The role of small-RNAs in regulating stress-induced responses in Nicotiana attenuata [Elektronische Ressource] / Shree Prakash Pandey

Ps2

Sujets

• Biologie

Informations

• Publié par: friedrich-schiller-universitat_jena
• Publié le: 01 janvier 2008
• Nombre de lectures: 33
• Langue: Deutsch
• Poids de l'ouvrage: 1 Mo

Extrait

The role of small-RNAs in regulating stress-induced
responses in Nicotiana attenuata



Dissertation

Zur Erlangung des akademischen Grades
doctor rerum naturalium (Dr. rer. nat.)


vorgelegt dem Rat der Biologisch-Pharmazeutischen Fakultät
der Friedrich-Schiller-Universität Jena



von Master of Science (Agriculture) in Genetics and Plant Breeding
Shree Prakash Pandey
geboren am 28. 07. 1978 in Varanasi, India



















Gutachter
1. Prof. Dr. Ian T. Baldwin

2. Prof. Dr. Ralf Oelmüller

3. Prof. Dr. Detlef Weigel



Tag der Doktoprüfung: 11.01.2008
Tag der öffentlichen verteidigung: 30.01.2008

Table of Contents

1. INTRODUCTION .................................................................................................................1
1.1 Stress and Stress responses ...........................................................................................1
1.2 Phenotypic plasticity......................................................................................................2
1.3 Nicotiana attenuata .......................................................................................................4
1.4 The world of small-RNAs...............................................................................................5
MANUSCRIPT OVERVIEW ..................................................................................................8
Manuscript I ........................................................................................................................8
Manuscript II .......................................................................................................................9
Manuscript III....................................................................................................................10
Manuscript IV....................................................................................................................11
2. MANUSCRIPTS..................................................................................................................12
2.1 Manuscript I ................................................................................................................12
2.2 Manuscript II ...............................................................................................................43
2.3 Manuscript III..............................................................................................................65
2.4 Manuscript IV............................................................................................................105
3. DISCUSSION.....................................................................................................................134
3.1 Small-RNA pathways: diversification and specialization .........................................134
3.2 Determining the role of small-RNAs .........................................................................136
3.3 Conclusions ...............................................................................................................140
4. SUMMARY........................................................................................................................143
5. ZUSSAMMENFASSUNG ................................................................................................145
6. REFERENCES ..................................................................................................................148
7. ACKNOWLEDGEMENT ................................................................................................150
8. DECLARATION OF INDEPENDENT ASSIGNMENT...............................................151
9. CURRICULUM VITAE ...................................................................................................152
10. APPENDIX ......................................................................................................................155
10.1 Supporting materials for Manuscript I....................................................................155
10.2 Supporting materials for Manuscript II...................................................................155
10.3 Supporting materials for Manuscript III .................................................................156
10.4 Supporting materials for Manuscript IV .................................................................157
1.1 Stress and Stress responses 1. Introduction
1. Introduction

Plants, which are mostly autotrophic, appear to be sessile. However, within the plants
are numerous pathways running to give them a stabilized appearance in nature. These
pathways allow the plants to develop, grow, reproduce, disperse, adapt and evolve. On the
other hand, cast-iron presence in the space puts plants under tremendous pressure from the
environment. Environmental heterogeneity is the most important selective force of nature.
Biotic and abiotic agents of environment constantly test plants: abiotic agents include limited
water and soil resources, salinity, cold, high temperatures, wind, mechanical damage, etc.;
biotic stresses include invading pathogens (viruses, bacteria, fungi), nematodes, herbivores
(e.g. insects, mammals), etc. Such abiotic and biotic stresses require the plants to make
maxium use of the available resources, and to design strategies for tolerance, defense and
escape. Whereas pathogens colonize and spread across plant parts, damage by herbivores
removes appreciable plant area and biomass. To check the loss of photosynthetic area, plants
need to evolve defense strategies; to compensate for the loss of photosynthetic area, they need
regeneration strategies.
In order to respond and adapt to their dynamic environments, plants derive “cues” (or
detectable information) from their abiotic and biotic surrounding. In abiotic environments,
these cues include changes in ionic strength, disruption of membranes, etc. (Bray, 1997;
Braam, 2005) , whereas in biotic environments, cues include chemical compounds, wounding
patterns, and volatile organic compounds emitted by neighboring plants, etc., (Alborn et al.,
1997; Schmelz et al., 2006; Gershenzon, 2007). In their natural habitats (and also elsewhere),
plants are constantly exposed to such cues. This exposure presents plants with challenges:
which changes in their environment should they respond to? More important, how should they
decide if a change is “a stress”?
1.1 Stress and Stress responses

Stress and Stress responses: conquering to adapt and adapting to conquer
Biological stress has been defined as any change in environment that might reduce or
adversely change a plant’s growth or development; biological strain refers to reduced or
changed function (Levitt, 1972, 1980). In their natural habitats, plants respond to a plethora of
- 1 - 1.2 Phenotypic plasticity 1. Introduction
stresses that impose high fitness costs. These responses involve the perception, processing,
and integration of external information into the cellular and physiological machinery. These
responses may be (i) a strategy to defend and/or to adapt to the changes in environment or (ii)
an outcome of an adaptation strategy evolved over time due to the presence of a persistent
stress across generations in the eco-physiological niche of the organism. As an outcome of
first the responses are more induced, and the second, more of constitutive nature.
Phytohormones are important compounds having multiple functions: they act as
signals, integrate different cellular processes, and sometimes regulate the biosynthesis of other
phytohormones. These chemical compounds amalgamate the externally perceived information
into regulatory processes such as stimulated or suppressed growth, apoptosis, immune
responses, metabolism, and reproduction. For a chemical compound to be a phytohormone
signal, it should (1) be synthesized or secreted, (2) be transported and perceived at the receiver
location, (3) activate an enzymatic reaction or process, and (4) be metabolized or excluded
from the site of action, so as to terminate the response at the end. Phytohormones traditionally
described as growth regulators are abscisic acid, auxins, cytokinins, ethylene, and gibberellins.
Phytohormones associated with plants’ defenses responses, especially to herbivores and
pathogens, are jasmonic acid and salicylic acid. Figuring out how these phytohormones act in
regulatory circuits and, further, how plant phenotypes evolve, are challenges plant researchers
face.

1.2 Phenotypic plasticity
Phenotypic plasticity as the driving force in circumventing stress
The ability of an individual to alter its physiology, morphology, and/or behavior in
response to a change in environment is called phenotypic plasticity. Phenotypic plasticity can
be defined simply as environmentally dependent phenotypic expression. Plants have the
capacity to respond differently to different envir