Contact
French Associates Institute for Agriculture and Biotechnology of Drylands

Jacob Blaustein Institute for Desert Research

BGU, Sede-Boqer Campus, 84990, Israel

Telephone: +972-8-6596750

Fax: +972-8-6596752

E-mail: simon@bgu.ac.il

 

Born: 1965, UK.

Associate Professor, The Jacob Blaustein Institute for Desert Research, BGU (2017)

 

Research Activities: 

 

1. Isolation and charaterization of genes regulating plant responses to environmental stress:

My lab's objective has been to isolate and characterize genes that regulate the overall response of plants to environmental stress and that might be good candidates for engineering crop plants for enhanced stress tolerance. We employ systems biology and classic molecular biology approaches using both Arabidopsis and stress-tolerant Arabidopsis relatives to identify and characterize potential stress-regulatory genes:

a) Systems biology approach to understanding global Arabidopsis responses to abiotic stress: Thanks to spectacular advances in the high-throughput “omics" disciplines and in information and communication technologies, systems biology approaches have the potential to provide a mechanistic understanding of the processes by which genetic change translates to phenotype. We are using systems biology to determine what constitutes the global genetic and metabolic response of Arabidopsis to specific abiotic stresses and what gene expression and metabolic changes are common between stresses. To facilitate answering these questions, we constructed a “stress gene" database incorporating hundreds of microarray datasets from public databases (GEO, ArrayExpress and AtGenExpress). Datasets were reanalyzed (quality control, normalization) and cover ten different abiotic stresses (abscisic acid (ABA) treatment, drought, high light, low and high temperatures, osmotic, oxidative, ozone, salinity and ultra-violet radiation) over a range of timecourse experiments. In collaboration with Prof. Gideon Grafi, Drs. Aaron Fait, Esti-Yeger Lotem, Vered Chalifa-Caspi (BGU), Dr. Matthew Hannah (Bayer CropScience), Prof. Laszlo Bogre and Dr. Alberto Paccanaro (University of London) we are using the database to: (i) explore common and specific stress responses;  (ii) examine whether a common response of cells to abiotic stress converges on cellular dedifferentiation whereby cells first acquire stem cell-like state before assuming a new cell fate; (iii) determine stress-specific and common gene and metabolic networks.

We have also used the stress gene database to identify and characterize genes that regulate Arabidopsis responses to a range of abiotic stresses. We queried the database for a set of genes whose expression was affected early on by multiple abiotic stresses. This gene set was further refined to include only those genes encoding regulatory proteins. T-DNA insertion mutants defective in each of these regulatory genes are being tested for altered sensitivity to different abiotic stresses [ref. 3]. This project is in collaboration with Bayer CropScience.

b) The role of DEAD-box RNA helicases in regulating Arabidopsis stress responses: Among the mutants identified using our stress gene database, two were defective in genes encoding different DEAD-box RNA helicases whose expression exhibits down-regulation in response to multiple stresses. The mutants showed increased tolerance to stress compared to wild-type and increased accumulation of transcripts encoding stress-responsive genes. We thus hypothesized that these two genes play a role in attenuating responses to abiotic stress. We designated the two genes STRESS RESPONSE SUPPRESSOR (STRS) 1 and STRS2 and showed that they represent nodes linking ABA-dependent and ABA-independent multiple stress signaling networks [ref. 5]. Although little is known regarding the function of the over 50 DEAD-box RNA helicase present in the Arabidopsis genome, in non-plant organisms these proteins are involved in all aspects of RNA metabolism particularly within supramolecular complexes (e.g. ribosome biogenesis, transcription, pre-mRNA splicing, mRNA export, RNA degradation, translation initiation) and are thought to function either as RNA chaperones that promote the formation of optimal RNA structure by local unwinding activity or by mediating RNA-protein association/dissociation We are continuing our research to understand the functions of these intriguing proteins and using GFP and RFP localization, we have recently shown that STRS1 and STRS2 are localized to the the nucleolus and nucleoplasm. We are now performing a detailed examination of the sub-nuclear localization of STRS1 and STRS2 as well as identifing STRS RNA targets and protein partners in collaboration with Prof. Gideon Grafi (BGU), Prof. Jian-Kang Zhu (University of California, Riverside) and Prof. Nam-Hai Chua (Rockefeller University).

 

2. Using Arabidopsis relatives to understand the mechanisms underlying wild-species adaptation to stress:

The model plant Arabidopsis thaliana is largely a stress-sensitive species and is unlikely to possess many stress tolerance mechanisms that are functional in naturally stress-tolerant plants. However, a major problem with studying naturally stress-tolerant plants such as those found in the desert is that it is often difficult to carry out in-depth molecular analyses due to the lack of molecular tools and the inability to introduce genes into these plants. On the other hand, wild stress-tolerant relatives of Arabidopsis belonging to the Cruciferae family are likely to be amenable to molecular studies due to their genetic similarity to Arabidopsis. This means that they can be brought into the lab and full arsenal of the molecular tools developed for Arabidopsis can be employed in investigating mechanisms underlying natural adaptation to stress.

a) Characterization of the mechanisms of salt tolerance of Thellungiella halophila. Thellungiella halophila (salt cress) is a highly salt-tolerant Arabidopsis relative. We have demonstrated that Thellungiella accumulates salt to a lower extent than Arabidopsis and that expression of the gene encoding the plasma membrane Na+/H+ antiporter, SOS1 is higher in unstressed Thellungiella and is more strongly induced by salt stress in Thellungiella than in Arabidopsis. Furthermore, Thellungiella exhibits both higher unstressed levels of the osmoprotectant proline and accumulates more proline under salt stress than Arabidopsis. Expression of a Thellungiella ortholog of the Arabidopsis gene encoding PROLINE DEHYDROGENASE (PDH), which degrades proline is undetectable in Thellungiella shoots while PDH enzyme activity is approximately half that of Arabidopsis. Taken together, these results suggest that differential regulation of gene expression between glycophytes and halophytes is a basis for the ability of halophytes to withstand extreme levels of salinity [ref. 7].

In collaboration with Prof. Steven Rothstein (University of Guelph), we have discovered that Thellungiella is also tolerant to nitrogen-limiting soil conditions. We were able to show that Thellungiella maintains growth under severe nitrate limitation by maintaining the level of nitrate-assimilating enzyme activity whereas in Arabidopsis (which is sensitive to N-limitation) enzyme activity declines. Furthermore, maintenance of nitrate-assimilating enzyme activity in Thellugiella is correlated with maintenance of expression of the corresponding genes. These results again support the idea that differential regulation of gene expression contributes to the higher tolerance to stress of Thellungiella compared to Arabidopsis [ref. 2].

We are now focusing on deep phenotyping (phenomics) of leaf development in Arabidopsis and Thellungiella under salt stress and linking phenotype to phosphoproteomic and metabolic responses in collaboration with Dr. Aaron Fait (BGU) and Prof. Laszlo Bogre (University of London).

(b) Multiple stress tolerance mechanisms in Arabidopsis relatives from the Negev Desert: We have been screening cruciferae from the Negev Desert for tolerance to multiple abiotic stresses. In collaboration with Prof. Yitzhak Gutterman, Dr. Shir-li Bar-David and Dr. Aaron Fait, we are evaluating the diversity of metabolic response to stress across stress-sensitive and stress-tolerant cruciferae to determine whether specific metabolites are associated with distinct stress-tolerant phylogenetic clade(s) and therefore indicate evolutionary adaptation.

One specific Negev crucifer that has been of particular interest is Anastatic heirochuntica (Rose of Jericho). We have found that this plant is tolerant to multiple abiotic stresses including salt, drought, heat and cold stresses. It also exhibits photochemistry suggesting adaptation to high light intensities. With the help of many of the French Associates Institute's plant scientists including Profs. Gideon Grafi, Yitzhak Gutterman, Moshe Sagi, and Drs. Shimon Rachmilevitch, Aaron Fait and Noemi Tel-Zur, we are now intensively investigating the physiological, biochemical and genetic mechanisms responsible for the natural stress tolerance of this species. We hope to sequence the Anastatica transcriptome using next generation sequencing techniques, which will also allow us to use systems biology approaches to establish Anastatica as a model stress tolerant plant.

 

3. The development of root architecture in response to salt stress:

Surprisingly little is understood regarding how plant roots respond to stress. This is particularly important since roots have an essential role in maintaining plant water status and in nutrient acquisition.  Effective water and nutrient acquisition depends not only on the amount of root but also on the three-dimensional deployment of the root (the root architecture), which is highly responsive to nutrient availability and distribution in the soil. Our objective is to understand how salt-stress affects the development of Arabidopsis root architecture. The main research strategy involves the growth of Arabidopsis seedlings on segmented nutrient agar plates that are placed vertically so that the roots grow along the plane of the agar and their development can be easily observed. Localized salt and/or nitrate treatments that cause lateral root (LR) proliferation are applied either to defined sections of the growing root or to the whole root. Our research has demonstrated that localized salt stress leads to stimulation of LR proliferation whereas LR length is reduced. Exposure of roots to nitrate (NO3-)-rich nutrient medium dramatically enhances salt stress stimulation of lateral root proliferation, thereby compensating for the decreased lateral root length and maintaining overall lateral root surface-area. Increased lateral root proliferation is specific to salt stress and is due to the progression of more lateral root primordia into mature lateral roots in salt-stressed plants. In salt-stressed roots, greater numbers of lateral root primordia exhibit expression of a reporter gene driven by the auxin-sensitive DR5 promoter than in unstressed roots. Moreover, in the auxin transporter mutant aux1-7, NO3--enhanced salt stress stimulation of lateral root proliferation is completely abrogated. The results suggest that salt stress promotes auxin accumulation in developing primordia thereby preventing their developmental arrest. Examination of ABA and ethylene mutants revealed that ABA synthesis and a component of the ethylene signaling pathway are also required for NO3--enhanced salt stress stimulation of lateral root proliferation [ref. 1].

 

Education:

1995-1999:   Ph.D, Ben-Gurion University of the Negev, Jacob Blaustein Insts. for Desert

                   Research. Thesis Title: The involvement of light and a light-dependent plastid

                   signal in control of expression of the tobacco gene encoding photorespiratory

                   glycolate oxidase.

1992-1994:   M.Sc. (magna cum laude) Ben-Gurion University of the Negev, Jacob Blaustein

                   Insts. for Desert Research. Thesis Title: Promoter identification of a gene

                   encoding glycolate oxidase, a peroxisomal enzyme of the photorespiratory

                   pathway

1985-1988:   B.Sc. (Hons), University of Nottingham, UK, Faculty of Agricultural Science.. 

 

Professional Activities:

Professional consulting

- Scientific manuscript reviewer for: Plant Physiology, Plant Journal, Planta, Physiologia   

   plantarum,BMC, Plant Biology, Plant Cell Reports.

Grant proposal reviewer for: Israel Science Foundation, BARD, Austrian Science Fund.

- Organizer of session entitled “Stress responses" at the 5th Congress of the Federation of the Israeli

   Societies for Experimental Biology, “ILANIT", Eilat, 2008.

 

Membership in professional/scientific societies

2004 to present: American Society of Plant Biologists

 

Awards, and Fellowships:

2002-2009: Ben-Gurion University of the Negev, Sonnenfeldt-Goldman Career Development Chair for

                   Desert Studies

 2010:          Marie Curie Intra-European Fellowship

 

Scientific Publications:

Editorship of collective volumes

1. Farrant G, Barak S (2016) Guest Editors, Special Issue: Extremophytes: Lessons learnt from plants living on the edge. Functional Plant Biology 43: 570-708.

2. Barak S (2015) Editorial - From systems biology to gene function: Discovering new determinants of plant tolerance to abiotic atresses. Transcriptomics 3: 1.

3. Grafi G, Barak S, Guest Editors. (2015) Special Issue: Stress as a fundamental theme in cell plasticity. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms 1849: 369-462.

 

Refereed articles in scientific journals:

 

Kazachkova Y, Eshel G, Pantha P, Cheeseman JM, Dassanayake M, Barak S (2018) Halophytism: What have we learnt from Arabidopsis relative Model Systems? Plant Physiology In press DOI

Tayeh Z, Dudai N, Schechter A, Chalifa-Caspi V, Barak S, Ofir R (2018) Molecular action of Asteriscus graveolens as an anticancer agent. International Journal of Molecular Sciences 19: E2162.

Oscar MA, Barak S, Winters G (2018) The tropical invasive seagrass, Halophila stipulacea, has a superior ability to tolerate dynamic changes in salinity levels compared to its freshwater relative, Vallisneria americana. Frontiers in Plant Science 9: 950

Eshel G, Shaked R, Kazachkova Y, Khan A, Eppel A, Cisneros A, Acuna T, Gutterman Y, Tel-Zur N, Rachmilevitch S, Fait A, Barak S (2017) Anastatica hierochuntica, an Arabidopsis desert relative, is tolerant to multiple abiotic stresses and exhibits species-specific and common stress tolerance strategies with its halophytic relative, Eutrema (Thellungiella) salsugineum. Frontiers in Plant Science 7: 1992.

Pal S, Zhao J, Khan A, Yadav NS, Batushansky A, Barak S, Rewald B, Fait A, Lazarovitch N, Rachmilevitch (2016) Paclobutrazol induces tolerance in tomato to deficit irrigation through diversified effects on plant morphology, physiology and metabolism. Scientific Reports 6: 39321.

Kazachkova Y, Khan A, Acuña T, López-Díaz I, Carrera E, Khozin-Goldberg I, Fait A, Barak S (2016) Salt induces features of a dormancy-like state in seeds of Eutrema (Thellungiella) salsugineum, a halophytic relative of Arabidopsis. Frontiers in Plant Science 7: 1071.

Meir M, Ransbotyn V, Raveh E, Barak S, Tel-Zur N, Zaccai, M (2016)  Dormancy release and flowering time in Ziziphus jujuba Mill., a “direct flowering" fruit tree, has a facultative requirement for chilling. Journal of Plant Physiology 192: 118-127.

Toubiana D, Batushansky A, Tzfadia O, Scossa F, Khan A, Barak S, Zamir D, Fernie A, Nikoloski, Z, Fait A (2015) Combined correlation-based network and mQTL analyses efficiently identified loci for branched chain amino acid, serine to threonine, and proline metabolism in tomato seeds. Plant Journal 81: 121-133.

Barak S, Yadav N, Khan A (2014) DEAD-box RNA helicases and epigenetic control of abiotic stress-responsive gene expression. Plant Signaling and Behavior 9: e977729.

Ransbotyn V, Yeger-Lotem E, Basha O, Acuna T, Verduyn C, Gordon M, Chalifa-Caspi V, Hannah MA, Barak S (2015) A combination of gene expression ranking and co expression network analysis increases discovery rate in large scale mutant screens for novel Arabidopsis thaliana abiotic stress genes. Plant Biotechnology Journal 13: 501-513.

Grafi G, Barak S (2015) Stress induces cell dedifferentiation in plants. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1849: 378-384.

Khan A, Garbelli A, Grossi S, Florentin A, Batelli G, Acuna T, Zolla G, Kaye Y, Paul LK, Zhu JK, Maga G, Grafi G, Barak S (2014) The Arabidopsis STRESS RESPONSE SUPPRESSOR DEAD-box RNA helicases are nucleolar- and chromocenter-localized proteins that undergo stress-mediated relocalization and are involved in epigenetic gene silencing. Plant Journal 79: 28-43.

║Eppel A, Shaked R, Eshel G, Barak S, Rachmilevitch S. (2014) Low induction of non-photochemical quenching and high photochemical efficiency in the annual desert plant Anastatica hierochuntica. Physiologia plantarum. 151: 544-558.

Kazachkova Y, Batushansky A, Cisneros A, Tel-Zur N, Fait A, Barak S (2013) Growth platform-dependent and -independent phenotypic and metabolic responses of Arabidopsis and its halophytic relative, Eutrema salsugineum, to salt stress. Plant Physiology, 162: 1583-1598.

Bai B, Sikron N, Gendler T, Kazachkova Y, . Bai B, Sikron N, Gendler T, Kazachkova Y, Barak S, Grafi G, Khozin-Goldberg I, Fait A ( 2011) Ecotypic variability in the metabolic response of seeds to diurnal hydration–dehydration cycles and its relationship to seed vigor. Plant and Cell Physiology, 53: 38-52.

Grafi G, Chalifa-Caspi V, Nagar T, Plaschkes I, Barak S, Ransbotyn V (2011) Plant response to stress meets dedifferentation. Planta 233: 433-438.

Zolla G, Heimer YM, Barak S (2010) Mild salinity stimulates a stress-induced morphogenic response in Arabidopsis thaliana roots. Journal of Experimental Botany, 61: 211-224.

Kant S, Bi YM, Weretilnyk E, Barak S and Rothstein SJ (2008) The Arabidopsis halophytic relative, Thellungiella halophila, tolerates nitrogen-limiting conditions by maintaining growth, nitrogen uptake and assimilation. Plant Physiology, 147: 1168-1180.

Kant P, Gordon M, Kant S, Davydov O, Heimer YM, Kalifa-Caspi V, Shaked R and Barak S (2008) Functional genomics-based identification of genes that regulate Arabidopsis responses to multiple abiotic stresses. Plant, Cell and Environment, 31: 697-714.

‡Andronis C, Barak S, Knowles SM, Sugano S and Tobin EM (2008) The clock protein CCA1 and the bZIP transcription factor HY5 physically interact to regulate gene expression in Arabidopsis. Molecular Plant, 1: 58-67.

Kant PK, Kant S, Gordon M, Shaked R and Barak S (2007) STRESS RESPONSE SUPPRESSOR1 and STRESS RESPONSE SUPPRESSOR2, two DEAD-Box RNA helicases that attenuate Arabidopsis responses to multiple abiotic stresses. Plant Physiology, 145: 814-830.

Kant S, Verma PK, Lips H and Barak S (2007). Partial substitution of NO3- by NH4+ fertilization increases ammonium assimilation enzyme activities and reduces the deleterious effects of salinity on the growth of barley. Journal of Plant Physiology, 164: 301-311.

Kant S, Kant PK, Raveh E and Barak S (2006) Evidence that differential gene expression between the halophyte Thellungiella halophila and Arabidopsis thaliana is responsible for higher levels of the compatible osmolyte proline and tight control of Na+ uptake in T. halophila. Plant, Cell and Environment, 29: 1220-1234.

Barak S, Heimer Y, Nejidat A and Volokita M (2001) Transcriptional and   posttranscriptional regulation of a glycolate oxidase gene in tobacco seedlings. Plant Molecular Biology, 45: 399-407.

Barak S, Tobin EM, Andronis C, Sugano S and Green RM (2000) All in good time: the Arabidopsis circadian clock. Trends in Plant Science, 5 (12): 517-522.

Barak S, Heimer Y, Nejidat A and Volokita M (2000) The peroxisomal glycolate oxidase gene is differentially expressed in yellow and white sectors of the D-P1 variegated tobacco mutant. Physiologia Plantarum, 110:120-126.

JH Li, J Gale, A Novoplansky, S Barak and M Volokita (1999) Response of tomato plants to saline water as affected by carbon dioxide supplementation. II: Physiological responses. Journal of Horticulture and Biotechnology, 74: 238-242.

Barak S, Nejidat A and Volokita M (1998) Promoter activity of the 5' flanking region of a tobacco glycolate oxidase gene in transgenic tobacco plants. Biochimica et Biophysica Acta, 1399: 105-110.

 

║These papers were featured on the cover of the journal.

‡Joint first author