Publications
List updated March. 2024
Carré C, Carluer JB, Chaux C, Estoup-Streiff C, Roche N, Hosy E, Mas A, Krouk G.
Genome Biol. 2024 Mar 25;25(1):76. doi: 10.1186/s13059-024-03202-0.
HERE https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03202-0
DeLoose M, Clúa J, Cho H, Zheng L, Masmoudi K, Desnos T, Krouk G, Nussaume L, Poirier Y, Rouached H.
Recent advances in unraveling the mystery of combined nutrient stress in plants.
Plant J. 2023 Nov 3. doi: 10.1111/tpj.16511.
Crabos A, Huang Y, Boursat T, Maurel C, Ruffel S, Krouk G, Boursiac Y.
Distinct early transcriptional regulations by turgor and osmotic potential in the roots of Arabidopsis.
J Exp Bot. 2023 Sep 29;74(18):5917-5930.
Nguyen NNT, Lamotte O, Alsulaiman M, Ruffel S, Krouk G, Berger N, Demolombre-Liozu V, Nespoulous C, Nguyet Dang TM, Aimé S, Berthomieu P, Dubos C, Wendehenne D, Vile D, Gosti F.
Reduction in PLANT DEFENSIN 1 expression in Arabidopsis thaliana results in increased resistance to pathogens and zinc toxicity.
J Exp Bot. 2023 Jun 16:erad228.
Krouk G, Szponarski W, Ruffel S
Unleashing the potential of peptides in agriculture and beyond
Trends in Plant Science. Trends Plant Sci. 2023 Jul;28(7):734-736.
Cho H, Banf M, Shahzad Z, Van Leene J, Bossi F, Ruffel S, Bouain N, Cao P, Krouk G, De Jaeger G, Lacombe B, Brandizzi F, Rhee SY, Rouached H.
ARSK1 activates TORC1 signaling to adjust growth to phosphate availability in Arabidopsis.
Current Biology. 2023 Mar 20:S0960-9822(23)00291-9. doi: 10.1016/j.cub.2023.03.005.
Jordan Courrèges-Clercq , Gabriel Krouk*
Two nitrate sensors, how many more?
Nature Plants . 2022 Nov 4. doi: 10.1038/s41477-022-01276
Baldwin Dumortier, Antoine Liutkus*, Clément Carré, Gabriel Krouk*
PeTriBERT : Augmenting BERT with tridimensional encoding for inverse protein folding and design
https://www.biorxiv.org/content/10.1101/2022.08.10.503344v1
Clément Carré*, Jean Baptiste Carluer, Christian Chaux, Nicolas Roche, André Mas*, Gabriel Krouk*
Full epistatic interaction maps retrieve part of missing heritability and improve phenotypic prediction
biorxiv.org/content/10.1101/2022.07.20.500572v1
Liu Y, Maniero RA, Giehl RFH, Melzer M, Steensma P, Krouk G, Fitzpatrick TB, von Wirén N.
PDX1.1-dependent biosynthesis of vitamin B6 protects roots from ammonium-induced oxidative stress.
Mol Plant. 2022
Camut L, Gallova B, Jilli L, Sirlin-Josserand M, Carrera E, Sakvarelidze-
Achard L, Ruffel S, Krouk G, Thomas SG, Hedden P, Phillips AL, Davière JM, Achard P.
Nitrate signaling promotes plant growth by upregulating gibberellin
biosynthesis and destabilization of DELLA proteins.
Current Biology. 2021
Nov 22;31(22):4971-4982.e4.
2: Safi A, Medici A, Szponarski W, Martin F, Clément-Vidal A, Marshall-Colon A,
Ruffel S, Gaymard F, Rouached H, Leclercq J, Coruzzi G, Lacombe B, Krouk G.
GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-
dependent and -independent pathways.
J Exp Bot. 2021
May 4;72(10):3881-3901.
3: Krouk G, Kiba T.
Nitrogen and Phosphorus interactions in plants: from
agronomic to physiological and molecular insights.
Curr Opin Plant Biol. 2020
Oct;57:104-109. doi: 10.1016/j.pbi.2020.07.002. Epub 2020 Sep 1. PMID: 32882570.
4: Parry G, Provart NJ, Brady SM, Uzilday B; Multinational Arabidopsis Steering Committee.
Current status of the multinational Arabidopsis community.
Plant Direct. 2020 Aug 2;4(7):e00248.
doi: 10.1002/pld3.248. PMID: 32775952; PMCID:
PMC7396448.
5: Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G,
Benková E, Nacry P, Gojon A, Bach L.
The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root
branching in response to nitrate.
J Exp Bot. 2020
Jul 25;71(15):4480-4494. doi:
10.1093/jxb/eraa242. PMID: 32428238.
6: Vidal EA, Alvarez JM, Araus V, Riveras E, Brooks MD, Krouk G, Ruffel S, Lejay
L, Crawford NM, Coruzzi GM, Gutiérrez RA. Nitrate in 2020: Thirty Years from
Transport to Signaling Networks.
Plant Cell. 2020
Jul;32(7):2094-2119.
doi:10.1105/tpc.19.00748. Epub 2020 Mar 13. PMID: 32169959; PMCID: PMC7346567.
7: Alvarez JM, Schinke AL, Brooks MD, Pasquino A, Leonelli L, Varala K, Safi A,
Krouk G, Krapp A, Coruzzi GM. Transient genome-wide interactions of the master
transcription factor NLP7 initiate a rapid nitrogen-response cascade.
Nat Commun. 2020
Mar 2;11(1):1157.
doi: 10.1038/s41467-020-14979-6. PMID: 32123177;
PMCID: PMC7052136.
8: Falter-Braun P, Brady S, Gutiérrez RA, Coruzzi GM, Krouk G. iPlant Systems
Biology (iPSB): An International Network Hub in the Plant Community.
Mol Plant. 2019
Jun 3;12(6):727-730.
doi: 10.1016/j.molp.2019.05.005. Epub 2019 May 21.
PMID: 31125688.
9: Bouain N, Krouk G, Lacombe B, Rouached H. Getting to the Root of Plant
Mineral Nutrition: Combinatorial Nutrient Stresses Reveal Emergent Properties.
Trends Plant Sci. 2019
Jun;24(6):542-552. doi: 10.1016/j.tplants.2019.03.008.
Epub 2019 Apr 18. PMID: 31006547.
10: Brooks MD, Cirrone J, Pasquino AV, Alvarez JM, Swift J, Mittal S, Juang CL,
Varala K, Gutiérrez RA, Krouk G, Shasha D, Coruzzi GM. Network Walking charts
transcriptional dynamics of nitrogen signaling by integrating validated and
predicted genome-wide interactions.
Nat Commun. 2019
Apr 5;10(1):1569. doi:
10.1038/s41467-019-09522-1. PMID: 30952851; PMCID: PMC6451032.
11: Medici A*, Szponarski W*, Dangeville P, Safi A, Dissanayake IM, Saenchai C,
Emanuel A, Rubio V, Lacombe B, Ruffel S, Tanurdzic M, Rouached H, Krouk G.
Identification of Molecular Integrators Shows that Nitrogen Actively Controls
the Phosphate Starvation Response in Plants.
Plant Cell. 2019
May;31(5):1171-1184. doi: 10.1105/tpc.18.00656. Epub 2019 Mar 14. PMID:
30872321; PMCID: PMC6533016.
12: Bellegarde F, Maghiaoui A, Boucherez J, Krouk G, Lejay L, Bach L, Gojon A,
Martin A. The Chromatin Factor HNI9 and ELONGATED HYPOCOTYL5 Maintain ROS
Homeostasis under High Nitrogen Provision.
Plant Physiol. 2019
May;180(1):582-592. doi: 10.1104/pp.18.01473. Epub 2019 Mar 1. PMID: 30824566;
PMCID: PMC6501088.
13: Poitout A, Crabos A, Petřík I, Novák O, Krouk G, Lacombe B, Ruffel S.
Responses to Systemic Nitrogen Signaling in Arabidopsis Roots Involve
<i>trans</i>-Zeatin in Shoots.
Plant Cell. 2018
Jun;30(6):1243-1257. doi:
10.1105/tpc.18.00011. Epub 2018 May 15. PMID: 29764985; PMCID: PMC6048791.
14: Kisko M, Bouain N, Safi A, Medici A, Akkers RC, Secco D, Fouret G, Krouk G,
Aarts MG, Busch W, Rouached H.
LPCAT1 controls phosphate homeostasis in a
zinc-dependent manner.
Elife. 2018
Feb 17;7:e32077. doi: 10.7554/eLife.32077.
PMID: 29453864; PMCID: PMC5826268.
15: Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V,
Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL,
Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk
G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith
R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware
D, Wilkins O, Williams C, Brady SM. The Next Generation of Training for
Arabidopsis Researchers: Bioinformatics and Quantitative Biology.
Plant Physiol. 2017
Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490. PMID: 29208732; PMCID:
PMC5717721.
16: Pal S, Kisko M, Dubos C, Lacombe B, Berthomieu P, Krouk G, Rouached H.
TransDetect Identifies a New Regulatory Module Controlling Phosphate Accumulation.
Plant Physiol. 2017
Oct;175(2):916-926. doi: 10.1104/pp.17.00568.
Epub 2017 Aug 21. PMID: 28827455; PMCID: PMC5619893.
17: Safi A, Medici A, Szponarski W, Ruffel S, Lacombe B, Krouk G. The world
according to GARP transcription factors.
Curr Opin Plant Biol. 2017
Oct;39:159-167. doi: 10.1016/j.pbi.2017.07.006. Epub 2017 Aug 10. PMID:
28802165.
18: Carré C, Mas A, Krouk G. Reverse engineering highlights potential principles
of large gene regulatory network design and learning.
NPJ Syst Biol Appl. 2017
Jun 22;3:17. doi: 10.1038/s41540-017-0019-y. PMID: 28649444; PMCID: PMC5481436.
19: Krouk G. Nitrate signalling: Calcium bridges the nitrate gap.
Nat Plants. 2017
Jun 19;3:17095. doi: 10.1038/nplants.2017.95. PMID: 28628086.
20: Ristova D, Carré C, Pervent M, Medici A, Kim GJ, Scalia D, Ruffel S,
Birnbaum KD, Lacombe B, Busch W, Coruzzi GM, Krouk G. Combinatorial interaction
network of transcriptomic and phenotypic responses to nitrogen and hormones in
the Arabidopsis thaliana root.
Science Signal. 2016
Oct 25;9(451):rs13. doi:
10.1126/scisignal.aaf2768. PMID: 27811143.
21: Bellati J, Champeyroux C, Hem S, Rofidal V, Krouk G, Maurel C, Santoni V.
Novel Aquaporin Regulatory Mechanisms Revealed by Interactomics.
Mol Cell Proteomics. 2016
Nov;15(11):3473-3487. doi: 10.1074/mcp.M116.060087. Epub 2016
Sep 8. PMID: 27609422; PMCID: PMC5098044.
22: Bouguyon E, Perrine-Walker F, Pervent M, Rochette J, Cuesta C, Benkova E,
Martinière A, Bach L, Krouk G, Gojon A, Nacry P. Nitrate Controls Root
Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter/Sensor.
Plant Physiol. 2016
Oct;172(2):1237-1248. doi:
10.1104/pp.16.01047. Epub 2016 Aug 19. PMID: 27543115; PMCID: PMC5047109.
23: O'Brien JA, Vega A, Bouguyon E, Krouk G, Gojon A, Coruzzi G, Gutiérrez RA.
Nitrate Transport, Sensing, and Responses in Plants.
Mol Plant. 2016
Jun 6;9(6):837-56. doi: 10.1016/j.molp.2016.05.004. Epub 2016 May 19. PMID:
27212387.
24: Krouk G. Hormones and nitrate: a two-way connection.
Plant Mol Biol. 2016
Aug;91(6):599-606. doi: 10.1007/s11103-016-0463-x. Epub 2016 Mar 22. PMID:
27003907.
25: Ruffel S, Poitout A, Krouk G, Coruzzi GM, Lacombe B. Long-distance nitrate
signaling displays cytokinin dependent and independent branches.
J Integr Plant Biol. 2016
Mar;58(3):226-9. doi: 10.1111/jipb.12453. Epub 2016 Feb 23. PMID:
26619818.
26: Medici A, Marshall-Colon A, Ronzier E, Szponarski W, Wang R, Gojon A,
Crawford NM, Ruffel S, Coruzzi GM, Krouk G. AtNIGT1/HRS1 integrates nitrate and
phosphate signals at the Arabidopsis root tip.
Nature Commun. 2015
Feb 27;6:6274.
doi: 10.1038/ncomms7274. PMID: 25723764; PMCID: PMC4373655.
27: Krouk G, Carré C, Fizames C, Gojon A, Ruffel S, Lacombe B. GeneCloud Reveals
Semantic Enrichment in Lists of Gene Descriptions.
Mol Plant. 2015
Jun;8(6):971-3. doi: 10.1016/j.molp.2015.02.005. Epub 2015 Feb 21. PMID:
25707756.
28: Li Y, Krouk G, Coruzzi GM, Ruffel S. Finding a nitrogen niche: a systems
integration of local and systemic nitrogen signalling in plants.
J Exp Bot. 2014
Oct;65(19):5601-10. doi: 10.1093/jxb/eru263. Epub 2014 Jun 24. PMID: 24963003.
29: Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards
MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM. Hit-
and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.
Proc Natl Acad Sci U S A. 2014
Jul 15;111(28):10371-6. doi:
10.1073/pnas.1404657111. Epub 2014 Jun 23. PMID: 24958886; PMCID: PMC4104873.
30: Medici A, Krouk G. The primary nitrate response: a multifaceted signalling pathway.
J Exp Bot. 2014
Oct;65(19):5567-76. doi: 10.1093/jxb/eru245. Epub 2014
Jun 18. PMID: 24942915.
31: Vidal EA, Moyano TC, Krouk G, Katari MS, Tanurdzic M, McCombie WR, Coruzzi
GM, Gutiérrez RA. Integrated RNA-seq and sRNA-seq analysis identifies novel
nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics. 2013 Oct
11;14:701. doi: 10.1186/1471-2164-14-701. PMID: 24119003; PMCID: PMC3906980.
32: Bargmann BO, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml
J, Bergmann DC, Estelle M, Birnbaum KD. A map of cell type-specific auxin
responses. Mol Syst Biol. 2013;9:688. doi: 10.1038/msb.2013.40. PMID: 24022006;
PMCID: PMC3792342.
33: Rosas U, Cibrian-Jaramillo A, Ristova D, Banta JA, Gifford ML, Fan AH, Zhou
RW, Kim GJ, Krouk G, Birnbaum KD, Purugganan MD, Coruzzi GM. Integration of
responses within and across Arabidopsis natural accessions uncovers loci
controlling root systems architecture. Proc Natl Acad Sci U S A. 2013 Sep
10;110(37):15133-8. doi: 10.1073/pnas.1305883110. Epub 2013 Aug 26. Erratum in:
Proc Natl Acad Sci U S A. 2015 May 12;112(19):E2555. PMID: 23980140; PMCID:
PMC3773737.
34: Krouk G, Lingeman J, Colon AM, Coruzzi G, Shasha D. Gene regulatory networks
in plants: learning causality from time and perturbation. Genome Biol. 2013 Jun
27;14(6):123. doi: 10.1186/gb-2013-14-6-123. PMID: 23805876; PMCID: PMC3707030.
35: Boursiac Y, Léran S, Corratgé-Faillie C, Gojon A, Krouk G, Lacombe B. ABA
transport and transporters. Trends Plant Sci. 2013 Jun;18(6):325-33. doi:
10.1016/j.tplants.2013.01.007. Epub 2013 Mar 1. PMID: 23453706.
36: Bargmann BO, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM,
Krouk G. TARGET: a transient transformation system for genome-wide transcription
factor target discovery. Mol Plant. 2013 May;6(3):978-80. doi:
10.1093/mp/sst010. Epub 2013 Jan 18. PMID: 23335732; PMCID: PMC3660954.
37: Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM. RootScape: a
landmark-based system for rapid screening of root architecture in Arabidopsis.
Plant Physiol. 2013 Mar;161(3):1086-96. doi: 10.1104/pp.112.210872. Epub 2013
Jan 18. PMID: 23335624; PMCID: PMC3585581.
38: Krouk G, Gojon A. Un mécanisme original de perception d'un ion minéral (le
nitrate): histoire de la découverte chez les plantes et perspectives [An
original ion (nitrate) sensing mechanism: story of the discovery in plants and
perspectives]. Med Sci (Paris). 2011 Dec;27(12):1045-7. French. doi:
10.1051/medsci/20112712002. Epub 2011 Dec 23. PMID: 22192735.
39: Ruffel S, Krouk G, Ristova D, Shasha D, Birnbaum KD, Coruzzi GM. Nitrogen
economics of root foraging: transitive closure of the nitrate-cytokinin relay
and distinct systemic signaling for N supply vs. demand. Proc Natl Acad Sci U S
A. 2011 Nov 8;108(45):18524-9. doi: 10.1073/pnas.1108684108. Epub 2011 Oct 24.
PMID: 22025711; PMCID: PMC3215050.
40: Ravet K, Reyt G, Arnaud N, Krouk G, Djouani el-B, Boucherez J, Briat JF,
Gaymard F. Iron and ROS control of the DownSTream mRNA decay pathway is
essential for plant fitness. EMBO J. 2012 Jan 4;31(1):175-86. doi:
10.1038/emboj.2011.341. Epub 2011 Sep 23. PMID: 21946558; PMCID: PMC3252566.
41: Widiez T, El Kafafi el S, Girin T, Berr A, Ruffel S, Krouk G, Vayssières A,
Shen WH, Coruzzi GM, Gojon A, Lepetit M. High nitrogen insensitive 9
(HNI9)-mediated systemic repression of root NO3- uptake is associated with
changes in histone methylation. Proc Natl Acad Sci U S A. 2011 Aug
9;108(32):13329-34. doi: 10.1073/pnas.1017863108. Epub 2011 Jul 25. PMID:
21788519; PMCID: PMC3156160.
42: Krouk G, Ruffel S, Gutiérrez RA, Gojon A, Crawford NM, Coruzzi GM, Lacombe
B. A framework integrating plant growth with hormones and nutrients. Trends
Plant Sci. 2011 Apr;16(4):178-82. doi: 10.1016/j.tplants.2011.02.004. Epub 2011
Mar 9. PMID: 21393048.
43: Gojon A, Krouk G, Perrine-Walker F, Laugier E. Nitrate transceptor(s) in
plants. J Exp Bot. 2011 Apr;62(7):2299-308. doi: 10.1093/jxb/erq419. Epub 2011
Jan 14. PMID: 21239382.
44: Krouk G, Mirowski P, LeCun Y, Shasha DE, Coruzzi GM. Predictive network
modeling of the high-resolution dynamic plant transcriptome in response to
nitrate. Genome Biol. 2010;11(12):R123. doi: 10.1186/gb-2010-11-12-r123. Epub
2010 Dec 23. PMID: 21182762; PMCID: PMC3046483.
45: Obertello M, Krouk G, Katari MS, Runko SJ, Coruzzi GM. Modeling the global
effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen
and light regulation in Arabidopsis. BMC Syst Biol. 2010 Aug 12;4:111. doi:
10.1186/1752-0509-4-111. PMID: 20704717; PMCID: PMC2933594.
46: Krouk G, Lacombe B, Bielach A, Perrine-Walker F, Malinska K, Mounier E,
Hoyerova K, Tillard P, Leon S, Ljung K, Zazimalova E, Benkova E, Nacry P, Gojon
A. Nitrate-regulated auxin transport by NRT1.1 defines a mechanism for nutrient
sensing in plants. Dev Cell. 2010 Jun 15;18(6):927-37. doi:
10.1016/j.devcel.2010.05.008. PMID: 20627075.
47: Krouk G, Crawford NM, Coruzzi GM, Tsay YF. Nitrate signaling: adaptation to
fluctuating environments. Curr Opin Plant Biol. 2010 Jun;13(3):266-73. doi:
10.1016/j.pbi.2009.12.003. Epub 2010 Jan 21. PMID: 20093067.
48: Ruffel S, Krouk G, Coruzzi GM. A systems view of responses to nutritional
cues in Arabidopsis: toward a paradigm shift for predictive network modeling.
Plant Physiol. 2010 Feb;152(2):445-52. doi: 10.1104/pp.109.148502. Epub 2009 Nov
25. PMID: 19939945; PMCID: PMC2815908.
49: Nero D, Krouk G, Tranchina D, Coruzzi GM. A system biology approach
highlights a hormonal enhancer effect on regulation of genes in a nitrate
responsive "biomodule". BMC Syst Biol. 2009 Jun 6;3:59. doi:
10.1186/1752-0509-3-59. PMID: 19500399; PMCID: PMC2702358.
50: Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM,
Gutiérrez RA. A systems approach uncovers restrictions for signal interactions
regulating genome-wide responses to nutritional cues in Arabidopsis. PLoS Comput
Biol. 2009 Mar;5(3):e1000326. doi: 10.1371/journal.pcbi.1000326. Epub 2009 Mar
20. PMID: 19300494; PMCID: PMC2652106.
51: Krouk G, Tillard P, Gojon A. Regulation of the high-affinity NO3- uptake
system by NRT1.1-mediated NO3- demand signaling in Arabidopsis. Plant Physiol.
2006 Nov;142(3):1075-86. doi: 10.1104/pp.106.087510. Epub 2006 Sep 22. PMID:
16998085; PMCID: PMC1630733.