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1. Protocol: analytical methods for visualizing the indolic precursor network leading to auxin biosynthesis

   https://doi.org/10.1186/s13007-021-00763-0  

   Tillmann, Molly ; Tang, Qian ; Cohen, Jerry D. ( June 2021 , Plant Methods)

   The plant hormone auxin plays a central role in regulation of plant growth and response to environmental stimuli. Multiple pathways have been proposed for biosynthesis of indole-3-acetic acid (IAA), the primary auxin in a number of plant species. However, utilization of these different pathways under various environmental conditions and developmental time points remains largely unknown.

   Monitoring incorporation of stable isotopes from labeled precursors into proposed intermediates provides a method to trace pathway utilization and characterize new biosynthetic routes to auxin. These techniques can be aided by addition of chemical inhibitors to target specific steps or entire pathways of auxin synthesis.

   Here we describe techniques for pathway analysis inArabidopsis thalianaseedlings using multiple stable isotope-labeled precursors and chemical inhibitors coupled with highly sensitive liquid chromatography-mass spectrometry (LC–MS) methods. These methods should prove to be useful to researchers studying routes of IAA biosynthesis in vivo in a variety of plant tissues.

    

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2. Biosynthesis and Roles of Salicylic Acid in Balancing Stress Response and Growth in Plants

   https://doi.org/10.3390/ijms222111672  

   Zhong, Qinling ; Hu, Hongliang ; Fan, Baofang ; Zhu, Cheng ; Chen, Zhixiang ( November 2021 , International Journal of Molecular Sciences)

   Salicylic acid (SA) is an important plant hormone with a critical role in plant defense against pathogen infection. Despite extensive research over the past 30 year or so, SA biosynthesis and its complex roles in plant defense are still not fully understood. Even though earlier biochemical studies suggested that plants synthesize SA from cinnamate produced by phenylalanine ammonia lyase (PAL), genetic analysis has indicated that in Arabidopsis, the bulk of SA is synthesized from isochorismate (IC) produced by IC synthase (ICS). Recent studies have further established the enzymes responsible for the conversion of IC to SA in Arabidopsis. However, it remains unclear whether other plants also rely on the ICS pathway for SA biosynthesis. SA induces defense genes against biotrophic pathogens, but represses genes involved in growth for balancing defense and growth to a great extent through crosstalk with the growth-promoting plant hormone auxin. Important progress has been made recently in understanding how SA attenuates plant growth by regulating the biosynthesis, transport, and signaling of auxin. In this review, we summarize recent progress in the biosynthesis and the broad roles of SA in regulating plant growth during defense responses. Further understanding of SA production and its regulation of both defense and growth will be critical for developing better knowledge to improve the disease resistance and fitness of crops. 

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3. Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome

   https://doi.org/10.1038/s41564-022-01244-3  

   Conway, Jonathan M. ; Walton, William G. ; Salas-González, Isai ; Law, Theresa F. ; Lindberg, Chloe A. ; Crook, Laura E. ; Kosina, Suzanne M. ; Fitzpatrick, Connor R. ; Lietzan, Adam D. ; Northen, Trent R. ; et al ( October 2022 , Nature Microbiology)

   Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genusVariovoraxvia an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect theVariovoraxauxin degradation locus to define the genesiadDEas necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products:iac-like andiad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizingArabidopsisplants show that while all degrade IAA, only strains containingiad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests thatiad-like operon-containing bacterial strains, includingVariovoraxspecies, play a key ecological role in modulating auxins in the plant microbiome.

    

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4. Auxin Plays Multiple Roles during Plant–Pathogen Interactions

   https://doi.org/10.1101/cshperspect.a040022  

   Kunkel, Barbara N. ; Johnson, Joshua M.B. ( January 2021 , Cold Spring Harbor Perspectives in Biology)

   Weijers, D. ; Ljung, K. ; Estelle, M. ; Leyser, O. (Ed.)

   The plant hormone auxin governs many aspects of normal plant growth and development. Auxin also plays an important role in plant–microbe interactions, including interactions between plant hosts and pathogenic microorganisms that cause disease. It is now well established that indole-3-acetic acid (IAA), the most well-studied form of auxin, promotes disease in many plant–pathogen interactions. Recent studies have shown that IAA can act both as a plant hormone that modulates host signaling and physiology to increase host susceptibility and as a microbial signal that directly impacts the pathogen to promote virulence, but large gaps in our understanding remain. In this article, we review recent studies on the roles that auxin plays during plant–pathogen interactions and discuss the virulence mechanisms that many plant pathogens have evolved to manipulate host auxin signaling and promote pathogenesis. 

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5. Dual Role of Auxin in Regulating Plant Defense and Bacterial Virulence Gene Expression During Pseudomonas syringae PtoDC3000 Pathogenesis

   https://doi.org/10.1094/MPMI-02-20-0047-R  

   Djami-Tchatchou, Arnaud T. ; Harrison, Gregory A. ; Harper, Chris P. ; Wang, Renhou ; Prigge, Michael J. ; Estelle, Mark ; Kunkel, Barbara N. ( August 2020 , Molecular Plant-Microbe Interactions®)

   null (Ed.)

   Modification of host hormone biology is a common strategy used by plant pathogens to promote disease. For example, the bacterial pathogen strain Pseudomonas syringae DC3000 (PtoDC3000) produces the plant hormone auxin (indole-3-acetic acid [IAA]) to promote PtoDC3000 growth in plant tissue. Previous studies suggest that auxin may promote PtoDC3000 pathogenesis through multiple mechanisms, including both suppression of salicylic acid (SA)-mediated host defenses and via an unknown mechanism that appears to be independent of SA. To test if host auxin signaling is important during pathogenesis, we took advantage of Arabidopsis thaliana lines impaired in either auxin signaling or perception. We found that disruption of auxin signaling in plants expressing an inducible dominant axr2-1 mutation resulted in decreased bacterial growth and that this phenotype was suppressed by introducing the sid2-2 mutation, which impairs SA synthesis. Thus, host auxin signaling is required for normal susceptibility to PtoDC3000 and is involved in suppressing SA-mediated defenses. Unexpectedly, tir1 afb1 afb4 afb5 quadruple-mutant plants lacking four of the six known auxin coreceptors that exhibit decreased auxin perception, supported increased levels of bacterial growth. This mutant exhibited elevated IAA levels and reduced SA-mediated defenses, providing additional evidence that auxin promotes disease by suppressing host defense. We also investigated the hypothesis that IAA promotes PtoDC3000 virulence through a direct effect on the pathogen and found that IAA modulates expression of virulence genes, both in culture and in planta. Thus, in addition to suppressing host defenses, IAA acts as a microbial signaling molecule that regulates bacterial virulence gene expression. 

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