Polar transport of the phytohormone auxin plays a crucial role in plant growth and response to environmental stimuli. Small-molecule tools that visualize auxin distribution in intact plants enable us to understand how plants dynamically regulate auxin transport to modulate growth. In this study, we developed a new fluorescent auxin probe, BODIPY-IAA2, which effectively visualizes auxin distribution in various plant tissues. We designed this probe to be transported by auxin transporters while lacking the ability to elicit auxin signaling. Using BODIPY as the fluorophore provides bright and stable fluorescence signals, making it suitable for live-imaging under standard fluorescent microscopy. We tested the probe with auxin reporter lines in Arabidopsis and performed yeast two-hybrid assays. The results showed that BODIPY-IAA2 did not activate auxin signaling through the auxin receptor TIR1. However, BODIPY-IAA2 did mildly compete with both exogenous and endogenous auxins for transport, indicating that the probe is transported by auxin transporters in vivo. The probe not only enables visualization of its tissue distribution but also allows sub-cellular staining, including the endoplasmic reticulum and tip regions in elongating cells in moss. We also observed unusual staining patterns in the main root of non-model parasitic plants where genetic transformation is not feasible. Our new fluorescent auxin probe demonstrates significant potential for detailed studies on auxin transport and distribution across diverse plant species.
{"title":"Development of bright fluorescent auxin","authors":"Tsuyoshi Aoyama, Masakazu Nambo, Jia Xin Yap, Ayami Nakagawa, Marina Hayashi, Yuko Ukai, Motoo Ohtsuka, Ken-ichiro Hayashi, Yoshikatsu Sato, Yuichiro Tsuchiya","doi":"10.1101/2024.09.11.612572","DOIUrl":"https://doi.org/10.1101/2024.09.11.612572","url":null,"abstract":"Polar transport of the phytohormone auxin plays a crucial role in plant growth and response to environmental stimuli. Small-molecule tools that visualize auxin distribution in intact plants enable us to understand how plants dynamically regulate auxin transport to modulate growth. In this study, we developed a new fluorescent auxin probe, BODIPY-IAA2, which effectively visualizes auxin distribution in various plant tissues. We designed this probe to be transported by auxin transporters while lacking the ability to elicit auxin signaling. Using BODIPY as the fluorophore provides bright and stable fluorescence signals, making it suitable for live-imaging under standard fluorescent microscopy. We tested the probe with auxin reporter lines in <em>Arabidopsis</em> and performed yeast two-hybrid assays. The results showed that BODIPY-IAA2 did not activate auxin signaling through the auxin receptor TIR1. However, BODIPY-IAA2 did mildly compete with both exogenous and endogenous auxins for transport, indicating that the probe is transported by auxin transporters <em>in vivo</em>. The probe not only enables visualization of its tissue distribution but also allows sub-cellular staining, including the endoplasmic reticulum and tip regions in elongating cells in moss. We also observed unusual staining patterns in the main root of non-model parasitic plants where genetic transformation is not feasible. Our new fluorescent auxin probe demonstrates significant potential for detailed studies on auxin transport and distribution across diverse plant species.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"125 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.10.612273
Radek Bezvoda, Yazmín Mónica Landeo-Ríos, Zdeňka Kubátová, Eva Kollárová, Ivan Kulich, Wolfgang Busch, Viktor Žárský, Fatima Cvrčková
We characterized the phenotypic variability of rosette leaf epidermis of 310 sequenced Arabidopsis thaliana accessions, focusing on trichome shape and distribution patterns, compositional characteristics of the trichome cell wall (callose contents, mechanical attachment strength and autofluorescence), and on histologically detectable metal ion distribution. A novel metal deposition pattern in stomatal guard cells was observed in some accessions. Subsequent GWAS analysis identified 1546 loci with protein sequence-altering SNPs associated with one or more traits, including five genes with previously reported relevant mutant phenotypes and 80 additional genes with known or predicted roles in relevant developmental and cellular processes. Several large gene families were overrepresented among the candidates, suggesting epidermal development-related functions. In particular, DUF1262, DUF3741 and receptor-like kinases associated with trichome shape traits, cytochrome P450 paralogs with cell wall composition, Cys/His-rich C1 domain proteins with trichome shape and metal deposition, and formin, DUF674, DUF784 and DUF1985 gene families with metal deposition. A possible participation of formins in guard cell metal deposition was supported by observations in available loss of function mutants. Screening of candidate gene lists against the STRING interactome database uncovered several predominantly nuclear protein interaction networks with possible novel roles in epidermal development.
{"title":"A genome-wide association screen for genes affecting leaf trichome development and epidermal metal accumulation in Arabidopsis","authors":"Radek Bezvoda, Yazmín Mónica Landeo-Ríos, Zdeňka Kubátová, Eva Kollárová, Ivan Kulich, Wolfgang Busch, Viktor Žárský, Fatima Cvrčková","doi":"10.1101/2024.09.10.612273","DOIUrl":"https://doi.org/10.1101/2024.09.10.612273","url":null,"abstract":"We characterized the phenotypic variability of rosette leaf epidermis of 310 sequenced Arabidopsis thaliana accessions, focusing on trichome shape and distribution patterns, compositional characteristics of the trichome cell wall (callose contents, mechanical attachment strength and autofluorescence), and on histologically detectable metal ion distribution. A novel metal deposition pattern in stomatal guard cells was observed in some accessions. Subsequent GWAS analysis identified 1546 loci with protein sequence-altering SNPs associated with one or more traits, including five genes with previously reported relevant mutant phenotypes and 80 additional genes with known or predicted roles in relevant developmental and cellular processes. Several large gene families were overrepresented among the candidates, suggesting epidermal development-related functions. In particular, DUF1262, DUF3741 and receptor-like kinases associated with trichome shape traits, cytochrome P450 paralogs with cell wall composition, Cys/His-rich C1 domain proteins with trichome shape and metal deposition, and formin, DUF674, DUF784 and DUF1985 gene families with metal deposition. A possible participation of formins in guard cell metal deposition was supported by observations in available loss of function mutants. Screening of candidate gene lists against the STRING interactome database uncovered several predominantly nuclear protein interaction networks with possible novel roles in epidermal development.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.12.612777
Xiao-Min Su, Dan-Yang Yuan, Lin Li, Minqi Yang, She Chen, Yue Zhou, Xin-Jian He
The histone H3K4 trimethylation (H3K4me3) is widely distributed at numerous actively transcribed protein-coding genes throughout the genome. However, the interplay between H3K4me3 and other chromatin modifications remains poorly understood in plants. In this study, we find that the Arabidopsis thaliana H3K4me3-binding ALFIN-LIKE (AL) proteins are associated with H3K4me3-enriched genes at the whole-genome level. The AL proteins contain a C-terminal PHD finger, which has a conserved role in recognizing H3K4me3, and a PHD-associated AL (PAL) domain, which is responsible for binding to diverse chromatin-related proteins. We demonstrate that the AL proteins not only act as subunits of the Polycomb repressive complex 1 (PRC1) to mediate H2A ubiquitination at H3K4me3-enriched genes but also interact with a variety of other chromatin-related proteins. Furthermore, we elucidate the mechanisms by which AL proteins interact with other chromatin-associated proteins to integrate H3K4me3, H2A ubiquitination, H2A.Z deposition, H3K27 demethylation, and chromatin accessibility across the genome. These findings underscore the critical role of AL proteins in linking H3K4me3 with a variety of other chromatin modifications in plants.
{"title":"The Arabidopsis histone H3K4me3-binding ALFIN-like proteins mediate histone H2A ubiquitination and coordinate diverse chromatin modifications","authors":"Xiao-Min Su, Dan-Yang Yuan, Lin Li, Minqi Yang, She Chen, Yue Zhou, Xin-Jian He","doi":"10.1101/2024.09.12.612777","DOIUrl":"https://doi.org/10.1101/2024.09.12.612777","url":null,"abstract":"The histone H3K4 trimethylation (H3K4me3) is widely distributed at numerous actively transcribed protein-coding genes throughout the genome. However, the interplay between H3K4me3 and other chromatin modifications remains poorly understood in plants. In this study, we find that the Arabidopsis thaliana H3K4me3-binding ALFIN-LIKE (AL) proteins are associated with H3K4me3-enriched genes at the whole-genome level. The AL proteins contain a C-terminal PHD finger, which has a conserved role in recognizing H3K4me3, and a PHD-associated AL (PAL) domain, which is responsible for binding to diverse chromatin-related proteins. We demonstrate that the AL proteins not only act as subunits of the Polycomb repressive complex 1 (PRC1) to mediate H2A ubiquitination at H3K4me3-enriched genes but also interact with a variety of other chromatin-related proteins. Furthermore, we elucidate the mechanisms by which AL proteins interact with other chromatin-associated proteins to integrate H3K4me3, H2A ubiquitination, H2A.Z deposition, H3K27 demethylation, and chromatin accessibility across the genome. These findings underscore the critical role of AL proteins in linking H3K4me3 with a variety of other chromatin modifications in plants.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.09.612066
Maria Florencia Bogino, Juan Marcos Lapegna Senz, Lucille Tihomirova Kourdova, Nicolas Tamagnone, Andres Romanowski, Lennart Wirthmueller, Georgina Fabro
Hyaloperonospora arabidopsidis (Hpa) is an oomycete pathogen that causes downy mildew disease on Arabidopsis. This obligate biotroph manipulates the homeostasis of its host plant by secreting numerous effector proteins, among which are the RxLR-effectors. Identifying the host targets of effectors and understanding how their manipulation facilitates colonization of plants is key to improve plant resistance to pathogens. Here we characterize the interaction between the RxLR effector HaRxL106 and BIM1, an Arabidopsis transcription factor (TF) involved in Brassinosteroid (BR) signaling. We report that HaRxL106 interacts with BIM1 in vitro and in planta. BIM1 is required by the effector to increase the host plant susceptibility to (hemi)biotrophic pathogens, and thus can be regarded as a susceptibility factor. Mechanistically, HaRxL106 requires BIM1 to induce the transcriptional activation of BR-responsive genes and cause alterations in plant growth patterns that phenocopy the shade avoidance syndrome. Our results support previous observations of antagonistic interactions between activation of BR signaling and suppression of plant immune responses and reveal that BIM1, a new player in this crosstalk, is manipulated by the pathogenic effector HaRxL106.
{"title":"Downy mildew effector HaRxL106 interacts with the transcription factor BIM1 altering plant growth, BR signaling and susceptibility to pathogens","authors":"Maria Florencia Bogino, Juan Marcos Lapegna Senz, Lucille Tihomirova Kourdova, Nicolas Tamagnone, Andres Romanowski, Lennart Wirthmueller, Georgina Fabro","doi":"10.1101/2024.09.09.612066","DOIUrl":"https://doi.org/10.1101/2024.09.09.612066","url":null,"abstract":"Hyaloperonospora arabidopsidis (Hpa) is an oomycete pathogen that causes downy mildew disease on Arabidopsis. This obligate biotroph manipulates the homeostasis of its host plant by secreting numerous effector proteins, among which are the RxLR-effectors. Identifying the host targets of effectors and understanding how their manipulation facilitates colonization of plants is key to improve plant resistance to pathogens. Here we characterize the interaction between the RxLR effector HaRxL106 and BIM1, an Arabidopsis transcription factor (TF) involved in Brassinosteroid (BR) signaling. We report that HaRxL106 interacts with BIM1 in vitro and in planta. BIM1 is required by the effector to increase the host plant susceptibility to (hemi)biotrophic pathogens, and thus can be regarded as a susceptibility factor. Mechanistically, HaRxL106 requires BIM1 to induce the transcriptional activation of BR-responsive genes and cause alterations in plant growth patterns that phenocopy the shade avoidance syndrome. Our results support previous observations of antagonistic interactions between activation of BR signaling and suppression of plant immune responses and reveal that BIM1, a new player in this crosstalk, is manipulated by the pathogenic effector HaRxL106.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.09.612018
Anna Kampova, Moritz K Nowack, Matyas Fendrych, Stanislav Vosolsobe
Anther dehiscence is the process that facilitates pollen release from mature anthers in flowering plants. Despite its crucial importance to reproduction, the underlying molecular regulations and the integration of environmental information remain poorly understood. Using controlled humidity treatments of Arabidopsis thaliana flowers, we show here that high humidity prevents anthers from opening. Lower and higher stomatal densities correlate with slower and faster dehiscence dynamics, respectively, suggesting that controlled transpiration regulates anther opening. Furthermore, analyses of subcellular markers revealed that specific anther tissues undergo a spatially controlled programmed cell death (PCD) process as anthers open. Notably, genetic inhibition of PCD networks delays, whereas precocious PCD induction promotes, anther dehiscence. Our data shed new light on the interplay between ambient humidity, controlled transpiration, and PCD processes in regulating timely pollen release in the model plant Arabidopsis.
{"title":"Programmed cell death and stomatal density regulate anther opening in response to ambient humidity","authors":"Anna Kampova, Moritz K Nowack, Matyas Fendrych, Stanislav Vosolsobe","doi":"10.1101/2024.09.09.612018","DOIUrl":"https://doi.org/10.1101/2024.09.09.612018","url":null,"abstract":"Anther dehiscence is the process that facilitates pollen release from mature anthers in flowering plants. Despite its crucial importance to reproduction, the underlying molecular regulations and the integration of environmental information remain poorly understood. Using controlled humidity treatments of Arabidopsis thaliana flowers, we show here that high humidity prevents anthers from opening. Lower and higher stomatal densities correlate with slower and faster dehiscence dynamics, respectively, suggesting that controlled transpiration regulates anther opening. Furthermore, analyses of subcellular markers revealed that specific anther tissues undergo a spatially controlled programmed cell death (PCD) process as anthers open. Notably, genetic inhibition of PCD networks delays, whereas precocious PCD induction promotes, anther dehiscence. Our data shed new light on the interplay between ambient humidity, controlled transpiration, and PCD processes in regulating timely pollen release in the model plant Arabidopsis.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.07.609951
Ivan Lopez-Valdivia, Harini Rangarajan, Miguel Vallebueno-Estrada, Jonathan Lynch
Integrated root phenotypes contribute to environmental adaptation and yield stability. We used the functional-structural plant/soil model OpenSimRoot_v2 to reconstruct the root phenotypes and environments of eight maize landraces to understand the phenotypic and environmental factors associated with broad adaptation. We found that accessions from low phosphorus regions have root phenotypes with shallow growth angles and greater nodal root numbers, allowing them to adapt to their native environments by improved topsoil foraging. We used machine learning algorithms to detect the most important phenotypes responsible for adaptation to multiple environments. The most important phene states responsible for stability across environments are large cortical cell size and reduced diameter of roots in nodes 5 and 6. When we dissected the components of root diameter, we observed that large cortical cell size improved growth by 28%, 23 % and 114%, while reduced cortical cell file number alone improved shoot growth by 137%, 66% and 216%, under drought, nitrogen and phosphorus stress, respectively. Functional-structural analysis of 96 maize landraces from the Americas, previously phenotyped in mesocosms in the greenhouse, suggested that parsimonious anatomical phenotypes, which reduce the metabolic cost of soil exploration, are the main phenotypes associated with adaptation to multiple environments, while root architectural traits were related to adaptation to specific environments. Our results indicate that integrated phenotypes with root anatomical phenes that reduce the metabolic cost of soil exploration will increase tolerance to stress across multiple environments and therefore improve yield stability, regardless of their root architecture.
{"title":"Exploring yield stability and the fitness landscape of maize landrace root phenotypes in silico","authors":"Ivan Lopez-Valdivia, Harini Rangarajan, Miguel Vallebueno-Estrada, Jonathan Lynch","doi":"10.1101/2024.09.07.609951","DOIUrl":"https://doi.org/10.1101/2024.09.07.609951","url":null,"abstract":"Integrated root phenotypes contribute to environmental adaptation and yield stability. We used the functional-structural plant/soil model OpenSimRoot_v2 to reconstruct the root phenotypes and environments of eight maize landraces to understand the phenotypic and environmental factors associated with broad adaptation. We found that accessions from low phosphorus regions have root phenotypes with shallow growth angles and greater nodal root numbers, allowing them to adapt to their native environments by improved topsoil foraging. We used machine learning algorithms to detect the most important phenotypes responsible for adaptation to multiple environments. The most important phene states responsible for stability across environments are large cortical cell size and reduced diameter of roots in nodes 5 and 6. When we dissected the components of root diameter, we observed that large cortical cell size improved growth by 28%, 23 % and 114%, while reduced cortical cell file number alone improved shoot growth by 137%, 66% and 216%, under drought, nitrogen and phosphorus stress, respectively. Functional-structural analysis of 96 maize landraces from the Americas, previously phenotyped in mesocosms in the greenhouse, suggested that parsimonious anatomical phenotypes, which reduce the metabolic cost of soil exploration, are the main phenotypes associated with adaptation to multiple environments, while root architectural traits were related to adaptation to specific environments. Our results indicate that integrated phenotypes with root anatomical phenes that reduce the metabolic cost of soil exploration will increase tolerance to stress across multiple environments and therefore improve yield stability, regardless of their root architecture.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"389 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.12.612472
Martijn de Roij, Jorge Hernandez Garcia, Shubhajit Das, Jan Willem Borst, Dolf Weijers
Auxin response critically depends on the concentrations and stoichiometry of competing A- and B-class AUXIN RESPONSE FACTOR (ARF) proteins. In Marchantia polymorpha, both A- and B-ARFs are unstable, and here we identify a minimal necessary and sufficient region for ARF degradation that is critical for development, and auxin response. Through comparative analysis, we find that ARF instability likely preceded the emergence of the auxin response system.
叶绿素反应关键取决于相互竞争的 A 级和 B 级叶绿素反应因子（ARF）蛋白的浓度和配比。在Marchantia polymorpha中，A-和B-ARF都不稳定，在此我们确定了ARF降解的最小必要和充分区域，该区域对发育和叶黄素响应至关重要。通过比较分析，我们发现ARF的不稳定性很可能出现在辅助素反应系统出现之前。
{"title":"ARF degradation defines a deeply conserved step in auxin response","authors":"Martijn de Roij, Jorge Hernandez Garcia, Shubhajit Das, Jan Willem Borst, Dolf Weijers","doi":"10.1101/2024.09.12.612472","DOIUrl":"https://doi.org/10.1101/2024.09.12.612472","url":null,"abstract":"Auxin response critically depends on the concentrations and stoichiometry of competing A- and B-class AUXIN RESPONSE FACTOR (ARF) proteins. In Marchantia polymorpha, both A- and B-ARFs are unstable, and here we identify a minimal necessary and sufficient region for ARF degradation that is critical for development, and auxin response. Through comparative analysis, we find that ARF instability likely preceded the emergence of the auxin response system.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.06.17.599020
Lei Hua, Na Wang, Susan Stanley, Ruth Donald, Satish Kumar Eeda, Kumari Billakurthi, Ana Rita Borba, Julian M Hibberd
C4 photosynthesis has evolved in over sixty plant lineages and improves photosynthetic efficiency by ~50%. One unifying character of C4 plants is photosynthetic activation of a compartment such as the bundle sheath, but gene regulatory networks controlling this cell type are poorly understood. In Arabidopsis a bipartite MYC-MYB transcription factor module restricts gene expression to these cells but in grasses the regulatory logic allowing bundle sheath gene expression has not been defined. Using the global staple and C3 crop rice we identified the SULFITE REDUCTASE promoter as sufficient for strong bundle sheath expression. This promoter encodes an intricate cis-regulatory logic with multiple activators and repressors acting combinatorially. Within this landscape we identified a distal enhancer activated by a quintet of transcription factors from the WRKY, G2-like, MYB-related, IDD and bZIP families. This module is necessary and sufficient to pattern gene expression to the rice bundle sheath. Oligomerisation of the enhancer and fusion to core promoters containing Y-patches allowed activity to be increased 220-fold. This enhancer generates bundle sheath-specific expression in Arabidopsis indicating deep conservation in function between monocotyledons and dicotyledons. In summary, we identify an ancient, short, and tuneable enhancer patterning expression to the bundle sheath that we anticipate will be useful for engineering this cell type in various crop species.
{"title":"A transcription factor quintet orchestrating bundle sheath expression in rice","authors":"Lei Hua, Na Wang, Susan Stanley, Ruth Donald, Satish Kumar Eeda, Kumari Billakurthi, Ana Rita Borba, Julian M Hibberd","doi":"10.1101/2024.06.17.599020","DOIUrl":"https://doi.org/10.1101/2024.06.17.599020","url":null,"abstract":"C4 photosynthesis has evolved in over sixty plant lineages and improves photosynthetic efficiency by ~50%. One unifying character of C4 plants is photosynthetic activation of a compartment such as the bundle sheath, but gene regulatory networks controlling this cell type are poorly understood. In Arabidopsis a bipartite MYC-MYB transcription factor module restricts gene expression to these cells but in grasses the regulatory logic allowing bundle sheath gene expression has not been defined. Using the global staple and C3 crop rice we identified the SULFITE REDUCTASE promoter as sufficient for strong bundle sheath expression. This promoter encodes an intricate cis-regulatory logic with multiple activators and repressors acting combinatorially. Within this landscape we identified a distal enhancer activated by a quintet of transcription factors from the WRKY, G2-like, MYB-related, IDD and bZIP families. This module is necessary and sufficient to pattern gene expression to the rice bundle sheath. Oligomerisation of the enhancer and fusion to core promoters containing Y-patches allowed activity to be increased 220-fold. This enhancer generates bundle sheath-specific expression in Arabidopsis indicating deep conservation in function between monocotyledons and dicotyledons. In summary, we identify an ancient, short, and tuneable enhancer patterning expression to the bundle sheath that we anticipate will be useful for engineering this cell type in various crop species.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"93 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.09.611861
Matanel Hipsch, Nardy Lampl, Raz Lev, Shilo Rosenwasser
Reductive and oxidative signals transmitted from the photosynthetic electron chain to target proteins through the redox signaling network are key regulators of carbon assimilation and downstream metabolism. However, despite their crucial role in activating and inhibiting photosynthetic activity, their relation to photosynthetic efficiency is hardly quantified due to the methodological gap between traditional spectroscopic approaches for investigating photosynthesis and biochemical analyses used in the redox regulation field. Here, we simultaneously quantified redox signals and photosynthetic activity by exploring time and wavelength-resolved fluorescence spectra that capture biosensor and chlorophyll fluorescence signals. Using a set of potato plants expressing genetically encoded redox biosensors capable of discerning between oxidized and reduced signals, we demonstrated how reductive and oxidative signals are amplified with elevated light intensities and revealed the tight connection between electron transport rate and the generation of oxidative signals. These results demonstrate how full spectrum analysis can pave the way for the integration of genetically encoded biosensors in photosynthesis research and demonstrate light-dependent activation of inhibitory oxidative signals in major crop plants.
{"title":"Quantification of electron transport-related oxidative signals by time and wavelength-resolved redox biosensors and chlorophyll fluorescence","authors":"Matanel Hipsch, Nardy Lampl, Raz Lev, Shilo Rosenwasser","doi":"10.1101/2024.09.09.611861","DOIUrl":"https://doi.org/10.1101/2024.09.09.611861","url":null,"abstract":"Reductive and oxidative signals transmitted from the photosynthetic electron chain to target proteins through the redox signaling network are key regulators of carbon assimilation and downstream metabolism. However, despite their crucial role in activating and inhibiting photosynthetic activity, their relation to photosynthetic efficiency is hardly quantified due to the methodological gap between traditional spectroscopic approaches for investigating photosynthesis and biochemical analyses used in the redox regulation field. Here, we simultaneously quantified redox signals and photosynthetic activity by exploring time and wavelength-resolved fluorescence spectra that capture biosensor and chlorophyll fluorescence signals. Using a set of potato plants expressing genetically encoded redox biosensors capable of discerning between oxidized and reduced signals, we demonstrated how reductive and oxidative signals are amplified with elevated light intensities and revealed the tight connection between electron transport rate and the generation of oxidative signals. These results demonstrate how full spectrum analysis can pave the way for the integration of genetically encoded biosensors in photosynthesis research and demonstrate light-dependent activation of inhibitory oxidative signals in major crop plants.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.06.611704
Trenton W Berrian, Matthew L Fabian, Conner J Rogan, Jeffrey C Anderson, Christopher R Clarke, Aymeric Goyer
Background: Previous reports in several plant species have shown that thiamin applied on foliage primes plant immunity and is effective in controlling fungal, bacterial, and viral diseases. However, the effectiveness of thiamin against potato (Solanum tuberosum) pathogens has seldom been investigated. Additionally, the transcriptomics and metabolomics of immune priming by thiamin have not previously been investigated. Here, we tested the effect of thiamin application against Alternaria solani, a necrotrophic fungus that causes early blight disease on potato foliage, and identified associated changes in gene expression and metabolite content. Results: Foliar applications of thiamin reduced lesion size by approximately 33% when applied at an optimal concentration of 10 mM. However, the effect of thiamin on preventing lesion growth was temporally limited, as we observed a reduction of lesion size when leaves were inoculated 4 h, but not 24 h, following thiamin treatment. Additionally, we found that the effect of thiamin on lesion size was restricted to the site of application and was not systemic. Gene expression analysis via RNA-seq showed that thiamin induced the expression of genes involved in the synthesis of salicylic acid (SA) and phenylpropanoids to higher levels than the pathogen alone, as well as fatty acid metabolism genes that may be related to jasmonic acid biosynthesis. Thiamin also delayed the downregulation of photosynthesis-associated genes in plants inoculated with A. solani, which is a typical plant response to pathogens, but could also induce a similar repression of primary metabolic pathways in non-infected leaves. Metabolite analyses revealed that thiamin treatment in the absence of pathogen decreased the amounts of several organic compounds involved in the citric acid cycle as well as sugars, sugar alcohols, and amino acids. Conclusions: Our study indicates that thiamin priming of plant defenses may occur through perturbation of primary metabolic pathways and a re-allocation of energy resources towards defense activities.
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