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Background: The ORI-EGI-02 study was designed to test the hypothesis that rectal mucus collected using a novel rectal sampling device (OriCol™), contains sufficient human deoxyribonucleic acid (DNA) of the required quality for Next Generation Sequencing (NGS), for colorectal disease genetic signature discovery., Methods: Using National Institute for Health and Care Research methodology, an internal pilot study was performed in January 2020-May 2021, at four sites in the United Kingdom, to assess the process of recruitment, consent, specimen acquisition and viability for analysis. Following an OriCol ™ test, the sample was stabilized with a buffer solution to preserve the material, which was posted to the laboratory. Samples were processed using QIAamp ® DNA Blood Midi kit to extract DNA and Quant-iT ™ PicoGreen ® dsDNA Reagent to quantify the retrieved DNA. DNA integrity was measured by Agilent TapeStation system. 25 ng of human amplifiable DNA was prepared for Next Generation Sequencing (NGS), which was performed on an Illumina NextSeq550 sequencer using the 300-cycle high output kit v2.5., Results: This study assessed the first 300 patients enrolled to the ORI-EGI-02 Study (n = 800). 290/300 (96.67%) were eligible to undergo OriCol ™ sampling procedure and 285/290 (98.27%) had a successful OriCol ™ sample taken. After transportation, extraction and quantification of DNA, 96.20% (279/290) of the samples had NGS successfully performed for bioinformatic analysis., Conclusions: Our internal pilot study demonstrated that the OriCol ™ sampling device can capture rectal mucus from unprepared bowel in subjects who could undergo a digital rectal examination. The technique could be applied irrespective of age, frailty, or co-morbidity. Completion of the study to 800 patients and analysis of NGS data for colorectal cancer mutations will now proceed., (© 2022. Springer Nature Switzerland AG.)

Growth at increased concentrations of CO 2 induces a reduction in seed zinc (Zn) and iron (Fe). Using Arabidopsis thaliana, we investigated whether this could be mitigated by reducing the elevated CO 2 -induced decrease in transpiration. We used an infrared imaging-based screen to isolate mutants in At1g08080 that encodes ALPHA CARBONIC ANHYDRASE 7 (ACA7). aca7 mutant alleles display wild-type (WT) responses to abscisic acid (ABA) and light but are compromised in their response to elevated CO 2 . ACA7 is expressed in guard cells. When aca7 mutants are grown at 1000 ppm CO 2 they exhibit higher transpiration and higher seed Fe and Zn content than WT grown under the same conditions. Our data show that by increasing transpiration it is possible to partially mitigate the reduction in seed Fe and Zn content when Arabidopsis is grown at elevated CO 2 ., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.)

Although UVA radiation (315-400 nm) represents 95% of the UV radiation reaching the earth's surface, surprisingly little is known about its effects on plants [1]. We show that in Arabidopsis, short-term exposure to UVA inhibits the opening of stomata, and this requires a reduction in the cytosolic level of cGMP. This process is independent of UVR8, the UVB receptor. A cGMP-activated phosphodiesterase (AtCN-PDE1) was responsible for the UVA-induced decrease in cGMP in Arabidopsis. AtCN-PDE1-like proteins form a clade within the large HD-domain/PDEase-like protein superfamily, but no eukaryotic members of this subfamily have been functionally characterized. These genes have been lost from the genomes of metazoans but are otherwise conserved as single-copy genes across the tree of life. In longer-term experiments, UVA radiation increased growth and decreased water-use efficiency. These experiments revealed that PDE1 is also a negative regulator of growth. As the PDE1 gene is ancient and not represented in animal lineages, it is likely that at least one element of cGMP signaling in plants has evolved differently to the system present in metazoans., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Stomata are leaf pores that regulate CO 2 uptake and evapotranspirational water loss. By controlling CO 2 uptake, stomata impact on photosynthesis and dry matter accumulation. The regulation of evapotranspiration is equally important because it impacts on nutrient accumulation and leaf cooling and enables the plant to limit water loss during drought [1]. Our work centers on stomatal closure [2-6]. This involves loss of potassium from the guard cell by a two-step process. Salt is released across the plasma membrane via anion channels such as SLAC1 [7-9] and depolarization-activated channels such as GORK [10, 11], with the net result that cations and anions exit guard cells. However, this critically depends on K + release from the vacuole; with ∼160 and 100 mM K + in cytoplasm and vacuole of open guard cells [12], vacuolar K + efflux is driven by the negative tonoplast potential, and this expels K + from the vacuole via tonoplast K + channels like TPK1. In all, guard cell salt release leads to a loss of turgor that brings about stomatal closure. First, we show that the TPK1 vacuolar K + channel is important for abscisic acid (ABA)- and CO 2 -mediated stomatal closure. Second, we reveal that, during ABA- and CO 2 -mediated closure, TPK1 is phosphorylated and activated by the KIN7 receptor-like protein kinase (RLK), which co-expresses in the tonoplast and plasma membrane. The net result is K + release from the vacuole. Taken together, our work reveals new components involved in guard cell signaling and describes a new mechanism potentially involved in fine-tuning ABA- and CO 2 -induced stomatal closure., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

All living organisms communicate with their environment, and part of this dialogue is mediated by secondary messengers such as cyclic guanosine mono phosphate (cGMP). In plants, most of the specific components that allow production and breakdown of cGMP have now been identified apart from cGMP dependent phosphodiesterases, enzymes responsible for cGMP catabolism. Irrespectively, the role of cGMP in plant signal transductions is now firmly established with involvement of this nucleotide in development, stress response, ion homeostasis and hormone function. Within these areas, several consistent themes where cGMP may be particularly relevant are slowly emerging: these include regulation of cation fluxes, for example via cyclic nucleotide gated channels and in stomatal functioning. Many details of signalling pathways that incorporate cGMP remain to be unveiled. These include downstream targets other than a small number of ion channels, in particular cGMP dependent kinases. Improved genomics tools may help in this respect, especially since many proteins involved in cGMP signalling appear to have multiple and often overlapping functional domains which hampers identification on the basis of simple homology searches. Another open question regards the topographical distribution of cGMP signals are they cell limited? Does long distance cGMP signalling occur and if so, by what mechanisms? The advent of non-disruptive fluorescent reporters with high spatial and temporal resolution will provide a tool to accelerate progress in all these areas. Automation can facilitate large scale screens of mutants or the action of effectors that impact on cGMP signalling.

Stomata respond to darkness by closing to prevent excessive water loss during the night. Although the reorganisation of actin filaments during stomatal closure is documented, the underlying mechanisms responsible for dark-induced cytoskeletal arrangement remain largely unknown. We used genetic, physiological and cell biological approaches to show that reorganisation of the actin cytoskeleton is required for dark-induced stomatal closure. The opal5 mutant does not close in response to darkness but exhibits wild-type (WT) behaviour when exposed to abscisic acid (ABA) or CaCl 2 . The mutation was mapped to At5g18410, encoding the PIR/SRA1/KLK subunit of the ArabidopsisSCAR/WAVE complex. Stomata of an independent allele of the PIR gene (Atpir-1) showed reduced sensitivity to darkness and F 1 progenies of the cross between opal5 and Atpir-1 displayed distorted leaf trichomes, suggesting that the two mutants are allelic. Darkness induced changes in the extent of actin filament bundling in WT. These were abolished in opal5. Disruption of filamentous actin using latrunculin B or cytochalasin D restored wild-type stomatal sensitivity to darkness in opal5. Our findings suggest that the stomatal response to darkness is mediated by reorganisation of guard cell actin filaments, a process that is finely tuned by the conserved SCAR/WAVE-Arp2/3 actin regulatory module., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)

An integral part of global environment change is an increase in the atmospheric concentration of CO2 ([CO2]) [1]. Increased [CO2] reduces leaf stomatal apertures and density of stomata that plays out as reductions in evapotranspiration [2-4]. Surprisingly, given the importance of transpiration to the control of terrestrial water fluxes [5] and plant nutrient acquisition [6], we know comparatively little about the molecular components involved in the intracellular signaling pathways by which [CO2] controls stomatal development and function [7]. Here, we report that elevated [CO2]-induced closure and reductions in stomatal density require the generation of reactive oxygen species (ROS), thereby adding a new common element to these signaling pathways. We also show that the PYR/RCAR family of ABA receptors [8, 9] and ABA itself are required in both responses. Using genetic approaches, we show that ABA in guard cells or their precursors is sufficient to mediate the [CO2]-induced stomatal density response. Taken together, our results suggest that stomatal responses to increased [CO2] operate through the intermediacy of ABA. In the case of [CO2]-induced reductions in stomatal aperture, this occurs by accessing the guard cell ABA signaling pathway. In both [CO2]-mediated responses, our data are consistent with a mechanism in which ABA increases the sensitivity of the system to [CO2] but could also be explained by requirement for a CO2-induced increase in ABA biosynthesis specifically in the guard cell lineage. Furthermore, the dependency of stomatal [CO2] signaling on ABA suggests that the ABA pathway is, in evolutionary terms, likely to be ancestral., (Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The cyclic nucleotide 3',5'-cyclic guanyl monophosphate (cGMP) has been implicated in the regulation of important plant processes. To unravel its physiological role further, accurate recording of dynamic changes in cGMP concentration is necessary. Fluorescent sensors based on biological molecules for "live imaging" are ideal for this since they have high specificity, a sensitivity that is in the range of biologically relevant concentrations, high spatial and dynamic resolution, and measurements with such sensors are nondestructive. In this chapter we describe the use of the cGMP FlincG sensor in plant materials that either transiently or stably express this sensor.

The cyclic nucleotide cGMP has been shown to play important roles in plant development and responses to abiotic and biotic stress. Yet much controversy remains regarding the exact role of this second messenger. Progress in unravelling cGMP function in plants was hampered by laborious and time-consuming methodology to measure changes in cellular [cGMP] but the development of fluorescence-based reporters has removed this disadvantage. This study used the FlincG cGMP reporter to investigate potential interactions between phytohormone and cGMP signalling and found a rapid and significant effect of the hormones abscisic acid (ABA), auxin (IAA), and jasmonic acid (JA) on cytoplasmic cGMP levels. In contrast, brassinosteroids and cytokinin did not evoke a cGMP signal. The effects of ABA, IAA, and JA were apparent at external concentrations in the nanomolar range with EC50 values of around 1000, 300, and 0.03 nmoles for ABA, IAA, and JA respectively. To examine potential mechanisms for how hormone-induced cGMP signals are propagated, the role of protein phosphorylation was tested. A phosphoproteomics analysis on Arabidopsis thaliana root microsomal proteins in the absence and presence of membrane-permeable cGMP showed 15 proteins that rapidly (within minutes) changed in phosphorylation status. Out of these, nine were previously shown to also alter phosphorylation status in response to plant hormones, pointing to protein phosphorylation as a target for hormone-induced cGMP signalling.

• Arsenic contamination has a negative impact on crop cultivation and on human health. As yet, no proteins have been identified in plants that mediate the extrusion of arsenic. Here, we heterologously expressed the yeast (Saccharomyces cerevisiae) arsenite efflux transporter ACR3 into Arabidopsis to evaluate how this affects plant tolerance and tissue arsenic contents. • ACR3 was cloned from yeast and transformed into wild-type and nip7;1 Arabidopsis. Arsenic tolerance was determined at the cellular level using vitality stains in protoplasts, in intact seedlings grown on agar plates and in mature plants grown hydroponically. Arsenic efflux was measured from protoplasts and from intact plants, and arsenic levels were measured in roots and shoots of plants exposed to arsenate. • At the cellular level, all transgenic lines showed increased tolerance to arsenite and arsenate and a greater capacity for arsenate efflux. With intact plants, three of four stably transformed lines showed improved growth, whereas only transgenic lines in the wild-type background showed increased efflux of arsenite into the external medium. The presence of ACR3 hardly affected tissue arsenic levels, but increased arsenic translocation to the shoot. • Heterologous expression of yeast ACR3 endows plants with greater arsenic resistance, but does not lower significantly arsenic tissue levels., (© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.)

Potassium (K) is one of the major nutrients that is essential for plant growth and development. The majority of cellular K+ resides in the vacuole and tonoplast K+ channels of the TPK (Two Pore K) family are main players in cellular K+ homeostasis. All TPK channels were previously reported to be expressed in the tonoplast of the large central lytic vacuole (LV) except for one isoform in Arabidopsis that resides in the plasma membrane. However, plant cells often contain more than one type of vacuole that coexist in the same cell. We recently showed that two TPK isoforms (OsTPKa and OsTPKb) from Oryza sativa localise to different vacuoles with OsTPKa predominantly found in the LV tonoplast and OsTPKb primarily in smaller compartments that resemble small vacuoles (SVs). Our study further revealed that it is the C-terminal domain that determines differential targeting of OsTPKa and OsTPKb. Three C-terminal amino acids were particularly relevant for targeting TPKs to their respective endomembranes. In this addendum we further evaluate how the different localisation of TPKa and TPKb impact on their physiological role and how TPKs provide a potential tool to study the physiology of different types of vacuole.

Potassium (K+) is a major nutrient for plant growth and development. Vacuolar K+ ion channels of the two-pore K+ (TPK) family play an important role in maintaining K+ homeostasis. Several TPK channels were previously shown to be expressed in the lytic vacuole (LV) tonoplast. Plants also contain smaller protein storage vacuoles (PSVs) that contain membrane transporters. However, the mechanisms that define how membrane proteins reach different vacuolar destinations are largely unknown. The Oryza sativa genome encodes two TPK isoforms (TPKa and TPKb) that have very similar sequences and are ubiquitously expressed. The electrophysiological properties of both TPKs were comparable, showing inward rectification and voltage independence. In spite of high levels of similarity in sequence and transport properties, the cellular localization of TPKa and TPKb channels was different, with TPKa localization predominantly at the large LV and TPKb primarily in smaller PSV-type compartments. Trafficking of TPKa was sensitive to brefeldin A, while that of TPKb was not. The use of TPKa:TPKb chimeras showed that C-terminal domains are crucial for the differential targeting of TPKa and TPKb. Site-directed mutagenesis of C-terminal residues that were different between TPKa and TPKb identified three amino acids that are important in determining ultimate vacuolar destination.

The cyclic nucleotide cGMP has been shown to play important roles in plant development and responses to abiotic and biotic stress. To date, the techniques that are available to measure cGMP in plants are limited by low spatial and temporal resolution. In addition, tissue destruction is necessary. To circumvent these drawbacks we have used the δ-FlincG fluorescent protein to create an endogenous cGMP sensor that can report cellular cGMP levels with high resolution in time and space in living plant cells. δ-FlincG in transient and stably expressing cells shows a dissociation constant for cGMP of around 200 nm giving it a dynamic range of around 20-2000 nm. Stimuli that were previously shown to alter cGMP in plant cells (nitric oxide and gibberrellic acid) evoked pronounced fluorescence signals in single cells and in root tissues, providing evidence that δ-FlincG reports changes in cellular cGMP in a physiologically relevant context., (© 2010 The Authors. The Plant Journal © 2010 Blackwell Publishing Ltd.)

Vacuoles play various roles in many physiologically relevant processes in plants. Some of the more prominent are turgor provision, the storage of minerals and nutrients, and cellular signalling. To fulfil these functions a complement of membrane transporters is present at the tonoplast. Prolific patch clamp studies have shown that amongst these, both selective and non-selective ion channels participate in turgor regulation, nutrient storage and signalling. This article reviews the physiological roles, expression patterns and structure function properties of plant vacuolar anion and cation channels that are gated by voltage and ligands., (Copyright 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.)

S-Adenosylmethionine (SAM) is formed exclusively in the cytosol but plays a major role in plastids; SAM can either act as a methyl donor for the biogenesis of small molecules such as prenyllipids and macromolecules or as a regulator of the synthesis of aspartate-derived amino acids. Because the biosynthesis of SAM is restricted to the cytosol, plastids require a SAM importer. However, this transporter has not yet been identified. Here, we report the molecular and functional characterization of an Arabidopsis thaliana gene designated SAM TRANSPORTER1 (SAMT1), which encodes a plastid metabolite transporter required for the import of SAM from the cytosol. Recombinant SAMT1 produced in yeast cells, when reconstituted into liposomes, mediated the counter-exchange of SAM with SAM and with S-adenosylhomocysteine, the by-product and inhibitor of transmethylation reactions using SAM. Insertional mutation in SAMT1 and virus-induced gene silencing of SAMT1 in Nicotiana benthamiana caused severe growth retardation in mutant plants. Impaired function of SAMT1 led to decreased accumulation of prenyllipids and mainly affected the chlorophyll pathway. Biochemical analysis suggests that the latter effect represents one prominent example of the multiple events triggered by undermethylation, when there is decreased SAM flux into plastids.

Carotenoids not only play a crucial role in their intact form but also are an important reservoir of lipid-derived bioactive mediators. The process is initiated by tailoring enzymes that cleave carotenoids into apocarotenoids. Apocarotenoids act as visual or volatile signals to attract pollinating and seed dispersal agents, and are also key players in allelopathic interactions and plant defense. Recent studies show that the loss of these cleavage enzymes induces the development of axillary branches, indicating that apocarotenoids convey signals that regulate plant architecture. Here, we describe these molecules and the current understanding of their biosynthesis and functions.