23/2018] [Accepted: 01/02/2019] [Indexed: 11/21/2022]
Abstract
The root cap surrounding the tip of plant roots is thought to protect the delicate stem cells in the root meristem. We discovered that the first layer of root cap cells is covered by an electron-opaque cell wall modification resembling a plant cuticle. Cuticles are polyester-based protective structures considered exclusive to aerial plant organs. Mutations in cutin biosynthesis genes affect the composition and ultrastructure of this cuticular structure, confirming its cutin-like characteristics. Strikingly, targeted degradation of the root cap cuticle causes a hypersensitivity to abiotic stresses during seedling establishment. Furthermore, lateral root primordia also display a cuticle that, when defective, causes delayed outgrowth and organ deformations, suggesting that it facilitates lateral root emergence. Our results show that the previously unrecognized root cap cuticle protects the root meristem during the critical phase of seedling establishment and promotes the efficient formation of lateral roots.
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