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1. Shared TIR enzymatic functions regulate cell death and immunity across the tree of life

   https://doi.org/10.1126/science.abo0001  

   Essuman, Kow ; Milbrandt, Jeffrey ; Dangl, Jeffery L. ; Nishimura, Marc T. ( July 2022 , Science)

   BACKGROUND Diverse organisms, from archaea and bacteria to plants and humans, use receptor systems to recognize both pathogens and dangerous self-derived or environmentally derived stimuli. These intricate, well-coordinated immune systems, composed of innate and adaptive components, ensure host survival. In the late 20th century, researchers identified the Toll/interleukin-1/resistance gene (TIR) domain as an evolutionarily conserved component of animal and plant innate immune systems. Today, TIR-domain proteins are known to be broadly distributed across the tree of life. The TIR domain was first recognized as an adaptor for the assembly of macromolecular signaling complexes in mammalian innate immune pathways. Work on axon degeneration in animals—as well as on plant, archaeal, and bacterial immune systems—has uncovered additional enzymatic activities for TIR domains. ADVANCES Mammalian axons initiate a self-destruct program upon injury and during disease that is mediated by the sterile alpha and TIR motif containing 1 (SARM1) protein. The SARM1 TIR domain enzymatically consumes the essential metabolic cofactor nicotinamide adenine dinucleotide (NAD + ) to promote axonal death. Identification of the SARM1 NAD + -consuming enzyme (NADase) revealed that TIR domains can function as enzymes. Given the evolutionary conservation of TIR domains, studies investigated whether the SARM1 TIR NADase was also conserved. Indeed, bacteria, archaea, and plant TIR domains possess NADase activity. In prokaryotes, TIR NADase activity is found in an ancient antiphage immune system. In plants, identification of TIR NADase activity and linkage of TIR enzymatic products to downstream signaling components addressed the question of how nucleotide-binding, leucine-rich repeat (NLR) receptors trigger hypersensitive cell death during an immune response. Studies in plants show that their TIR domains can cleave nucleic acids and possess 2′,3′ cyclic adenosine monophosphate (2′,3′-cAMP) and 2′,3′ cyclic guanosine monophosphate (2′,3′-cGMP) synthetase activity that aids cell death programs in plant innate immunity. Thus, TIR domains constitute an ancient family of enzymes that are activated in immune and cell death pathways. OUTLOOK The discovery of TIR-domain enzyme activities carries implications for innate immunity and neurodegeneration. The identification of the SARM1 NADase defined a drug target for a wide number of neurodegenerative diseases that is being exploited in both preclinical and clinical studies. Hyperactive mutations in the SARM1 NADase have been discovered in amyotrophic lateral sclerosis (ALS) patients. Future work will seek to clarify the contribution of the SARM1 axon degeneration pathway to ALS pathogenesis. NAD + biology influences cellular processes from metabolism to DNA repair to aging. How TIR enzymes influence the NAD + metabolome and its associated pathways in bacteria, archaea, plants, and animals will be an exciting area for upcoming investigation. The discovery of the diversity of TIR enzymatic products is revealing signaling pathways across kingdoms. Discovery of TIR enzymatic function in plants and animals may yet inspire studies of enzymatic functions for Toll-like receptors in animals. We anticipate that cross-kingdom studies of TIR-domain function will guide interventions that will span the tree of life, from treating human neurodegenerative disorders and bacterial infections to preventing plant diseases. Conserved TIR-domain enzymatic activity. TIR-domain proteins from prokaryotes and eukaryotes cleave NAD + into nicotinamide (Nam), ADP-ribose (ADPR), cyclic ADP-ribose (cADPR), isomers of cyclic ADP-ribose (2′ or 3′cADPR), and related molecules [e.g., phosphoribosyl adenosine monophosphate (pRib-AMP)]. Plant TIR domains also possess a nuclease activity, can degrade DNA and RNA, and can function as a 2′,3′-cAMP or 2′,3′-cGMP synthetase. TIR enzymatic activity drives cell death and immune pathways across kingdoms. TIR activity can kill cells directly through NAD + depletion or indirectly using enzymatic products as signal molecules. The representative TIR domain structure shown here is Protein Data Bank ID 6O0Q. EDS1, enhanced disease susceptibility 1; ThsA, Thoeris A. 

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2. Arabidopsis Ca2+-ATPases 1, 2, and 7 in the endoplasmic reticulum contribute to growth and pollen fitness

   https://doi.org/10.1093/plphys/kiab021  

   Rahmati Ishka, Maryam ; Brown, Elizabeth ; Rosenberg, Alexa ; Romanowsky, Shawn ; Davis, James A ; Choi, Won-Gyu ; Harper, Jeffrey F ( January 2021 , Plant Physiology)

   null (Ed.)

   Abstract Generating cellular Ca2+ signals requires coordinated transport activities from both Ca2+ influx and efflux pathways. In Arabidopsis (Arabidopsis thaliana), multiple efflux pathways exist, some of which involve Ca2+-pumps belonging to the Autoinhibited Ca2+-ATPase (ACA) family. Here, we show that ACA1, 2, and 7 localize to the endoplasmic reticulum (ER) and are important for plant growth and pollen fertility. While phenotypes for plants harboring single-gene knockouts (KOs) were weak or undetected, a triple KO of aca1/2/7 displayed a 2.6-fold decrease in pollen transmission efficiency, whereas inheritance through female gametes was normal. The triple KO also resulted in smaller rosettes showing a high frequency of lesions. Both vegetative and reproductive phenotypes were rescued by transgenes encoding either ACA1, 2, or 7, suggesting that all three isoforms are biochemically redundant. Lesions were suppressed by expression of a transgene encoding NahG, an enzyme that degrades salicylic acid (SA). Triple KO mutants showed elevated mRNA expression for two SA-inducible marker genes, Pathogenesis-related1 (PR1) and PR2. The aca1/2/7 lesion phenotype was similar but less severe than SA-dependent lesions associated with a double KO of vacuolar pumps aca4 and 11. Imaging of Ca2+ dynamics triggered by blue light or the pathogen elicitor flg22 revealed that aca1/2/7 mutants display Ca2+ transients with increased magnitudes and durations. Together, these results indicate that ER-localized ACAs play important roles in regulating Ca2+ signals, and that the loss of these pumps results in male fertility and vegetative growth deficiencies. 

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3. Electronic relaxation dynamics in [Au 25 (SR) 18 ] −1 (R = CH 3 , C 2 H 5 , C 3 H 7 , MPA, PET) thiolate-protected nanoclusters

   https://doi.org/10.1039/C9CP04039K  

   Senanayake, Ravithree D. ; Aikens, Christine M. ( March 2020 , Physical Chemistry Chemical Physics)

   null (Ed.)

   We investigate the excited electron dynamics in [Au 25 (SR) 18 ] −1 (R = CH 3 , C 2 H 5 , C 3 H 7 , MPA, PET) [MPA = mercaptopropanoic acid, PET = phenylethylthiol] nanoparticles to understand how different ligands affect the excited state dynamics in this system. The population dynamics of the core and higher excited states lying in the energy range 0.00–2.20 eV are studied using a surface hopping method with decoherence correction in a real-time DFT approach. All of the ligated clusters follow a similar trend in decay for the core states (S 1 –S 6 ). The observed time constants are on the picosecond time scale (2–19 ps), which agrees with the experimental time scale, and this study confirms that the time constants observed experimentally could originate from core-to-core transitions and not from core-to-semiring transitions. In the presence of higher excited states, R = H, CH 3 , C 2 H 5 , C 3 H 7 , and PET demonstrate similar relaxations trends whereas R = MPA shows slightly different relaxation of the core states due to a smaller gap between the LUMO+1 and LUMO+2 gap in its electronic structure. The S 1 (HOMO → LUMO) state gives the slowest decay in all ligated clusters, while S 7 has a relatively long decay. Furthermore, separate electron and hole relaxations were performed on the [Au 25 (SCH 3 ) 18 ] −1 nanocluster to understand how independent electron and hole relaxations contribute to the overall relaxation dynamics. 

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4. The Arabidopsis LHT1 Amino Acid Transporter Contributes to Pseudomonas simiae-Mediated Plant Growth Promotion by Modulating Bacterial Metabolism in the Rhizosphere

   https://doi.org/10.3390/plants12020371  

   Agorsor, Israel D. ; Kagel, Brian T. ; Danna, Cristian H. ( January 2023 , Plants)

   The root microbiome structure ensures optimal plant host health and fitness, and it is, at least in part, defined by the plant genotype. It is well documented that root-secreted amino acids promote microbial chemotaxis and growth in the rhizosphere. However, whether the plant-mediated re-uptake of amino acids contributes to maintaining optimal levels of amino acids in the root exudates, and, in turn, microbial growth and metabolism, remains to be established. Here, we show that Lysine-Histidine Transporter-1 (LHT1), an amino acid inward transporter expressed in Arabidopsis thaliana roots, limits the growth of the plant-growth-promoting bacteria Pseudomonas simiae WCS417r (Ps WCS417r). The amino acid profiling of the lht1 mutant root exudates showed increased levels of glutamine, among other amino acids. Interestingly, lht1 exudates or Gln-supplemented wild-type exudates enhance Ps WCS417r growth. However, despite promoting bacterial growth and robust root colonization, lht1 exudates and Gln-supplemented wild-type exudates inhibited plant growth in a Ps WCS417r-dependent manner. The transcriptional analysis of defense and growth marker genes revealed that plant growth inhibition was not linked to the elicitation of plant defense but likely to the impact of Ps WCS417r amino acids metabolism on auxin signaling. These data suggest that an excess of amino acids in the rhizosphere impacts Ps WCS417r metabolism, which, in turn, inhibits plant growth. Together, these results show that LHT1 regulates the amino-acid-mediated interaction between plants and Ps WCS417r and suggest a complex relationship between root-exuded amino acids, root colonization by beneficial bacteria, bacterial metabolism, and plant growth promotion. 

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5. Soil-derived fulvic acid and root exudates, modified by soil bacteria, alter CuO nanoparticle-induced root stunting of wheat via Cu complexation

   https://doi.org/10.1039/c9en00728h  

   Hortin, J. M. ; Anderson, A. J. ; Britt, D. W. ; Jacobson, A. R. ; McLean, J. E. ( December 2019 , Environmental Science: Nano)

   CuO nanoparticles (NPs) are explored as fungicides and fertilizers, and are increasingly likely to be applied to agricultural soils. Consequently, interactions of CuO NPs with soil pore water (SPW) components, plants, and microbes must be understood. These experiments examined whether dissolved natural organic matter (DNOM) from SPW, or root/bacterial exudates, changed wheat ( Triticum aestivum L. v. Deloris) responses to 100 mg kg −1 (Cu/sand) as CuO NPs. Seedlings were grown in sand with 3.34 mM Ca(NO 3 ) 2 or one of three SPWs, differing in DNOM concentration and composition. At 10 days post-germination, CuO NPs stunted roots by 59% in the 3.34 mM Ca(NO 3 ) 2 and 26–35% in the three SPWs compared to plants grown without NPs. Malate, citrate, gluconate, and 2′-deoxymugineic acid (DMA), were elevated 1.3 to 5-fold in the rhizosphere with CuO NPs present. Cu was bioavailable through metallo-organic complexes, including Cu–DMA and Cu–gluconate. Fulvic acid in SPWs mitigated CuO NP-induced wheat root shortening. Pseudomonas chlororaphis O6 eliminated malate and citrate in the rhizospheres, reduced rhizosphere dissolved Cu ∼18–66%, and reduced root Cu 39% across all SPWs while enhancing root stunting ∼17% more across all SPWs than non-inoculated wheat grown with CuO NPs. Thus, both SPW components and root microbial colonization influenced wheat responses to CuO NPs. These interactions are likely in agricultural soils with additional processes, such as ion sorption, to influence CuO NP phytotoxicity, highlighting the importance of considering not just the target plant, but soil properties and associated microbiomes when evaluating impacts of NPs in agricultural usage. 

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