Bioinformatics acid (ABA) signaling and drought stress tolerance.

Bioinformatics
in Environment

 

Biotic
& Abiotic Stress in Plants

We Will Write a Custom Essay Specifically
For You For Only $13.90/page!


order now

 

Introduction

Facing stressful
conditions imposed by their environment that could affect their growth and
their development throughout their life cycle, plants must be able to perceive,
to process, and to translate different stimuli into adaptive responses.
Understanding the organism-coordinated responses involves fine description of
the mechanisms occurring at the cellular and molecular level. These mechanisms
involve numerous components that are organized into complex transduction
pathways and networks, from signal perception to physiological responses. The
major challenge of plant signalling is to understand how the large diversity of
molecules identified as signals, sensors, or effectors could drive a cell to
the appropriate plant response, to cope with various environmental challenges.
The objective of this Research Topic is to give an overview of various signalling
mechanisms or to present new molecular signals involved in stress response and
to demonstrate how basic/fundamental research on cell signalling will help to
understand stress responses at the whole plant level. Under a changing climate,
drought becomes one of the most critical abiotic stresses that severely reduces
crop production. Molecular mechanisms involved in plant drought adaptation are
addressed in several articles/contributions. Reversible protein
phosphorylation, catalyzed by antagonistic activities of protein kinases and
phosphatases, is a predominant molecular switch controlling the outcome of cell
signaling after stress perception. Vilela et al. present an extensive review of
the role of Casein Kinase 2 (CK2), an evolutionary conserved Ser/Thr protein
kinase found in all eukaryotes, during abscisic acid (ABA) signaling and
drought stress tolerance. For instance CK2 has a pivotal role in the regulation
of ABA signaling through its action on Zea mays OST1/SnRK2.6 (Open Stomata
1/Sucrose Non Fermenting Kinase 2.6) a well-known Ser/Thr protein kinase
involved in ABA signaling (Kulik et al., 2011). Furthermore, CK2-dependent
phosphorylation enhances the stabilization and degradation of targeted
proteins. CK2 is thought to be a housekeeping kinase which finely controls ABA
signaling by mediating dynamic protein turnover. Another protein, this time
involved in genome reprogramming during ABA signaling was identified by Li et
al. They present new evidence showing interrelation between the transcription
factor NAC072 and ABA responsive element binding factor ABF3, a positive
regulator of ABA responsive gene expression. Interestingly, these two proteins
could cooperate or act antagonistically, revealing a dual function of NAC072.
ABA and other phytohormones could cooperate to orchestrate plant responses to
stress. The research article of Jia and Li reports an example of this process
known as hormone crosstalk in Arabidopsis, where ABA and ethylene accelerate
senescence. The authors show that the suppression of phospholipase D (PLD)
retards ethylene-promoted senescence (as previously reported for the
ABA-promoted senescence) through an elusive mechanism resulting in the
modification of plastidic lipid metabolism and maintenance of plasma membrane
integrity. Lovieno et al. using a RNA sequencing approach, report on global
transcriptomic changes associated with drought and rehydration in tomato.
Transcriptomic analyses together with physiological measurements,
quantification of metabolites and biometric parameters, yielded promising
candidate genes and that could be used as specific physiological markers of
plant drought response. Using a transgenic approach, two studies have
functionally validated the role of two transcription factors during drought
stress in rice and in soybean (Glycine max, Gm). Jiang et al. improved rice
drought tolerance by overexpressing the Arabidopsis thaliana transcription
factor WRKY57 (AtWRKY57) which was previously shown to enhanced drought
resistance in Arabidopsis (Jiang et al., 2012). AtWRKY57 is a positive regulator
of drought responses and appears to be a potential candidate gene for crop
improvement but, as reported by the authors the effect on plant productivity
should be analysed to validate this strategy. However, Zhang et al. show that
GmZFP3 (Gl. max Zinc Finger Protein 3) negatively regulates drought responses
when overexpressed in Arabidopsis. GIGANTEA (GI), a plant specific nuclear
protein, is a key component of flowering time regulation but is also known to
be involved in a multitude of physiological responses. Finally, Li et al.
report that mutation of Oryza sativa GI confers tolerance to osmotic stress and
regulates transcript abundance of some gene encoding ABA-induced proteins.
Tolerance to salinity and high temperature is also reviewed by Hanumanth Rao et
al. who presented an integrative view of mungbean responses from physiological,
biochemical, and molecular aspects to agronomical perspectives and field
management practices. Lastly, although Boron is considered as an essential  micronutrients for plants, abnormal
concentrations can be toxic and limit crop productivity. Fang et al. report
that boron could alter calcium signaling and actin filament organization thus
impacting on plant development (Malus domestica pollen tube growth). In
addition to their essential function in plant primary metabolism, several
molecules have now been considered as signal molecules. For instance, the
signaling function of sugars has become the focus of numerous research efforts.
Nguyen et al. using transgenic plants overexpressing sucrose synthase, reveal a
novel sugar signaling pathway controlling pronounced phenotypic changes in
tobacco. We can expect that future research will confirm the role of sugars
throughout all stages of the plant’s life cycle since sugar-signaling pathways
could interact with other stimuli such as phytohormones or light (Smeekens,
2000). Lipids could also be considered at the interface of plant stress
response and cellular primary metabolism. Levels of very long chain fatty acids
(>18C, VLCFA) are known to be modified under stressful conditions. Based on
preexisting data, De Bigault Du Grandrut and Cacas investigate through three
scenarios, the concept that these VLCFA could also participate in stress
signaling pathways. The authors proposed a model depicting the hypothetic role
of VLCFA in a very informative and synthetic figure. Small molecule such as the
diatomic gas carbon monoxide (CO), widely considered as detrimental, also
emerges as signaling molecule in plants. The review of Wang and Liao provides
brief update on its role in growth, development and abiotic stress tolerance.
CO has a positive effects on salt or heavy metal stresses in relation with
other signaling molecules, such as phytohormones or NO and ROS. Last but not
least, research conducted by Kim et al. reveals links between N metabolism and
epigenetics (gene methylation). They report that ammonium treatment inhibits chloromethylated
3-mediated methylation of the gene encoding one of the two nitrate reductase
isoform (Nia2) in Arabidopsis. These results bring new insights concerning the
regulation of nitrate assimilation and its signaling properties and open
interesting perspectives for the role of epigenetics in plant responses to
stress. Biotic stresses also cause major losses in crop productivity.
Deciphering mechanisms involved in plant defence to pathogens will help to
develop breeding and biotechnological strategies for crop protection. Durian et
al. provide an overview of the Protein Phosphatase 2A (PP2A) functions, a
crucial component that controls pathogenic responses in various plant species.
The authors describe, in an exhaustive manner, the connections of these
multifunctional enzymes with the signaling pathway that controls plant
immunity, cell death and more globally primary and secondary metabolism. Using
an elegant biochemical and targeted approach, Sheikh et al. reveal a
post-translational regulation of AtWKRY46 transcription factor by a
MAPK3-dependent phosphorylation that mediates the stability of this
transcription factor after PAMP elicitation in Arabidopsis. It is noteworthy
that knowledge about plant molecular responses to biotic stress is obtained
from model plants as well as from cultivated species. Thus, this topic reports
the identification of regulators of plant immunity in different economically
important crops. In soybean, Cheng et al. report the characterization of a
novel member of the isoflavone reductase gene family, GmIFR, regulated by
phytohormones (SA, ET, ABA) and involved in the resistance to the oomycete Phytophthora
sojae. Using a quite similar functionally transgenic approach, Dai et al. have
identified and characterized a new defense protein PR4-1 from a wild chinese
grape Vitis pseudoreticula. When overexpressed in Vitis vinifera, it improved
tolerance to powdery mildew. RNAseq methodology is now widely used to
investigate gene expression in response to microbes in non-model species. Based
on the analysis of the differentially expressed genes, Gao et al. propose a
model illustrating the main molecular responses and gum polysaccharide
formation in peach tree (Prunus persica) infected by Lasiodiplodia theobromae,
the fungal agent of peach tree gummosis.Yuan et al. compare by a RNAseq
approach two symbiotic systems with notable different nodulation phenotypes in
soybean roots. Many of the differentially expressed genes identified are
related to plant immunity and could explain the different nodulation
phenotypes. Their work highlights the delicate balance between beneficial and
detrimental effects of microbes and, as written by the authors, it “sheds new
light on the host legume control of nodulation specificity.”Crosstalk between
abiotic and biotic stress responses are the last aspect developed in this
topic. Comparative approaches can be interesting to test the hypotheses of
common signaling pathways and of physiological responses that are subject to
pleiotropic gene action. In a mini-review article, Ranty et al.provide a broad
perspective on the role of Ca 2+ in plant responses to abiotic and biotic
stress. The specific effects of this ubiquitous second messenger and the role
of calcium sensor proteins are discussed. The authors put forward hypotheses to
explain one crucial question of cell signaling: how are signals perceived and
how do cells respond spatially and temporally to these signals to program a
specific response at the organism level? More specifically, Sinha et al. have
examined the transcriptome dynamics in chickpea plants exposed to a combination
of water deficit stress and Ralstonia solanacearum infection and have
identified a set of genes uniquely expressed in response to combined stress.
Also comparing pathogenic and drought stress but focusing on the analysis of
redox homeostasis and the role phytohormones, Cui et al show that co-stress by
virus and drought had much severer effects than single stress in V. vinifera.
Finally, Singh and Jha have studied crosstalk between salt stress and the
bacteria Bacillus licheniformis HSW-16. They report biochemical and
physiological characterization associated with bacteria-induced systemic
tolerance to salt stress.

 

 

 

 

Mechanism
of Abiotic stress Tolerance in plant

Abiotic stresses such as drought, salinity and mineral toxicity
negatively impact growth, development, yield and seed quality of plants.
Similarly, large losses of grain yields in plants occur as a result of pathogen
attack, in particular during vulnerable stages of grain development and
germination. Stress perception and plant response occurs via signal transduction pathways that regulate expression of
several classes of stress responsive genes. Products of these genes include
those that are directly involved in plant protection and those that fulfil
regulatory functions. The first group of the gene products include chaperones,
osmotins, anti-freeze proteins, mRNA binding proteins, enzymes involved in
osmolyte biosynthesis, water channel proteins, sugar and proline transport
proteins, detoxification enzymes and a variety of proteases, as well as a range
of antimicrobial, insecticidal and other proteins and peptides. The proteins
with regulatory function involve transcription factors and those that are
engaged in signal transduction pathways, such as protein kinases and hormone
biosynthetic enzymes. Both classes of genes encoding these proteins are being
investigated using the tools of forward and reverse genetics. Once the stress
response pathways are defined and the key players during the plant response to
stress are demarcated by forward genetics approaches. Gene function can be
enhanced through reverse genetics approaches such as genetic engineering or
novel alleles can be sought through germplasm screening or mutagenesis. The
latter avenues offer alternatives to traditional breeding. The new knowledge
acquired through research of abiotic and biotic stress tolerance mechanisms in
plants will help in the application of stress responsive determinants and in
engineering plants with enhanced tolerance to stress.

 

 

 

 

Productivity
losses due to stress

 Loss due to diseases range from 20 to 30 %, in
case of severe infection, total crop may be lost

 Estimated
global loss due to insect pests in potential yields of all crops is ~14%.

 In India losses
due to insect pests ranges from 10 to 20 %

Abiotic stresses reduce average yield of crops by upto
50% (Bray EA 1997)

In India also 67% of the area is rain-fed and crops in
these areas invariably experience droughts of different magnitudes

Annually about 42% of the crop productivity is lost
owing to various abiotic stress factors ( Oerke et.al., 1994).

 

Stress
resistant crops are a dire need

  • Human population continues to increase: Nine
billion expected by 2050.

  • Global
warming and climate perturbations are likely to accentuate biotic as well as
abiotic         stresses

 

 

 

Plants must be stress resistant to survive

·       
Avoidance
also possible by morphological adaptations

·       
Deep
tap roots in alfalfa allow growth in arid conditions

·        
Desert
CAM plants store H2O in fleshy photosynthetic stems

·        
Stress resistant plants can tolerate a particular stress

·        
Resurrection
plants (ferns) can tolerate dessication of protoplasm to <7% H2O à can rehydrate dried leaves ·         Plants may become stress tolerant through     How Factors are Affecting to plants ·         View how they affect metabolism ·         Determine how the plant responds to counter the stress ·         ABIOTIC STRESS: Temperature ·         Plants exhibit a wide range of Topt (optimum temperature) for growth ·         We know this is because their enzymes have evolved for optimum activity at a particular T ·         Properly acclimated plants can survive overwintering at extremely low Ts ·         Environmental conditions frequently oscillate outside ideal T range ·         Deserts and high altitudes: hot days, cold nights ·         Three types of temperature stress affect plant growth ·         Chilling, freezing, heat   Responding to challenges posed by biotic and abiotic stresses through crop improvement • Every new objective added to a breeding programme almost doubles the magnitude of work • Unlike past successes (e.g., dwarf varieties), future increases in productivity potential are not likely to be accompanied by enhanced inputs • Genetic improvements need to be accomplished under demanding time frames Can routine   Anticipated abiotic stress induced crisis in Indo-Gangetic plains • Conventional rice cultivation may become unsustainable in the Indo-Gangetic plains due to ground water exploitation greatly in excess of recharge. Recharging of aquifers to be hit further by less rain and snow and shrinking of himalayan snow cover • Temperature effects predicted to be more pronounced in this region. Wheat with already strained adaptation in the region is likely to be hit hard. For every 1 C increase in mean temperature above normal, grain yield is reduced by 12-23 per cent.               Examples Of Some Stress Tolerance Plants     If a single abiotic stress is to be identified as the most common in limiting the growth of crops worldwide, it most probably is low water supply (Boyer, 1982; Araus et al., 2002). However, other abiotic stresses, notably salinity and acidity, are becoming increasingly significant in limiting growth of both forage grasses and the cereals. Globally, low temperature also is a major limitation of plant growth, and this has a major impact on grasses via, for example, vernalization and low temperature damage at anthesis. In this focus issue, there are articles addressing three aspects of these abiotic stresses. Traditional approaches to breeding crop plants with improved abiotic stress tolerances have so far met limited success (Richards, 1996). This is due to a number of contributing factors, including: (1) the focus has been on yield rather than on specific traits; (2) the difficulties in breeding for tolerance traits, which include complexities introduced by genotype by environment, or G × E, interactions and the relatively infrequent use of simple physiological traits as measures of tolerance, have been potentially less subject to G × E interferences; and (3) desired traits can only be introduced from closely related species. Most cereals are moderately sensitive to a wide range of abiotic stresses, and variability in the gene pool generally appears to be relatively small and may provide few opportunities for major step changes in tolerance. Of potentially larger impact on abiotic stress tolerance is the use of genetic manipulation technologies to generate such step changes. Having said this, more immediately achievable, if modest, increases in tolerance may be introgressed into commercial lines from tolerant landraces using marker-assisted breeding approaches (Dubcovsky, 2004), facilitated by recent breakthroughs with positional cloning (e.g. Yan et al., 2003, 2004) that are likely to enable identification of extant tolerance genes within cereal germplasms (see www.acpfg.com.au). Of course, the sequencing of the rice (Oryza sativa) genome provides an invaluable resource for work on rice and, by exploiting syntenic alignment with many other grasses (Devos and Gale, 2000), facilitates fine mapping in the unsequenced genomes of many other grasses. It is exploitation of this latest resource that, combined with steadily increasing transformation frequencies for many grasses, is making the functional genomics approach to the study and manipulation of abiotic stresses in grasses increasingly tractable. The need to use a model plant such as Arabidopsis (Arabidopsis thaliana) for such work is steadily decreasing, and will continue to do so, as the principles uncovered in this model organism are refined (or even supplanted) by knowledge gained in the plants that are the ones in which this knowledge needs to be applied (this means, of course, primarily the grasses, both cereals and forage species). Furthermore, in addition to the obvious fundamental differences in development and anatomy between monocotyledons and dicotyledons, many of the mechanisms of tolerance to abiotic stresses can have fundamentally different characteristics between these two major plant groups, so transferring knowledge from Arabidopsis to the major crops often is not possible. For example, when grown in saline soils, many dicotyledonous halophytes accumulate much higher concentrations of Na+ in their shoots than monocotyledonous halophytes, a feature that may be related to the observation that succulence is observed more commonly in dicotyledons than monocotyledons, particularly the grasses.The possibilities for increasing tolerance to abiotic stresses are enormous, although it is notable that the actual production of transgenic plants with demonstrably improved abiotic stress tolerance has been slow.                               Fig.  Examples Of Heat Stress Tolerance Plants                                 Fig. Effects On Plant Leaf Due to Some Abiotic Factors           References 1. Genome-Wide Characterization of Heat-Shock Protein 70s from Chenopodium quinoa and   Expression Analyses of Cqhsp70s in Response to Drought Stress. Liu J1, Wang R2, Liu W3, Zhang H4, Guo Y5, Wen R6. 2. A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.). Huynh BL1, Ehlers JD2, Huang BE3, Munoz-Amatriain M2, Lonardi S4, Santos JRP1, Ndeve A1, Batieno BJ5, Boukar O6, Cisse N7, Drabo I8, Fatokun C9, Kusi F10, Agyare RY10, Guo YN2, Herniter I2, Lo S2, Wanamaker SI2, Xu S2, Close TJ2, Roberts PA1. 3. Arabidopsis MLO2 is a negative regulator of sensitivity to extracellular ROS. Cui F1,2, Wu H3, Safronov O1, Zhang P1, Kumar R4, Kollist H5, Salojärvi J1, Panstruga R3, Overmyer K1. 4. Genome-wide analysis and expression profiles of glyoxalase gene families in Chinese cabbage (Brassica rapa L).Yan G1, Xiao X1, Wang N1, Zhang F1, Gao G1, Xu K1, Chen B1, Qiao J1, Wu X1. 5. Functional and DNA-protein binding studies of WRKY transcription factors and their expression analysis in response to biotic and abiotic stress in wheat (Triticum aestivum L.).Satapathy L1, Kumar D1, Kumar M1, Mukhopadhyay K1.