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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id>
<journal-title>Frontiers in Plant Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Plant Sci.</abbrev-journal-title>
<issn pub-type="epub">1664-462X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fpls.2022.1039041</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Plant Science</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Functional characterization of the sugarcane (<italic>Saccharum</italic> spp.) ammonium transporter AMT2;1 suggests a role in ammonium root-to-shoot translocation</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Koltun</surname>
<given-names>Alessandra</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2072988"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Maniero</surname>
<given-names>Rodolfo A.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2091979"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Vitti</surname>
<given-names>Marielle</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>de Setta</surname>
<given-names>Nathalia</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Giehl</surname>
<given-names>Ricardo F. H.</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/49951"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Lima</surname>
<given-names>Joni E.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2072819"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Figueira</surname>
<given-names>Antonio</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/329662"/>
</contrib>
</contrib-group>    <aff id="aff1">
<sup>1</sup>
<institution>Centro de Energia Nuclear na Agricultura, Universidade de S&#xe3;o Paulo</institution>, <addr-line>Piracicaba, SP</addr-line>, <country>Brazil</country>
</aff>    <aff id="aff2">
<sup>2</sup>
<institution>Centro de Ci&#xea;ncias Naturais e Humanas, Universidade Federal do ABC</institution>, <addr-line>S&#xe3;o Bernardo do Campo, SP</addr-line>, <country>Brazil</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Instituto de Bioci&#xea;ncias, Universidade de S&#xe3;o Paulo</institution>, <addr-line>S&#xe3;o Paulo, SP</addr-line>, <country>Brazil</country>
</aff>    <aff id="aff4">
<sup>4</sup>
<institution>Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</institution>, <addr-line>Gatersleben</addr-line>, <country>Germany</country>
</aff>
<aff id="aff5">
<sup>5</sup>
<institution>Departamento de Bot&#xe2;nica, Universidade Federal de Minas Gerais</institution>, <addr-line>Belo Horizonte, MG</addr-line>, <country>Brazil</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Jing Che, Institute of Soil Science (CAS), China</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Jiang Wang, University of Illinois at Urbana-Champaign, United States; Hongmei Cai, Huazhong Agricultural University, China</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Joni E. Lima, <email xlink:href="mailto:limajoni@googlemail.com">limajoni@googlemail.com</email>; Antonio Figueira, <email xlink:href="mailto:figueira@cena.usp.br">figueira@cena.usp.br</email>
</p>
</fn>
<fn fn-type="equal" id="fn003">
<p>&#x2020;These authors have contributed equally to this work</p>
</fn>
<fn fn-type="other" id="fn002">
<p>This article was submitted to Plant Nutrition, a section of the journal Frontiers in Plant Science</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>18</day>
<month>11</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>13</volume>
<elocation-id>1039041</elocation-id>
<history>
<date date-type="received">
<day>07</day>
<month>09</month>
<year>2022</year>
</date>
<date date-type="accepted">
<day>31</day>
<month>10</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2022 Koltun, Maniero, Vitti, de Setta, Giehl, Lima and Figueira</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Koltun, Maniero, Vitti, de Setta, Giehl, Lima and Figueira</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>AMMONIUM TRANSPORTER/METHYLAMMONIUM PERMEASE/RHESUS (AMT) family members transport ammonium across membranes in all life domains. Plant AMTs can be categorized into AMT1 and AMT2 subfamilies. Functional studies of AMTs, particularly AMT1-type, have been conducted using model plants but little is known about the function of AMTs from crops. Sugarcane (<italic>Saccharum</italic> spp.) is a major bioenergy crop that requires heavy nitrogen fertilization but depends on a low carbon-footprint for competitive sustainability. Here, we identified and functionally characterized sugarcane <italic>ScAMT2;1</italic> by complementing ammonium uptake-defective mutants of <italic>Saccharomyces cerevisiae</italic> and <italic>Arabidopsis thaliana</italic>. Reporter gene driven by the <italic>ScAMT2;1</italic> promoter in <italic>A. thaliana</italic> revealed preferential expression in the shoot vasculature and root endodermis/pericycle according to nitrogen availability and source. Arabidopsis quadruple mutant plants expressing <italic>ScAMT2;1</italic> driven by the CaMV35S promoter or by a sugarcane endogenous promoter produced significantly more biomass than mutant plants when grown in NH<sub>4</sub>
<sup>+</sup> and showed more <sup>15</sup>N-ammonium uptake by roots and nitrogen translocation to shoots. In <italic>A. thaliana</italic>, ScAMT2;1 displayed a K<sub>m</sub> of 90.17 &#xb5;M and V<sub>max</sub> of 338.99 &#xb5;moles h<sup>-1</sup> g<sup>-1</sup> root DW. Altogether, our results suggest that ScAMT2;1 is a functional high-affinity ammonium transporter that might contribute to ammonium uptake and presumably to root-to-shoot translocation under high NH<sub>4</sub>
<sup>+</sup> conditions.</p>
</abstract>
<kwd-group>
<kwd>ammonium uptake</kwd>
<kwd>AMT2 subfamily</kwd>
<kwd>nitrogen use efficiency</kwd>
<kwd>quadruple mutant</kwd>
<kwd>transport kinetics</kwd>
<kwd>xylem loading</kwd>
</kwd-group>    <contract-sponsor id="cn001">Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo<named-content content-type="fundref-id">10.13039/501100001807</named-content>
</contract-sponsor>
<counts>
<fig-count count="7"/>
<table-count count="0"/>
<equation-count count="0"/>
<ref-count count="80"/>
<page-count count="16"/>
<word-count count="8524"/>
</counts>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>    <p>Nitrogen (N) is the most abundant mineral element present in plant tissues, and nitrate (<mml:math display="inline" id="im3">
<mml:mrow>
<mml:msubsup>
<mml:mrow>
<mml:mtext>NO</mml:mtext>
</mml:mrow>
<mml:mn>3</mml:mn>
<mml:mo>-</mml:mo>
</mml:msubsup>
</mml:mrow>
</mml:math>) and ammonium (NH<sub>4</sub>
<sup>+</sup>) are the primary inorganic sources absorbed by roots of higher plants. NH<sub>4</sub>
<sup>+</sup> is transported across cell membranes by proteins of the AMMONIUM TRANSPORTER/METHYLAMMONIUM PERMEASE/RHESUS (AMT/MEP/Rh) family (<xref ref-type="bibr" rid="B17">Gazzarrini et&#xa0;al., 1999</xref>; <xref ref-type="bibr" rid="B41">Loqu&#xe9; and von Wir&#xe9;n, 2004</xref>), which are present in all living organisms (<xref ref-type="bibr" rid="B39">Li et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B49">McDonald et&#xa0;al., 2012</xref>). Plant AMTs can be further categorized into AMT1 and AMT2 (<xref ref-type="bibr" rid="B41">Loqu&#xe9; and von Wir&#xe9;n, 2004</xref>; <xref ref-type="bibr" rid="B49">McDonald et&#xa0;al., 2012</xref>). AMT1-type proteins share an evolutionary history related to prokaryotic NH<sub>4</sub>
<sup>+</sup> transporters, while AMT2-type proteins are homologues of the methylammonium permease (MEP) family (<xref ref-type="bibr" rid="B74">von Wittgenstein et&#xa0;al., 2014</xref>). The number of AMT family members varies considerably among plant species, displaying a variety of expression patterns, spatial regulations, substrate affinities, and presumed functions (<xref ref-type="bibr" rid="B79">Yuan et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B22">Guether et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B78">Yuan et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B49">McDonald et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B35">Li et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B64">Song et&#xa0;al., 2017</xref>).</p>    <p>In <italic>Arabidopsis thaliana</italic>, four root-expressed AMT1 proteins are responsible for high-affinity NH<sub>4</sub>
<sup>+</sup> uptake, namely, AtAMT1;1, AtAMT1;2, AtAMT1;3, and AtAMT1;5 (<xref ref-type="bibr" rid="B42">Loqu&#xe9; et&#xa0;al., 2006</xref>; <xref ref-type="bibr" rid="B79">Yuan et&#xa0;al., 2007</xref>), while AtAMT1;4 plays a major role in NH<sub>4</sub>
<sup>+</sup> uptake in pollen grains (<xref ref-type="bibr" rid="B78">Yuan et&#xa0;al., 2009</xref>). Functional studies revealed that the membrane proteins AtAMT1;1 and AtAMT1;3 are active in the rhizodermis, cortex, and root hairs and are responsible for approximately two-thirds of the NH<sub>4</sub>
<sup>+</sup> uptake capacity by the symplastic route, further supported by AtAMT1;5 in radial transport (<xref ref-type="bibr" rid="B42">Loqu&#xe9; et&#xa0;al., 2006</xref>; <xref ref-type="bibr" rid="B79">Yuan et&#xa0;al., 2007</xref>). In addition, the apoplastic NH<sub>4</sub>
<sup>+</sup> pool can enter the root symplast by AtAMT1;2 activity in the plasma membrane of endodermal and cortical cells (<xref ref-type="bibr" rid="B79">Yuan et&#xa0;al., 2007</xref>). Functional and regulatory characterization of AMT1 proteins in other plant species, including crops (<xref ref-type="bibr" rid="B73">von Wir&#xe9;n et&#xa0;al., 2000</xref>; <xref ref-type="bibr" rid="B65">Suenaga et&#xa0;al., 2003</xref>; <xref ref-type="bibr" rid="B7">D&#x2019;Apuzzo et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B5">Couturier et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B21">Gu et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B30">Koegel et&#xa0;al., 2013</xref>), have confirmed their dominant role in high-affinity NH<sub>4</sub>
<sup>+</sup> uptake in roots (<xref ref-type="bibr" rid="B42">Loqu&#xe9; et&#xa0;al., 2006</xref>; <xref ref-type="bibr" rid="B79">Yuan et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B21">Gu et&#xa0;al., 2013</xref>).</p>
<p>In contrast to AMT1-type proteins, there is less information about the physiological functions of AMT2 proteins. The sole AMT2 member present in the <italic>A. thaliana</italic> genome, AtAMT2;1, was shown to have a minor role in ammonium uptake under N-deficient conditions (<xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>). However, at elevated N levels, AtAMT2;1 mediates ammonium accumulation in xylem sap and contributes to long-distance ammonium translocation from roots to shoots (<xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>). AMT2 members have been investigated in a few crops, such as wheat (<xref ref-type="bibr" rid="B37">Li et&#xa0;al., 2017b</xref>; <xref ref-type="bibr" rid="B28">Jiang et&#xa0;al., 2019</xref>), sorghum (<xref ref-type="bibr" rid="B30">Koegel et&#xa0;al., 2013</xref>) and maize (<xref ref-type="bibr" rid="B9">Dechorgnat et&#xa0;al., 2019</xref>), but various aspects of AMT2 function and regulation remain to be addressed.</p>
<p>Sugarcane (<italic>Saccharum</italic> spp.) is a robust feedstock for bioenergy production due to its remarkably high aboveground biomass, including culms with high sucrose content (<xref ref-type="bibr" rid="B71">Tilman et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B75">Waclawovsky et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B25">Hoang et&#xa0;al., 2015</xref>). High N fertilizer rates are applied to boost sugarcane production; however, the crop responds poorly to N fertilization, and N losses can reach up to 50% (<xref ref-type="bibr" rid="B15">Franco et&#xa0;al., 2008</xref>; <xref ref-type="bibr" rid="B55">Robinson et&#xa0;al., 2011</xref>). The reason behind the high N loss in sugarcane remains elusive (<xref ref-type="bibr" rid="B69">Thorburn et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B8">de Castro et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B38">Lima et&#xa0;al., 2022</xref>). The low nitrogen use efficiency (NUE) of sugarcane represents high economic and environmental costs (<xref ref-type="bibr" rid="B70">Thorburn et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B61">Skocaj et&#xa0;al., 2013</xref>), reducing the long-term sustainability of this bioenergy crop (<xref ref-type="bibr" rid="B13">Erisman et&#xa0;al., 2010</xref>). Various forms of N losses from the soil (volatilization, N<sub>2</sub>O emission, nitrate leaching, and run-off) negatively impact ecosystems (<xref ref-type="bibr" rid="B48">McAllister et&#xa0;al., 2012</xref>). Therefore, it is essential to improve sugarcane NUE to help maintain its competitiveness and sustainability as a bioenergy crop (<xref ref-type="bibr" rid="B69">Thorburn et&#xa0;al., 2017</xref>).</p>    <p>NUE is a complex trait involving N uptake, assimilation, and remobilization during plant development (<xref ref-type="bibr" rid="B11">Dobermann, 2005</xref>; <xref ref-type="bibr" rid="B36">Li et&#xa0;al., 2017a</xref>; <xref ref-type="bibr" rid="B59">Sharma and Bali, 2018</xref>). Prospecting genes involved in NUE is challenging, particularly in crops with a highly polyploid and complex genome, such as modern sugarcane cultivars (<xref ref-type="bibr" rid="B67">Thirugnanasambandam et&#xa0;al., 2018</xref>). Sugarcane achieves optimal growth and yield under the supply of mixed ammonium and nitrate sources (<xref ref-type="bibr" rid="B53">Otto et&#xa0;al., 2016</xref>), yet sugarcane roots have a physiological preference for ammonium over nitrate uptake under N-sufficient (<xref ref-type="bibr" rid="B55">Robinson et&#xa0;al., 2011</xref>) or N-limited conditions (<xref ref-type="bibr" rid="B38">Lima et&#xa0;al., 2022</xref>). Therefore, the sugarcane preference for NH<sub>4</sub>
<sup>+</sup> may also mean that transporters that are potentially involved in radial NH<sub>4</sub>
<sup>+</sup> transport in roots and/or root-to-shoot NH<sub>4</sub>
<sup>+</sup> translocation may affect the overall NUE of sugarcane, which led us to investigate AMTs to determine the potential role of AMTs in improving NUE in sugarcane. We started by functionally characterizing AMT1-type ammonium transporter members of sugarcane (unpublished results).</p>    <p>In the present work, we searched for AMT2-type ammonium transporters in the sugarcane genome by screening clones from a bacterial artificial chromosome (BAC) library (<xref ref-type="bibr" rid="B72">Tomkins et&#xa0;al., 1999</xref>). We then functionally characterized <italic>ScAMT2;1</italic> by complementing ammonium transport-defective mutants of <italic>Saccharomyces cerevisiae</italic> (triple <italic>mep</italic>&#x394;) and <italic>A. thaliana</italic> (<italic>qko</italic>). The analysis of the <italic>ScAMT2;1</italic> expression profile in response to various N conditions in sugarcane, together with promoter analysis driving a reporter gene, allowed some insight on the regulation of AMT2;1 in NH<sub>4</sub>
<sup>+</sup> transport in response to changes in external N availability and source. Altogether, the evidence suggests a role for AMT2;1 in ammonium uptake and a presumed contribution to root-to-shoot translocation.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<title>Materials and methods</title>
<sec id="s2_1">
<title>Biological materials</title>
<p>AMT2 sequences were searched in a sugarcane BAC library from the commercial cultivar &#x2018;R570&#x2019; (<xref ref-type="bibr" rid="B72">Tomkins et&#xa0;al., 1999</xref>). Analyses of <italic>ScAMT2;1</italic> expression in sugarcane organs upon various N sources and levels were performed using the commercial cultivar SP80-3280. The <italic>S. cerevisiae</italic> mutant 31019b (triple <italic>mep</italic>&#x394;: <italic>mep1, mep2::LEU2, mep3::KanMX2, ura3</italic>) (<xref ref-type="bibr" rid="B45">Marini et&#xa0;al., 1997</xref>) defective for ammonium uptake was complemented with <italic>AtAMT1;1</italic> or <italic>ScAMT2;1</italic>. The Arabidopsis genotype Columbia-0 (Col-0), the quadruple AMT-knockout mutant <italic>qko</italic> (<italic>amt1;1</italic>, <italic>amt1;2</italic>, <italic>amt1;3</italic>, and <italic>amt2;1</italic>) (<xref ref-type="bibr" rid="B79">Yuan et&#xa0;al., 2007</xref>), and the respective complemented lines were used in complementation assays.</p>
</sec>
<sec id="s2_2">
<title>Search for AMT2 and <italic>in silico</italic> analyses of <italic>ScAMT2;1</italic> coding and regulatory regions</title>
<p>Sugarcane <italic>AMTs</italic> were sought in a BAC library that consists of 269 plates with 384 clones each in a total of 103,296 clones representing a 4.5X coverage of the sugarcane genome (<xref ref-type="bibr" rid="B72">Tomkins et&#xa0;al., 1999</xref>). The search was performed by real-time PCR amplification of the three-dimensional pool of clones (<xref ref-type="bibr" rid="B10">de Setta et&#xa0;al., 2014</xref>). For that, <italic>A. thaliana</italic> and <italic>Oryza sativa AMT2;1</italic> were used to find orthologue sequences in the sugarcane expressed sequence tag (SUCEST) database (<uri xlink:href="https://sucest-fun.org/">https://sucest-fun.org/</uri>) to design the primers (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>). First, superpools were screened for positive blocks, and positive blocks were further screened for the specific coordinates of positive clones, which were then isolated for confirmation and sequenced using the 454/Roche sequencing platform, assembled, and automated annotated as previously described (<xref ref-type="bibr" rid="B10">de Setta et&#xa0;al., 2014</xref>).</p>
<p>
<italic>AMT</italic> gene automated annotation was curated using Artemis Genome Browser and Annotation Tool (v. 16.0.11) (<xref ref-type="bibr" rid="B57">Rutherford et&#xa0;al., 2000</xref>), and sorghum <italic>AMT2</italic> was used as a reference. <italic>ScAMTs</italic> were aligned with <italic>AMTs</italic> from maize, rice, sorghum, and <italic>S. spontaneum</italic> by ClustalW (<xref ref-type="bibr" rid="B68">Thompson et&#xa0;al., 2003</xref>), including a sugarcane (&#x2018;SP80-3280&#x2019;) <italic>AMT2;1</italic> root-expressed sequence, identified here as &#x2018;comp105883&#x2019; (NCBI id# OM966894). The evolutionary history was inferred by using the Maximum Likelihood method and JTT matrix-based model using MEGA11 (<xref ref-type="bibr" rid="B66">Tamura et&#xa0;al., 2021</xref>). A discrete Gamma distribution was used to model evolutionary rate differences among sites [5 categories (+<italic>G</italic>, parameter = 1,1177)]. This analysis involved a total of 537 positions in the final amino acid alignment. A physical map of genomic sequences (~100 kb) containing <italic>AMT2;1</italic> from sugarcane (<italic>Saccharum</italic> spp. &#x2018;R570&#x2019;) BAC clones (032_A12, 038_G02, 118_C18, 216_D16, and 235_F05) and <italic>S. bicolor</italic> (chromosome 9; NC_012878) was manually generated.</p>
<p>
<italic>ScAMT2;1</italic> identified in the BAC clones were analyzed to select the sequence to be functionally characterized. Regulatory upstream (~ 3 kb from the start codon) and coding regions were aligned and compared by ClustalW using BioEdit (<xref ref-type="bibr" rid="B23">Hall, 1999</xref>). Conceptually translated amino acid sequences were analyzed for specific elements/domains of the MEP/AMT/Rh transporter superfamily using Prosite (<xref ref-type="bibr" rid="B26">Hulo et&#xa0;al., 2006</xref>), TMHMM (<xref ref-type="bibr" rid="B32">Krogh et&#xa0;al., 2001</xref>), and WebLogo (<xref ref-type="bibr" rid="B6">Crooks et&#xa0;al., 2004</xref>). The presence of transposable elements (TEs) in the <italic>ScAMT2;1</italic> regulatory region was predicted by Censor (<xref ref-type="bibr" rid="B31">Kohany et&#xa0;al., 2006</xref>) using the Viridiplantae database, and the co-occurrence of transcription factor-binding sites (TFBSs) was analyzed by PlantPAN 2.0 (<xref ref-type="bibr" rid="B4">Chow et&#xa0;al., 2016</xref>).</p>
</sec>
<sec id="s2_3">
<title>Sugarcane plant growth and experimental conditions for gene expression analysis</title>    <p>&#x2018;SP80-3280&#x2019; plantlets derived from <italic>in vitro</italic> meristem culture were grown hydroponically in 5 L plastic pots with full-strength nutrient solution (<xref ref-type="bibr" rid="B24">Hoagland and Arnon, 1950</xref>) containing 1 mM NH<sub>4</sub>NO<sub>3</sub> (pH adjusted to 5.8) under greenhouse conditions for three months. The nutrient solution was aerated and renewed weekly. Prior to treatment, plants received a nutrient solution containing 2 mM NH<sub>4</sub>NO<sub>3</sub> for 2&#xa0;d. Subsequently, the plants were subjected to either an N-free nutrient solution (-N), 2 mM NH<sub>4</sub>NO<sub>3</sub> (+N), 4 mM KNO<sub>3</sub> (<mml:math display="inline" id="im17">
<mml:mrow>
<mml:msubsup>
<mml:mrow>
<mml:mtext>NO</mml:mtext>
</mml:mrow>
<mml:mn>3</mml:mn>
<mml:mo>-</mml:mo>
</mml:msubsup>
</mml:mrow>
</mml:math>), 4 mM NH<sub>4</sub>Cl (<mml:math display="inline" id="im18">
<mml:mrow>
<mml:msubsup>
<mml:mrow>
<mml:mtext>NH</mml:mtext>
</mml:mrow>
<mml:mn>4</mml:mn>
<mml:mo>+</mml:mo>
</mml:msubsup>
</mml:mrow>
</mml:math>), or 5 mM NH<sub>4</sub>NO<sub>3</sub> (high N) for 14&#xa0;d. Roots, culms, and young (+1) and mature (+3) leaves were collected, frozen in liquid N and stored at -80&#xb0;C. Three plants per treatment were used for <italic>ScAMT2;1</italic> tissue-specific expression.</p>
</sec>
<sec id="s2_4">
<title>Arabidopsis genotype growth and experimental conditions</title>
<p>Arabidopsis seeds were surface sterilized and grown for 30&#xa0;d in substrate and vermiculite (1:1) in a growth chamber at 22&#xb0;C, 80% humidity, and a 16/8&#xa0;h light/dark phase at 200 &#xb5;mol m<sup>-2</sup> s<sup>-1</sup>. For the selection of transgenic events and experiments in agar plates, seeds were sown onto modified half-strength MS with 1 mM NH<sub>4</sub>NO<sub>3</sub> as the sole N source, with the pH adjusted to 5.8. After a 4&#xa0;d vernalization at 4&#xb0;C in the dark, plates were placed in a growth cabinet at 24&#xb0;C, 16/8&#xa0;h light/dark phases, and 100 &#x3bc;mol m<sup>-2</sup> s<sup>-1</sup>. For experiments in agar plates, Arabidopsis seeds were kept for 3&#xa0;d in half-strength MS medium with 5 mM KNO<sub>3</sub>, with plates positioned vertically. Seedlings were then transferred onto media supplemented with various N sources at the indicated concentrations under the same environmental conditions. Treatments included either 0.5 mM KNO<sub>3</sub> or 2 mM NH<sub>4</sub>Cl for experiments with plants bearing p35S::<italic>ScAMT2;1</italic> and 2 mM KNO<sub>3</sub> or 0.2, 2, and 4 mM NH<sub>4</sub>Cl for experiments with <italic>qko</italic>+p2<italic>ScAMT2;1::ScAMT2;1</italic> plants (sugarcane endogenous promoter). After 14&#xa0;d of treatment, seedlings were harvested, and the dry or fresh weight was measured.</p>
</sec>
<sec id="s2_5">
<title>
<italic>AMT2;1</italic> expression analysis by quantitative reverse transcription amplification</title>
<p>Total RNA was isolated from sugarcane leaves as described (<xref ref-type="bibr" rid="B34">Leal et&#xa0;al., 2007</xref>) or from Arabidopsis using TRIzol (Thermo Fisher Scientific; Waltham, MS, USA). cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). Primers were designed based on the <italic>ScAMT2;1</italic> sequence from clone BAC 118_C18 (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>). RT&#x2013;qPCR was performed with 5 &#xb5;L of KAPA SYBR FAST (Kapa Biosystems, Wilmington, MA, USA), 0.2 &#xb5;M of each primer (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>), and 1 &#xb5;L of diluted cDNA (1:10) in a final volume of 10 &#xb5;L. Reactions were run in a RotorGene-6000 (Qiagen) with the following settings: 50&#xb0;C for 10&#xa0;min and 95&#xb0;C for 2&#xa0;min, followed by 40 cycles of 95&#xb0;C for 20 s, 62&#xb0;C for 25 s, and 72&#xb0;C for 25 s. <italic>UBIQUITIN2</italic> was used as a reference gene in sugarcane (<italic>ScUBQ2</italic>) and Arabidopsis (<italic>AtUBQ2</italic>) (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>). All reactions were performed in triplicate with three biological replicates. Relative expression levels were calculated as described (<xref ref-type="bibr" rid="B40">Livak and Schmittgen, 2001</xref>). Normalization is indicated for each experiment.</p>
</sec>
<sec id="s2_6">
<title>Functional analysis of ScAMT2;1 by complementation of the yeast triple <italic>mep</italic>&#x394; mutant</title>    <p>The full-length <italic>ScAMT2;1</italic> coding sequence from clone BAC 118_C18 was synthesized (Biomatik; Cambridge, Ontario, Canada); <italic>AtAMT1;1</italic> was used as a positive control because of its well-established function, and the empty vector was used as a negative control (final constructs in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S2</bold>
</xref>). <italic>AtAMT1;1</italic> and <italic>ScAMT2;1</italic> sequences were amplified from Arabidopsis cDNA or synthetic vector, respectively, with primers containing restriction enzyme sites (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>), cloned into pGEM-T Easy (Promega, Madison, WI, USA), sequenced, and subcloned into the expression vector pDR196 (<xref ref-type="bibr" rid="B54">Rentsch et&#xa0;al., 1995</xref>). Triple <italic>mep</italic>&#x394; (strain 31019b) yeast cells were transformed by the lithium acetate method (<xref ref-type="bibr" rid="B19">Gietz and Schiestl, 2007</xref>). Confirmed positive clones were inoculated in liquid YNB-AA/AS (0.17% yeast nitrogen base without amino acids or ammonium sulfate) containing 1 mM arginine (positive control) and 50 mg L<sup>-1</sup> ampicillin for 36&#xa0;h at 30&#xb0;C at 200 rpm. A growth test was performed with a serial dilution (DO<sub>600nm</sub>= 1, and subsequent dilution of 10<sup>-1</sup>, 10<sup>-2</sup>, and 10<sup>-3</sup>) plated onto YNB-AA/AS supplemented with 3% glucose and one source of N [0.5, 2, 3, or 5 mM NH<sub>4</sub>Cl (NH<sub>4</sub>
<sup>+</sup>), 100 mM methylammonium (MeA), or 1 mM arginine (Arg)]. MES-Tris was added at 20 mM to maintain the pH at 5.0, 6.0, or 7.5. The plates were incubated at 30&#xb0;C for 6&#xa0;d.</p>
</sec>
<sec id="s2_7">
<title>Promoter analysis and <italic>ScAMT2;1</italic> functional complementation of the Arabidopsis <italic>qko</italic> mutant</title>
<p>The <italic>ScAMT2;1</italic> promoter region fragment from clones BAC 118_C18 (2,936 bp; p1<italic>ScAMT2;1</italic>) and BAC 235_F05 (2,962 bp; p2<italic>ScAMT2;1</italic>), hereafter called endogenous promoters, as well as the coding region from the synthetic <italic>ScAMT2;1</italic> gene, were amplified (see above). The amplified products were cloned into pDONR or pCR8 (Thermo Fisher Scientific) and then subcloned into the final pMDC vectors (primers in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>; vectors and final constructs in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S2</bold>
</xref>) using the Gateway system (Thermo Fisher Scientific). Arabidopsis plants (Col-0 or <italic>qko</italic>) were transformed by floral dipping (<xref ref-type="bibr" rid="B50">Narusaka et&#xa0;al., 2010</xref>) using <italic>Agrobacterium tumefaciens</italic> GV3101 bearing the constructs indicated in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S2</bold>
</xref>. Transformed lines were selected for hygromycin resistance. Homozygous lines were confirmed by PCR and RT&#x2013;qPCR.</p>
</sec>
<sec id="s2_8">
<title>Localization of promoter activity in Arabidopsis</title>
<p>Seedlings of Arabidopsis transgenic lines containing the GUS reporter gene (<italic>uidA</italic>, pMDC164) driven by <italic>ScAMT2;1</italic> endogenous promoter were cultivated on half-strength MS media without N (-N) or supplied with 2 mM NH<sub>4</sub>Cl or 1 mM NH<sub>4</sub>NO<sub>3</sub> as the sole N source for up to 10&#xa0;d. For GUS staining, plants were transferred to buffer containing 5&#x2010;bromo&#x2010;4&#x2010;chloro&#x2010;3&#x2010;indolyl glucuronide (X-Gluc; Jersey Lab and Glove Supply, Livingston, NJ, USA) at 37&#xb0;C for 4&#xa0;h 30&#xa0;min and then washed in 70% ethanol (<xref ref-type="bibr" rid="B27">Jefferson et&#xa0;al., 1987</xref>). Plant tissues were analyzed and photographed under a Nikon SMZ18 stereo microscope.</p>
</sec>
<sec id="s2_9">
<title>
<sup>15</sup>N uptake and accumulation in Arabidopsis plants</title>    <p>Wild-type Arabidopsis and homozygous (T<sub>3</sub>) <italic>ScAMT2;1</italic>-complemented <italic>qko</italic> plants were hydroponically grown in N-sufficient conditions (2 mM NH<sub>4</sub>NO<sub>3</sub>) with pH adjusted to 5.8 with 2-(N-morpholino)ethanesulfonic acid (MES) for 40&#xa0;d. For <italic>qko</italic>+<italic>p35S</italic>::<italic>ScAMT2;1</italic> lines, plants were subjected to N deficiency (-N, no N) or N sufficiency (+N, 1 mM NH<sub>4</sub>NO<sub>3</sub>), whereas <italic>qko</italic>+<italic>p2ScAMT2;1::ScAMT2;1</italic> plants were transferred to -N, 2 mM KNO<sub>3</sub> or NH<sub>4</sub>Cl as sole N sources. After 3&#xa0;d under treatment, plants were exposed to a short-term <sup>15</sup>N-ammonium influx assay with a 10&#xa0;min incubation in a full-strength nutrient solution containing 0.2 mM (<sup>15</sup>NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub> (60% of <sup>15</sup>N-ammonium). To assess <sup>15</sup>N accumulation in roots and shoots, plants were subjected to -N for 3&#xa0;d and then transferred to a <sup>15</sup>N-labelled nutrient solution with 2 mM (<sup>15</sup>NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub> (60% of <sup>15</sup>N-ammonium) for 1&#xa0;h. For concentration-dependent influx of NH<sub>4</sub>
<sup>+</sup> into roots of <italic>qko</italic> and <italic>qko</italic>+p35S::<italic>ScAMT2;1</italic> lines, 40-d-old plants grown hydroponically under the same conditions mentioned above were transferred to -N for 3&#xa0;d. Roots were then incubated for 10&#xa0;min in full nutrient solution containing increasing concentrations 0, 25, 50 100, 150, 200, 300, and 500 mM of (<sup>15</sup>NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub> (60% of <sup>15</sup>N-ammonium). To further assess the contribution of AMT2;1 to <sup>15</sup>N root-to-shoot translocation, 40-d-old hydroponically grown <italic>qko</italic> and <italic>qko</italic>+ <italic>p2ScAMT2</italic>::<italic>ScAMT2;1</italic> plants were subjected to -N for 3&#xa0;d followed by one h-root exposure to a nutrient solution containing 0.2 mM or 4 mM (<sup>15</sup>NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub> (60% of <sup>15</sup>N-ammonium). In all <sup>15</sup>N experiments, roots were first rinsed with 1 mM CaSO<sub>4</sub> for 1&#xa0;min before exposure to <sup>15</sup>N, followed by washing with 1 mM CaSO<sub>4</sub> prior to sample collection. Roots and shoots were collected separately, dried, ground, and analyzed for total <sup>15</sup>N content using continuous-flow isotope ratio mass spectrometry (ANCA SL, Sercon, Cheshire, UK).</p>
</sec>
<sec id="s2_10">
<title>Data analysis</title>
<p>A completely randomized design was used in all experiments. The number of biological replicates is indicated for each experiment. Analysis of variance (ANOVA) was performed, and means were compared using Tukey&#x2019;s test at 5% significance or <italic>t</italic> test (<italic>p</italic> &#x2264; 0.10 and <italic>p</italic> &#x2264; 0.05), as indicated for each experiment, using SAS software (SAS Institute Inc., Cary, NC, USA).</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<title>Results</title>
<sec id="s3_1">
<title>Identification of <italic>ScAMT2;1</italic> in BAC clones and selection of sequences for functional characterization</title>
<p>Through real-time amplification of the three-dimensional pool of BAC clones using <italic>AMT2;1</italic>-specific primers followed by screening for the specific coordinates of positive clones, we identified five clones containing sequences closely related to <italic>ScAMT2;1</italic> transcript, namely, BAC 032_A12, BAC 038_G02, BAC 118_C18, BAC 216_D16, and BAC 235_F05 (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S1</bold>
</xref>). Each BAC clone contained a unique locus, except for BAC 216_D16 and BAC 235_F05, which shared the same protein sequence. The BAC 032_A12, BAC 038_G02, and BAC 118_C18 <italic>AMT2.1</italic> loci were phylogenetically closer to the root-expressed assembled transcript (comp105883). On the other hand, BAC 216_D16 and BAC 235_F05 did not group closely with the transcript sequence (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S1</bold>
</xref>).</p>
<p>As sugarcane cultivars are polyploids derived from interspecific crosses between <italic>S. officinarum</italic> and <italic>S. spontaneum</italic> (<xref ref-type="bibr" rid="B52">Nogueira et&#xa0;al., 2005</xref>; <xref ref-type="bibr" rid="B20">Graff et&#xa0;al., 2011</xref>), the identified BAC clones containing distinct <italic>ScAMT2;1</italic> loci are expected to differ for the surrounding topology (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>). Of the five clones, BAC 216_D16 and BAC 235_F05 were highly similar, with 62.0% identity.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Physical map of genomic sequences (100 Kb) containing <italic>AMT2;1</italic> from sugarcane (<italic>Saccharum</italic> spp. &#x2018;R570&#x2019;) BAC clones (032_A12, 038_G02, 118_C18, 216_D16, and 235_F05) and <italic>S. bicolor</italic> (chromosome 9; NC_012878).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1039041-g001.tif"/>
</fig>
<p>The alignment of the deduced amino acid of AMT2;1 sequences from the BAC clones, comp105883, and one <italic>S. spontaneum AMT2;1</italic> (<xref ref-type="bibr" rid="B77">Wu et&#xa0;al., 2021</xref>) indicated that BAC 118_C18 had an identical protein sequence as the transcribed assembled sequence (comp105883) (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S3A</bold>
</xref>). The complete <italic>ScAMT2;1</italic> gene from BAC 118_C18 (NCBI# OM471796) is 1,473 bp long with three exons encoding 490 amino acids, conceptually estimated to be a protein of 52 kDa (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S2B</bold>
</xref>). Similar gene structure and protein features were observed for <italic>S. spontaneum SsAMT2;1</italic> from the chromosome 7 (Sspon.03G0003380-4D; Wu et&#xa0;al., 2021) (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S2B</bold>
</xref>; <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S3A</bold>
</xref>). In addition, the presumed ScAMT2;1 amino acid sequence from BAC 118_C18 was identical to the SsAMT2;1 protein Sspon.03G0003380-4D (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S3A</bold>
</xref>) and contained the expected 11 transmembrane domains predicted by TMHMM (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S3B</bold>
</xref>), along with the conserved signature motif for the MEP/AMT/Rh superfamily (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S3C</bold>
</xref>).</p>
<p>Various plant AMT1 and AMT2 sequences, including the identified sugarcane members, were compared to verify the conservation of C- and N-terminal regions concerning amino acids essential for transport function (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S4</bold>
</xref>). In the N-terminus of the tomato protein LeAMT1;1, two cysteines (C3 and C27) have been proven to be fundamental for AMT1 oligomer stability (<xref ref-type="bibr" rid="B20">Graff et&#xa0;al., 2011</xref>). While AMT1 proteins except for SlAMT1;3 contained these two conserved Cys residues, these residues were absent in all AMT2 homologues (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figures S4A, C</bold>
</xref>). In the C-terminus, some residues have been associated with transport regulation, including glycine-456 (G456; SlAMT1;1) and threonine-460 (T460) (<xref ref-type="bibr" rid="B43">Ludewig et&#xa0;al., 2003</xref>). G456 was found in all AMTs evaluated to date, whereas T460 was absent in all AMT2 subfamily members, including ScATM2;1 (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figures S4B, D</bold>
</xref>).</p>
<p>Multiple alignment of the various <italic>ScAMT2;1</italic> promoter sequences identified in the BAC clones (approximately 3 kb upstream of the predicted translation start codon) allowed the arbitrary separation of the clones into two groups, in which sequences from BAC 032_A12, BAC 038_G02, and BAC 118_C18 were more similar between each other, differing from BAC 216_D16 and BAC 235_F05 (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S5A</bold>
</xref>). We analyzed whether this separation could be due to transposable element (TE) insertions, which are commonly found in promoter regions of sugarcane sequences (<xref ref-type="bibr" rid="B10">de Setta et&#xa0;al., 2014</xref>). TE insertion was assessed by Censor, which identified repetitive elements by comparison with known repeats and assigned a score for probability. The results reinforced the similarity of BAC 216_D16 and BAC 235_F05, showing a similar TE insertion profile (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S5C</bold>
</xref>). To further investigate the presence of regulatory elements and presumed synteny of regulatory motifs, we chose clones from each group, BAC 118_C18 and BAC 235_F05. Only a few conserved regions exist between the selected regulatory regions, indicating significant variation between the two <italic>ScAMT2;1</italic> promoters (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S5C</bold>
</xref>). As loci from BAC 118_C18 were not functional in driving the expression of <italic>uidA</italic> in the GUS assay (see below), the sequence from the BAC 235_F05 clone was chosen to be further analyzed as a functional <italic>ScAMT2;1</italic> endogenous promoter. Concerning the gene sequence, <italic>ScAMT2;1</italic> from BAC 118_C18 was selected for functional validation due to greater similarity with the root-expressed <italic>ScAMT2;1</italic> sequence comp105883 and <italic>S. spontaneum</italic> Sspon.03G0003380-4D (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S2B</bold>
</xref>).</p>
</sec>
<sec id="s3_2">
<title>
<italic>ScAMT2;1</italic> is expressed in sugarcane roots and shoots and it is regulated according to inorganic N source and level</title>
<p>The transcriptional profile of <italic>ScAMT2;1</italic> was examined in the organs of sugarcane plants grown under various N conditions. At the stage of generative growth (90-d-old plants) under N-sufficient conditions, <italic>ScAMT2;1</italic> was expressed in all organs analyzed, with more transcript accumulation in roots, but it was also largely expressed in mature leaves, followed by young leaves, and less abundant in culms (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>). To assess how <italic>ScAMT2;1</italic> expression is regulated by N supply, transcript levels were determined in various organs in plants grown in nutrient solution containing distinct N sources or without N for 14&#xa0;d and compared with the +N treatment (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2B</bold>
</xref>). In the presence of nitrate as the sole N source, <italic>ScAMT2;1</italic> transcripts accumulated approximately 2- to 3-fold more in roots, mature leaves, and culms but not in young leaves compared with plants grown in ammonium nitrate (+N). Thus, exposing the plants at the same high N level (4 mM) but changing the source from 2 mM NH<sub>4</sub>NO<sub>3</sub> to 4 mM KNO<sub>3</sub> (4 mM N with no ammonium) was sufficient to induce <italic>ScAMT2;1</italic> expression in roots and shoots more than the change from 2 mM NH<sub>4</sub>NO<sub>3</sub> to 4 mM NH<sub>4</sub>Cl.</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Expression of <italic>ScAMT2;1</italic> in sugarcane organs after subjecting plants to distinct inorganic N sources or no N. <bold>(A)</bold> RT&#x2013;qPCR analysis of <italic>ScAMT2;1</italic> expression in roots, culms, and young (+1) or mature (+3) leaves of sugarcane grown under 2 mM NH<sub>4</sub>NO<sub>3</sub> for 2&#xa0;d. Bars indicate &#xb1; SE (<italic>n</italic> = 3). <italic>ScUBQ2</italic> was adopted as a reference gene. Gene expression levels were normalized to expression levels in culms. Asterisks represent significant differences in relation to culms according to Student&#x2019;s <italic>t</italic> test (<italic>p</italic> &lt; 0.01). <bold>(B)</bold> <italic>ScAMT2;1</italic> relative expression levels in sugarcane roots, culm, young, and mature leaves of plants under +N: 2 mM NH<sub>4</sub>NO<sub>3</sub>, -N: no N; <mml:math display="inline" id="im21">
<mml:mrow>
<mml:msubsup>
<mml:mrow>
<mml:mtext>NO</mml:mtext>
</mml:mrow>
<mml:mn>3</mml:mn>
<mml:mo>-</mml:mo>
</mml:msubsup>
</mml:mrow>
</mml:math>: 4 mM KNO<sub>3</sub>, or NH<sub>4</sub>
<sup>+</sup>: 4 mM NH<sub>4</sub>Cl for 14&#xa0;d. <italic>ScUBQ2</italic> was used as a reference gene. The gene expression level was normalized to the +N treatment. Bars indicate &#xb1; SE (<italic>n</italic> = 3). Asterisks represent significant differences between treatments and +N according to Student&#x2019;s <italic>t</italic> test (<italic>p</italic> &lt; 0.01).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1039041-g002.tif"/>
</fig>
<p>To further investigate whether <italic>ScAMT2;1</italic> is transcriptionally modulated by N availability, the expression profile was evaluated in sugarcane plants grown under 5 mM NH<sub>4</sub>NO<sub>3</sub> (high N) or no N (-N) for 10&#xa0;d (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S6</bold>
</xref>). Transient and temporal transcript accumulation was detected in N-deficient mature leaves relative to high N supply. In culms, <italic>ScAMT2;1</italic> transcripts showed some accumulation in both treatments; however, this transcriptional response was not observed in roots or young leaves. Altogether, these observations indicate that the N source and the plant N status modulate the expression of <italic>ScAMT2;1</italic> in sugarcane.</p>
</sec>
<sec id="s3_3">
<title>
<italic>ScAMT2;1</italic> marginally facilitates ammonium uptake in a defective mutant yeast</title>    <p>To investigate whether the selected <italic>ScAMT2;1</italic> gene (BAC118_C18) encodes a functional ammonium transporter, we complemented the <italic>S. cerevisiae</italic> triple <italic>mep</italic> mutant (31019b) (<xref ref-type="bibr" rid="B45">Marini et&#xa0;al., 1997</xref>). The positive control (triple <italic>mep</italic> complemented with AtAMT1;1) completely restored growth under all N conditions tested (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3</bold>
</xref>). By increasing the external NH<sub>4</sub>
<sup>+</sup> concentration, triple <italic>mep</italic> cells complemented with <italic>ScAMT2;1</italic> showed slightly more growth than the negative control suggesting that ScAMT2;1 is a functional protein that mediates ammonium transport. At 5 mM ammonium, the growth of the triple <italic>mep</italic> complemented with ScAMT2;1 was strongly pH dependent. The ScAMT2;1-expressing triple <italic>mep</italic> grew slightly better than the negative control (empty pDR196) at a pH of 5.0 and 6.0. Raising the pH further to 7.5 may have increased the concentration of ammonia (NH<sub>3</sub>), resulting in similar growth between triple <italic>mep</italic> expressing ScAMT2;1 and the negative control.</p>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Functional complementation of the yeast mutant defective for ammonium uptake. Growth of the ammonium transporter-deficient yeast strain triple <italic>mep</italic>&#x394; (31019b) expressing <italic>AtAMT1;1</italic> (positive control), the empty pDR196 vector (negative control), or <italic>ScAMT2;1</italic> on media supplied with 0.5 to 5 mM ammonium chloride (NH<sub>4</sub>
<sup>+</sup>), 100 mM methylammonium (MeA), or 1 mM arginine (Arg; positive control) as the sole N source. Culture media pH was adjusted to 6.0 when not indicated otherwise. Each transformant line was grown to OD<sub>600nm</sub> = 1 and plated in concentrated and sequential four 10-fold dilutions.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1039041-g003.tif"/>
</fig>
<p>In contrast to type 1 AMT proteins, AMT2 has been proposed to be impermeable to the transport of the ammonium toxic analogue methylammonium (MeA) (<xref ref-type="bibr" rid="B62">Sohlenkamp et&#xa0;al., 2000</xref>; <xref ref-type="bibr" rid="B63">Sohlenkamp et&#xa0;al., 2002</xref>). The growth of triple <italic>mep</italic> complemented with ScAMT2;1 was evaluated on media supplemented with 100 mM MeA (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3</bold>
</xref>). The toxic effect of MeA drastically reduced the growth of triple <italic>mep</italic> cells expressing AtAMT1;1, whereas those complemented with ScAMT2;1 or the empty vector displayed no visible sensitivity towards MeA.</p>
</sec>
<sec id="s3_4">
<title>
<italic>ScAMT2;1</italic> complements the ammonium uptake-defective Arabidopsis quadruple mutant</title>    <p>
<italic>ScAMT2;1</italic> driven by the CaMV<italic>35S</italic> promoter (p35S) was expressed in the Arabidopsis quadruple <italic>AMT</italic> mutant line (<italic>qko</italic>) (<xref ref-type="bibr" rid="B79">Yuan et&#xa0;al., 2007</xref>). Three independent T<sub>3</sub> homozygous lines were characterized for <italic>ScAMT2;1</italic> expression in relation to Col-0 plants (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S7</bold>
</xref>) and then used for phenotypic evaluation. <italic>ScAMT2;1-</italic>complemented events grown in the presence of ammonium as the only N source accumulated significantly more total dry biomass than <italic>qko</italic>, with values approximately 65% (event #1) and 51% (event #2) higher under 2 mM NH<sub>4</sub>
<sup>+</sup> (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4A, B</bold>
</xref>). In contrast, no significant difference between <italic>qko</italic> and the complemented lines was observed when only nitrate was supplied (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4A, B</bold>
</xref>), suggesting that the ectopic expression of <italic>ScAMT2;1</italic> restored the <italic>qko</italic> mutant growth phenotype only under ammonium nutrition, likely by mediating ammonium uptake into roots.</p>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Functional evaluation of complemented Arabidopsis <italic>qko</italic> mutant. <bold>(A)</bold> Total biomass (DW, dry weight) of homozygous lines of Arabidopsis overexpressing <italic>ScAMT2;1</italic> (<italic>qko</italic>+p35S::<italic>ScAMT2;1</italic>) subjected to either 0.5 mM KNO<sub>3</sub> (<mml:math display="inline" id="im26">
<mml:mrow>
<mml:msubsup>
<mml:mrow>
<mml:mtext>NO</mml:mtext>
</mml:mrow>
<mml:mn>3</mml:mn>
<mml:mo>-</mml:mo>
</mml:msubsup>
</mml:mrow>
</mml:math>) or 2 mM NH<sub>4</sub>Cl (NH<sub>4</sub>
<sup>+</sup>) for 14&#xa0;d. Bars indicate means &#xb1; SE (<italic>n</italic> = 6). Different letters indicate significant differences among means according to Tukey&#x2019;s test (<italic>p</italic> &#x2264; 0.05). <bold>(B)</bold> Phenotype of <italic>qko</italic> and transgenic events grown <italic>in vitro</italic> under different N sources. <bold>(C)</bold> Influx of <sup>15</sup>N-labeled ammonium into the roots of <italic>qko</italic> and a transgenic line (#1) overexpressing <italic>ScAMT2;1</italic> subjected to either N-free (-N) or 0.2 mM NH<sub>4</sub>
<sup>+</sup> (+N) nutrient solution for 3&#xa0;d. Bars indicate means &#xb1; SE (<italic>n</italic> = 4). Asterisks indicate significant differences between <italic>qko</italic> and the transgenic line according to Student&#x2019;s <italic>t</italic> test (<italic>p</italic> &lt; 0.05). <bold>(D)</bold> Concentration-dependent influx of <sup>15</sup>NH<sub>4</sub>
<sup>+</sup> into roots of <italic>qko</italic> or <italic>qko</italic>+p35S::<italic>ScAMT2;1</italic> (#1). Symbols indicate six biological replicates (<italic>n</italic> = 6).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1039041-g004.tif"/>
</fig>    <p>We then evaluated the short-term influx of <sup>15</sup>N-NH<sub>4</sub>
<sup>+</sup> in the <italic>qko ScAMT2;1</italic>-complemented lines. Under -N, the root ammonium uptake capacity of <italic>qko</italic>+p35S::<italic>ScAMT2;1</italic> increased by 87% compared with <italic>qko</italic> (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4C</bold>
</xref>), corroborating the function of ScAMT2;1 in NH<sub>4</sub>
<sup>+</sup> uptake in roots. To estimate the substrate affinity of ScAMT2;1, six-week-old <italic>ScAMT2;1-</italic>overexpressing (p35S) <italic>qko</italic> plants were grown under -N for 3&#xa0;d, followed by concentration-dependent <sup>15</sup>N-NH<sub>4</sub>
<sup>+</sup> influx analyses. In this experiment, ScAMT2;1 function was saturated above 90 &#xb5;M (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4D</bold>
</xref>). The estimated net ammonium influx fitted the Michaelis&#x2013;Menten equation well, resulting in a K<sub>m</sub> = 90.17 &#xb5;M and a V<sub>max</sub> of 338.99 &#xb5;moles h<sup>-1</sup> g<sup>-1</sup> root DW, determined by subtracting the values of <italic>qko</italic> (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4D</bold>
</xref>). These results demonstrate that the ScAMT2;1 protein can contribute to high-affinity ammonium transport <italic>in planta</italic>.</p>
</sec>
<sec id="s3_5">
<title>
<italic>ScAMT2;1</italic> regulatory region drives expression in Arabidopsis root and shoot vascular tissues and is regulated by N source and availability</title>
<p>To help determining the ScAMT2;1 function, we conducted localization experiments in Arabidopsis by expressing the <italic>GUS</italic> reporter gene driven by the <italic>ScAMT2;1</italic> regulatory region from BAC 118_C18 (p1<italic>ScAMT2;1</italic>) and BAC 235_F05 (p2<italic>ScAMT2;1</italic>). No reporter expression was detected with the promoter p1<italic>ScAMT2;1</italic>, which was apparently nonfunctional (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S8</bold>
</xref>). Arabidopsis lines expressing p2<italic>ScAMT2;1</italic>::<italic>GUS</italic> allowed tracing promoter activity in vascular bundles and outermost cells in leaves, either under ammonium or ammonium nitrate (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5A</bold>
</xref>). In contrast, leaves from N-deficient plants displayed no p2<italic>ScAMT2;1</italic> activity in outer cells, and activity appeared to predominate at vascular bundles (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5A</bold>
</xref>). In roots, GUS was mainly detected in the innermost tissues (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5B</bold>
</xref>). Altogether, these results suggest that the <italic>ScAMT2;1</italic> regulatory region is associated with root and leaf vascular tissues, but tissue-specific expression depends particularly on the N status in leaves rather than roots.</p>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>Endogenous <italic>ScAMT2;1</italic> promoter <bold>(</bold>p2<bold>)</bold> driving GUS expression in Col-0 Arabidopsis plants subjected to 1 mM NH<sub>4</sub>NO<sub>3</sub>, 2 mM NH<sub>4</sub>
<sup>+</sup>, or no N for 1, 3, 5, and 10&#xa0;d in <bold>(A)</bold> shoots; and <bold>(B)</bold> roots. The blue color shows GUS activity. Bars = 200 &#x3bc;m.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1039041-g005.tif"/>
</fig>
</sec>
<sec id="s3_6">
<title>Sugarcane <italic>ScAMT2;1</italic> promoter regulates ammonium uptake according to external N level and source</title>    <p>We then assessed the contribution of ScAMT2;1 to ammonium uptake by generating <italic>qko</italic> lines complemented with <italic>ScAMT2;1</italic> driven by the endogenous regulatory region p2<italic>ScAMT2;1</italic>. While all p2<italic>ScAMT2;1</italic>::<italic>ScAMT2;1-</italic>complemented lines and <italic>qko</italic> grew similarly on agar medium supplemented with either 2 mM nitrate or 0.2 mM ammonium (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>), the total biomass of <italic>qko</italic>+p2<italic>ScAMT2;1</italic>::<italic>ScAMT2;1</italic> plants was clearly superior to that of <italic>qko</italic> under higher external NH<sub>4</sub>
<sup>+</sup> concentrations. At 2 mM NH<sub>4</sub>
<sup>+</sup>, <italic>qko</italic>+p2<italic>ScAMT2;1</italic>::<italic>ScAMT2;1</italic> accumulated approximately 83% (#1), 103% (#2), or 28% (#3) more shoot biomass than <italic>qko</italic> (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>). The biomass accumulation for plants grown at 4 mM NH<sub>4</sub>
<sup>+</sup> was 102% (event #1), 75% (event #2), or 107% (event #3) higher than the control plants (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>). These results suggest that ScAMT2;1 under the control of the sugarcane endogenous promoter significantly increased biomass at elevated external ammonium levels and confirm the functionality of ScAMT2;1 in facilitating NH<sub>4</sub>
<sup>+</sup> uptake.</p>
<fig id="f6" position="float">
<label>Figure&#xa0;6</label>
<caption>
<p>Biomass accumulation in Arabidopsis mutant plants and lines complemented with <italic>ScAMT2;1</italic> driven by the sugarcane endogenous promoter. <bold>(A)</bold> Fresh weight of homozygous lines of <italic>qko</italic>+p2<italic>ScAMT2;1</italic>::<italic>ScAMT2;1</italic> subjected to 2 mM KNO<sub>3</sub> (<mml:math display="inline" id="im38">
<mml:mrow>
<mml:msubsup>
<mml:mrow>
<mml:mtext>NO</mml:mtext>
</mml:mrow>
<mml:mn>3</mml:mn>
<mml:mo>-</mml:mo>
</mml:msubsup>
</mml:mrow>
</mml:math>) or 0.2, 2, and 4 mM NH<sub>4</sub>Cl (NH<sub>4</sub>
<sup>+</sup>) for 14&#xa0;d. Bars indicate means &#xb1; SE (<italic>n</italic> = 30). Different letters indicate significant differences among means according to Tukey&#x2019;s test (<italic>p</italic> &#x2264; 0.05). <bold>(B)</bold> Influx of <sup>15</sup>N-labeled ammonium (NH<sub>4</sub>
<sup>+</sup>) into roots of <italic>qko</italic> and <italic>qko</italic>+p2<italic>ScAMT2;1</italic>::<italic>ScAMT2;1</italic> lines upon 3-d exposure to N-free (-N), 2 mM <mml:math display="inline" id="im41">
<mml:mrow>
<mml:msubsup>
<mml:mrow>
<mml:mtext>NO</mml:mtext>
</mml:mrow>
<mml:mn>3</mml:mn>
<mml:mo>-</mml:mo>
</mml:msubsup>
</mml:mrow>
</mml:math>, or 2 mM NH<sub>4</sub>
<sup>+</sup> nutrient solution. Bars indicate means &#xb1; SE (<italic>n</italic> = 4). Asterisks indicate significant differences between <italic>qko</italic> and transgenic plants according to Student&#x2019;s <italic>t</italic> test (*<italic>p</italic> &lt; 0.10 and **<italic>p</italic> &lt; 0.05).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1039041-g006.tif"/>
</fig>    <p>To evaluate the regulatory level of the response of the <italic>ScAMT2;1</italic> promoter to high external N supply, short-term <sup>15</sup>N-ammonium influx analysis was performed with <italic>qko+</italic>p2<italic>ScAMT2;1</italic>::<italic>ScAMT2;1</italic> plants in the presence of 2 mM of either ammonium or nitrate or no N (-N). The influx of <sup>15</sup>N-NH<sub>4</sub>
<sup>+</sup> into the roots of <italic>qko</italic> and complemented lines subjected to -N was similar and nonsignificant (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6B</bold>
</xref>). Complementation with <italic>ScAMT2;1</italic> significantly increased uptake levels by 6% (#1) and 43% (#2) compared with <italic>qko</italic> when subjected to 2 mM nitrate and by 61% (#1) and 78% (#2) in complemented plants subjected to 2 mM ammonium (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6B</bold>
</xref>). Altogether, these results indicate that the regulation of ScAMT2;1 in ammonium uptake depends strictly on the preconditioning of plants to an externally high N form but not to -N.</p>
</sec>
<sec id="s3_7">
<title>The <italic>ScAMT2;1</italic> regulatory region appears to drive ammonium root-to-shoot translocation</title>    <p>Our experiments indicated that ScAMT2;1 contributes to root ammonium uptake mainly in NH<sub>4</sub>
<sup>+</sup>-supplied plants (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6</bold>
</xref>) and that the <italic>ScAMT2;1</italic> promoter (p2) drives gene expression in the inner vascular root cells (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5</bold>
</xref>). These results prompted us to evaluate whether ScAMT2;1 mediates root-to-shoot ammonium transport under ammonium supply. To this end, we evaluated ScAMT2;1-specific functions by estimating <sup>15</sup>N accumulation in roots and shoots of <italic>qko</italic> and <italic>qko+</italic>p2<italic>ScAMT2;1</italic>::<italic>ScAMT2;1</italic> lines subjected to either 0.2 mM or 4 mM <sup>15</sup>N-NH<sub>4</sub>
<sup>+</sup> for 1&#xa0;h to allow time for root-to-shoot translocation (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7A</bold>
</xref>). At 0.2 mM <sup>15</sup>N-NH<sub>4</sub>
<sup>+</sup> supply, no significant <sup>15</sup>N was accumulated in shoots compared with <italic>qko</italic>, whereas some <sup>15</sup>N accumulation in roots occurred for one transgenic line (event #2). When plants were grown in the presence of 4 mM <sup>15</sup>N-NH<sub>4</sub>
<sup>+</sup>, roots of <italic>qko</italic> and complemented lines accumulated <sup>15</sup>N in a similar pattern. In contrast, significantly more <sup>15</sup>N accumulated in the shoots of both <italic>qko</italic>+p2<italic>ScAMT2;1</italic>::<italic>ScAMT2;1</italic> lines, approximately 35% and 25% more than in <italic>qko</italic> shoots (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7A</bold>
</xref>). The rate of <sup>15</sup>N accumulated in the shoot in relation to the whole plant was 7 and 6.3% for the <italic>qko+</italic>p2<italic>ScAMT2;1</italic>::<italic>ScAMT2;1</italic> lines, significantly superior to the 4.8% observed in <italic>qko</italic> when plants were subjected to 4 mM <sup>15</sup>N-NH<sub>4</sub>
<sup>+</sup> (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7B</bold>
</xref>). These results suggest that ScAMT2;1 activity in roots might contribute to ammonium translocation to shoots under high external ammonium conditions.</p>
<fig id="f7" position="float">
<label>Figure&#xa0;7</label>
<caption>
<p>
<sup>15</sup>N accumulation in roots and shoots of <italic>qko</italic> and complemented <italic>qko</italic> transgenic lines expressing <italic>ScAMT2;1</italic> under the regulation of its sugarcane endogenous promoter (p2). The assay was performed in plants after 3&#xa0;d of exposure to an N-free nutrient solution, followed by 1&#xa0;h of treatment in either a 0.2 mM or 4.0 mM <sup>15</sup>NH<sub>4</sub>
<sup>+</sup> solution. Bars indicate means &#xb1; SE (<italic>n</italic> = 5). Asterisks indicate significant differences in root and shoot <sup>15</sup>NH<sub>4</sub>
<sup>+</sup> accumulation between <italic>qko</italic> and transgenic plants according to Student&#x2019;s <italic>t</italic> test (*<italic>p</italic> &lt; 0.1 and **<italic>p</italic> &lt; 0.05). <bold>(B)</bold> Root-to-shoot translocation of <sup>15</sup>N in percent of <sup>15</sup>N accumulation in shoots in relation to the whole plant. Asterisks indicate significant differences between <italic>qko</italic> and transgenic plants according to Student&#x2019;s <italic>t</italic> test (** <italic>p</italic> &lt; 0.05).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1039041-g007.tif"/>
</fig>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<title>Discussion</title>
<p>AMT2 proteins have been demonstrated to exhibit transport properties distinct from those of the AMT1 subfamily (<xref ref-type="bibr" rid="B63">Sohlenkamp et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B47">Mayer and Ludewig, 2006</xref>; <xref ref-type="bibr" rid="B51">Neuh&#xe4;user et&#xa0;al., 2009</xref>). However, little is known about the physiological roles of AMT2-type ammonium transporters. In <italic>Arabidopsis thaliana</italic>, the only AMT2 member was shown to play a critical role in root-to-shoot partitioning of ammonium (<xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>). Here, we provide evidence that ScAMT2;1 might be involved in sugarcane root ammonium uptake at elevated external substrate levels.</p>
<p>We started by identifying AMT2s in the sugarcane genome by searching a BAC library from the commercial cultivar R570 (<xref ref-type="bibr" rid="B72">Tomkins et&#xa0;al., 1999</xref>). The screening allowed the identification of five <italic>ScAMT2;1</italic> sequences. Modern sugarcane cultivars are derived from interspecific crosses between <italic>S. officinarum</italic> and <italic>S. spontaneum</italic>, followed by backcrossing to <italic>S. officinarum</italic>, producing a highly complex genome (<xref ref-type="bibr" rid="B67">Thirugnanasambandam et&#xa0;al., 2018</xref>). Therefore, considering the high polyploidy and redundant character of the sugarcane genome (<xref ref-type="bibr" rid="B16">Garsmeur et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B80">Zhang et&#xa0;al., 2018</xref>), a series of <italic>in silico</italic> conceptual analyses was performed with the various upstream regulatory regions and gene sequences of the <italic>ScAMT2;1</italic> loci found in the five BAC clones to define the target for functional characterization. Based on the phylogenetic analysis, it was possible to infer that BAC 216_D16 and BAC 235_F05 clones contained <italic>ScAMT2;1</italic> alleles distinct from BAC 038_G02, BAC 032_A12, and BAC 118_C18, which was corroborated by analyzing their regulatory regions. The <italic>ScAMT2;1</italic> coding sequence from BAC 118_C18 was chosen because it demonstrated the highest similarity to a root-expressed sequence detected by us in sugarcane (NCBI# OM966894). In addition, <italic>ScAMT2;1</italic> from BAC 118_C18 was structurally identical to an <italic>AMT2;1</italic> from <italic>S. spontaneum</italic> (Sspon.03G0003380-4D; <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S2</bold>
</xref>), with an identical deduced protein (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S3A</bold>
</xref>). The conceptually translated ScAMT2;1 protein from clone BAC 118_C18 displays the conserved 11 presumed transmembrane domains, amino and carboxy-terminal, facing the inner and outer parts of the plasma membrane, respectively, and contains the superfamily signature motif, strongly indicating that this gene is an ammonium transporter (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Figure S2</bold>
</xref>) (<xref ref-type="bibr" rid="B45">Marini et&#xa0;al., 1997</xref>; <xref ref-type="bibr" rid="B44">Marini and Andr&#xe9;, 2000</xref>; <xref ref-type="bibr" rid="B58">Schwacke et&#xa0;al., 2003</xref>; <xref ref-type="bibr" rid="B41">Loqu&#xe9; and von Wir&#xe9;n, 2004</xref>; <xref ref-type="bibr" rid="B12">Ellerbeck et&#xa0;al., 2013</xref>). It will be necessary to evaluate whether the other ScAMT2;1 alleles are functional and present the same expression and regulation patterns and transport characteristics as the one evaluated here.</p>    <p>
<italic>ScAMT2;1</italic> expression in sugarcane was more pronounced in roots and, to a minor extent, in aboveground organs, especially mature leaves (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>). Similar patterns were found for <italic>AMT2;1</italic> expression in <italic>A. thaliana</italic> (<xref ref-type="bibr" rid="B63">Sohlenkamp et&#xa0;al., 2002</xref>), <italic>O. sativa</italic> (<xref ref-type="bibr" rid="B65">Suenaga et&#xa0;al., 2003</xref>), <italic>Lotus japonicus</italic> (<xref ref-type="bibr" rid="B60">Simon-Rosin et&#xa0;al., 2003</xref>), and <italic>S. bicolor</italic> (<xref ref-type="bibr" rid="B30">Koegel et&#xa0;al., 2013</xref>), in all cases showing expression in distinct plant organs. For instance, the homologue <italic>PbAMT2</italic> from <italic>Pyrus betulaefolia</italic> was shown to be expressed in stems, petioles, and leaves but primarily in roots (<xref ref-type="bibr" rid="B35">Li et&#xa0;al., 2016</xref>), similar to the <italic>ScAMT2;1</italic> expression pattern described here for sugarcane. Conversely, <italic>PtAMT2;1</italic> from <italic>P. trichocarpa</italic> was shown to be exclusively expressed in roots (<xref ref-type="bibr" rid="B5">Couturier et&#xa0;al., 2007</xref>). Analysis of the expression profile in sugarcane roots showed that <italic>ScAMT2;1</italic> transcription was slightly but significantly induced by the N status and significantly induced by <mml:math display="inline" id="im51">
<mml:mrow>
<mml:msubsup>
<mml:mrow>
<mml:mtext>NO</mml:mtext>
</mml:mrow>
<mml:mn>3</mml:mn>
<mml:mo>-</mml:mo>
</mml:msubsup>
</mml:mrow>
</mml:math> (possibly sensing the lack of NH<sub>4</sub>
<sup>+</sup>) in roots, culms, and mature leaves (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2B</bold>
</xref>). In Arabidopsis roots, <italic>AtAMT2;1</italic> is induced by N starvation and weakly repressed by nitrate (<xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>), whereas the poplar homologue <italic>PtrAMT2;1</italic> is not regulated by N (<xref ref-type="bibr" rid="B5">Couturier et&#xa0;al., 2007</xref>), suggesting distinct regulation according to species.</p>
<p>The <italic>ScAMT2;1</italic> endogenous promoter drove the expression of GUS in Arabidopsis mainly at endodermal and pericycle cells in the innermost root tissue, with apparently more expression in roots subjected to ammonium compared with N deficiency. Previously, the activity of the Arabidopsis <italic>AMT2;1</italic> promoter was shown to become more confined to root endodermal and particularly pericycle cells when plants were exposed to high ammonium concentrations (<xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>). N deficiency, in turn, shifted the expression of <italic>AtAMT2;1</italic> towards the outer cells (<xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>). Our results with the heterologous expression of the <italic>ScAMT2;1</italic> promoter in Arabidopsis provide initial evidence that <italic>ScAMT2;1</italic> expression is concentrated on vascular and immediately surrounding tissues in roots and shoots. To confirm the predicted tissue-specific localization of <italic>ScAMT2;1</italic> in sugarcane, future studies based on <italic>in situ</italic> hybridization or transient or stable expression of <italic>AMT2;1::GUS/GFP</italic> directly in sugarcane will be necessary. Nevertheless, functional evaluation of sugarcane sequences, such as genes and regulatory regions, in a model plant provides initial inference before narrowing down to the target organism, such as described for sugarcane gene functional analysis (<xref ref-type="bibr" rid="B76">Wang et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B3">Chai et&#xa0;al., 2022</xref>).</p>    <p>Complementation of the ammonium uptake-defective yeast mutant (triple <italic>mep</italic>&#x394;) suggested that ScAMT2;1 is a functional NH<sub>4</sub>
<sup>+</sup> transporter, despite its lower substrate affinity than AtAMT1;1, similar to what had been previously described for AtAMT2;1 (<xref ref-type="bibr" rid="B62">Sohlenkamp et&#xa0;al., 2000</xref>). The expression of OsAMT2;1 in the same yeast mutant supported cell growth on media containing 5 mM NH<sub>4</sub>
<sup>+</sup> but not on 1 mM NH<sub>4</sub>
<sup>+</sup> (<xref ref-type="bibr" rid="B65">Suenaga et&#xa0;al., 2003</xref>). The poplar homologue PtrAMT2;1 complemented the triple <italic>mep</italic>&#x394; cells on 1 mM NH<sub>4</sub>
<sup>+</sup> (<xref ref-type="bibr" rid="B5">Couturier et&#xa0;al., 2007</xref>), while the homologues AtAMT2;1 (<xref ref-type="bibr" rid="B62">Sohlenkamp et&#xa0;al., 2000</xref>), LjAMT2;1 (<xref ref-type="bibr" rid="B60">Simon-Rosin et&#xa0;al., 2003</xref>), PbAMT2, and PbAMT3 (<xref ref-type="bibr" rid="B35">Li et&#xa0;al., 2016</xref>) restored the growth of the same yeast mutant strain cells on 0.5 mM NH<sub>4</sub>
<sup>+</sup> or even lower N concentrations, indicating a diverse biochemical transport capacity of the various AMT2 homologues.</p>    <p>Sugarcane ScAMT2;1 restored the growth of the triple <italic>mep</italic>&#x394; yeast in a pH-dependent manner, increasing activity consistently as the pH was raised from 5.0 to 6.0 while achieving the same growth of the negative control triple <italic>mep</italic>&#x394;+pDR196 at pH 7.5 (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3</bold>
</xref>), suggesting NH<sub>3</sub> diffusion (<xref ref-type="bibr" rid="B46">Martinelle et&#xa0;al., 1996</xref>; <xref ref-type="bibr" rid="B63">Sohlenkamp et&#xa0;al., 2002</xref>). The apparent V<sub>max</sub> of AtAMT2;1 determined in yeast also increased at higher pH values (<xref ref-type="bibr" rid="B63">Sohlenkamp et&#xa0;al., 2002</xref>). Ammonia is a weak base (pK<sub>a</sub> 9.25), with more than 99% protonated at neutral external pH. Thus, elevating the pH from 5.0 to 7.5 increases the concentration of NH<sub>3</sub> by 30-fold, while that of NH<sub>4</sub>
<sup>+</sup> remains almost constant (<xref ref-type="bibr" rid="B63">Sohlenkamp et&#xa0;al., 2002</xref>). The complementation of triple <italic>mep</italic>&#x394; by ScAMT2;1 at lower pH suggests that NH<sub>4</sub>
<sup>+</sup> rather than NH<sub>3</sub> is the substrate for ScAMT2;1. Notably, as a common transport mechanism performed by AMT2 proteins, NH<sub>4</sub>
<sup>+</sup> appears to be deprotonated before transport, and NH<sub>3</sub> permeates through the transporter pore (<xref ref-type="bibr" rid="B29">Khademi et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B22">Guether et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B51">Neuh&#xe4;user et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B1">Akgun and Khademi, 2011</xref>; <xref ref-type="bibr" rid="B2">Ariz et&#xa0;al., 2018</xref>). In yeast, ScAMT2;1 was unable to transport methylammonium (MeA), as triple <italic>mep</italic>&#x394; cells expressing ScAMT2;1 exhibited similar growth as cells expressing the empty vector (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3</bold>
</xref>). Previously, LjAMT2;1 and AtAMT2;1 were shown to be impermeable to MeA and to perform electroneutral transport of uncharged ammonia with a low transport capacity (<xref ref-type="bibr" rid="B60">Simon-Rosin et&#xa0;al., 2003</xref>; <xref ref-type="bibr" rid="B51">Neuh&#xe4;user et&#xa0;al., 2009</xref>). Thus, these three plant AMT2 homologues exhibit pH-dependent activity, being less active in acidic extracellular environments and displaying similar biochemical properties for NH<sub>4</sub>
<sup>+</sup> uptake and possible cotransport of NH<sub>3</sub>/H<sup>+</sup> through the protein lumen (<xref ref-type="bibr" rid="B51">Neuh&#xe4;user et&#xa0;al., 2009</xref>). Certainly, expression analysis in <italic>Xenopus</italic> oocyte cells would be needed to validate this hypothesis.</p>    <p>The function of ScAMT2;1 was further supported by ectopic expression in the Arabidopsis <italic>qko</italic> mutant. Arabidopsis <italic>qko</italic> lines overexpressing <italic>ScAMT2;1</italic> accumulated more biomass under NH<sub>4</sub>
<sup>+</sup> nutrition as the only N source (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4</bold>
</xref>). Short-term influx analysis in <italic>qko</italic> complemented lines expressing <italic>ScAMT2;1</italic> allowed us to estimate a K<sub>m</sub> equal to 90.17 &#xb5;M and a V<sub>max</sub> of 338.99 &#xb5;mol h<sup>-1</sup> g<sup>-1</sup> root DW, suggesting that ScAMT2;1 contributes to high-affinity ammonium transport <italic>in planta</italic>. The estimated K<sub>m</sub> value of ScAMT2;1 is higher than those determined for AtAMT1;1 and AtAMT2;1 <italic>via</italic> <sup>13</sup>N-ammonium in yeast (22 and 21 &#xb5;M at pH 6.1, respectively) (<xref ref-type="bibr" rid="B63">Sohlenkamp et&#xa0;al., 2002</xref>). However, despite the similar K<sub>m</sub> values, the ammonium transport capacity of AtAMT2;1 was at least 10 times lower than that of AtAMT1;1 at a pH of 5.0 and 6.1. Nevertheless, at a pH of 7.5, the transport capacity of the two transporters appeared to be similar (<xref ref-type="bibr" rid="B63">Sohlenkamp et&#xa0;al., 2002</xref>).</p>
<p>Initial evidence for the possible function of ScAMT2;1 was obtained by heterologous expression of <italic>ScAMT2;1</italic> in Arabidopsis driven by one of its endogenous promoters (p2<italic>ScAMT2;1</italic>). Expression of p2<italic>ScAMT2;1::ScAMT2;1</italic> complemented the growth of <italic>qko</italic> plants under ammonium supply and significantly increased net ammonium influx only at high external N concentrations (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6</bold>
</xref>). These results and the localization of p2<italic>ScAMT2;1</italic> promoter activity (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5</bold>
</xref>) suggest that ScAMT2;1 mediates ammonium import from the apoplast, which is in agreement with previous studies with AtAMT2;1 (<xref ref-type="bibr" rid="B63">Sohlenkamp et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B79">Yuan et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B51">Neuh&#xe4;user et&#xa0;al., 2009</xref>). In Arabidopsis roots, AtAMT2;1 contributes to 10%&#x2013;25% of the overall ammonium uptake rate at high external ammonium concentrations, whereas under N deficiency, AtAMT2;1 activity occurs in outer cell layers and supports root ammonium uptake capacity in the millimolar concentration range (<xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>).</p>    <p>Based on the localization of p2<italic>ScAMT2;1</italic> promoter activity, we hypothesized that ScAMT2;1 might be involved in root-to-shoot NH<sub>4</sub>
<sup>+</sup> translocation. Our findings indicated a contribution of ScAMT2;1 to shoot ammonium translocation only in fully ammonium- or nitrate-supplied plants (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7</bold>
</xref>). The increased root-to-shoot NH<sub>4</sub>
<sup>+</sup> translocation may have resulted from an increased ScAMT2;1-facilitated radial transport of ammonium towards the root vascular tissue, altering N partitioning between roots and shoots and impacting the N nutrition of the shoot. Although glutamine is the predominant organic N form translocated in the xylem of ammonium-supplied oilseed rape (<xref ref-type="bibr" rid="B14">Finnemann and Schjoerring, 1999</xref>) and <italic>A. thaliana</italic> plants (<xref ref-type="bibr" rid="B33">Lam et&#xa0;al., 1995</xref>), ammonium can represent 11% of the total N translocated in the xylem sap, reaching up to 18 mM in Arabidopsis vasculature (<xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>). Hence, increased root-to-shoot translocation of ammonium provides a stable supply of N to the shoots in response to high N availability. In Arabidopsis, a concerted function of AtAMT2;1 and GLN1;2 in roots is proposed to determine ammonium translocation and assimilation in response to high N supply (<xref ref-type="bibr" rid="B18">Giehl et&#xa0;al., 2017</xref>). Likewise, our results showing ScAMT2;1 activity in the innermost root cell suggest that this protein might also provide ammonium for the N assimilation pathway in sugarcane roots upon high ammonium supply. While GS1 activity has not been linked to yield gain or improved NUE in sugarcane genotypes (<xref ref-type="bibr" rid="B56">Robinson et&#xa0;al., 2007</xref>), ammonium is preferentially acquired by sugarcane roots (<xref ref-type="bibr" rid="B55">Robinson et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B38">Lima et&#xa0;al., 2022</xref>). Therefore, the critical role of ammonium translocation to shoots in response to plant nutritional status might significantly impact vegetative biomass in sugarcane plants. The mechanisms involved in root-to-shoot N transport, recycling, and remobilization are paramount for improving plant performance and NUE and can certainly decrease the need for fertilizers and strengthen sustainable sugarcane crop production. Our preliminary findings suggest that ScAMT2;1 might contribute to ammonium uptake in sugarcane roots in response to high external N availability in addition to presumably contributing to root-to-shoot ammonium translocation by facilitating its radial transport towards the vascular system, which may finally contribute to enhanced shoot growth under abundant N supply.</p>
<p>We conclude that ScAMT2;1 is a functional ammonium transporter as it was able to complement the defective Arabidopsis mutant and partially complement yeast. Estimation of K<sub>m</sub> and V<sub>max</sub> indicated ScAMT2;1 to be a high-affinity ammonium transporter. In sugarcane, <italic>ScAMT2;1</italic> is expressed in different organs, with the highest expression in roots induced by external nitrate (possibly lack of ammonium). When expressed in <italic>A. thaliana</italic>, <italic>ScAMT2;1</italic> promoter activity can be detected in the innermost cell layers of roots and the vasculature of leaves, and it can increase ammonium translocation from root to shoot. Our findings suggest that ScAMT2;1 might contribute to ammonium uptake in sugarcane roots in response to high external N availability and to probably contribute to root-to-shoot ammonium translocation by facilitating its radial transport towards the vascular system.</p>
</sec>
<sec id="s5" sec-type="data-availability">
<title>Data availability statement</title>
<p>The original contributions presented in the study are included in the article/<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Material</bold>
</xref>. Further inquiries can be directed to the corresponding authors.</p>
</sec>
<sec id="s6" sec-type="author-contributions">
<title>Author contributions</title>
<p>AF and JL designed the research project. AK and RM performed experiments. JL, RM, and AK analyzed and interpreted the data. AK, RM, and NS performed bioinformatic analysis. NS helped to analyze/interpret the genomic data from BAC clones. MV contributed with analyses and protocols. AK and JL wrote the manuscript. RG critically reviewed the manuscript and helped with data interpretation. AF and JL supervised the project and experiments. All authors contributed to the article and approved the submitted version.</p>
</sec>
<sec id="s7" sec-type="funding-information">
<title>Funding</title>
<p>This work was supported by FAPESP (The Sao Paulo Research Foundation) through Regular Research Grants (16/14669-8; 2013/15989-8), and fellowships to JL (2010/11313-1), and RM (2017/00460-2). Additional support came from CNPq (Brazilian National Council for Scientific and Technological Development) and CAPES (Coordination for the Improvement of Higher Education Personnel). AF is a recipient of a CNPq research fellowship (310645/2021-2).</p>
</sec>
<sec id="s8" sec-type="acknowledgement">
<title>Acknowledgments</title>
<p>Seeds of <italic>qko</italic> were gently provided by Prof. Dr. Nicolaus von Wir&#xe9;n from the Leibniz Institute of Plant Genetics and Crop Plant Research.</p>
</sec>
<sec id="s9" sec-type="COI-statement">
<title>Conflict of interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s10" sec-type="disclaimer">
<title>Publisher&#x2019;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
</body>
<back>
<sec id="s11" sec-type="supplementary-material">
<title>Supplementary material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fpls.2022.1039041/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fpls.2022.1039041/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="DataSheet_1.docx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document"/>
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