Mohamed Zouine

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Short CV


Actual Research Project:

Title: Auxin signalling, epigenetic factors and molecular mechanisms controlling the transition from flower to fruit 

My research project is related to the study of fruit set and fruit development in tomato as a model with special emphasis on the role of auxin-induced transcription factors and epigenetics using modern methodological tools and resources available in the laboratory.

I am also actively involved in programs including the generation of genomic ressources and  tools in tomato like the international tomato genome sequencing project and actually leading the development of the TomExpress RNAseq platform which is intended to standardize all RNAseq tomato data available in public databases.

Updated publications liste on ResearchGateGoogle Scholar

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Short CV



Bioinformatics, Genome Sequencing and Annotation, RNA-Seq, ChIP-Seq,  Epigenetics, genome editing.



- Since  2020, PI and Work package leader in the EU-H2020 project HARNESSTOM

- Since 2019, Member of the management committee and Working Group leaderof the EU COST Action RoxyCOST

- 2016-20, Coordinator of the ANR Project "TomEpiSet"

- 2016-20, Work package leader (WP3) of the EU-TOMGEM H2020 project

- 2011-19, Leader of the structuring project « Epigenetic control of the fruit set process» in the frame of the laboratory of excellence Labex-TULIP.

- 2013-16, Coordinator of the working group WG2 “Bioinformatics tools for genomic high-throughput data analysis” in the frame of the Pan-European COST action FA1106



- Since 2020,Vice-President of Toulouse INP

- Since 2020, Elected member of the administration council of Toulouse INP (Conseil d'administration)

- 2016-19, Elected member of the Labex-TULIP research council

- 2016-19, Member of the Labex-TULIP innovation comitte

- 2016-19, Elected member of the doctoral school SEVAB scientific council.

- Since 2014-19, Manager of the INP-NSAT digital services user council related to education and research activities.



- 2015-2019, Coordinator of the “ERASMUS+ Capacity Building in the field of Higher Education” project (ref 561964-EPP-1-2015-1-FR-EPPKA2-CBHE-JP) including four countries and ten university/institution partners: MABIOVA

- Since 2015, Responsible for the bioinformatics-biostatistics specialization, joint between INP-ENSAT and INSA engineer schools: BioComp



- Since 2012, Holder for the scientific excellence bonus.

- 2016, Price “rayonnement international“ INP-INNOV' for my coordination of the project ERSAMUS+ Capacity Building in High Education MABIOVA.

- 2012, Price INP-INNOV' in the category "Discovery / major advance" for my involvement in the sequencing of the tomato genome.




2012 « Accreditation to supervise research » (Habilitation à dirriger les recherches : HDR) delivered at Institute Nationale Polytechnique Toulouse

Since 2005 Associate Professor (Maître de conférences)

2001-2005 Post-doc in comparative genomics and transcriptomics of pathogenic bacteria, Pasteur Institute, Paris.

1999-2001 Assistant professor (ATER) in bioinformatics, University Paris XI, France

1999 PhD in Molecular Genetics, University Paris XI, France

1994 Master (DEA) in Genetics and Microbiology, University Paris XI, France



Histone Post Translational Modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato.  Hu G, Huang B, Wang K, Frasse P, Maza E, Djari A, Benhamed M, Gallusci P, Li Z, Zouine M*, Bouzayen M*. New Phytol. 2020 Sep 2. doi: 10.1111/nph.16902. Online ahead of print. PMID: 32875585

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato.  Petek M, Zagorščak M, Ramšak Ž, Sanders S, Tomaž Š, Tseng E, Zouine M, Coll A, Gruden K.Sci Data. 2020 Jul 24;7(1):249. doi: 10.1038/s41597-020-00581-4.PMID: 32709858

Bouzroud S, Gasparini K, Hu G, Barbosa MAM, Rosa BL, Fahr M, Bendaou N, Bouzayen M, Zsögön A, Smouni A, Zouine M. Down Regulation and Loss of Auxin Response Factor 4 Function Using CRISPR/Cas9 Alters Plant Growth, Stomatal Function and Improves Tomato Tolerance to Salinity and Osmotic Stress. Genes (Basel). 2020 Mar 3;11(3), 272.

An J, Althiab Almasaud R, Bouzayen M, Zouine M*, Chervin C*. Auxin and ethylene regulation of fruit set. Plant Sci. 2020 Mar;292:110381.


Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Muños S, Bendahmane A, Bergès H, Niebel A, Buitink J, Frugier F, Benhamed M, Crespi M, Gouzy J, Gamas P. 2018. Whole-genome landscape of Medicago truncatula symbiotic genes. Nat Plants. 2018 Nov 5. doi:10.1038/s41477-018-0286-7.

Ambrosino L, Ruggieri V, Bostan H, Miralto M, Vitulo N, Zouine M, Barone A, Bouzayen M, Frusciante L, Pezzotti P, Valle G and Luisa Chiusano M. Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. 2018, BMC Bioinformatics. doi: 10.1186/s12859-018-2420-y.

Liu M, Yao C, Ya; Shin J,  Mila I,  Audran C, Zouine M, Pirrello J, Bouzayen M. The tomato Ethylene Response Factor Sl-ERF.B3 integrates ethylene and auxin signaling via direct regulation of Sl-Aux/IAA27. In press in New Phytologist

Lamarre S, Frasse P, Zouine M, Labourdette D, Sainderichin E, Hu G, Le Berre-Anton V, Bouzayen M, Maza E. Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size. Front Plant Sci. 2018 Feb 14;9:108. doi: 10.3389/fpls.2018.00108.

Bouzroud S, Gouiaa S, Hu N, Bernadac A, Mila I, Bendaou N, Smouni A, Bouzayen  M, Zouine M. Auxin Response Factors (ARFs) are potential mediators of auxin action in tomato response to biotic and abiotic stress (Solanum lycopersicum). PLoS One. 2018 Feb 28;13(2):e0193517. doi: 10.1371/journal.pone.0193517.

Pirrello J, Deluche C, Frangne N, Gévaudant F, Maza E, Djari A, Bourge M, Renaudin JP, Brown S, Bowler C, Zouine M, Chevalier C, Gonzalez N. Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation. The Plant Journal 2018 Jan;93(2):387-398. doi: 10.1111/tpj.13783.

2017 :

Zouine M, Maza E, Djari A, Lauvernier M,Frasse P, smouni A, Pirrello J, Bouzayen M.  TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks. Plant J. 2017 Sep 5. doi: 10.1111/tpj.13711.

Huang B, Routaboul JM,  Liu M,  Deng W,  Maza E,  Mila I,  Hu G,  Zouine M,  Frasse P,  Vrebalov JT,  Giovannoni J,  Li Z,  van der Rest B and  Bouzayen MOverexpression of class D MADS-box Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruit.  J Exp Bot. 2017 Sep 14. doi: 10.1093/jxb/erx303.

2016 :

Breitel D, Chappell-Maor, Sagit Meir L, Panizel I, Pons Puig C, Hao Y, Yifhar T, Yasuor H, Zouine M, Bouzayen M, Granell Richart A, Rogachev I and Aharoni A. (2016) AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening. PLoS Genet (in press).

Liu M, Lima Gomes B, Mila I, Purgatto E, Peres LE, Frasse P, Maza E, Zouine M, Roustan JP, Bouzayen M and Pirrello J. (2016) Comprehensive profiling of Ethylene Response Factors expression identifies ripening-associated ERF genes and their link to key regulators of fruit ripening in tomato (Solanum lycopersicum). Plant Physiol. 2016 Jan 6. pii: pp.01859.2015. [Epub ahead of print] PubMed PMID: 26739234.

Corso M, Vannozzi A, Ziliotto F, Zouine M, Nicolato T, Maza E, Vitulo N, Meggio F, Valle G, Bouzayen M, Müller M, Munné-Bosch S, Lucchin M, Bonghi C (2016). Grapevine rootstocks differentially affect the rate of ripening and modulate auxin-related genes in Cabernet Sauvignon berries. Front Plant Sci (in press)

2015 :

Hao Y., Hu G., Breitel D., Liu M., Mila I., Frasse P., Aharoni A., Bouzayen M. and Zouine M. (2015) Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato. PLoS Genet Dec 30;11(12):e1005649. doi: 10.1371/journal.pgen.1005649. eCollection 2015.

Mazzucato, A., Cellini, F., Bouzayen, M., Zouine, M., Mila, I., Minoia, S., Petrozza, A., Picarella, M.E., Ruiu, F. and Carriero, F. (2015) A TILLING allele of the tomato Aux/IAA9 gene offers new insights into fruit set mechanisms and perspectives for breeding seedless tomatoes. Molecular Breeding, 35, 1-15.

Su, L., Diretto, G., Purgatto, E., Danoun, S., Zouine, M., Li, Z., Roustan, J.-P., Bouzayen, M., Giuliano, G. and Chervin, C. (2015) Carotenoid accumulation during tomato fruit ripening is modulated by the auxin-ethylene balance. BMC plant biology, 15, 114.

 2014 :

Zouine, M., Fu, Y., Chateigner-Boutin, A.-L., Mila, I., Frasse, P., Wang, H., Audran, C., Roustan, J.-P. and Bouzayen, M. (2014) Characterization of the tomato ARF gene family uncovers a multi-levels post-transcriptional regulation including alternative splicing.

Etemadi, M., Gutjahr, C., Couzigou, J.-M., Zouine, M., Lauressergues, D., Timmers, A., Audran, C., Bouzayen, M., Bécard, G. and Combier, J.-P. (2014) Auxin perception is required for arbuscule development in arbuscular mycorrhizal symbiosis. Plant physiology, 166, 281-292.

Hao, Y., Wang, X., Li, X., Bassa, C., Mila, I., Audran, C., Maza, E., Li, Z., Bouzayen, M., Van der Rest, B. and Zouine, M (2014) Genome-wide identification, phylogenetic analysis, expression profiling, and protein–protein interaction properties of TOPLESS gene family members in tomato. Journal of experimental botany, 65, 1013-1023.

 2013 :

Maza, E., Frasse, P., Senin, P., Bouzayen, M. and Zouine, M. (2013) Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes. Communicative & Integrative Biology, 6, e25849.

Sagar, M., Chervin, C., Mila, I., Hao, Y., Roustan, J.-P., Benichou, M., Gibon, Y., Biais, B., Maury, P.,  Latché, A., Bouzayen, M. and Zouine, M. (2013) SlARF4, an auxin response factor involved in the control of sugar metabolism during tomato fruit development. Plant physiology, 161, 1362-1374.

Sagar, M., Chervin, C., Roustan, J.-P., Bouzayen, M. and Zouine, M. (2013) Under-expression of the Auxin Response Factor Sl-ARF4 improves post-harvest behavior of tomato fruits. Plant signaling & behavior, 8, e25647.

2012 :

Sato S, Tabata S, …(including Zouine M)… Consortium TG (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641

Lesic B, Zouine M, Ducos-Galand M, Huon C, Rosso ML, Prevost MC, Mazel D, Carniel E (2012) A natural system of chromosome transfer in Yersinia pseudotuberculosis. PLoS Genet 8: e1002529

Barsan C, Zouine M, Maza E, Bian W, Egea I, Rossignol M, Bouyssie D, Pichereaux C, Purgatto E, Bouzayen M, Latche A, Pech JC (2012) Proteomic Analysis of Chloroplast-to-Chromoplast Transition in Tomato Reveals Metabolic Shifts Coupled with Disrupted Thylakoid Biogenesis Machinery and Elevated Energy-Production Components. Plant Physiol 160: 708-725

Audran-Delalande C, Bassa C, Mila I, Regad F, Zouine M, Bouzayen M (2012) Genome-wide identification, functional analysis and expression profiling of the Aux/IAA gene family in tomato. Plant Cell Physiol 53: 659-672

Pirrello J, Prasad N, Zhang W, Chen K, Mila I, Zouine M, Latche A, Pech JC, Ohme-Takagi M, Regad F, Bouzayen M (2012)Functional analysis and binding affinity of tomato ethylene response factors provide insight on the molecular bases of plant differential responses to ethylene. BMC Plant Biol 12: 190

Li J, Li Z, Tang L, Yang Y, Zouine M, Bouzayen M (2012) A conserved phosphorylation site regulates the transcriptional function of ETHYLENE-INSENSITIVE3-like1 in tomato. Journal of Experimental Botany 63: 427-439


Barsan C, Sanchez-Bel P, Rombaldi C, Egea I, Rossignol M, Kuntz M, Zouine M, Latche A, Bouzayen M, Pech JC (2010)Characteristics of the tomato chromoplast revealed by proteomic analysis.
Journal of Experimental Botany 61: 2413-2431

Lefebvre-Pautigny F, Wu FN, Philippot M, Rigoreau M, Priyono, Zouine M, Frasse P, Bouzayen M, Broun P, Petiard V, Tanksley SD, Crouzillat D (2010)High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes.
Tree Genetics & Genomes 6: 565-577


Le Roux F, Zouine M, Chakroun N, Binesse J, Saulnier D, Bouchier C, Zidane N, Ma L, Rusniok C, Lajus A, Buchrieser C, Medigue C, Polz MF, Mazel D (2009)Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity.Environmental Microbiology 11: 1959-1970

Wang H, Schauer N, Usadel B, Frasse P, Zouine M, Hernould M, Latche A, Pech JC, Fernie AR, Bouzayen M (2009)Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling. Plant Cell 21: 1428-1452



A naturally occurring gene amplification leading to sulfonamide and trimethoprim resistance in Streptococcus agalactiae.

Journal of Bacteriology 190: 672-680

Stimulation of the grape berry expansion by ethylene and effects on related gene transcripts, over the ripening phase.

Physiologia Plantarum 134: 534-546




Biochemical and catalytic properties of three recombinant alcohol acyltransferases of melon. Sulfur-containing ester formation, regulatory role of CoA-SH in activity, and sequence elements conferring substrate preference.

Journal of Agricultural and Food Chemistry 55: 5213-5220




Genomic diversity and evolution within the species Streptococcus agalactiae.

Microbes and Infection 8: 1227-1243

The mitochondrial elongation factor LeEF-Ts-mt is regulated during tomato fruit ripening and upon wounding and ethylene treatment.

Postharvest Biology and Technology 42: 1-7


Before 2006:

The SrtA sortase of Streptococcus agalactiae is required for cell wall anchoring of proteins containing the LPXTG motif, for adhesion to epithelial cells, and for colonization of the mouse intestine.

Infection and Immunity 73: 3342-3350

The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens.

Nature Biotechnology 21: 1307-1313

Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease.

Molecular Microbiology 45: 1499-1513

CovS/CovR of group B streptococcus: a two-component global regulatory system involved in virulence.

Molecular Microbiology 54: 1250-1268

A possible role for L24 of Bacillus subtilis in nucleoid organization and segregation.

Biochimie 83: 269-275

Characterization of LrpC DNA-binding properties and regulation of Bacillus subtilis lrpC gene expression.

Journal of Bacteriology 182: 4414-4424

The L17 ribosomal protein of Bacillus subtilis binds preferentially to curved DNA.

Biochimie 82: 85-91

Correct assignment of homology is crucial when genomics meets molecular evolution.

Comparative and Functional Genomics 3: 488-493

Overproduction, purification and characterization of the HPB12-L24 ribosomal protein of Bacillus subtilis.

Fems Microbiology Letters 145: 41-48