Arabidopsis Molecular Genetics Group

Research

History of the Arabidopsis group.

The Arabidopsis Molecular Genetics Group has been established in 1990, to employ the Arabidopsis thaliana as model plant to study plant stress biology, and decipher regulatory pathways in abiotic stress responses. Our group was the first which used the arabidopsis model for molecular genetic research in Hungary. First years have passed by establishing and adapting genetic and molecular technologies for Arabidopsis. With the valuable help and support of Csaba Koncz (Max-Planck-Institute für Züchtungsforschung, Cologne, Germany) we have developed T-DNA insertion mutagenesis programs, adapted promoter trapping technologies which facilitated the identification and molecular and genetic characterization of stress genes. We have developed a novel genetic system to identify regulatory genes in Arabidopsis and other plants. Following the initial period, we have focused on the regulatory processes which control cellular and physiological responses to drought and salinity in higher plants.

Research topics

Extreme environmental conditions such as drought and high soil salinity lead to osmotic, ionic and oxidative stresses which hinders plant growth and limits agricultural productivity. Using Arabidopsis thaliana as model organism, we study the regulation of molecular and physiological responses to these stress conditions. Using various genetic techniques, we have identified several regulatory genes from Arabidopsis or its halophytic relatives which encode novel transcription factors, protein kinases or enzymes which control growth, metabolic responses or cellular defences in stress conditions. 

Regulation and function of proline metabolism in stress conditions. 

Proline accumulation during drought or salt stress is a well-known phenomenon in plants. Proline is a multifunctional amino acid, which can contribute to stress tolerance in several ways including osmoprotection, regulation of redox balance or function as metabolic signal (Szabados and Savouré, 2010, Alvarez et al., 2022). Regulation of proline biosynthesis has been studied in our laboratory for decades and included the identification and characterization of key Arabidopsis genes P5CS1 and P5CS2, which control the glutamate-derived biosynthetic pathway (Strizhov et al., 1987, Ábrahám et al., 2003, Fabro et al., 2004, Székely et al., 2008). We have confirmed the importance of proline accumulation in maintaining cellular homeostasis and redox balance in plants under salt stress (Székely et al., 2008). We showed that proline accumulates during phosphate starvation, and such response is regulated by PHR1 and PHL1 transcription factors which recognize a cis regulatory motif in the first intron of P5CS1 (Aleksza et al., 2017). Stress-dependent proline accumulation is controlled by ABA-dependent and independent signals, and is influenced by light, which upregulates proline biosynthesis and reduces catabolism (Ábrahám et al., 2003, Kovács et al., 2019). We found that light regulation of P5CS1 is controlled by the bZIP factor HY5, which binds to G-box and C-box motifs of P5CS1 promoter region (Kovács et al., 2019). 

Ongoing research tries to decipher the role of proline metabolism in coordinating plastid and mitochondrial functions during stress, understand the importance of proline metabolism in stabilizing photosynthesis and reveal the interaction of stress, ABA and light signals which control proline accumulation in plants. 

Figure 1. Regulation of proline metabolism in Arabidopsis, sygnalling systems controlling responses to environmental effects (Alvarez et al., 2022).

Characterization of novel stress regulatory genes. 

Using novel genetic screens we have identified several regulatory genes which control responses to extreme environmental conditions.

Mitochondrial respiration is sensitive to changes in environmental conditions. By screening our T-DNA insertion collection, we have identified the Arabidopsis genes which encoded the mitochondrial PPR40 protein. Germination of the ppr40 mutant turned to be hypersensitive to salt and ABA (Zsigmond et al., 2008). Interestingly, the enhanced ABA sensitivity of the mutant could promote drought tolerance (Kant et al., 2023).

The Arabidopsis Heat Shock Factor A4A (HSFA4A) controls stress tolerance by regulating redox balance of Arabidopsis plants exposed to salinity, oxidative stress or combination of heat and salt stresses. HSFA4A is phosphorylated by MAP kinases MPK3, MPK4 and MPK6, which promotes its multimerisation and activity (Pérez-Salamó et al., 2014, Faragó et al., 2018, Andrási et al., 2019). Heat shock factors are not only key regulators of responses to high temperatures, but are essential to coordinate responses to a number of environmental effects (Andrási et al., 2021).

Figure 2. Function and interactions of HSFA4A in stress signaling (Andrási et al., 2019).

The zinc finger factor ZFP3 regulates ABA sensitivity of germinating seedlings, interfere with red light signals and plant development (Joseph et al., 2014).

The ERFVII-type transcription factor RAP2.12 together with its close relatives RAP2.2 and RAP2.3 was found to regulates responses to low oxygen conditions, osmotic and oxidative stresses and interfere with ABA signals (Papdi et al., 2008, Papdi et al., 2015).

The CRK5 kinase controls geotropism through modulating auxing transport. Various PIN transporters are targets of CRK5, which modulates their activity and therefore controls auxin levels of elongating tissues (Rigó et al., 2013, Baba et al., 2018, Cséplő et al., 2021).

Several genes have been identifdied in the halophyte plant Lepidium crassifolium which could enhance tolerance of transgenic Arabidopsis plants to salt, osmotic or oxidative stress conditions (Rigó et al., 2016). The small Lepidium peptide called SPQ could enhance drought tolerance of Arabidopsis by modulating ABA sensitivity in overexpressing plants (Faragó et al., 2022).

Development of genetic and imaging tools

Genetics offer powerful tools to identify novel regulatory genes controlling plant development, stress responses or hormonal signals. In collaboration with Csaba Koncz in the Max-Planck Institut für Züchtungsforschung, several genetic technologies were developed or improved in our laboratory to identify novel regulatory genes in Arabidopsis (Papdi et al., 2009, Papdi et al., 2010). Firefly luciferase was employed for gene trapping and could be used to identify mutants of stress-responsive genes (Alvarado et al., 2004). The Conditional cDNA Overexpression System (COS) was developed for random cDNA transfer and conditional overexpression of the inserted cDNA and to facilitate gene identification in transgenic Arabidopsis lines. The COS system generates conditional dominant phenotypes which is particularly suitable for the identification of stress regulatory genes (Papdi et al., 2008). We have adapted the COS technology for large-scale interspecific gene transfer to identify genes in extremophile plants such as Lepidium crassifolium, which can enhance stress tolerance of Arabidopsis and other stress sensitive plants (Rigó et al., 2016). 

Plant size, shape and color are important parameters of plants, which have traditionally been measured by destructive and time-consuming methods. We have developed a non-invasive image-based technology, which measures basic morphological and physiological parameters of in vitro cultured plants. Images are analyzed with the new computer application PlantSize, which calculates plant parameters such as rosette size, convex area, convex ratio, chlorophyll and anthocyanin contents of plants (Faragó et al., 2018).

Recently we have acquired an automatic plant phenotyping platform (PSI, Czech Republic) which is being used to characterize multiple morphological and physiological parameters of large number of plants in controlled environmental conditions (Faragó et al., 2022). 

Figure 3. Change of chlorophyll fluorescence of drought-treated Arabidopsis lines, imaged by the complex phenotyping platform. A) Fv/Fm values in water-stressed plants. B) Fv/Fm values after stress recovery.

Translational research

In order to characterize epigenetic changes associated with water deficit in rapeseed, in the frame of an international collaboration we are characterizing genome-wide histone modification and DNA methylation patterns in rapeseed.

Using our Arabidopsis model, several regulatory genes have been identified from this plant or from halophytic species, which can contribute to improve tolerance of higher plants to extreme environments (Zsigmond et al., 2008, Pérez-Salamó et al., 2014, Papdi et al., 2015, Rigó et al., 2016, Andrási et al., 2019, Faragó et al., 2022). In order to facilitate biotechnological applications and apply the acquired knowledge to crop plants, we have initiated research on rapeseed, aiming the transformation or engineering its genes to improve stress tolerance. In case the legal constraints og genetic transformation and genome editing will be eliminated, such technologies can contribute to the development of more tolerant varieties, to alleviate the damaging effects of klimate change on Agriculture.

Figure 4. SPQ overexpressing Arabidopsis lines survive better desiccation than wild type ones. Upper row: recovery of Wild type Arabidopsis, middle and lower row: recovery of SPQ overexpressing lines after rewatering.

Research material and service 

Pooled 40.000 transgenic Arabidopsis lines are available for research, carrying random cDNA clones of the halophytic plant Lepidium crassifolium (Rigó et al., 2016). 

PlantSize image analysis softvare (Faragó et al., 2018).

Image-based plant phenotyping suitable for characterization of shoot and root system of small and medium-sized plants.

Education activity

We are actively involved in pre and postgraduate training of Hungarian and Foreign students. 15 students have acquired their Ms.C. degree who made their thesis work under guidance of senior group members. 16 Ph.D. students made their research program in our group, succesfully defended their thesis and got their degree. Our group is active in other educational activities such as training of ITC students (one-year International Training Course, offered by BRC for foreign postgraduate students). Group members are participating in educational programs by giving lectures and courses in the University of Szeged, Hungary and the Babes-Bólyai University of Cluj, Romania. Presently one hungarian and two foreign PhD students are involved in our research activities.

Public outreach

We are actively participating in events and educational programs which target the larger public, such as the „Night of Scientists”.  We were involved in writing or editing publications on different subjects aiming the larger public (Szabados, 2014, Szabados and Györgyey, 2015). A book is being published by L. Szabados about the extromphile plants in the series of Kaleidoszkóp Könyvek (Szabados, 2023).

National and international collaborations

Dr. Koncz Csaba, Max-Planck-Institute für Züchtungsforschung, Köln, Germany,

Prof. Arnould Savouré, University of Paris Marie-Curie, Paris, France

Prof. Aviah Zilberstein, Tel-Aviv University, Tel-Aviv, Israel,

Prof. Sabina Vidal, University of Montevideo, Uruguay

Dr. Santiago Signorelli, University of Montevideo, Uruguay

Prof. Maria Elena Alvarez, University of Córdoba, Argentina

Prof. P.V.Shivaprasad, NCBS, Bangalore, India

Dr. Csiszár Jolán, Szegedi Tudományegyetem, Szeged

Dr. Kolbert Zsuzsanna, Szegedi Tudományegyetem, Szeged

Dr. Szarka András, Budapesti Műszaki Egyetem, Budapest

Seloected publications

1.          Ábrahám E, Rigó G, Székely G, Nagy R, Koncz Cs, Szabados L (2003) Light-dependent induction of proline biosynthesis by abscisic acid and salt stress is inhibited by brassinosteroid in Arabidopsis. Plant Mol. Biol 51:363-372.

2.          Aleksza D, Horváth GV, Sándor Gy, Szabados L (2017) Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation. Plant Physiol 175:555-567

3.          Alvarez ME, Savouré, A, Szabados, L. (2022) Proline metabolism as regulatory hub. Trends Plant Sci 27: 39-55.

4.          Andrási N, Rigó G, Zsigmond Zs, Pérez-Salamó I, Papdi Cs, Klement E, Pettkó-Szandtner A, Baba A-I, Ayaydin F, Dasari R, Cséplő A, Szabados L (2019)  The MPK4-phosphorylated Heat Shock Factor A4A regulates responses to combined salt and heat stresses. J. Exp. Bot. 70:4903-4918.

5.          Andrási N, Pettko-Szandtner A, Szabados L (2021) Diversity of Plant Heat Shock Factors: Regulation, Interactions and Functions. J. Exp. Bot. 72(5):1558-1575.

6.          Baba AI, Rigó G, Ayaydin F, Rehman AU, Andrási N, Zsigmond L, Valkai I, Urbancsok J, Vass I, Pasternak T, Palme K, Szabados L, Cséplő Á (2018) Functional analysis of the Arabidopsis thaliana CDPK-Related kinase family: AtCRK1 regulates responses to continuous light. Int. J. Mol. Sci. 19: 1282.

7.          Cséplő Á, Zsigmond, L, Andrási, N, Baba, A.i., Labhane, N., Pető, A., Kolbert, Zs., Kovács, H.E., Steinbach, G., Szabados, L., Fehér, A., Rigó, G. (2021) The AtCRK5 Protein Kinase Is Required to Maintain the ROS NO Balance Affecting the PIN2-Mediated Root Gravitropic Response in Arabidopsis. Int J Mol Sci. 22:5979.

8.          Fabro G, Kovács I, Pavet, V, Szabados L, Alvarez, ME (2004) Proline accumulation and AtP5CS2 gene activation are induced by plant-pathogen incompatible interactions in Arabidopsis. Mol Plant Micr Interaction 17:343-350.

9.          Faragó D, Sass L, Valkai I, Andrási N, Szabados L (2018) PlantSize offers an affordable, non-destructive method to measure plant size and color in vitro. Front. Plant Sci. 9:219.

10.        Faragó D, Zsigmond L, Benyó D, Alcázar R, Rigó G, Ayaydin F, Rabilu S-A, Hunyadi-Gulyás É, Szabados L (2022) Small paraquat resistance proteins modulate paraquat and ABA responses and confer drought tolerance to overexpressing Arabidopsis plants. Plant Cell Environ, 45:1985-2003

11.        Joseph MP, Papdi C, Kozma-Bognar L, Nagy I, Lopez-Carbonell M, Koncz C, Szabados L (2014) The Arabidopsis Zinc Finger Protein 3 interferes with ABA and light signaling in seed germination and plant development. Plant Physiol 165(3):1203-1220

12.        Kant K, Rigó G, Faragó D, Benyó D, Szabados L, Zsigmond L (2023) The Arabidopsis mitochondrial Pentatricopeptide repeat 40 protein modulates drought tolerance. Planta (accepted).

13.        Kováts H, Aleksza D, Baba AI, Hajdu A, Kiraly AM, Zsigmond L, Tóth SZ, Kozma-Bognár L, Szabados L (2019) Light control of salt-induced proline accumulation is mediated by ELONGATED HYPOCOTYL 5 in Arabidopsis. Front. Plant Sci. 10:1584.

14.        Papdi Cs, Ábrahám E, Joseph MP, Popescu C, Koncz Cs, Szabados L (2008) Functional identification of Arabidopsis stress regulatory genes using the Controlled cDNA Overexpression System, COS. Plant Physiol. 147: 528–542.

15.        Papdi Cs, Pérez-Salamó I, Joseph MP, Giuntoli B, Bögre L, Koncz Cs, Szabados L (2015) The low oxygen, oxidative and osmotic stress responses synergistically act through the Ethylene Response Factor-VII genes RAP2.12, RAP2.2 and RAP2.3. Plant J. 82: 772-784

16.        Perez-Salamo I, Papdi C, Rigó G, Zsigmond L, Vilela B, Lumbreras V, Nagy I, Horvath B, Domoki M, Darula Z, Medzihradszky K, Bögre L, Koncz C, Szabados L (2014) The Heat Shock Factor A4A Confers Salt Tolerance and Is Regulated by Oxidative Stress and the Mitogen-Activated Protein Kinases MPK3 and MPK6. Plant Physiol 165: 319-334.

17.        Rigó G, Tietz O, Ayaydin F, Zsigmond L, Kovács H, Páy A, Salchert K, Szabados L, Palme K, Koncz Cs, Cséplö Á (2013) Inactivation of plasma-membrane localized CDPK-related kinase 5 decelerates PIN2 exocytosis and root gravitropic response. Plant Cell  25:1592-1608.

18.        Rigó, G., Valkai, I., Faragó, D., Kiss, E., Van Houdt, S., Van de Steene, N., Hannah, M. A., and Szabados, L. (2016) Gene mining in halophytes: functional identification of stress tolerance genes in Lepidium crassifolium. Plant, Cell & Environment, 39:2074-2084.

19.        Szabados L, Savouré A (2010) Proline: a multifunctional amino acid. Trends Plant Sci 15:89-97.

20.        Strichov N, Ábrahám E, Ökrész L, Blickling S, Zilberstein A, Schell J, Koncz C, Szabados L (1997) Differential expression of two P5CS genes controlling proline accumulation during salt-stress is regulated by ABA1, ABI1 and AXR2 in Arabidopsis.  Plant J. 12:557-569.

21.        Székely Gy, Ábrahám E, Cséplő Á, Rigó G, Zsigmond L, Csiszár J, Ayaydin F, Strizhov N, Jásik J, Schmelzer E, Koncz Cs, Szabados L (2008) Duplicated P5CS genes of Arabidopsis play distinct roles in stress regulation and developmental control of proline biosynthessis. Plant J. 53:11-28.

22.        Zsigmond L, Rigó G, Székely Gy, Ötvös K, Szarka A, Darula Zs, Medzihradszky KF, Koncz Cs, Koncz Zs, Szabados L (2008) Arabidopsis PPR40 connects abiotic stress responses to mitochondrial electron transport. Plant Physiol. 146:1721-1737.

Publications for the public

Szabados L (2014) A szárazság és sótűrés szabályozása a virágos növényekben. In.: A Növények Molekuláris Biológiájától a Zöld Biotechnológiáig. Ed.: Fehér A., Györgyey J. Akadémiai Kiadó, Budapest, pp. 192-210.

Szabados L., Györgyey J (2015) Molecular background of stress tolerance: lessons from plant systems. In: Selected Topics from Contemporary Experimental Biology. Biological Research Centre, Szeged, Hungary, Eds: Csaba Vágvölgyi, László Siklós, Vol. 2.  pp. 209-224.

Szabados L (2023) Extremofil növények. Növényi élet szélsőséges körülmények között. Kaleidoszkóp Könyvek kiadványsorozat, Libri Könyvkiadó, Budapest. 136 pages.

Patent applications

Szabados L, Zsigmond L, Koncz Cs: Improvement of stress tolerance in higher plants. Patent Application No.: P0500811, date:  31/08/2005

Szabados L, Koncz C, Ábrahám E, Papdi C, Joseph MP (2008) Controlled cDNA Overexpression System in Arabidopsis, Hungarian Patent No.: P0800351, 2008.05.30.