Publications by authors named "Felix Hauser"

25 Publications

  • Page 1 of 1

The SLIM1 transcription factor is required for arsenic resistance in Arabidopsis thaliana.

FEBS Lett 2021 06 19;595(12):1696-1707. Epub 2021 May 19.

Division of Biological Sciences, Cell and Developmental Biology Section, University of California, La Jolla, CA, USA.

The transcriptional regulators of arsenic-induced gene expression remain largely unknown. Sulfur assimilation is tightly linked with arsenic detoxification. Here, we report that mutant alleles in the SLIM1 transcription factor are substantially more sensitive to arsenic than cadmium. Arsenic treatment caused high levels of oxidative stress in the slim1 mutants, and slim1 alleles were impaired in both thiol accumulation and sulfate accumulation. We further found enhanced arsenic accumulation in roots of slim1 mutants. Transcriptome analyses indicate an important role for SLIM1 in arsenic-induced tolerance mechanisms. The present study identifies the SLIM1 transcription factor as an essential component in arsenic tolerance and arsenic-induced gene expression. Our results suggest that the severe arsenic sensitivity of the slim1 mutants is caused by altered redox status.
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http://dx.doi.org/10.1002/1873-3468.14096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8238853PMC
June 2021

An amiRNA screen uncovers redundant CBF and ERF34/35 transcription factors that differentially regulate arsenite and cadmium responses.

Plant Cell Environ 2021 May 25;44(5):1692-1706. Epub 2021 Feb 25.

Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, California, USA.

Arsenic stress causes rapid transcriptional responses in plants. However, transcriptional regulators of arsenic-induced gene expression in plants remain less well known. To date, forward genetic screens have proven limited for dissecting arsenic response mechanisms. We hypothesized that this may be due to the extensive genetic redundancy present in plant genomes. To overcome this limitation, we pursued a forward genetic screen for arsenite tolerance using a randomized library of plants expressing >2,000 artificial microRNAs (amiRNAs). This library was designed to knock-down diverse combinations of homologous gene family members within sub-clades of transcription factor and transporter gene families. We identified six transformant lines showing an altered response to arsenite in root growth assays. Further characterization of an amiRNA line targeting closely homologous CBF and ERF transcription factors show that the CBF1,2 and 3 transcription factors negatively regulate arsenite sensitivity. Furthermore, the ERF34 and ERF35 transcription factors are required for cadmium resistance. Generation of CRISPR lines, higher-order T-DNA mutants and gene expression analyses, further support our findings. These ERF transcription factors differentially regulate arsenite sensitivity and cadmium tolerance.
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http://dx.doi.org/10.1111/pce.14023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068611PMC
May 2021

MAP3Kinase-dependent SnRK2-kinase activation is required for abscisic acid signal transduction and rapid osmotic stress response.

Nat Commun 2020 01 2;11(1):12. Epub 2020 Jan 2.

Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, 92093, USA.

Abiotic stresses, including drought and salinity, trigger a complex osmotic-stress and abscisic acid (ABA) signal transduction network. The core ABA signalling components are snf1-related protein kinase2s (SnRK2s), which are activated by ABA-triggered inhibition of type-2C protein-phosphatases (PP2Cs). SnRK2 kinases are also activated by a rapid, largely unknown, ABA-independent osmotic-stress signalling pathway. Here, through a combination of a redundancy-circumventing genetic screen and biochemical analyses, we have identified functionally-redundant MAPKK-kinases (M3Ks) that are necessary for activation of SnRK2 kinases. These M3Ks phosphorylate a specific SnRK2/OST1 site, which is indispensable for ABA-induced reactivation of PP2C-dephosphorylated SnRK2 kinases. ABA-triggered SnRK2 activation, transcription factor phosphorylation and SLAC1 activation require these M3Ks in vitro and in plants. M3K triple knock-out plants show reduced ABA sensitivity and strongly impaired rapid osmotic-stress-induced SnRK2 activation. These findings demonstrate that this M3K clade is required for ABA- and osmotic-stress-activation of SnRK2 kinases, enabling robust ABA and osmotic stress signal transduction.
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http://dx.doi.org/10.1038/s41467-019-13875-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6940395PMC
January 2020

Insights into the Molecular Mechanisms of CO-Mediated Regulation of Stomatal Movements.

Curr Biol 2018 12;28(23):R1356-R1363

Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093, USA. Electronic address:

Plants must continually balance the influx of CO for photosynthesis against the loss of water vapor through stomatal pores in their leaves. This balance can be achieved by controlling the aperture of the stomatal pores in response to several environmental stimuli. Elevation in atmospheric [CO] induces stomatal closure and further impacts leaf temperatures, plant growth and water-use efficiency, and global crop productivity. Here, we review recent advances in understanding CO-perception mechanisms and CO-mediated signal transduction in the regulation of stomatal movements, and we explore how these mechanisms are integrated with other signaling pathways in guard cells.
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http://dx.doi.org/10.1016/j.cub.2018.10.015DOI Listing
December 2018

A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses.

J Exp Bot 2019 01;70(2):641-651

Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA.

The identification of homologous genes with functional overlap in forward genetic screens is severely limited. Here, we report the generation of over 14000 artificial microRNA (amiRNA)-expressing plants that enable screens of the functionally redundant gene space in Arabidopsis. A protocol was developed for isolating robust and reproducible amiRNA mutants. Examples of validation approaches and essential controls are presented for two new amiRNA mutants that exhibit genetically redundant phenotypes and circumvent double mutant lethality. In a forward genetic screen for abscisic acid (ABA)-mediated inhibition of seed germination, amiRNAs that target combinations of known redundant ABA receptor and SnRK2 kinase genes were rapidly isolated, providing a strong proof of principle for this approach. A new ABA-insensitive amiRNA line that targets three avirulence-induced gene 2(-like) genes was isolated . A thermal imaging screen for plants with impaired stomatal opening in response to low CO2 exposure led to the isolation of a new amiRNA targeting two essential proteasomal subunits, PAB1 and PAB2. The seed library of 11000 T2 amiRNA lines (with 3000 lines in progress) generated here provides a new platform for forward genetic screens and has been made available to the Arabidopsis Biological Resource Center (ABRC). Optimized procedures for amiRNA screening and controls are described.
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http://dx.doi.org/10.1093/jxb/ery363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322574PMC
January 2019

A transportome-scale amiRNA-based screen identifies redundant roles of Arabidopsis ABCB6 and ABCB20 in auxin transport.

Nat Commun 2018 10 11;9(1):4204. Epub 2018 Oct 11.

School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 69978, Israel.

Transport of signaling molecules is of major importance for regulating plant growth, development, and responses to the environment. A prime example is the spatial-distribution of auxin, which is regulated via transporters to govern developmental patterning. A critical limitation in our ability to identify transporters by forward genetic screens is their potential functional redundancy. Here, we overcome part of this functional redundancy via a transportome, multi-targeted forward-genetic screen using artificial-microRNAs (amiRNAs). We generate a library of 3000 plant lines expressing 1777 amiRNAs, designed to target closely homologous genes within subclades of transporter families and identify, genotype and quantitatively phenotype, 80 lines showing reproducible shoot growth phenotypes. Within this population, we discover and characterize a strong redundant role for the unstudied ABCB6 and ABCB20 genes in auxin transport and response. The unique multi-targeted lines generated in this study could serve as a genetic resource that is expected to reveal additional transporters.
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http://dx.doi.org/10.1038/s41467-018-06410-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182007PMC
October 2018

Identification of SLAC1 anion channel residues required for CO/bicarbonate sensing and regulation of stomatal movements.

Proc Natl Acad Sci U S A 2018 10 9;115(44):11129-11137. Epub 2018 Oct 9.

Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116;

Increases in CO concentration in plant leaves due to respiration in the dark and the continuing atmospheric [CO] rise cause closing of stomatal pores, thus affecting plant-water relations globally. However, the underlying CO/bicarbonate (CO/HCO ) sensing mechanisms remain unknown. [CO] elevation in leaves triggers stomatal closure by anion efflux mediated via the SLAC1 anion channel localized in the plasma membrane of guard cells. Previous reconstitution analysis has suggested that intracellular bicarbonate ions might directly up-regulate SLAC1 channel activity. However, whether such a CO/HCO regulation of SLAC1 is relevant for CO control of stomatal movements in planta remains unknown. Here, we computationally probe for candidate bicarbonate-interacting sites within the SLAC1 anion channel via long-timescale Gaussian accelerated molecular dynamics (GaMD) simulations. Mutations of two putative bicarbonate-interacting residues, R256 and R321, impaired the enhancement of the SLAC1 anion channel activity by CO/HCO in oocytes. Mutations of the neighboring charged amino acid K255 and residue R432 and the predicted gate residue F450 did not affect HCO regulation of SLAC1. Notably, gas-exchange experiments with -transformed plants expressing mutated SLAC1 proteins revealed that the SLAC1 residue R256 is required for CO regulation of stomatal movements in planta, but not for abscisic acid (ABA)-induced stomatal closing. Patch clamp analyses of guard cells show that activation of S-type anion channels by CO/HCO , but not by ABA, was impaired, indicating the relevance of R256 for CO signal transduction. Together, these analyses suggest that the SLAC1 anion channel is one of the physiologically relevant CO/HCO sensors in guard cells.
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http://dx.doi.org/10.1073/pnas.1807624115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6217375PMC
October 2018

SnapShot: Abscisic Acid Signaling.

Cell 2017 Dec;171(7):1708-1708.e0

Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA.

Abscisic acid is a key phytohormone produced in response to abiotic stress conditions and is an activator of abiotic stress resistance mechanisms and a regulator during diverse developmental stages in plants. This SnapShot explores how ABA signaling operates and coordinates resistance during stress responses and modulates plant development.
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http://dx.doi.org/10.1016/j.cell.2017.11.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895850PMC
December 2017

Molecular and systems approaches towards drought-tolerant canola crops.

New Phytol 2016 06 16;210(4):1169-89. Epub 2016 Feb 16.

Biology Department, Pennsylvania State University, University Park, PA, 16802, USA.

1169 I. 1170 II. 1170 III. 1172 IV. 1176 V. 1181 VI. 1182 1183 References 1183 SUMMARY: Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.
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http://dx.doi.org/10.1111/nph.13866DOI Listing
June 2016

Mechanisms of abscisic acid-mediated control of stomatal aperture.

Curr Opin Plant Biol 2015 Dec 19;28:154-62. Epub 2015 Nov 19.

Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, USA. Electronic address:

Drought stress triggers an increase in the level of the plant hormone abscisic acid (ABA), which initiates a signaling cascade to close stomata and reduce water loss. Recent studies have revealed that guard cells control cytosolic ABA concentration through the concerted actions of biosynthesis, catabolism as well as transport across membranes. Substantial progress has been made at understanding the molecular mechanisms of how the ABA signaling core module controls the activity of anion channels and thereby stomatal aperture. In this review, we focus on our current mechanistic understanding of ABA signaling in guard cells including the role of the second messenger Ca(2+) as well as crosstalk with biotic stress responses.
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http://dx.doi.org/10.1016/j.pbi.2015.10.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679528PMC
December 2015

HKT transporters mediate salt stress resistance in plants: from structure and function to the field.

Curr Opin Biotechnol 2015 Apr 18;32:113-120. Epub 2014 Dec 18.

Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan. Electronic address:

Plant cells are sensitive to salinity stress and do not require sodium as an essential element for their growth and development. Saline soils reduce crop yields and limit available land. Research shows that HKT transporters provide a potent mechanism for mediating salt tolerance in plants. Knowledge of the molecular ion transport and regulation mechanisms and the control of HKT gene expression are crucial for understanding the mechanisms by which HKT transporters enhance crop performance under salinity stress. This review focuses on HKT transporters in monocot plants and in Arabidopsis as a dicot plant, as a guide to efforts toward improving salt tolerance of plants for increasing the production of crops and bioenergy feedstocks.
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http://dx.doi.org/10.1016/j.copbio.2014.11.025DOI Listing
April 2015

A genomic-scale artificial microRNA library as a tool to investigate the functionally redundant gene space in Arabidopsis.

Plant Cell 2013 Aug 16;25(8):2848-63. Epub 2013 Aug 16.

Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California 92093-0116.

Traditional forward genetic screens are limited in the identification of homologous genes with overlapping functions. Here, we report the analyses and assembly of genome-wide protein family definitions that comprise the largest estimate for the potentially redundant gene space in Arabidopsis thaliana. On this basis, a computational design of genome-wide family-specific artificial microRNAs (amiRNAs) was performed using high-performance computing resources. The amiRNA designs are searchable online (http://phantomdb.ucsd.edu). A computationally derived library of 22,000 amiRNAs was synthesized in 10 sublibraries of 1505 to 4082 amiRNAs, each targeting defined functional protein classes. For example, 2964 amiRNAs target annotated DNA and RNA binding protein families and 1777 target transporter proteins, and another sublibrary targets proteins of unknown function. To evaluate the potential of an amiRNA-based screen, we tested 122 amiRNAs targeting transcription factor, protein kinase, and protein phosphatase families. Several amiRNA lines showed morphological phenotypes, either comparable to known phenotypes of single and double/triple mutants or caused by overexpression of microRNAs. Moreover, novel morphological and abscisic acid-insensitive seed germination mutants were identified for amiRNAs targeting zinc finger homeodomain transcription factors and mitogen-activated protein kinase kinase kinases, respectively. These resources provide an approach for genome-wide genetic screens of the functionally redundant gene space in Arabidopsis.
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http://dx.doi.org/10.1105/tpc.113.112805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784584PMC
August 2013

Natural variation in small molecule-induced TIR-NB-LRR signaling induces root growth arrest via EDS1- and PAD4-complexed R protein VICTR in Arabidopsis.

Plant Cell 2012 Dec 28;24(12):5177-92. Epub 2012 Dec 28.

Division of Biological Sciences, Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093-0116, USA.

In a chemical genetics screen we identified the small-molecule [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione (DFPM) that triggers rapid inhibition of early abscisic acid signal transduction via PHYTOALEXIN DEFICIENT4 (PAD4)- and ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)-dependent immune signaling mechanisms. However, mechanisms upstream of EDS1 and PAD4 in DFPM-mediated signaling remain unknown. Here, we report that DFPM generates an Arabidopsis thaliana accession-specific root growth arrest in Columbia-0 (Col-0) plants. The genetic locus responsible for this natural variant, VICTR (VARIATION IN COMPOUND TRIGGERED ROOT growth response), encodes a TIR-NB-LRR (for Toll-Interleukin1 Receptor-nucleotide binding-Leucine-rich repeat) protein. Analyses of T-DNA insertion victr alleles showed that VICTR is necessary for DFPM-induced root growth arrest and inhibition of abscisic acid-induced stomatal closing. Transgenic expression of the Col-0 VICTR allele in DFPM-insensitive Arabidopsis accessions recapitulated the DFPM-induced root growth arrest. EDS1 and PAD4, both central regulators of basal resistance and effector-triggered immunity, as well as HSP90 chaperones and their cochaperones RAR1 and SGT1B, are required for the DFPM-induced root growth arrest. Salicylic acid and jasmonic acid signaling pathway components are dispensable. We further demonstrate that VICTR associates with EDS1 and PAD4 in a nuclear protein complex. These findings show a previously unexplored association between a TIR-NB-LRR protein and PAD4 and identify functions of plant immune signaling components in the regulation of root meristematic zone-targeted growth arrest.
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http://dx.doi.org/10.1105/tpc.112.107235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556982PMC
December 2012

Long-distance transport, vacuolar sequestration, tolerance, and transcriptional responses induced by cadmium and arsenic.

Curr Opin Plant Biol 2011 Oct 5;14(5):554-62. Epub 2011 Aug 5.

Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, La Jolla, CA 92093-0116, USA.

Iron, zinc, copper and manganese are essential metals for cellular enzyme functions while cadmium, mercury and the metalloid arsenic lack any biological function. Both, essential metals, at high concentrations, and non-essential metals and metalloids are extremely reactive and toxic. Therefore, plants have acquired specialized mechanisms to sense, transport and maintain essential metals within physiological concentrations and to detoxify non-essential metals and metalloids. This review focuses on the recent identification of transporters that sequester cadmium and arsenic in vacuoles and the mechanisms mediating the partitioning of these metal(loid)s between roots and shoots. We further discuss recent models of phloem-mediated long-distance transport, seed accumulation of Cd and As and recent data demonstrating that plants posses a defined transcriptional response that allow plants to preserve metal homeostasis. This research is instrumental for future engineering of reduced toxic metal(loid) accumulation in edible crop tissues as well as for improved phytoremediation technologies.
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http://dx.doi.org/10.1016/j.pbi.2011.07.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191310PMC
October 2011

Chemical genetics reveals negative regulation of abscisic acid signaling by a plant immune response pathway.

Curr Biol 2011 Jun 27;21(11):990-7. Epub 2011 May 27.

Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116, USA.

Coordinated regulation of protection mechanisms against environmental abiotic stress and pathogen attack is essential for plant adaptation and survival. Initial abiotic stress can interfere with disease-resistance signaling [1-6]. Conversely, initial plant immune signaling may interrupt subsequent abscisic acid (ABA) signal transduction [7, 8]. However, the processes involved in this crosstalk between these signaling networks have not been determined. By screening a 9600-compound chemical library, we identified a small molecule [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione (DFPM) that rapidly downregulates ABA-dependent gene expression and also inhibits ABA-induced stomatal closure. Transcriptome analyses show that DFPM also stimulates expression of plant defense-related genes. Major early regulators of pathogen-resistance responses, including EDS1, PAD4, RAR1, and SGT1b, are required for DFPM-and notably also for Pseudomonas-interference with ABA signal transduction, whereas salicylic acid, EDS16, and NPR1 are not necessary. Although DFPM does not interfere with early ABA perception by PYR/RCAR receptors or ABA activation of SnRK2 kinases, it disrupts cytosolic Ca(2+) signaling and downstream anion channel activation in a PAD4-dependent manner. Our findings provide evidence that activation of EDS1/PAD4-dependent plant immune responses rapidly disrupts ABA signal transduction and that this occurs at the level of Ca(2+) signaling, illuminating how the initial biotic stress pathway interferes with ABA signaling.
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http://dx.doi.org/10.1016/j.cub.2011.04.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109272PMC
June 2011

Evolution of abscisic acid synthesis and signaling mechanisms.

Curr Biol 2011 May;21(9):R346-55

Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093-0116, USA.

The plant hormone abscisic acid (ABA) mediates seed dormancy, controls seedling development and triggers tolerance to abiotic stresses, including drought. Core ABA signaling components consist of a recently identified group of ABA receptor proteins of the PYRABACTIN RESISTANCE (PYR)/REGULATORY COMPONENT OF ABA RECEPTOR (RCAR) family that act as negative regulators of members of the PROTEIN PHOSPHATASE 2C (PP2C) family. Inhibition of PP2C activity enables activation of SNF1-RELATED KINASE 2 (SnRK2) protein kinases, which target downstream components, including transcription factors, ion channels and NADPH oxidases. These and other components form a complex ABA signaling network. Here, an in depth analysis of the evolution of components in this ABA signaling network shows that (i) PYR/RCAR ABA receptor and ABF-type transcription factor families arose during land colonization of plants and are not found in algae and other species, (ii) ABA biosynthesis enzymes have evolved to plant- and fungal-specific forms, leading to different ABA synthesis pathways, (iii) existing stress signaling components, including PP2C phosphatases and SnRK kinases, were adapted for novel roles in this plant-specific network to respond to water limitation. In addition, evolutionarily conserved secondary structures in the PYR/RCAR ABA receptor family are visualized.
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http://dx.doi.org/10.1016/j.cub.2011.03.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119208PMC
May 2011

A conserved primary salt tolerance mechanism mediated by HKT transporters: a mechanism for sodium exclusion and maintenance of high K(+)/Na(+) ratio in leaves during salinity stress.

Plant Cell Environ 2010 Apr 4;33(4):552-65. Epub 2009 Nov 4.

Center for Molecular Genetics, University of California, San Diego, La Jolla, 92093-0116, USA.

Increasing soil salinity is a serious threat to agricultural productions worldwide in the 21st century. Several essential Na(+) transporters such as AtNHX1 and AtSOS1 function in Na(+) tolerance under salinity stress in plants. Recently, evidence for a new primary salt tolerance mechanism has been reported, which is mediated by a class of HKT transporters both in dicots such as Arabidopsis and monocot crops such as rice and wheat. Here we present a review on vital physiological functions of HKT transporters including AtHKT1;1 and OsHKT1;5 in preventing shoot Na(+) over-accumulation by mediating Na(+) exclusion from xylem vessels in the presence of a large amount of Na(+) thereby protecting leaves from salinity stress. Findings of the HKT2 transporter sub-family are also updated in this review. Subjects regarding function and regulation of HKT transporters, which need to be elucidated in future research, are discussed.
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http://dx.doi.org/10.1111/j.1365-3040.2009.02056.xDOI Listing
April 2010

HKT transporter-mediated salinity resistance mechanisms in Arabidopsis and monocot crop plants.

Trends Plant Sci 2009 Dec 25;14(12):660-8. Epub 2009 Sep 25.

Group of Molecular and Functional Plant Biology, Research Institute for Bioresources, Okayama University, Kurashiki, Okayama 710-0046, Japan.

The salinization of irrigated lands is increasingly detrimental to plant biomass production and agricultural productivity, as most plant species are sensitive to high concentrations of sodium (Na(+)), which causes combined Na(+) toxicity and osmotic stress. Plants have multiple Na(+)-transport systems to circumvent Na(+) toxicity. Essential physiological functions of major Na(+) transporters and their mechanisms mediating salinity resistance have been identified in Arabidopsis , including the AtSOS1, AtNHX and AtHKT1;1 transporters. As we discuss here, recent studies have demonstrated that a class of xylem-parenchyma-expressed Na(+)-permeable plant HKT transporters represent a primary mechanism mediating salt tolerance and Na(+) exclusion from leaves in Arabidopsis, and that major salt-tolerance quantitative trait loci in monocot crop plants are also based on this HKT-mediated mechanism.
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http://dx.doi.org/10.1016/j.tplants.2009.08.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2787891PMC
December 2009

Comprehensive assessment of the regulons controlled by the FixLJ-FixK2-FixK1 cascade in Bradyrhizobium japonicum.

J Bacteriol 2008 Oct 8;190(20):6568-79. Epub 2008 Aug 8.

Institute of Microbiology, ETH, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland.

Symbiotic N(2) fixation in Bradyrhizobium japonicum is controlled by a complex transcription factor network. Part of it is a hierarchically arranged cascade in which the two-component regulatory system FixLJ, in response to a moderate decrease in oxygen concentration, activates the fixK(2) gene. The FixK(2) protein then activates not only a number of genes essential for microoxic respiration in symbiosis (fixNOQP and fixGHIS) but also further regulatory genes (rpoN(1), nnrR, and fixK(1)). The results of transcriptome analyses described here have led to a comprehensive and expanded definition of the FixJ, FixK(2), and FixK(1) regulons, which, respectively, consist of 26, 204, and 29 genes specifically regulated in microoxically grown cells. Most of these genes are subject to positive control. Particular attention was addressed to the FixK(2)-dependent genes, which included a bioinformatics search for putative FixK(2) binding sites on DNA (FixK(2) boxes). Using an in vitro transcription assay with RNA polymerase holoenzyme and purified FixK(2) as the activator, we validated as direct targets eight new genes. Interestingly, the adjacent but divergently oriented fixK(1) and cycS genes shared the same FixK(2) box for the activation of transcription in both directions. This recognition site may also be a direct target for the FixK(1) protein, because activation of the cycS promoter required an intact fixK(1) gene and either microoxic or anoxic, denitrifying conditions. We present evidence that cycS codes for a c-type cytochrome which is important, but not essential, for nitrate respiration. Two other, unexpected results emerged from this study: (i) specifically FixK(1) seemed to exert a negative control on genes that are normally activated by the N(2) fixation-specific transcription factor NifA, and (ii) a larger number of genes are expressed in a FixK(2)-dependent manner in endosymbiotic bacteroids than in culture-grown cells, pointing to a possible symbiosis-specific control.
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http://dx.doi.org/10.1128/JB.00748-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566219PMC
October 2008

The genistein stimulon of Bradyrhizobium japonicum.

Mol Genet Genomics 2008 Mar 24;279(3):203-11. Epub 2008 Jan 24.

Institute of Genetics, Dresden University of Technology, Helmholtzstrasse 10, 01069, Dresden, Germany.

An initializing step in the rhizobia-legume symbiosis is the secretion of flavonoids by plants that leads to the expression of nodulation genes in rhizobia. Here we report the genome-wide transcriptional response of Bradyrhizobium japonicum to genistein, an isoflavone secreted by soybean. About 100 genes were induced in the wild type. This included all nod box-associated genes, the flagellar cluster and several genes that are likely to be involved in transport processes. To elucidate the role of known regulators, we analysed mutant strains. This revealed that the two-component response regulator NodW is essential for induction of almost all genistein-inducible genes, with the exception of 8 genes. The phenotype of the nodW mutant could be partially suppressed by overexpression of NwsB, which is also a two-component response regulator. These data indicate that genistein has a much broader function than mere induction of nod genes.
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http://dx.doi.org/10.1007/s00438-007-0280-7DOI Listing
March 2008

Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules.

Mol Plant Microbe Interact 2007 Nov;20(11):1353-63

Institute of Microbiology, Eidgenössische Technische Hochschule, CH-8093 Zürich, Switzerland.

The transcriptome of endosymbiotic Bradyrhizobium japonicum bacteroids was assessed, using RNA extracted from determinate soybean root nodules. Results were compared with the transcript profiles of B. japonicum cells grown in either aerobic or microaerobic culture. Microoxia is a known trigger for the induction of symbiotically relevant genes. In fact, one third of the genes induced in bacteroids at day 21 after inoculation are congruent with those up-regulated in culture by a decreased oxygen concentration. The other induced genes, however, may be regulated by cues other than oxygen limitation. Both groups of genes provide a rich source for the possible discovery of novel functions related to symbiosis. Samples taken at different timepoints in nodule development have led to the distinction of genes expressed early and late in bacteroids. The experimental approach applied here is also useful for B. japonicum mutant analyses. As an example, we compared the transcriptome of wild-type bacteroids with that of bacteroids formed by a mutant defective in the RNA polymerase transcription factor sigma54. This led to a collection of hitherto unrecognized B. japonicum genes potentially transcribed in planta in a sigma54-dependent manner.
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http://dx.doi.org/10.1094/MPMI-20-11-1353DOI Listing
November 2007

New target genes controlled by the Bradyrhizobium japonicum two-component regulatory system RegSR.

J Bacteriol 2007 Dec 19;189(24):8928-43. Epub 2007 Oct 19.

Institute of Microbiology, Eidgenössische Technische Hochschule, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland.

RegSR-like proteins, members of the family of two-component regulatory systems, are present in a large number of proteobacteria in which they globally control gene expression mostly in a redox-responsive manner. The controlled target genes feature an enormous functional diversity. In Bradyrhizobium japonicum, the facultative root nodule symbiont of soybean, RegSR activate the transcription of the nitrogen fixation regulatory gene nifA, thus forming a RegSR-NifA cascade which is part of a complex regulatory network for gene regulation in response to changing oxygen concentrations. Whole-genome transcription profiling was performed here in order to assess the full regulatory scope of RegSR. The comparative analysis of wild-type and delta regR cells grown under oxic and microoxic conditions revealed that expression of almost 250 genes is dependent on RegR, a result that underscores the important contribution of RegR to oxygen- or redox-regulated gene expression in B. japonicum. Furthermore, transcription profiling of delta regR bacteroids compared with wild-type bacteroids revealed expression changes for about 1,200 genes in young and mature bacteroids. Incidentally, many of these were found to be induced in symbiosis when wild-type bacteroids were compared with free-living, culture-grown wild-type cells, and they appeared to encode diverse functions possibly related to symbiosis and nitrogen fixation. We demonstrated direct RegR-mediated control at promoter regions of several selected target genes by means of DNA binding experiments and in vitro transcription assays, which revealed six novel direct RegR target promoters.
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http://dx.doi.org/10.1128/JB.01088-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168637PMC
December 2007

Dissection of the Bradyrhizobium japonicum NifA+sigma54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation.

Mol Genet Genomics 2007 Sep 15;278(3):255-71. Epub 2007 Jun 15.

Institute of Microbiology, Eidgenössische Technische Hochschule, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland.

Hierarchically organized regulatory proteins form a complex network for expression control of symbiotic and accessory genes in the nitrogen-fixing soybean symbiont Bradyrhizobium japonicum. A genome-wide survey of regulatory interactions was made possible with the design of a custom-made gene chip. Here, we report the first use of the microarray in a comprehensive and complete characterization of the B. japonicum NifA+sigma(54) regulon which forms an important node in the entire network. Comparative transcript profiles of anaerobically grown wild-type, nifA, and rpoN (1/2) mutant cells were complemented with a position-specific frequency matrix-based search for NifA- and sigma(54)-binding sites plus a simple operon definition. One of the newly identified NifA+sigma(54)-dependent genes, fdxN, encodes a ferredoxin required for efficient symbiotic nitrogen fixation, which makes it a candidate for being a direct electron donor to nitrogenase. The fdxN gene has an unconventional, albeit functional sigma(54 )promoter with the dinucleotide GA instead of the consensus GC motif at position -12. A GC-containing mutant promoter and the atypical GA-containing promoter of the wild type were disparately activated. Expression analyses were also carried out with two other NifA+sigma(54) targets (ectC; ahpC). Incidentally, the tiling-like design of the microarray has helped to arrive at completely revised annotations of the ectC- and ahpC-upstream DNA regions, which are now compatible with promoter locations. Taken together, the approaches used here led to a substantial expansion of the NifA+sigma(54 )regulon size, culminating in a total of 65 genes for nitrogen fixation and diverse other processes.
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http://dx.doi.org/10.1007/s00438-007-0246-9DOI Listing
September 2007

Bradyrhizobium japonicum senses iron through the status of haem to regulate iron homeostasis and metabolism.

Mol Microbiol 2006 Apr;60(2):427-37

Department of Biochemistry, 140 Farber Hall, State University of New York at Buffalo, Buffalo, New York 14214, USA.

The Irr protein from the bacterium Bradyrhizobium japonicum is expressed under iron limitation to mediate iron control of haem biosynthesis. The regulatory input to Irr is the status of haem and its precursors iron and protoporphyrin at the site of haem synthesis. Here, we show that Irr controls the expression of iron transport genes and many other iron-regulated genes not directly involved in haem synthesis. Irr is both a positive and negative effector of gene expression, and in at least some cases the control is direct. Loss of normal iron responsiveness of those genes in an irr mutant, as well as a lower total cellular iron content, suggests that Irr is required for the correct perception of the cellular iron status. Degradation of Irr in iron replete cells requires haem. Accordingly, control of Irr-regulated genes by iron was aberrant in a haem-defective strain, and iron replete mutant cells behave as if they are iron-limited. In addition, the haem mutant had an abnormally high cellular iron content. The findings indicate that B. japonicum senses iron via the status of haem biosynthesis in an Irr-dependent manner to regulate iron homeostasis and metabolism.
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http://dx.doi.org/10.1111/j.1365-2958.2006.05101.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1424673PMC
April 2006

The Iron control element, acting in positive and negative control of iron-regulated Bradyrhizobium japonicum genes, is a target for the Irr protein.

J Bacteriol 2006 Jan;188(2):733-44

Institute of Microbiology, Eidgenössische Technische Hochschule, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland.

Bradyrhizobium japonicum, the nitrogen-fixing soybean symbiont, possesses a heme uptake system encoded by the gene cluster hmuVUT-hmuR-exbBD-tonB. Transcription of the divergently oriented hmuT and hmuR genes was previously found to be induced by iron limitation and to depend on a 21-bp promoter-upstream iron control element (ICE). Here, we show by deletion analysis that the full-length ICE is needed for this type of positive control. Additional genes associated with ICE-like motifs were identified in the B. japonicum genome, of which bll6680 and blr7895 code for bacterioferritin and rubrerythrin homologs, respectively. Transcription start site mapping revealed that their ICEs directly overlap with either the -10 promoter region or the transcription initiation site, suggesting an involvement of the ICE in negative control of both genes. Consistent with this inference was the observed down-regulation of both genes under iron limitation, which in the case of bll6680 was shown to require an intact ICE motif. Using a yeast one-hybrid system, we demonstrated in vivo interaction of the iron response regulator (Irr) with all three ICEs. Moreover, specific in vitro binding of purified Irr protein to the ICE motifs of bll6680 and blr7895 was shown in electrophoretic mobility shift experiments. A genome-wide survey for iron-regulated genes with a custom-made Affymetrix gene chip revealed 17 genes to be induced and 68 to be repressed under iron-replete conditions. Remarkably, ICE-like motifs are associated with a large subset of those B. japonicum genes. We propose the ICE as an important cis-acting element in B. japonicum which represents the DNA-binding site for the Irr protein and, depending on its location within promoter regions, is involved in positive or negative control of the associated iron-regulated genes.
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http://dx.doi.org/10.1128/JB.188.2.733-744.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347296PMC
January 2006
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