Photosynthesis : genetic, environmental and evolutionary aspects

336 Pages·2011·9.273 MB·337 p.) ill., maps\336

by  Philip Stewart, Sabine Globig

Photosynthesis
Genetic, Environmental and
Evolutionary Aspects
© 2011 by Apple Academic Press, Inc.
Research Progress in Botany
Photosynthesis
Genetic, Environmental and
Evolutionary Aspects
Philip Stewart, PhD
Head, Multinational Plant Breeding Program; Author;
Member, US Rosaceae Genomics, Genetics and
Breeding Executive Committee; North Central Regional Association
of State Agricultural Experiment Station Directors, U.S.A.
Sabine Globig
Associate Professor of Biology, Hazard Community
and Technical College, Kentucky, U.S.A.

Apple Academic Press
© 2011 by Apple Academic Press, Inc.
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Contents
Introduction 7
1. Chloroplast Two-Component Systems: Evolution of the Link 9
between Photosynthesis and Gene Expression
Sujith Puthiyaveetil and John F. Allen
2. Ecological Selection Pressures for C Photosynthesis in the Grasses 38
4
Colin P. Osborne and Robert P. Freckleton
3. Modeling the Fitness Consequences of a Cyanophage-Encoded 56
Photosynthesis Gene
Jason G. Bragg and Sallie W. Chisholm

4. An Evaluation of the Effects of Exogenous Ethephon, an 78
Ethylene Releasing Compound, on Photosynthesis of Mustard
(Brassica juncea) Cultivars that Differ in Photosynthetic Capacity
N. A. Khan
5. High-Susceptibility of Photosynthesis to Photoinhibition in the 88
Tropical Plant Ficus Microcarpa L. f. cv. Golden Leaves
Shunichi Takahashi, Ayumu Tamashiro, Yasuko Sakihama,
Yasusi Yamamoto, Yoshinobu Kawamitsu and Hideo Yamasaki
6. The Role of Chlorophyll b in Photosynthesis: Hypothesis 103
Laura L. Eggink, Hyoungshin Park and J. Kenneth Hoober
© 2011 by Apple Academic Press, Inc.
6 Photosynthesis: Genetic, Environmental and Evolutionary Aspects
7. Exploring Photosynthesis Evolution by Comparative Analysis of 118
Metabolic Networks between Chloroplasts and Photosynthetic
Bacteria
Zhuo Wang, Xin-Guang Zhu, Yazhu Chen, Yuanyuan Li, Jing Hou
and Yixue Li and Lei Liu
8. Effects of Cu2+, Ni2+, Pb2+, Zn2+ and Pentachlorophenol on 139
Photosynthesis and Motility in Chlamydomonas Reinhardtii in
Short-Term Exposure Experiments
Roman A. Danilov and Nils G. A. Ekelund
9. Comparative Genomic Analysis of C Photosynthetic Pathway 154
4
Evolution in Grasses
Xiyin Wang, Udo Gowik, Haibao Tang, John E. Bowers,
Peter Westhoff and Andrew H. Paterson
10. The Accent-Vocbas Field Campaign on Biosphere-Atmosphere 188
Interactions in a Mediterranean Ecosystem of Castelporziano (Rome):
Site Characteristics, Climatic and Meteorological Conditions,
and Eco-Physiology of Vegetation
S. Fares, S. Mereu, G. Scarascia Mugnozza, M. Vitale, F. Manes,
M. Frattoni, P. Ciccioli, G. Gerosa and F. Loreto
11. Molecular Adaptation During Adaptive Radiation in the Hawaiian 221
Endemic Genus Schiedea
Maxim V. Kapralov and Dmitry A. Filatov
12. Analysis of the Chloroplast Protein Kinase Stt7 during State 239
Transitions
Sylvain Lemeille, Adrian Willig, Nathalie Depège-Fargeix,
Christian Delessert, Roberto Bassi and Jean-David Rochaix

13. A Rapid, Non-Invasive Procedure for Quantitative Assessment 266
of Drought Survival Using Chlorophyll Fluorescence
Nick S. Woo, Murray R. Badger and Barry J. Pogson
14. CO Assimilation, Ribulose-1,5-Bisphosphate Carboxylase/ 289
2
Oxygenase, Carbohydrates and Photosynthetic Electron
Transport Probed by the JIP-Test, of Tea Leaves in Response to
Phosphorus Supply
Zheng-He Lin, Li-Song Chen, Rong-Bing Chen, Fang-Zhou Zhang,
Huan-Xin Jiang and Ning Tang
Index 316
© 2011 by Apple Academic Press, Inc.
introduCtion
Although photosynthesis can happen in different ways in different species, some
features are always the same. For example, the process always begins when energy
from light is absorbed by proteins called photosynthetic reaction centers that con-
tain chlorophylls. In plants, these proteins are held inside organelles called chloro-
plasts embedded within the cell membranes, while in bacteria they are embedded
in the plasma membrane. This membrane may be tightly folded into cylindrical
sheets called thylakoids, or bunched up into round vesicles called intra cytoplas-
mic membranes. These structures can fill most of the interior of a cell, giving the
membrane a very large surface area and therefore increasing the amount of light
that the bacteria can absorb. Meanwhile, a typical plant cell contains about 10
to 100 chloroplasts. The chloroplast is enclosed by a membrane composed of a
phospholipid inner membrane, a phospholipid outer membrane, and an inter-
membrane space between them. Within the membrane is an aqueous fluid called
the stroma. The stroma contains stacks (grana) of thylakoids, which are the site of
photosynthesis. The thylakoids are flattened disks, bounded by a membrane with
a lumen or thylakoid space within it. The site of photosynthesis is the thylakoid
membrane, which contains integral and peripheral membrane protein complexes,
including the pigments that absorb light energy, which form the photosystems.
Although all cells in the green parts of a plant have chloroplasts, most of the
energy is captured in the leaves. The cells in the interior tissues of a leaf, called
themesophyll, can contain between 450,000 and 800,000 chloroplasts for every
© 2011 by Apple Academic Press, Inc.
8 Photosynthesis: Genetic, Environmental and Evolutionary Aspects
square millimeter of leaf. The surface of the leaf is uniformly coated with a water-
resistant waxy cuticle that protects the leaf from excessive evaporation of water
and decreases the absorption of ultraviolet or blue light to reduce heating. The
transparent epidermis layer allows light to pass through to the palisade mesophyll
cells where most of the photosynthesis takes place.
At its most basic level, the genetic, environmental and evolutionary aspects of
photosynthesis can be summarized as we have done here, but research into this
process is ongoing. This volume brings to light the most recent studies of this top-
ic. The detailed information provided here will allow readers to stay current with
our ever-developing knowledge of the structures that carry out photosynthesis.
— Philip Stewart, PhD

© 2011 by Apple Academic Press, Inc.
Chloroplast two-Component
systems: evolution of the Link
between Photosynthesis and
Gene expression
Sujith Puthiyaveetil and John F. Allen
AbstrACt
Two-component signal transduction, consisting of sensor kinases and response
regulators, is the predominant signalling mechanism in bacteria. This sig-
nalling system originated in prokaryotes and has spread throughout the eu-
karyotic domain of life through endosymbiotic, lateral gene transfer from the
bacterial ancestors and early evolutionary precursors of eukaryotic, cytoplas-
mic, bioenergetic organelles—chloroplasts and mitochondria. Until recently,
it was thought that two-component systems inherited from an ancestral cy-
anobacterial symbiont are no longer present in chloroplasts. Recent research
now shows that two-component systems have survived in chloroplasts as prod-
ucts of both chloroplast and nuclear genes. Comparative genomic analysis of
© 2011 by Apple Academic Press, Inc.
10 Photosynthesis: Genetic, Environmental and Evolutionary Aspects
photosynthetic eukaryotes shows a lineage-specific distribution of chloroplast
two-component systems. The components and the systems they comprise have
homologues in extant cyanobacterial lineages, indicating their ancient cy-
anobacterial origin. Sequence and functional characteristics of chloroplast
two-component systems point to their fundamental role in linking photosyn-
thesis with gene expression. We propose that two-component systems provide
a coupling between photosynthesis and gene expression that serves to retain
genes in chloroplasts, thus providing the basis of cytoplasmic, non-Mendelian
inheritance of plastid-associated characters. We discuss the role of this cou-
pling in the chronobiology of cells and in the dialogue between nuclear and
cytoplasmic genetic systems.
Keywords: cytoplasmic inheritance, endosymbiosis, redox response regulator,
redox sensor kinase, signal transduction, transcription
two-Component systems enter the eukaryotic
domain of Life
The name ‘two-component system’ is used to describe members of a class of signal
transduction pathways found in eubacteria and made up of two conserved protein
components (Stock et al. 1985; Nixon et al. 1986). These two conserved protein
components are a sensor kinase and a response regulator (figure 1).
Of these two, the component that is first to detect and respond to an environ-
mental change is the sensor kinase. A sensor kinase is a histidine protein kinase
that combines a variable sensor domain with an invariable kinase domain (Figure
1). The sensor domain perceives different specific signals in different histidine
sensor kinases. The nature of the signal sensed and the structure of the protein’s
sensor domain are specific for each histidine sensor kinase. By contrast, the kinase
domain is highly conserved in structure and function, being made up of an inde-
pendent dimerization motif and a catalytic core. The catalytic core of the kinase
domain consists of five conserved amino acid motifs: H-box, N, G1, F and G2
(figure 1). The H-box contains the conserved histidine residue that is the site of
phosphorylation and is usually located in the dimerization motif. N, G1, F and
G2 boxes form the ATP-binding pocket of the catalytic core (Stock et al. 2000).
The second component of any two-component system is its response regula-
tor. The response regulator protein is also made up of two domains (figure 1). The
first domain of a response regulator is its invariable receiver domain. The second
domain of a response regulator is its variable effector domain, which mediates
the specific output response. The chemistry of signal transduction is common to
different pathways: two-component systems use a phosphotransfer mechanism
© 2011 by Apple Academic Press, Inc.
Chloroplast Two-Component Systems 11
from the invariant kinase domain of the sensor to the invariant receiver domain
of the response regulator (figure 1). The sequence of events that leads to an out-
put response from a two-component signalling pathway begins when histidine
kinases, in their functional dimeric form, and upon sensing the signal, undergo
an ATP-dependent trans-autophosphorylation reaction, whereby one histidine
kinase monomer phosphorylates a second monomer within the dimer. The phos-
phate group becomes covalently, though weakly, bound to a conserved histidine
residue of the catalytic core. The receiver domain of the response regulator protein
then catalyses the transfer of the phosphate group from the histidine residue of
the kinase to a conserved aspartate residue within the receiver domain of the re-
sponse regulator protein. This creates a high-energy acyl phosphate that activates
the effector domain of the response regulator (Stock et al. 2000).
Figure 1. Schematic of a two-component system. The sensor kinase and the response regulator components
and their domain architecture are shown. The kinase domain consists of a dimerization domain (diamond)
and an ATP-binding domain (rectangle). The H, N, G1, F and G2 motifs of the kinase domain are indicated.
Conserved sequence motifs of the response regulator receiver domain, DD, D1 and K, are also indicated. The
phosphotransfer signalling mechanism of the two-component systems is depicted as phosphate group transfer
from ATP to the conserved aspartate residue of the response regulator via the conserved histidine residue of the
sensor kinase.
There are actually two reactions catalysed by the ‘sensor kinase’ enzyme. The
first is transfer of the γ-phosphate of ATP to a histidine side chain of the protein
itself, to form a phosphoamide linkage (autophosphorylation; equation (1.1)).
The second reaction is transfer of the phosphate moiety from the histidine of the
sensor kinase to an aspartate on the corresponding response regulator (equation
(1.2)). Thus, the phosphohistidine acts as a covalent chemical intermediate in
transfer of the phosphate group between ATP and the response regulator, and
so sensor kinases are, in a biochemical sense, really ‘response regulator kinases’
(equation (1.3)).
Sensor-His + ATPSensor-His~ADP (1.1)
Regulator-Asp + Sensor-His~PRegulator-Asp ~ P + Sensor-His (1.2)
Sum:Regulator-Asp + ATP  Regulator-Asp ~ P + ADP (1.3)
The histidine sensor kinase becomes autophosphorylated (equation (1.1)) if,
and only if, the specific environmental precondition is met, and on an invariant
© 2011 by Apple Academic Press, Inc.