Integrative systems approaches to study plant stress responses

Abstract

The world’s population is growing at an alarming rate. As of 2010, out of 7 billion people in the world, 925 million are hungry. It represents 13.1 percent of the total world population, or almost 1 in 7 people are hungry (FAO). Climate change is increasingly viewed as a current and future cause of hunger and poverty. In the scenario of global climatic change, different biotic and abiotic stresses are severe threats to the agricultural production worldwide. In nature, plants are continuously stressed by exposure to multiple adverse conditions. The combined effect of multiple biotic and abiotic stresses is a major yield-limiting factor in agriculture. In such a situation, it is of utmost importance to take initiatives for genome scale molecular understanding of stress response mechanisms in plants, so that new stress resistant crop varieties can be developed. Recent developments in omics technologies (metabolomic, proteomic, transcriptomic, phenomics and more) have opened up a new dimension for conducting genome scale molecular studies to understand stress response mechanisms in plants. These studies have led to the revelation of extremely complex and interacting networks of various stress response processes. Statistical, mathematical and informatics driven analysis and integration of the enormous amount of data produced is a challenge. The combination of high throughput profiling techniques, bioinformatics tools and the knowledge of genetics will provide the ways by which to achieve a comprehensive understanding of biological processes related to stress responses in plants. Such knowledge can be translated further to develop better crop varieties.

This thesis presents a few such integrated studies, exploring different aspects of plant stress responses at the molecular and systems levels. I believe that the works presented in this thesis will significantly contribute towards a molecular understanding of plant stress response mechanisms at the systems level. The entire thesis has been divided into seven chapters.

Chapter 1 gives a brief introduction about the adverse effect of global climatic change on plant productivity due to intensified effects of various stress factors and its negative socioeconomic impact on human society. This chapter also briefly summarises the background of seven research papers presented in this thesis along with a review of contemporary works.

Chapter 2 (Paper I) describes why systems biology is useful to study plant stress biology, reviewing various approaches and computational tools available to plant biologists till date.

Chapter 3 (Paper II) explores common and stress specific response signatures by the host plant to two different biotic stresses. It provides a comparative understandings of Arabidopsis – Brevicoryne brassicae (aphid) and Arabidopsis –Pseudomonas syringae(bacteria) interactions at the systems level.

Chapter 4 (Paper III) uncovers the molecular stress response patterns in plants during the co-occurrence of multiple abiotic and biotic stresses. The main outcome is that transcriptome changes in response to combined stresses could not be predicted from the responses to single stress treatments. This chapter also presents a modular network topology based approach to identify functionally related stress responsive gene modules.

Chapter 5 (Paper IV) presents the intraspecific variation in stress response patterns among 10 Arabidopsis ecotypes during cold stress exposure. Using an in silico transcriptional regulatory network model during cellular responses to cold stress in Arabidopsis thaliana, a hypothesis is presented that differentially evolving regulatory networks play a crucial role in climate adaptation of plants.

Chapter 6 (Paper V) presents an in silico transcriptional regulatory network model in responses to 11 stresses (5 single and 6 combined) conditions in Arabidopsis thaliana reconstructed from microarray data using a robust algorithm - Network Component Analysis (NCA).

Chapter 7 presents two application cases as examples of translational research, how knowledge developed in lab can be used in crop plants.

a. (Paper VI) demonstrates how the omics and systems biology approach is useful in improving crop productivity and abiotic stress tolerance in cultivated Fragaria.

b. (Paper VII) presents a case study on developing transgenic Brassica napus MINELESS as a new model system to study plant insect interactions. During this study, activation of plant defense in Brassica napus L. cv. Westar and transgenic MINELESS plants after attack by Mamestra brassicae (cabbage moth) were analysed.