Understanding plant responses to environmental stress for improvement of crop productivity

1.  Understand responses to adverse environmental stresses like drought, high salinity or heavy metal stress or limited nutrients by investigating hormonal regulatory networks, and efficiency of nitrogen fixation and nutrient use (Fig. 1)
2.  Use this knowledge to improve productivity of crops like soybean, chickpea and maize through translational genomics

Lam-Son Phan Tran


Unit Leader
Signaling Pathway Research Unit

How would you express the theme of your work?

Our work has two sides. Ultimately, our lab undertakes a variety of activities that can lead to know-how gained in basic research using model plants, such as Arabidopsis and Medicago truncatula, to improve the productivity of crops, such as soybean, chickpea, maize, rice, radish and mustard, under adverse conditions.

To do this, (i) we are working on two basic research goals:
(a) Elucidate the hormonal regulatory networks and roles of signaling molecules in plant responses to drought, high salinity and heavy metals by studying the functions of various hormones, with the main focus on abscisic acid (ABA), cytokinin and strigolactone, and signaling molecules, and their interactions in plant adaptation to these stresses.
(b) Understand the specific mechanisms regulating symbiotic nitrogen fixation in various legume crops under drought and nutrient deficiency, such as phosphorous deficiency.

Then, (ii) we have the applied research goal focused on:
Applying what we learn to enhance crop productivity under adverse stress conditions to develop super crop plants (soybean for example) using translational genomics, which produce higher yield under field conditions with low nutrient input and/or under adverse environments.

Mission (1): Understanding plant responses to environmental stresses to improve crop productivity
(Figure by Tran L.S.)

How would you describe your Laboratory and working in CSRS at RIKEN?

We offer interesting and realistic research projects that are achievable by younger researchers and students, and good opportunities for training in many kinds of disciplines to help them build up their research careers. Currently, there are two international researchers in our lab; one research scientist from China and one International Program Associate (RIKEN IPA) graduate student from Vietnam. In addition, my lab has one Japanese technical staff and two Japanese part-timers. Thus, my lab is a quite international lab. In the past, we also hosted scientists from China, Iran, Sudan and Vietnam. We have established a large collaboration network that is crucial for our research.

I believe that both our basic and translational genomics research programs are original, competitive and quite attractive to researchers around the world. It is appealing as my research programs are interesting and have produced a good achievement in publication every year, and because I am an international PI who has built up a wide collaboration network.

How does your team act as a hub for signaling pathway-related science?

The most important strategy for us is to pursue basic science, and then to translate our know-how into application in collaboration with labs in Japan and around the world.

Our collaborators and we here do complementary research. It’s a win-win situation through collaborations with researchers from either developed or developing countries. Especially, in the field of translational genomics, collaborations from several developing countries can complement our needs very well. From our side, we advise our collaborators in developing countries to carry out their research in a publishable manner, so that they can publish their data. They can get advice and training from us, such as learning about and using our high technology as well as acquiring research techniques to publish. In balance, labs in developing countries have more manpower, greater greenhouse and field facilities to help us test our findings under more “real” conditions. They can do what we can’t do here. The research environment in some developing countries can be open to field research using transgenic and GMO-related technologies. We can benefit from their people’s field experience and their ability to test in the field and larger greenhouse facilities, so we need them. We try to do the maximum we can from here, and think how well we can translate this into applied research. At the end the final goal is we want to develop the super plant.

The combination means that we can work effectively with scientists around the world to achieve the common goal. That’s why you see other Japanese Institutions and those including Mexico, USA, Czech Republic, Germany, Egypt, Nigeria, Sudan, Bangladesh, China, India, Iran, Pakistan, Saudi Arabia and Vietnam among our collaborators to carry out basic research and to translate our knowledge from shared basic research to shared applied goals. This makes a situation beneficial for all parties.

How do signaling molecules and hormonal regulatory networks respond to abiotic stress?

One of the most exciting recent research that our lab has carried out was the original discovery that the strigolactone hormone plays key positive regulatory roles in plant responses to drought and salt stress (Ref.1). Under environmental stresses, such as drought and salinity, plants experience restricted growth and productivity. To cope with stresses, plants develop various mechanisms that are mediated by complex molecular signaling networks. Together with an international team of researchers in Vietnam, Mexico and Japan, we identified for the first time the previously unknown signaling pathway based on the hormone strigolactone that plays a key role in stress tolerance (Ref.2).

For our team’s groundbreaking research into this original idea about the function of strigolactone, we had to solve several areas together: the expressed characteristic of the phenotype, and the biochemical, physiological and molecular mechanisms. Most research on strigolactone has focused on its role in plant growth and development. We were the first to look at its role in regulation of abiotic stress responses in Arabidopsis. The synthesis and signaling of strigolactone in Arabidopsis plants are controlled by several genes known as More Axillary Growth (MAX) genes. Loss-of-function of these genes makes max mutant plants more sensitive to drought and salt stress than wild-type (WT) plants, indicating the positive regulatory role of strigolactone in plant responses to drought and high salinity.

In their potential crosstalk, strigolactone and ABA act as positive regulators, while cytokinin acts as a negative regulator
Plants integrate multiple hormonal pathways to provide complex and finely tuned responses to drought (Figure by Tran L.S.).

By examining differential gene expression between WT and max2 signaling mutant plants, we uncovered multiple genetic targets of the strigolactone pathway (Fig. 2). The expression of many of these genes were already known to be induced by drought, or the famous stress-related hormone ABA or both. In addition, several genes involved in cytokinin (CK) degradation were repressed in max2 mutant under normal and dehydration conditions. These results together suggest that plants integrate multiple hormonal pathways to provide complex and finely tuned responses to stress (Fig. 3). Our differential gene expression analysis also implied that under environmental stress plants reduce demands on resources by using strigolactone signaling to suppress photosynthesis. It’s possible that stress-inducible promoters could be used to switch on the strigolactone pathway when plants encounter stress. Thus, under normal growing conditions, the plants could grow without any yield penalty. This provides a basis to move, by manipulating genes in the strigolactone synthesis and response pathway, from the model plant Arabidopsis to developing genetically modified drought- and salt-tolerant crops.

There is an intriguing further possibility for growing crops under tough conditions. The application of artificial strigolactone, although expensive to manufacture at present, could possibly be used to increase tolerance to drought stress as an alternative to developing drought-tolerant transgenic crops.
In addition, we have been also studying the roles of CK and CK signaling in plant adaptation to drought and salt stress.

People who have interest in our CK-related research can read our papers below:

– Nishiyama et al. Plant Cell 23 (2011) DOI: 10.1105/tpc.111.087395
– Nishiyama et al. PLoS One 7 (2012) DOI: 10.1371/journal.pone.0032124
– Nishiyama et al. Proc Natl Acad Sci USA 110 (2013) DOI: 10.1073/pnas.1302265110
– Nguyen et al. Proc Natl Acad Sci USA 113 (2016) DOI: 10.1073/pnas.1600399113

How might studying nitrogen fixation lead to better crop performance?

For symbiotic N2-fixation (SNF)-related research, we are studying the mechanisms involved in SNF inhibition in soils suffering from phosphorus (P) deficiency, as well as drought (Ref.3,4). Phosphorus is one of the most important macronutrients for plant growth and development.  It is required for essential metabolic processes, such as photosynthesis, respiration and energy generation, especially in SNF legume plants. Because of the high energy requirements of N2-fixing nodules, P deficiency represents an important constraint for legume growth and crop production. On the other hand high P concentrations restrict nodule growth and symbiotic machinery with bacteria. Potentially, nodules play a part in maintaining P level balance, known as homeostasis, while acting as a strong sink for P allocation.  For this research, we have collaboration with researchers in Sudan, Iran, Nigeria and Germany.

Strategies to enhance N2 fixation efficiency under normal, drought and low phosphorus conditions
(Figure by Tran L.S.)

We were able to document that the SNF capacity of M. truncatula plants was greatly affected by P deficiency and that carbon metabolic capacity in this model plant was unexpectedly modified by activating the metabolic pathway for certain distinct organic acids. Additionally, we could begin to understand what concentrations of P are needed for legume plants to establish an efficient symbiotic association (Ref.5,6). Collectively, these findings have particular importance as basic information for future design of genetically modified legume crops.

We also conducted research to improve the SNF of chickpea, an important annual legume-type crop grown in over 50 countries across the Indian subcontinent, North Africa, the Middle East, Southern Europe, the Americas and Australia (Ref.7). We identified a Mesorhizobium ciceri strain that formed the best association with chickpea because it could induce nodules exhibiting enhanced malate formation. This finding suggests that genetically engineering malate formation in nodules might be a promising strategy for improving N2 fixation efficiency in chickpea and perhaps other leguminous crops.


1. Ha, C.V., Leyva-González, M.A., Osakabe, Y., Tran, U.T., Nishiyama, R., Watanabe, Y., Tanaka, M., Seki, M., Yamaguchi, S., Dong, N.V., Yamaguchi-Shinozaki, K., Shinozaki, K., Herrera-Estrella, L., Tran, L.S.
Positive regulatory role of strigolactone in plant responses to drought and salt stress.
Proc. Natl. Acad. Sci. USA, 111, 851-856 (2014)
DOI: 10.1073/pnas.1322135111
2. RIKEN Research Highlights Online: Surviving stressful situations (Mar. 2014) 
3. Nasr, E.M., Sulieman, S., Schulze, J., Yamaguchi-Shinozaki, K., Shinozaki, K., Tran, L.S.
Mechanisms of physiological adjustment of N2 fixation in Cicer arietinum L. (chickpea) during early stages of water deficit: single or multi-factor controls.
Plant J. 79, 964-980 (2014)
DOI: 10.1111/tpj.12599
4. Nasr, E.M., Kusano, M., Nguyen, K.H., Watanabe, Y., Ha, C.V., Saito, K., Sulieman, S., Herrera-Estrella, L., Tran, L.S.
Adaptation of the symbiotic Mesorhizobium-chickpea relationship to phosphate deficiency relies on reprogramming of whole-plant metabolism.
Proc. Natl. Acad. Sci. USA 113, E4610-4619 (2016)
DOI: 10.1073/pnas.1609440113
5. Sulieman, S., Schulze, J., Tran, L.S.
Comparative Analysis of the Symbiotic Efficiency of Medicago truncatula and Medicago sativa under Phosphorus Deficiency.
Int. J. Mol. Sci. 14, 5198-5213 (2013)
DOI: 10.3390/ijms14035198
6. Sulieman, S., Ha, C.V., Schulze, J., Tran, L.S.
Growth and nodulation of symbiotic Medicago truncatula at different levels of phosphorus availability.
J. Exp. Bot. 64, 2701-2712 (2013)
DOI: 10.1093/jxb/ert122
7. Nasr, E.M., Sulieman, S., Schulze, J., Yamaguchi-Shinozaki, K., Shinozaki, K., Tran, L.S.
Approaches for enhancement of N2 fixation efficiency of chickpea (Cicer arietinum L.) under limiting nitrogen conditions.
Plant Biotechnol J. 12, 387-397 (2014)
DOI: 10.1111/pbi.12146