The enigma of environmental ph sensing in plants

ABSTRACT Environmental pH is a critical parameter for innumerable chemical reactions, myriad biological processes and all forms of life. The mechanisms that underlie the perception of

external pH (pHe) have been elucidated in detail for bacteria, fungi and mammalian cells; however, little information is available on whether and, if so, how pHe is perceived by plants. This

is particularly surprising since hydrogen ion activity of the substrate is of paramount significance for plants, governing the availability of mineral nutrients, the structure of the soil

microbiome and the composition of natural plant communities. Rapid changes in soil pH require constant readjustment of nutrient acquisition strategies, which is associated with dynamic

alterations in gene expression. Referring to observations made in diverse experimental set-ups that unambiguously show that pHe per se affects gene expression, we hypothesize that sensing of

pHe in plants is mandatory to prioritize responses to various simultaneously received environmental cues. Access through your institution Buy or subscribe This is a preview of subscription

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* Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS CONTINUOUS MONITORING OF CHEMICAL SIGNALS IN PLANTS UNDER

STRESS Article 12 December 2022 ADAPTATION TO CHRONIC DROUGHT MODIFIES SOIL MICROBIAL COMMUNITY RESPONSES TO PHYTOHORMONES Article Open access 03 May 2021 GENERALIST HERBIVORE RESPONSE TO

VOLATILE CHEMICAL INDUCTION VARIES ALONG A GRADIENT IN SOIL SALINIZATION Article Open access 01 February 2022 REFERENCES * Gregory, P. J. & Hinsinger, P. New approaches to studying

chemical and physical changes in the rhizosphere: an overview. _Plant Soil_ 211, 1–9 (1999). Article  CAS  Google Scholar  * Misra, A. & Tyler, G. Influence of soil moisture on soil

solution chemistry and concentrations of minerals in the calcicoles _Phleum phleoides_ and _Veronica spicata_ grown on a limestone soil. _Ann. Bot._ 84, 401–410 (1999). Article  CAS  Google

Scholar  * Göttlein, A., Heim, A. & Matzner, E. Mobilization of aluminium in the rhizosphere soil solution of growing tree roots in an acidic soil. _Plant Soil_ 211, 41–49 (1999).

Article  Google Scholar  * Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. _ISME J._ 4, 1340–1351 (2010). Article  PubMed  Google Scholar  *

Arnon, D. I. & Johnson, C. M. Influence of hydrogen ion concentration on the growth of higher plants under controlled conditions. _Plant Physiol._ 17, 525–539 (1942). Article  CAS 

PubMed  PubMed Central  Google Scholar  * Raven, J. A. Sensing pH? _Plant Cell Environ._ 13, 721–729 (1990). Article  CAS  Google Scholar  * Krulwich, T. A., Sachs, G. & Padan, E.

Molecular aspects of bacterial pH sensing and homeostasis. _Nat. Rev. Microbiol._ 9, 330–343 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Tohidifar, P., Plutz, M. J.,

Ordal, G. W. & Rao, C. V. The mechanism of bidirectional pH taxis in _Bacillus subtilis_. _J. Bacteriol._ 202, e00491-19 (2020). Article  PubMed  PubMed Central  Google Scholar  * Yang,

Y. & Sourjik, V. Opposite responses by different chemoreceptors set a tunable preference point in _Escherichia coli_ pH taxis. _Mol. Microbiol._ 86, 1482–1489 (2012). Article  CAS 

PubMed  Google Scholar  * Hu, B. & Tu, Y. Precision sensing by two opposing gradient sensors: how does _Escherichia coli_ find its preferred pH level? _Biophys. J._ 105, 276–285 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar  * Haneburger, I., Eichinger, A., Skerra, A. & Jung, K. New insights into the signaling mechanism of the pH-responsive,

membrane-integrated transcriptional activator CadC of _Escherichia coli_. _J. Biol. Chem._ 286, 10681–10689 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Buchner, S.,

Schlundt, A., Lassak, J., Sattler, M. & Jung, K. Structural and functional analysis of the signal-transducing linker in the pH-responsive one-component system CadC of _Escherichia coli_.

_J. Mol. Biol._ 427, 2548–2561 (2015). Article  CAS  PubMed  Google Scholar  * Schlundt, A. et al. Structure–function analysis of the DNA-binding domain of a transmembrane transcriptional

activator. _Sci. Rep._ 7, 1051 (2017). Article  PubMed  PubMed Central  Google Scholar  * Taglicht, D., Padan, E. & Schuldiner, S. Overproduction and purification of a functional Na+/H+

antiporter coded by _nhaA_ (_ant_) from _Escherichia coli_. _J. Biol. Chem._ 266, 11289–11294 (1991). Article  CAS  PubMed  Google Scholar  * Padan, E. The enlightening encounter between

structure and function in the NhaA Na+–H+ antiporter. _Trends Biochem. Sci._ 33, 435–443 (2008). Article  CAS  PubMed  Google Scholar  * Herz, K., Rimon, A., Olkhova, E., Kozachkov, L. &

Padan, E. Transmembrane segment II of NhaA Na+/H+ antiporter lines the cation passage, and Asp65 is critical for pH activation of the antiporter. _J. Biol. Chem._ 285, 2211–2220 (2010).

Article  CAS  PubMed  Google Scholar  * Călinescu, O. et al. Lysine 300 is essential for stability but not for electrogenic transport of the _Escherichia coli_ NhaA Na+/H+ antiporter. _J.

Biol. Chem._ 292, 7932–7941 (2017). Article  PubMed  PubMed Central  Google Scholar  * Gerchman, Y. et al. Histidine-226 is part of the pH sensor of NhaA, a Na+/H+ antiporter in _Escherichia

coli_. _Proc. Natl Acad. Sci. USA_ 90, 1212–1216 (1993). Article  CAS  PubMed  Google Scholar  * Wen, Y., Feng, J., Scott, D. R., Marcus, E. A. & Sachs, G. The HP0165–HP0166

two-component system (ArsRS) regulates acid-induced expression of HP1186 α-carbonic anhydrase in _Helicobacter pylori_ by activating the pH-dependent promoter. _J. Bacteriol._ 189, 2426–2434

(2007). Article  CAS  PubMed  PubMed Central  Google Scholar  * Müller, S., Götz, M. & Beier, D. Histidine residue 94 is involved in pH sensing by histidine kinase ArsS of _Helicobacter

pylori_. _PLoS ONE_ 4, e6930 (2009). Article  PubMed  PubMed Central  Google Scholar  * Yu, X. J., McGourty, K., Liu, M., Unsworth, K. E. & Holden, D. W. pH sensing by intracellular

_Salmonella_ induces effector translocation. _Science_ 328, 1040–1043 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * Wimmi, S. et al. Dynamic relocalization of the cytosolic

type III secretion system components prevents premature protein secretion at low external pH. Preprint at _bioRxiv_ https://doi.org/10.1101/869214 (2019). * Tresguerres, M., Buck, J. &

Levin, L. R. Physiological carbon dioxide, bicarbonate, and pH sensing. _Pflugers Arch. Eur. J. Phy._ 460, 953–964 (2010). Article  CAS  Google Scholar  * Deyev, I. E. et al. Insulin

receptor-related receptor as an extracellular alkali sensor. _Cell Metab._ 13, 679–689 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Deyev, I. E., Chachina, N. A.,

Shayahmetova, D. M., Serova, O. V. & Petrenko, A. G. Mapping of alkali-sensing sites of the insulin receptor-related receptor. The role of L2 and fibronectin domains. _Biochimie_ 111,

1–9 (2015). Article  CAS  PubMed  Google Scholar  * Reyes, R. et al. Cloning and expression of a novel pH-sensitive two pore domain K+ channel from human kidney. _J. Biol. Chem._ 273,

30863–30869 (1998). Article  CAS  PubMed  Google Scholar  * Zúñiga, L. et al. Gating of a pH-sensitive K2P potassium channel by an electrostatic effect of basic sensor residues on the

selectivity filter. _PLoS ONE_ 6, e16141 (2011). Article  PubMed  PubMed Central  Google Scholar  * Levin, L. R. & Buck, J. Physiological roles of acid–base sensors. _Annu. Rev.

Physiol._ 77, 347–362 (2015). Article  CAS  PubMed  Google Scholar  * Ludwig, M. et al. Proton-sensing G-protein-coupled receptors. _Nature_ 425, 93–98 (2003). Article  CAS  PubMed  Google

Scholar  * Tobo, M. et al. Previously postulated “ligand-independent” signaling of GPR4 is mediated through proton-sensing mechanisms. _Cell. Signal._ 19, 1745–1753 (2007). Article  CAS 

PubMed  Google Scholar  * Wang, J. Q. et al. TDAG8 is a proton-sensing and psychosine-sensitive G-protein-coupled receptor. _J. Biol. Chem._ 279, 45626–45633 (2004). Article  CAS  PubMed 

Google Scholar  * Jasti, J., Furukawa, H., Gonzales, E. B. & Gouaux, E. Structure of acid-sensing ion channel 1 at 1.9 Å resolution and low pH. _Nature_ 449, 316–323 (2007). Article  CAS

  PubMed  Google Scholar  * Paukert, M., Chen, X., Polleichtner, G., Schindelin, H. & Gründer, S. Candidate amino acids involved in H+ gating of acid-sensing ion channel 1a. _J. Biol.

Chem._ 283, 572–581 (2008). Article  CAS  PubMed  Google Scholar  * Vullo, S. et al. Role of acidic pocket in ASIC gating. _Proc. Natl Acad. Sci. USA_ 114, 3768–3773 (2017). Article  CAS 

PubMed  Google Scholar  * Vullo, S. & Kellenberger, S. A molecular view of the function and pharmacology of acid-sensing ion channels. _Pharmacol. Res._ 154, 104166 (2020). Article  CAS

  PubMed  Google Scholar  * Ikeda, M., Kihara, A., Denpoh, A. & Igarashi, Y. The Rim101 pathway is involved in Rsb1 expression induced by altered lipid asymmetry. _Mol. Biol. Cell_ 19,

1922–1931 (2008). Article  CAS  PubMed  PubMed Central  Google Scholar  * Obara, K., Yamamoto, H. & Kihara, A. Membrane protein Rim21 plays a central role in sensing ambient pH in

_Saccharomyces cerevisiae_. _J. Biol. Chem._ 287, 38473–38481 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Xu, W., Smith, F. J., Subaran, R. & Mitchell, A. P.

Multivesicular body-ESCRT components function in pH response regulation in _Saccharomyces cerevisiae_ and _Candida albicans_. _Mol. Biol. Cell_ 15, 5528–5537 (2004). Article  CAS  PubMed 

PubMed Central  Google Scholar  * Peñalva, M. A., Lucena-Agell, D. & Arst, H. N. Jr. Liaison alcaline: Pals entice non-endosomal ESCRTs to the plasma membrane for pH signaling. _Curr.

Opin. Microbiol._ 22, 49–59 (2014). Article  PubMed  Google Scholar  * Nishino, K., Obara, K. & Kihara, A. The C-terminal cytosolic region of Rim21 senses alterations in plasma membrane

lipid composition: insights into sensing mechanisms for plasma membrane lipid asymmetry. _J. Biol. Chem._ 290, 30797–30805 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Obara, K. & Kihara, A. Signaling events of the Rim101 pathway occur at the plasma membrane in a ubiquitination-dependent manner. _Mol. Cell. Biol._ 34, 3525–3534 (2014). Article  PubMed

  PubMed Central  Google Scholar  * Hayashi, M., Fukuzawa, T., Sorimachi, H. & Maeda, T. Constitutive activation of the pH-responsive Rim101 pathway in yeast mutants defective in late

steps of the MVB/ESCRT pathway. _Mol. Cell. Biol._ 25, 9478–9490 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  * Doyle, D. A. et al. The structure of the potassium channel:

molecular basis of K+ conduction and selectivity. _Science_ 280, 69–77 (1998). Article  CAS  PubMed  Google Scholar  * Pandey, S., Zhang, W. & Assmann, S. M. Roles of ion channels and

transporters in guard cell signal transduction. _FEBS Lett._ 581, 2325–2336 (2007). Article  CAS  PubMed  Google Scholar  * Clark, M. D., Contreras, G. F., Shen, R. & Perozo, E.

Electromechanical coupling in the hyperpolarization-activated K+ channel KAT1. _Nature_ 583, 145–149 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Hoth, S. et al. Molecular

basis of plant-specific acid activation of K+ uptake channels. _Proc. Natl Acad. Sci. USA_ 94, 4806–4810 (1997). Article  CAS  PubMed  Google Scholar  * Hoth, S. & Hedrich, R. Distinct

molecular bases for pH sensitivity of the guard cell K+ channels KST1 and KAT1. _J. Biol. Chem._ 274, 11599–11603 (1999). Article  CAS  PubMed  Google Scholar  * González, W. et al. The pH

sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids. _Biochem. J._ 442, 57–63 (2012). Article  PubMed  Google Scholar  * Wang, L.

et al. The S1–S2 linker determines the distinct pH sensitivity between ZmK2.1 and KAT 1. _Plant J._ 85, 675–685 (2016). Article  CAS  PubMed  Google Scholar  * Toyota, M. et al. Glutamate

triggers long-distance, calcium-based plant defense signaling. _Science_ 14, 1112–1115 (2018). Article  Google Scholar  * Shao, Q. et al. Two glutamate- and pH-regulated Ca2+ channels are

required for systemic wound signaling in _Arabidopsis_. _Sci. Signal._ 13, eaba1453 (2020). Article  CAS  PubMed  Google Scholar  * Causton, H. C. et al. Remodeling of yeast genome

expression in response to environmental changes. _Mol. Biol. Cell_ 12, 323–337 (2001). Article  CAS  PubMed  PubMed Central  Google Scholar  * Canadell, D. et al. Impact of high pH stress on

yeast gene expression: a comprehensive analysis of mRNA turnover during stress responses. _Biochim. Biophys. Acta Gene Regul. Mech._ 1849, 653–664 (2015). Article  CAS  Google Scholar  *

Serra-Cardona, A., Canadell, D. & Ariño, J. Coordinate responses to alkaline pH stress in budding yeast. _Microb. Cell_ 2, 182–196 (2015). Article  CAS  PubMed  PubMed Central  Google

Scholar  * Barad, S. et al. Fungal and host transcriptome analysis of pH-regulated genes during colonization of apple fruits by _Penicillium expansum_. _BMC Genomics_ 17, 330 (2016). Article

  PubMed  PubMed Central  Google Scholar  * Payá-Milans, M. et al. Regulation of gene expression in roots of the pH-sensitive _Vaccinium corymbosum_ and the pH-tolerant _Vaccinium arboreum_

in response to near neutral pH stress using RNA-seq. _BMC Genomics_ 18, 580 (2017). Article  PubMed  PubMed Central  Google Scholar  * Lager, I. D. A. et al. Changes in external pH rapidly

alter plant gene expression and modulate auxin and elicitor responses. _Plant Cell Environ._ 33, 1513–1528 (2010). CAS  PubMed  PubMed Central  Google Scholar  * Tsai, H. H. & Schmidt,

W. pH-dependent transcriptional profile changes in iron-deficient _Arabidopsis_ roots. _BMC Genomics_ 21, 694 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Von Uexküll, H.

R. & Mutert, E. Global extent, development and economic impact of acid soils. _Plant Soil_ 171, 1–15 (1995). Article  Google Scholar  * Parker, J. L. & Newstead, S. Molecular basis

of nitrate uptake by the plant nitrate transporter NRT1.1. _Nature_ 507, 68–72 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  * Tsay, Y. F., Schroeder, J. I., Feldmann, K. A.

& Crawford, N. M. The herbicide sensitivity gene _CHL1_ of _Arabidopsis encodes_ a nitrate-inducible nitrate transporter. _Cell_ 72, 705–713 (1993). Article  CAS  PubMed  Google Scholar

  * Iuchi, S. et al. Zinc finger protein STOP1 is critical for proton tolerance in _Arabidopsis_ and coregulates a key gene in aluminum tolerance. _Proc. Natl Acad. Sci. USA_ 104, 9900–9905

(2007). Article  PubMed  Google Scholar  * Kidd, P. S. & Proctor, J. Why plants grow poorly on very acid soils: are ecologists missing the obvious? _J. Exp. Bot._ 52, 791–799 (2001).

Article  CAS  PubMed  Google Scholar  * Ikka, T. et al. Natural variation of _Arabidopsis thaliana_ reveals that aluminum resistance and proton resistance are controlled by different genetic

factors. _Theor. Appl. Genet._ 115, 709–719 (2007). Article  CAS  PubMed  Google Scholar  * Jiang, F. et al. Identification and characterization of suppressor mutants of stop1. _BMC Plant

Biol._ 17, 128 (2017). Article  PubMed  PubMed Central  Google Scholar  * Kobayashi, Y. et al. STOP2 activates transcription of several genes for Al-and low pH-tolerance that are regulated

by STOP1 in _Arabidopsis_. _Mol. Plant_ 7, 311–322 (2014). Article  CAS  PubMed  Google Scholar  * Balzergue, C. et al. Low phosphate activates STOP1–ALMT1 to rapidly inhibit root cell

elongation. _Nat. Comm._ 8, 15300 (2017). Article  CAS  Google Scholar  * Boukhalfa, H. & Crumbliss, A. L. Chemical aspects of siderophore mediated iron transport. _Biometals_ 15,

325–339 (2002). Article  CAS  Google Scholar  * Römheld, V. & Marschner, H. Evidence for a specific uptake system for iron phytosiderophores in roots of grasses. _Plant Physiol._ 80,

175–180 (1986). Article  PubMed  PubMed Central  Google Scholar  * Siwinska, J. et al. Scopoletin 8-hydroxylase: a novel enzyme involved in coumarin biosynthesis and iron-deficiency

responses in _Arabidopsis_. _J. Exp. Bot._ 69, 1735–1748 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Rajniak, J. et al. Biosynthesis of redox-active metabolites in

response to iron deficiency in plants. _Nat. Chem. Biol._ 14, 442–450 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Tsai, H. H. et al. Scopoletin 8-hydroxylase-mediated

fraxetin production is crucial for iron mobilization. _Plant Physiol._ 177, 194–207 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Sisó-Terraza, P. et al. Accumulation and

secretion of coumarinolignans and other coumarins in _Arabidopsis thaliana_ roots in response to iron deficiency at high pH. _Front. Plant Sci._ 7, 1711 (2016). Article  PubMed  PubMed

Central  Google Scholar  * Kim, S. A., LaCroix, I. S., Gerber, S. A. & Guerinot, M. L. The iron deficiency response in _Arabidopsis thaliana_ requires the phosphorylated transcription

factor URI. _Proc. Natl Acad. Sci. USA_ 116, 24933–24942 (2019). Article  CAS  PubMed  Google Scholar  * Colangelo, E. P. & Guerinot, M. L. The essential basic helix-loop-helix protein

FIT1 is required for the iron deficiency response. _Plant Cell_ 16, 3400–3412 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  * Ahn, Y. O. et al. Scopolin-hydrolyzing

β-glucosidases in roots of _Arabidopsis_. _Plant Cell Physiol._ 51, 132–143 (2010). Article  CAS  PubMed  Google Scholar  * Zamioudis, C., Hanson, J. & Pieterse, C. M. J. β-Glucosidase

BGLU 42 is a MYB 72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in _Arabidopsis_ roots. _N. Phytol._ 204, 368–379 (2014).

Article  CAS  Google Scholar  * Oba, K., Conn, E. E., Canut, H. & Boudet, A. M. Subcellular localization of 2-(β-d-glucosyloxy)-cinnamic acids and the related β-glucosidase in leaves of

_Melilotus alba_ Desr. _Plant Physiol._ 68, 1359–1363 (1981). Article  CAS  PubMed  PubMed Central  Google Scholar  * Dietz, K. J., Sauter, A., Wichert, K., Messdaghi, D. & Hartung, W.

Extracellular β-glucosidase activity in barley involved in the hydrolysis of ABA glucose conjugate in leaves. _J. Exp. Bot._ 51, 937–944 (2000). Article  CAS  PubMed  Google Scholar  *

Morant, A. et al. β-Glucosidases as detonators of plant chemical defense. _Phytochemistry_ 69, 1795–1813 (2008). Article  CAS  PubMed  Google Scholar  * Martinière, A. et al. Uncovering pH

at both sides of the root plasma membrane interface using noninvasive imaging. _Proc. Natl Acad. Sci. USA_ 115, 6488–6493 (2018). Article  PubMed  Google Scholar  * Cosgrove, D. J. Diffuse

growth of plant cell walls. _Plant Physiol._ 176, 16–27 (2018). Article  CAS  PubMed  Google Scholar  * Hager, A., Menzle, H. & Krauss, A. Versuche und hypothese zur primarwirkung des

auxins beim streckungswachstum. _Planta_ 100, 47–75 (1971). Article  CAS  PubMed  Google Scholar  * Geilfus, C. M., Tenhaken, R. & Carpentier, S. C. Transient alkalinization of the leaf

apoplast stiffens the cell wall during onset of chloride salinity in corn leaves. _J. Biol. Chem._ 292, 18800–18813 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar  * Pearce,

G., Moura, D. S., Stratmann, J. & Ryan, C. A. RALF, a 5-kDa ubiquitous polypeptide in plants, arrests root growth and development. _Proc. Natl Acad. Sci. USA_ 98, 12843–12847 (2001).

Article  CAS  PubMed  Google Scholar  * Amano, Y., Tsubouchi, H., Shinohara, H., Ogawa, M. & Matsubayashi, Y. Tyrosine-sulfated glycopeptide involved in cellular proliferation and

expansion in _Arabidopsis_. _Proc. Natl Acad. Sci. USA_ 104, 18333–18338 (2007). Article  CAS  PubMed  Google Scholar  * Gjetting, S. K. et al. Evidence for multiple receptors mediating

RALF–triggered Ca2+ signaling and proton pump inhibition. _Plant J._ https://doi.org/10.1111/tpj.14935 (2020). * Fuglsang, A. T. et al. Receptor kinase-mediated control of primary active

proton pumping at the plasma membrane. _Plant J._ 80, 951–964 (2014). Article  CAS  PubMed  Google Scholar  * Haruta, M., Sabat, G., Stecker, K., Minkoff, B. B. & Sussman, M. R. A

peptide hormone and its receptor protein kinase regulate plant cell expansion. _Science_ 343, 408–411 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  * Masachis, S. et al. A

fungal pathogen secretes plant alkalinizing peptides to increase infection. _Nat. Microbiol._ 1, 16043 (2016). Article  CAS  PubMed  Google Scholar  * Stegmann, M. et al. The receptor kinase

FER is a RALF-regulated scaffold controlling plant immune signaling. _Science_ 355, 287–289 (2017). Article  CAS  PubMed  Google Scholar  * Li, C. Y. et al. Two _FERONIA-like receptor_

(_FLR_) genes are required to maintain architecture, fertility, and seed yield in rice. _Mol. Breed._ 36, 151 (2016). Article  Google Scholar  * Xu, G. et al. FERONIA phosphorylates E3

ubiquitin ligase ATL6 to modulate the stability of 14-3-3 proteins in response to the carbon/nitrogen ratio. _J. Exp. Bot._ 70, 6375–6388 (2019). Article  CAS  PubMed  PubMed Central  Google

Scholar  * Zhu, S. et al. The RALF1–FERONIA complex phosphorylates eIF4E1 to promote protein synthesis and polar root hair growth. _Mol. Plant_ 13, 698–716 (2020). Article  CAS  PubMed 

Google Scholar  * Roberts, J. K. M., Wade-Jardetzky, N. & Jardetsky, O. Intracellular pH measurements by phosphorus-31 nuclear magnetic resonance. Influence of factors other than pH on

phosphorus-31 chemical shifts. _Biochemistry_ 20, 5389–5394 (1981). Article  CAS  PubMed  Google Scholar  * Pfeffer, P. E., Tu, S., Gerasimowicz, W. V. & Borswell, R. T. Effects of

aluminum on the release and-or immobilization of soluble phosphate in corn root tissue. _Planta_ 172, 200–208 (1987). Article  CAS  PubMed  Google Scholar  * Lacombe, B. et al. pH control of

the plant outwardly-rectifying potassium channel SKOR. _FEBS Lett._ 466, 351–354 (2000). Article  CAS  PubMed  Google Scholar  * Weisenseel, M. H., Dorn, A. & Jaffe, L. F. Natural H+

currents traverse growing roots and root hairs of barley (_Hordeum vulgare_ L.). _Plant Physiol._ 64, 512–518 (1979). Article  CAS  PubMed  PubMed Central  Google Scholar  * Marschner, H.

& Römheld, V. In vivo measurement of root-induced pH changes at the soil–root interface: effect of plant species and nitrogen source. _Z. Pflanzenphysiol._ 111, 241–251 (1983). Article 

CAS  Google Scholar  * Moorby, H., White, R. E. & Nye, P. H. The influence of phosphate nutrition on H ion efflux from the roots of young rape plants. _Plant Soil_ 105, 247–256 (1988).

Article  CAS  Google Scholar  * Zhao, Q. et al. Ubiquitination-related MdBT scaffold proteins target a bHLH transcription factor for iron homeostasis. _Plant Physiol._ 172, 1973–1988 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar  * Wang, Y. & Lambers, H. Root-released organic anions in response to low phosphorus availability: recent progress, challenges and

future perspectives. _Plant Soil_ 447, 135–156 (2020). Article  CAS  Google Scholar  * Penny, M. G. & Bowling, D. J. F. Direct determination of pH in the stomatal complex of _Commelina_.

_Planta_ 122, 209–212 (1975). Article  CAS  PubMed  Google Scholar  * Felle, H. H. The apoplastic pH of the _Zea mays_ root cortex as measured with pH-sensitive microelectrodes: aspects of

regulation. _J. Exp. Bot._ 49, 987–995 (1998). Article  CAS  Google Scholar  * Geilfus, C. M. The pH of the apoplast: dynamic factor with functional impact under stress. _Mol. Plant_ 10,

1371–1386 (2017). Article  CAS  PubMed  Google Scholar  * Hoffmann, B., Plänker, R. & Mengel, K. Measurements of pH in the apoplast of sunflower leaves by means of fluorescence.

_Physiol. Plant._ 84, 146–153 (1992). Article  CAS  Google Scholar  * Brauer, D., Otto, J. & Tu, S.-I. Selective accumulation of the fluorescent pH indicator, BCECF, in vacuoles of maize

root-hair cells. _J. Plant Physiol._ 145, 57–61 (1995). Article  CAS  Google Scholar  * Sano, T., Kutsuna, N. & Hasezawa, S. Improved cytoplasmic pH measurements in SNARF-1 stained

plant cells by image processing. _Plant Signal. Behav._ 5, 406–408 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * Barbez, E., Dünser, K., Gaidora, A., Lendl, T. & Busch,

W. Apoplastic pH regulation in _A. thaliana_ roots. _Proc. Natl Acad. Sci. USA_ 114, E4884–E4893 (2017). Article  CAS  PubMed  Google Scholar  * Kneen, M., Farinas, J., Li, Y. &

Verkman, A. S. Green fluorescent protein as a non-invasive intracellular pH indicator. _Biophys. J._ 74, 1591–1599 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  * Miesenböck,

G., De Angelis, D. & Rothman, J. Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins. _Nature_ 394, 192–195 (1998). Article  PubMed  Google

Scholar  * Haseloff, J., Siemering, K. R., Prasher, D. C. & Hodge, S. Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark

transgenic _Arabidopsis_ plants brightly. _Proc. Natl Acad. Sci. USA_ 94, 2122–2127 (1997). Article  CAS  PubMed  Google Scholar  * Moseyko, N. & Feldman, L. J. Expression of

pH-sensitive green fluorescent protein in _Arabidopsis thaliana_. _Plant Cell Environ._ 24, 557–563 (2001). Article  CAS  PubMed  Google Scholar  * Shen, J. et al. Organelle pH in the

_Arabidopsis_ endomembrane system. _Mol. Plant_ 6, 1419–1437 (2013). Article  CAS  PubMed  Google Scholar  * Gjetting, K. S., Ytting, C. K., Schulz, A. & Fuglsang, A. T. Live imaging of

intra-and extracellular pH in plants using pHusion, a novel genetically encoded biosensor. _J. Exp. Bot._ 63, 3207–3218 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Zhang,

Y., Xie, Q., Robertson, J. B. & Johnson, C. H. pHlash: a new genetically encoded and ratiometric luminescence sensor of intracellular pH. _PLoS ONE_ 7, e43072 (2012). Article  CAS 

PubMed  PubMed Central  Google Scholar  * Dinkelaker, B., Römheld, V. & Marschner, H. Citric acid excretion and precipitation of calcium citrate in the rhizosphere of white lupin

(_Lupinus albus_ L.). _Plant Cell Environ._ 12, 285–292 (1989). Article  CAS  Google Scholar  * Falhof, J., Pedersen, J. T., Fuglsang, A. T. & Palmgren, M. Plasma membrane H+-ATPase

regulation in the center of plant physiology. _Mol. Plant_ 9, 323–337 (2016). Article  CAS  PubMed  Google Scholar  * Canarini, A., Wanek, W., Merchant, A., Richter, A. & Kaiser, C. Root

exudation of primary metabolites: mechanisms and their roles in plant responses to environmental stimuli. _Front. Plant Sci._ 10, 157 (2019). Article  PubMed  PubMed Central  Google Scholar

  * Zhou, L. J. et al. The SUMO E3 ligase MdSIZ1 targets MdbHLH104 to regulate plasma membrane H+-ATPase activity and iron homeostasis. _Plant Physiol._ 179, 88–106 (2019). Article  CAS 

PubMed  Google Scholar  * Martinière, A. et al. In vivo intracellular pH measurements in tobacco and _Arabidopsis_ reveal an unexpected pH gradient in the endomembrane system. _Plant Cell_

25, 4028–4043 (2013). Article  PubMed  PubMed Central  Google Scholar  Download references ACKNOWLEDGEMENTS Research in the Schmidt Laboratory is funded by Academia Sinica and the Ministry

of Science and Technology (MOST). AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan Huei-Hsuan Tsai & Wolfgang

Schmidt * Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan Wolfgang Schmidt * Genome and Systems Biology Degree Program, College of Life Science, National Taiwan

University, Taipei, Taiwan Wolfgang Schmidt Authors * Huei-Hsuan Tsai View author publications You can also search for this author inPubMed Google Scholar * Wolfgang Schmidt View author

publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS H.-H.T. conducted research that led to the hypothesis put forward in the manuscript, composed the

figures and contributed to the writing. W.S. initiated the research and wrote the paper. CORRESPONDING AUTHOR Correspondence to Wolfgang Schmidt. ETHICS DECLARATIONS COMPETING INTERESTS The

authors declare no competing interests. ADDITIONAL INFORMATION PEER REVIEW INFORMATION _Nature Plants_ thanks the anonymous reviewers for their contribution to the peer review of this work.

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THIS ARTICLE CITE THIS ARTICLE Tsai, HH., Schmidt, W. The enigma of environmental pH sensing in plants. _Nat. Plants_ 7, 106–115 (2021). https://doi.org/10.1038/s41477-020-00831-8 Download

citation * Received: 09 June 2020 * Accepted: 08 December 2020 * Published: 08 February 2021 * Issue Date: February 2021 * DOI: https://doi.org/10.1038/s41477-020-00831-8 SHARE THIS ARTICLE

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