MICROBIAL

PHOTOSYNTHESIS
TABLE OF CONTENT
CERTIFICATION PAGE
DEDICATION
ACKNOWLEDGEMENT
SUMMARY
Chapter one
1.1 Introduction
Chapter Two
Literature Review
2.1 Origins of Microbial Photosynthesis
2.1.1 Historical perspective
2.2 Classification of photosynthesis organisms
2.3 The Constituent Processes of Photosynthesis
2.4 Absorption and Transfer of Light Energy
2.4.1 The Light-Absorbing Chromophores
2.4.1.1 Primary Chromophores
2.4.1.2 Accessory Chromophores
2.4.2 The Light-Gathering Structures and Resonance Energy Transfer
2.5 Photosynthetic membranes and organelles
2.6 Stages of photosynthesis
2.6.1 Light dependent reaction
2.6.1.1 Photosystems
2.6.1.2 Reaction Centre
2.6.1.3 Photosystem I
2.6.1.4 Photosystem II
2.6.2 Light independent reaction
2.6.2.1 Calvin Cycle
2.6.2.2 Carbon Concentration mechanism
2.7 Anoxygenic Photosynthesis
2.8 Experimental History
2.9 Cyanobacteria and the evolution of photosynthesis
2.10 Factors
2.10.1 Light irradiance, wavelength and temperature
2.10.2 Carbon dioxide levels and photorespiration
Chapter 3
3.1 Recommendation
3.2 Conclusion
3.3 Reference
Summary
The primary source of energy for nearly all life is the Sun. The energy in
sunlight is introduced into the biosphere by a process known as
photosynthesis, which occurs in plants, algae and some types of bacteria.
Photosynthesis can be defined as the physico-chemical process by which
photosynthetic organisms use light energy to drive the synthesis of organic
compounds. The photosynthetic process depends on a set of complex protein
molecules that are located in and around a highly organized membrane.
Through a series of energy transducing reactions, the photosynthetic
machinery transforms light energy into a stable form that can last for
hundreds of millions of years. This introductory chapter focuses on the
structure of the photosynthetic machinery and the reactions essential for
transforming light energy into chemical energy.
CHAPTER 1

1.1 Introduction

Photosynthesis is the biochemical process carried out by certain bacteria,

algae, and higher plants in which light is converted into chemical bond energy.
The process is crucial, since nearly all life on earth depends on sunlight either
directly or indirectly for energy, food, and O2 . The advent of photosynthetic
prokaryotes with the ability to consume CO2 and produce O2 from H2O
resulted in a hospitable environment on earth for advanced forms of life.
Fossil records indicate that the first oxygenic photosynthetic bacteria
appeared around 3.5 109 years ago. Earlier, organisms survived by anaerobic
metabolism, a process that generates only a fraction of the energy produced
by aerobic metabolism. It is likely that in the absence of oxygenic
photosynthesis, advanced forms of life would not have emerged and only
microorganisms would now exist. Today, as the primary means of carbon
fixation, oxygenic photosynthesis forms one half of the energy-carbon cycle.
Phototrophic organisms reduce CO2 to carbohydrates, which are oxidized
back to CO2 by heterotrophic (as well as phototrophic) organisms. The energy
released during the oxidation reaction is stored in the form of NADH and ATP,
which are subsequently used for growth, metabolism, and reproduction. In
addition, prehistoric plants and algae were largely responsible for the
generation of the vast reserves of fossil fuels that are now being mined for
their energy value. They provided a large portion of the initial biomass, which
was converted into oil and coal over millions of years through pressure, heat,
and microbial action. The general process of photosynthesis is described by
Van Niel’s equation: 2H2A + CO2  2A + CH2O + H2O (1) Where H2A is the
reductant and A is the oxidized product. Van Niel’s equation can be applied to
oxygenic photosynthesis as: 6CO2 + 6H2O + light  C6H12O6 + 6O2 (2)
Although complete, this equation belies the overwhelming complexity of the
process. For example, the generation of the light-induced charge-separated
state and its subsequent stabilization over time requires a large number of
pigments and cofactors arranged in a specific protein environment. The
splitting of H2O into O2 is extremely difficult to replicate in the laboratory, yet
plants and cyanobacteria perform the task repeatedly with seeming ease. The
conversion of CO2 into sugars is another intricate process that requires an
extensive set of physical and chemical reactions to occur in a highly
coordinated fashion. In this article, we will expand on this simple equation. In
addition to describing the general design principles behind the sophisticated
biomachinery involved in photosynthesis, we will provide structural and
functional details, placing special emphasis on light-induced electron transfer
in aerobic and anaerobic organisms.
CHAPTER 2

LITERATURE REVIEW

2.1 Origins of Microbial Photosynthesis

We know very little about the earliest origins of photosynthesis. There have
been numerous suggestions as to where and how the process originated, but
there is no direct evidence to support any of the possible origins (Olson and
Blankenship, 2004). There is suggestive evidence that photosynthetic
organisms were present approximately 3.2 to 3.5 billion years ago, in the form
of stromatolites, layered structures similar to forms that are produced by
some modern cyanobacteria, as well as numerous microfossils that have been
interpreted as arising from phototrophs (Des Marais, 2000). In all these cases,
phototrophs are not certain to have been the source of the fossils, but are
inferred from the morphology or geological context. There is also isotopic
evidence for autotrophic carbon fixation at 3.7 to 3.8 billion years ago,
although there is nothing that indicates that these organisms were
photosynthetic. All of these claims for early photosynthesis are highly
controversial and have engendered a great deal of spirited discussion in the
literature (Buick, 2008). Evidence for the timing of the origin of oxygenic
photosynthesis and the rise of oxygen in the atmosphere is discussed below.
The accumulated evidence suggests that photosynthesis began early in Earth’s
history, but was probably not one of the earliest metabolisms and that the
earliest forms of photosynthesis were anoxygenic, with oxygenic forms arising
significantly later.

2.1.1 Historical Perspective

The first experiments on photosynthetic organisms were performed in the

1770s when Joseph Priestley showed that plants were capable of generating a
gas that could support combustion. Building on his work, Jan Ingenhousz
established that sunlight was required, and Jean Senebier and Nicolas
Theodore de Saussure demonstrated the indispensability of CO2 and H2O. In
1845, Julius Robert von Meyer postulated that plants convert light into
chemical energy during photosynthesis. Early scientists believed that the O2
was produced from the splitting of CO2 , and it was not until the 1930s that
Cornelius van Niel proposed, correctly, that H2O was the source of O2 . It is
interesting that 75 years later the exact biochemical mechanism of H2O
splitting remains to be elucidated. Photosynthesis research has had its share
of Nobel laureates. Melvin Calvin won the chemistry prize in 1961 for
identifying most of the intermediates in the conversion of CO2 into
carbohydrates. Peter Mitchell was the sole recipient of the chemistry award in
1978 for his work on the chemi-osmotic theory of proton translocation.
Johann Deisenhofer, Robert Huber, and Hartmut Michel won the chemistry
prize in 1988 for solving the first crystal structure of a photosynthetic
reaction center. Rudolph Marcus’s investigation of the factors guiding electron
transfer in chemical systems remains the paradigm for theoretical calculations
of electron transfer in photosynthetic reaction centers. He was awarded the
Nobel Prize in chemistry in 1992. More recently, Paul Boyer and John Walker
were awarded the prize in chemistry in 1997 for elucidating the enzymatic
mechanism underlying the synthesis of ATP. Artificial photosynthesis has seen
a recent spurt of activity, largely due to an increased awareness of the
depletion of fossil fuel reserves and the effect of their combustion products on
the earth’s climate. The goal is to synthesize inexpensive and long-lasting
organic and inorganic molecules that convert light into chemical energy,
thereby mimicking the basic process of photosynthesis. This has brought new
disciplines such as material science and bioengineering into photosynthesis,
making the field truly interdisciplinary.

2.2 Classification of Photosynthetic Organisms

There exist five bacterial phyla with members capable of chlorophyll-based
phototrophy: Firmicutes, Chloroflexi, Chlorobi, Proteobacteria, and
Cyanobacteria. With the recent discovery of Chloracidobacterium
thermophilum, Acidobacteria have become the sixth known phylum to carry
out the process of photosynthesis. All photosynthetic organisms can be
classified as either oxygenic or anoxygenic. Oxygenic phototrophs employ
H2O as the source of electrons and liberate O2 as the byproduct. Anoxygenic
phototrophs derive their electrons from organic or inorganic molecules, and
hence they do not evolve O2. Of the five well-established phototrophic
bacterial phyla, only the Cyanobacteria are capable of performing oxygenic
photosynthesis. In addition, all eukaryotic phototrophs such as higher plants
and algae, which evolved later than cyanobacteria, produce O2 during
photosynthesis. The remaining four phyla include anaerobes such as the
purple nonsulfur bacteria, purple sulfur bacteria, green sulfur bacteria, and
heliobacteria, which survive only under low concentrations of O2 . The
recently discovered Acidobacteria have been reported to live under oxic
conditions, although a detailed physiological characterization of this organism
remains to be carried out. We will discuss oxygenic photosynthesis first, using
cyanobacteria as the model organism. Cyanobacteria are photosynthetic
prokaryotes that are found in every conceivable habitat from oceans to fresh
water to soil. These Gram-negative bacteria are responsible for generating the
majority of the O2 in the earth’s atmosphere. The most widely used
cyanobacterial strains for current experimental research are Synechocystis sp.
PCC 6803, Synechococcus sp. PCC 7002, and Thermosynechococcus elongatus.
In cyanobacteria, photosynthesis is associated with a well-organized system
of internal membranes in the cytoplasm. These are called thylakoids, from the
Greek word thylakos meaning sac. These membranes are highly folded,
allowing the cell to pack a large amount of surface area into a small space. The
interior space enclosed by the thylakoid membrane is termed the lumen and
the matrix surrounding the thylakoids is termed the stroma. The thylakoids
are home to the integral membrane protein complexes that are involved in the
light reactions of photosynthesis. Eukaryotic organisms such as higher plants
and algae conduct photosynthesis in membrane-bound organelles called
chloroplasts. They consist of an outer, freely permeable membrane and a
selectively permeable inner membrane that encloses the stroma. The sac-like
thylakoids immersed in the stroma are similar in organization to the
comparable membranes in cyanobacteria. Chloroplast thylakoids, however,
tend to form well-defined stacks called grana, which are connected to other
stacks by intergrana thylakoids called lamellae. It is widely thought that
chloroplasts evolved from an endosymbiotic relationship of a heterotrophic
prokaryote with a cyanobacterium.

2.3 The Constituent Processes of Photosynthesis

Eqn [1] is the end product of a large number of events that occur during a
typical photosynthetic cycle. The basic processes that constitute oxygenic
photosynthesis are:

• Absorption of light by pigment molecules and transfer of the excitation

energy to two reaction centers, Photosystem II (PS II) and Photosystem I (PS
I).
• Light-induced transfer of an electron across the photosynthetic membrane
and splitting of H2O into O2 by PS II.
• Light-induced excitation and transfer of an electron across the
photosynthetic membrane, generating reducing equivalents in the form of
nicotinamide adenine dinucleotide phosphate (NADPH) by PS I.
• Production of ATP using the proton gradient generated across the
membrane from both H2O splitting and electron transfer through the
cytochrome b6 f complex.
• Conversion of CO2 into carbohydrates using ATP and the reducing power of
NADPH.

The division of photosynthetic labor is relatively straightforward. All the light

reactions occur within or on the thylakoid membrane. The ATP and NADPH
produced by the light reactions are released into the stroma where the dark
reactions of CO2 fixation are carried out. We focus first on the overall design
philosophy of the process of converting light to stable chemical energy.

2.4 Absorption and Transfer of Light Energy

2.4.1 The Light-Absorbing Chromophores
Photosynthesis in cyanobacteria and plants is driven by light in the visible
(380–750 nm) region of the electromagnetic spectrum. Phototrophic
organisms such as purple bacteria, green sulfur bacteria, and heliobacteria
extend this region to the near-infrared so as to exploit unique ecological
niches. All of this makes evolutionary sense as the majority of the sun’s energy
that reaches the earth’s surface lies in this range. Ultraviolet radiation and
farinfrared radiation are both limited in amount; also, the former is too
energetic and is capable of breaking chemical bonds, while the latter contains
insufficient energy to be useful for most photochemical processes.

2.4.1.1 Primary Chromophores

Photosynthetic organisms use a range of chromophores to efficiently capture
photons in the visible and near-IR regions. The most abundant chromophore
involved in photosynthesis is chlorophyll, a molecule structurally similar to,
and produced by, the same metabolic pathway as porphyrin pigments such as
heme. The basic structure of the chlorophyll molecule is a chlorin ring
coordinated to a central magnesium atom (Figure 1). The addition of a long
phytol tail makes chlorophyll insoluble in water. There are four common
types of chlorophyll molecules in photosynthetic organisms, named
chlorophyll a, b, c, and d. Their overall structure is similar, with minor changes
in the side-chain groups that result in slightly different absorption spectra
(Figure 2). Cyanobacteria employ chlorophyll a, while plants utilize both
chlorophyll a and b. Some species of algae contain chlorophyll c, and a few
species of cyanobacteria contain chlorophyll d. Chlorophylls absorb primarily
in the blue and red regions of the visible spectrum and have a high molar
extinction coefficient. They have an inherently high fluorescence yield, which
guarantees a long-lived excited singlet state, making them the ideal
chromophore.

2.4.1.2 Accessory Chromophores

Besides containing chlorophylls, photosynthetic organisms contain accessory
pigments that extend the range of absorbed wavelengths. Carotenoids are the
main accessory pigment found in cyanobacteria, algae, and higher plants. They
belong to the tetraterpenoid family, that is, contain 40 carbon atoms, and
absorb light in the 400–500 nm region. Structurally, these compounds are
composed of two small six-carbon rings connected by a polyene chain of
carbon atoms. They are insoluble in water and are normally attached to
proteins that are attached to the membrane. There are over 600 types of
carotenoids, which are classified as either carotenes or xanthophylls.
Carotenes consist exclusively of carbon and hydrogen, while xanthophylls also
contain oxygen. The most abundant carotenoid in cyanobacteria is - carotene,
which is the same pigment that gives carrots its distinctive color. In addition
to functioning as an accessory pigment, carotenoids play a vital role in
dissipating excess light energy, which would otherwise lead to the generation
of superoxide radicals. These radicals are highly reactive to chemical bonds
and could be potentially lethal to the cell if left unchecked. Cyanobacteria and
certain types of algae contain additional pigments called phycobilins, which
absorb light between 500 and 650 nm. Phycobilins consist of an open chain of
four pyrrole rings and are water-soluble. They are attached to proteins
termed phycobiliproteins and they pass on the absorbed light energy to
nearby antenna chlorophyll molecules. Plants and cyanobacteria therefore use
a combination of chlorophylls and accessory pigments to effectively blanket a
large majority of the visible spectrum. Both appear dark green or blue-green
because the few photons that are not absorbed lie between the blue and red
regions of the spectrum.

2.4.2 The Light-Gathering Structures and Resonance Energy Transfer

The task of the photosynthetic reaction center is to convert the energy stored
in the excited singlet state of chlorophyll to a form useful for work. In
photosynthesis, work refers to the creation of a charge-separated state
consisting of a donor, Dþ, and an acceptor, A—, pair. At one extreme of time,
the creation of the singlet excited state occurs within 10—15 s of absorbing a photon.
At the other extreme, the captured light energy must be utilized within 10—8 s,
otherwise the energy will be lost as heat or fluorescence as the excited state
decays. The generation of the charge-separated state must occur within this
window of time.
A network of closely spaced chlorophyll molecules, termed the antenna system,
absorbs the photon and the resulting excited state migrates to neighboring
antenna chlorophyll by a process known as resonance energy transfer. This
occurs on a timescale of 10—12 s and is a non-radiative process. The excited state,
known as an exciton, randomly wanders about the antenna system until it
chances upon the specialized reaction center chlorophylls associated with PS
I and PS II. The energy levels of these specialized chlorophylls are slightly
lower than the antenna chlorophylls because they are in a different protein
environment. This allows these specialized chlorophylls to trap the exciton and
use it to create a charge-separated state. In most photosynthetic reaction centers,
this state is generated within 10—10 s following photon absorption. Accessory
pigments also transmit the absorbed energy to antenna chlorophylls by a
similar process of resonance energy transfer.

2.5 Photosynthetic membranes and organelles

In photosynthetic bacteria, the proteins that gather light for photosynthesis
are embedded in cell membranes. In its simplest form, this involves the
membrane surrounding the cell itself. However, the membrane may be tightly
folded into cylindrical sheets called thylakoids, or bunched up into round
vesicles called intracytoplasmic 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. In plants
and algae, photosynthesis takes place in organelles called chloroplasts. A
typical plant cell contains about 10 to 100 chloroplasts. The chloroplast is
enclosed by a membrane. This membrane is composed of a phospholipid inner
membrane, a phospholipid outer membrane, and an intermembrane space.
Enclosed by the membrane is an aqueous fluid called the stroma. Embedded
within the stroma are stacks of thylakoids (grana), which are the site of
photosynthesis. The thylakoids appear as flattened disks. The thylakoid itself
is enclosed by the thylakoid membrane, and within the enclosed volume is a
lumen or thylakoid space. Embedded in the thylakoid membrane are integral
and peripheral membrane protein complexes of the photosynthetic system.
Carbon dioxide arsenite light energy arsenate carbon monoxide.
Photosynthetic membranes and organelles Light-dependent reactions of
photosynthesis at the thylakoid membrane Plants absorb light primarily using
the pigment chlorophyll. The green part of the light spectrum is not absorbed
but is reflected which is the reason that most plants have a green color.
Besides chlorophyll, plants also use pigments such as carotenes and
xanthophylls. Algae also use chlorophyll, but various other pigments are
present, such as phycocyanin, carotenes, and xanthophylls in green algae,
phycoerythrin in red algae (rhodophytes) and fucoxanthin in brown algae and
diatoms resulting in a wide variety of colors. These pigments are embedded in
plants and algae in complexes called antenna proteins. In such proteins, the
pigments are arranged to work together. Such a combination of proteins is
also called a light-harvesting complex. Although all cells in the green parts of
a plant have chloroplasts, the majority of those are found in specially adapted
structures called leaves. Certain species adapted to conditions of strong
sunlight and aridity, such as many Euphorbia and cactus species, have their
main photosynthetic organs in their stems. The cells in the interior tissues of a
leaf, called the mesophyll, can contain between 450,000 and 800,000
chloroplasts for every square millimeter of leaf. The surface of the leaf is
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 minimize heating. The transparent epidermis layer allows light to
pass through to the palisade mesophyll cells where most of the
Photosynthesis Takes Place.

2.6 Stages of Photosynthesis

The process of photosynthesis takes place in two consecutive stages, light
dependent reaction and light independent reaction (Calvin cycle).
2.6.1 Light Dependent Reaction
Just as the name implies, this step requires sunlight. Energy from sunlight is
absorbed by chlorophyll and converted into chemical energy. The absorption
of light energy and transfer to electrons in chemical energy will take place in a
protein complex called photosystems. The end products for this reaction are
ATP and NADPH, which are picked up in the light independent reaction to fix
carbon dioxide producing organic carbon molecules.
The two photosystems are photosystem 1 (PS 1) and photosystem 11 (PS 11),
and they contain light-harvesting pigments that absorb light energy. Different
types of light-harvesting pigments take in distinctive patterns of the
wavelength of visible light. The light-harvesting complex transports the
energy to the reaction center, which delivers the high-energy electrons to the
electron transport system.
2.6.1.1 Photosystems 
Are functional and structural units of protein complexes involved
in photosynthesis. Together they carry out the
primary photochemistry of photosynthesis: the absorption of light and the
transfer of energy and electrons. Photosystems are found in the thylakoid
membranes of plants, algae, and cyanobacteria. These membranes are located
inside the chloroplasts of plants and algae, and in the cytoplasmic membrane
of photosynthetic bacteria. There are two kinds of photosystems: PSI and PSII.
PSII will absorb red light, and PSI will absorb far-red light. Although
photosynthetic activity will be detected when the photosystems are exposed
to either red or far-red light, the photosynthetic activity will be the greatest
when plants are exposed to both wavelengths of light. Studies have actually
demonstrated that the two wavelengths together have a synergistic effect on
the photosynthetic activity, rather than an additive one.
Each photosystem has two parts: a reaction center, where the photochemistry
occurs, and an antenna complex, which surrounds the reaction center. The
antenna complex contains hundreds of chlorophyll molecules which funnel
the excitation energy to the center of the photosystem. At the reaction center,
the energy will be trapped and transferred to produce a high energy molecule.
The main function of PSII is to efficiently split water into oxygen molecules
and protons. PSII will provide a steady stream of electrons to PSI, which will
+ +
boost these in energy and transfer them to NADP  and H  to make NADPH.
The hydrogen from this NADPH can then be used in a number of different
processes within the plant.
2.6.1.2 Reaction Center
Reaction centers are multi-protein complexes found within the thylakoid
membrane.
At the heart of a photosystem lies the reaction center, which is an enzyme that
uses light to reduce and oxidize molecules (give off and take up electrons).
This reaction center is surrounded by light-harvesting complexes that
enhance the absorption of light.
In addition, surrounding the reaction center are pigments which will absorb
light. The pigments which absorb light at the highest energy level are found
furthest from the reaction center. On the other hand, the pigments with the
lowest energy level are more closely associated with the reaction center.
Energy will be efficiently transferred from the outer part of the antenna
complex to the inner part. This funneling of energy is performed via
resonance transfer, which occurs when energy from an excited molecule is
transferred to a molecule in the ground state. This ground state molecule will
be excited, and the process will continue between molecules all the way to the
reaction center. At the reaction center, the electrons on the special chlorophyll
molecule will be excited and ultimately transferred away by electron carriers.
(If the electrons were not transferred away after excitation to a high energy
state, they would lose energy by fluorescence back to the ground state, which
would not allow plants to drive photosynthesis.) The reaction center will
drive photosynthesis by taking light and turning it into chemical energy that
can then be used by the chloroplast.
Two families of reaction centers in photosystems can be distinguished: type I
reaction centers (such as photosystem I (P700) in chloroplasts and in green-
sulfur bacteria) and type II reaction centers (such as photosystem II (P680) in
chloroplasts and in non-sulfur purple bacteria). The two photosystems
originated from a common ancestor, but have since diversified.
Each of the photosystem can be identified by the wavelength of light to which
it is most reactive (700 nanometers for PSI and 680 nanometers for PSII in
chloroplasts), the amount and type of light-harvesting complex present, and
the type of terminal electron acceptor used.
Type I photosystems use ferredoxin-like iron-sulfur cluster proteins as
terminal electron acceptors, while type II photosystems ultimately shuttle
electrons to a quinone terminal electron acceptor. Both reaction center types
are present in chloroplasts and cyanobacteria, and work together to form a
unique photosynthetic chain able to extract electrons from water, creating
oxygen as a byproduct.
2.6.1.3 Photosystem I
Photosystem I (PSI, or plastocyanin–ferredoxin oxidoreductase) is one of
two photosystems in the photosynthetic light reactions of algae, plants,
and cyanobacteria. Photosystem I is an integral membrane
protein complex that uses light energy to catalyze the transfer of
electrons across the thylakoid membrane from plastocyanin to ferredoxin.
Ultimately, the electrons that are transferred by Photosystem I are used to
produce the moderate-energy hydrogen carrier NADPH. The photon energy
absorbed by Photosystem I also produces a proton-motive force that is used
to generate ATP. PSI is composed of more than 110 cofactors, significantly
more than Photosystem II.
History
This photosystem is known as PSI because it was discovered before
Photosystem II, although future experiments showed that Photosystem II is
actually the first enzyme of the photosynthetic electron transport chain.
Aspects of PSI were discovered in the 1950s, but the significance of these
discoveries was not yet recognized at the time. Louis Duysens first proposed
the concepts of Photosystems I and II in 1960, and, in the same year, a
proposal by Fay Bendall and Robert Hill assembled earlier discoveries into a
coherent theory of serial photosynthetic reactions. Hill and Bendall's
hypothesis was later confirmed in experiments conducted in 1961 by the
Duysens and Witt groups.
2.6.1.4 Photosystem II
Photosystem II (or water-plastoquinone oxidoreductase) is the first protein
complex in the light-dependent reactions of oxygenic photosynthesis. It is
located in the thylakoid membrane of plants, algae, and cyanobacteria. Within
the photosystem, enzymes capture photons of light to energize electrons that
are then transferred through a variety of coenzymes and cofactors to
reduce plastoquinone to plastoquinol. The energized electrons are replaced
by oxidizing water to form hydrogen ions and molecular oxygen.
By replenishing lost electrons with electrons from the splitting of water,
photosystem II provides the electrons for all of photosynthesis to occur. The
hydrogen ions (protons) generated by the oxidation of water help to create
a proton gradient that is used by ATP synthase to generate ATP. The
energized electrons transferred to plastoquinone are ultimately used to
reduce NADP+
 to NADPH or are used in non-cyclic electron flow. DCMU is a chemical often
used in laboratory settings to inhibit photosynthesis. When present, DCMU
inhibits electron flow from photosystem II to plastoquinone.
Water Splitting
Photosynthetic water splitting (or oxygen evolution) is one of the most
important reactions on the planet, since it is the source of nearly all the
atmosphere's oxygen. Moreover, artificial photosynthetic water-splitting may
contribute to the effective use of sunlight as an alternative energy-source.
The mechanism of water oxidation is understood in substantial detail. The
oxidation of water to molecular oxygen requires extraction of four electrons
and four protons from two molecules of water. The experimental evidence
that oxygen is released through cyclic reaction of oxygen evolving complex
(OEC) within one PSII was provided by Pierre Joliot et al. They have shown
that, if dark-adapted photosynthetic material (higher plants, algae, and
cyanobacteria) is exposed to a series of single turnover flashes, oxygen
evolution is detected with typical period-four damped oscillation with
maxima on the third and the seventh flash and with minima on the first and
the fifth flash. Based on this experiment, Bessel Kok and co-
workers introduced a cycle of five flash-induced transitions of the so-called S-
states, describing the four redox states of OEC: When four oxidizing
equivalents have been stored (at the S4-state), OEC returns to its basic S0-state.
In the absence of light, the OEC will "relax" to the S 1 state; the S1 state is often
described as being "dark-stable". The S1 state is largely considered to consist
of manganese ions with oxidation states of Mn3+, Mn3+, Mn4+, Mn4+. Finally,
the intermediate S-states were proposed by Jablonsky and Lazar as a
regulatory mechanism and link between S-states and tyrosine Z.
In 2012, Renger expressed the idea of internal changes of water molecules
into typical oxides in different S-states during water splitting.

2.6.2 Light-Independent Reactions

2.6.2.1 Calvin Cycle
In the light-independent (or "dark") reactions, the enzyme RuBisCO captures
CO2 from the atmosphere and, in a process called the Calvin cycle, uses the
newly formed NADPH and releases three-carbon sugars, which are later
combined to form sucrose and starch. The overall equation for the light-
independent reactions in green plants is: 3CO2 + 9ATP + 6NADPH + 6H+ →
C3H6O3-phosphate + 9ADP + 8Pi + 6NADP + 3H2O Carbon fixation produces
the three-carbon sugar intermediate, which is then converted into the final
carbohydrate products. The simple carbon sugars produced by
photosynthesis are then used to form other organic compounds, such as the
building material cellulose, the precursors for lipid and amino acid
biosynthesis, or as a fuel in cellular respiration. The latter occurs not only in
plants but also in animals when the carbon and energy from plants is passed
through a food chain. The fixation or reduction of carbon dioxide is a process
in which carbon dioxide combines with a five-carbon sugar, ribulose 1,5-
bisphosphate, to yield two molecules of a three-carbon compound, glycerate
3-phosphate, also known as 3- phosphoglycerate. Glycerate 3-phosphate, in
the presence of ATP and NADPH produced during the light-dependent stages,
is reduced to glyceraldehyde 3-phosphate. This product is also referred to as
3- phosphoglyceraldehyde (PGAL) or, more generically, as triose phosphate.
Most (5 out of 6 molecules) of the glyceraldehyde 3-phosphate produced are
used to regenerate ribulose 1,5-bisphosphate so the process can continue. The
triose phosphates not thus "recycled" often condense to form hexose
phosphates, which ultimately yield sucrose, starch and cellulose. The sugars
produced during carbon metabolism yield carbon skeletons that can be used
for other metabolic reactions like the production of amino acids and lipids.
2.6.2.2 Carbon concentrating mechanisms
On land
In hot and dry conditions, plants close their stomata to prevent water loss.
Under these conditions, CO2 will decrease and oxygen gas, produced by the
light reactions of photosynthesis, will increase, causing an increase of
photorespiration by the oxygenase activity of ribulose-1,5-bisphosphate
carboxylase/oxygenase Light-independent reactions Calvin cycle Carbon
concentrating mechanisms On land Overview of C4 carbon fixation and
decrease in carbon fixation. Some plants have evolved mechanisms to increase
the CO2 concentration in the leaves under these conditions. Plants that use the
C4 carbon fixation process chemically fix carbon dioxide in the cells of the
mesophyll by adding it to the three-carbon molecule phosphoenolpyruvate
(PEP), a reaction catalyzed by an enzyme called PEP carboxylase, creating the
fourcarbon organic acid oxaloacetic acid. Oxaloacetic acid or malate
synthesized by this process is then translocated to specialized bundle sheath
cells where the enzyme RuBisCO and other Calvin cycle enzymes are located,
and where CO2 released by decarboxylation of the four-carbon acids is then
fixed by RuBisCO activity to the three-carbon 3- phosphoglyceric acids. The
physical separation of RuBisCO from the oxygen-generating light reactions
reduces photorespiration and increases CO2 fixation and, thus, the
photosynthetic capacity of the leaf. C4 plants can produce more sugar than C3
plants in conditions of high light and temperature. Many important crop
plants are C4 plants, including maize, sorghum, sugarcane, and millet. Plants
that do not use PEP-carboxylase in carbon fixation are called C3 plants
because the primary carboxylation reaction, catalyzed by RuBisCO, produces
the three-carbon 3-phosphoglyceric acids directly in the Calvin-Benson cycle.
Over 90% of plants use C3 carbon fixation, compared to 3% that use C4
carbon fixation; however, the evolution of C4 in over 60 plant lineages makes
it a striking example of convergent evolution. C2 photosynthesis, which
involves carbon-concentration by selective breakdown of photorespiratory
glycine, is both an evolutionary precursor to C4 and a useful CCM in its own
right. Xerophytes, such as cacti and most succulents, also use PEP carboxylase
to capture carbon dioxide in a process called Crassulacean acid metabolism
(CAM). In contrast to C4 metabolism, which spatially separates the CO2
fixation to PEP from the Calvin cycle, CAM temporally separates these two
processes. CAM plants have a different leaf anatomy from C3 plants, and fix
the CO2 at night, when their stomata are open. CAM plants store the CO2
mostly in the form of malic acid via carboxylation of phosphoenolpyruvate to
oxaloacetate, which is then reduced to malate. Decarboxylation of malate
during the day releases CO2 inside the leaves, thus allowing carbon fixation to
3-phosphoglycerate by RuBisCO. CAM is used by 16,000 species of plants.
Calcium oxalate accumulating plants, such as Amaranthus hybridus and
Colobanthus quitensis, show a variation of photosynthesis where calcium
oxalate crystals function as dynamic carbon pools, supplying carbon dioxide
(CO2) to photosynthetic cells when stomata are partially or totally closed.
This process was named Alarm photosynthesis. Under stress conditions (e.g.
water deficit) oxalate released from calcium oxalate crystals is converted to
CO2 by an oxalate oxidase enzyme and the produced CO2 can support the
Calvin cycle reactions. Reactive hydrogen peroxide (H2O2), the byproduct of
oxalate oxidase reaction, can be neutralized by catalase. Alarm photosynthesis
represents a photosynthetic variant to be added to the well-known C4 and
CAM pathways. However, alarm photosynthesis, in contrast to these
pathways, operates as a biochemical pump that collects carbon from the organ
interior (or from the soil) and not from the atmosphere.
In Water
Cyanobacteria possess carboxysomes, which increase the concentration of
CO2 around RuBisCO to increase the rate of photosynthesis. An enzyme,
carbonic anhydrase, located within the carboxysome releases CO2 from
dissolved hydrocarbonate ions (HCO−3). Before the CO2 diffuses out it is
quickly sponged up by RuBisCO, which is concentrated within the
carboxysomes. HCO − 3 ions are made from CO2 outside the cell by another
carbonic anhydrase and are actively pumped into the cell by a membrane
protein. They cannot cross the membrane as they are charged, and within the
cytosol they turn back into CO2 very slowly without the help of carbonic
anhydrase. This causes the HCO − 3 ions to accumulate within the cell from
where they diffuse into the carboxysomes. Pyrenoids in algae and hornworts
also act to concentrate CO2 around RuBisCO.
2.7 Anoxygenic Photosynthesis
As the name suggests, anoxygenic photosynthetic bacteria do not evolve O2 as
a by-product of photosynthesis. These descendants of ancient microbes
contain only one type of reaction center and hence the electrons used to
reduce CO2 are taken from highly reduced molecules such as succinate and
sulfide. Although most photosynthetic bacteria use the CCB cycle to fix carbon,
some are able to fix atmospheric CO2 by other biochemical pathways. Most
anaerobic phototrophs can survive only under very low concentrations of O2.
Despite these differences, the general principles of energy transduction in
anoxygenic photosynthesis are similar to those in oxygenic photosynthesis.
The primary chromophore belongs to a family of molecules called
bacteriochlorophylls. There are six types of bacteriochlorophylls, denoted
bacteriochlorophyll (BChl) a, b, c, d, e, and g. They are similar to chlorophylls,
but absorb light in the near-infrared region. As in aerobic photosynthesis,
electron transfer is coupled to the generation of a proton gradient that is used
to synthesize ATP. The energy required to reduce CO2 is provided by ATP and
NADH, a molecule similar to NADPH but lacking the phosphate.

Purple Bacteria
Purple photosynthetic bacteria are a versatile group of proteobacteria that
can be classified further into purple nonsulfur bacteria and purple sulfur
bacteria. All purple bacteria use a Type II reaction center to generate a proton
gradient for ATP synthesis, that is, there is no formation of NADPH. The
reductant for carbon fixation is derived from organic compounds such as
succinate and malate (nonsulfur bacteria) or from inorganic sulfide (sulfur
bacteria). Light-driven electron transfer in purple bacteria is cyclic and hence
no net oxidation or reduction occurs. Purple nonsulfur bacteria are found in
ponds, mud, and sewage. Purple sulfur bacteria are obligate anaerobes and
are found in illuminated anoxic zones of lakes where H2S accumulates and
also in geothermal sulfur springs. Both fix carbon via the CBB cycle. All purple
bacteria have a very efficient antenna system consisting of BChl a, BChl b, and
carotenoids. The presence of purple carotenoids such as spirilloxanthin gives
these bacteria their distinct color. The first three-dimensional X-ray crystal
structures of a photosynthetic reaction center were from purple nonsulfur
bacteria (Rhodopseudomonas viridis and Rhodobacter sphaeroides). The
basic composition of their reaction centers is similar to that of PS II. The
primary donor is a special pair of BChl a molecules, which, after excitation by
light, transfer the electron to bacteriopheophytin, the primary electron
acceptor. The chargeseparated state is stabilized by successive electron
transfer to two ubiquinone molecules, QA and QB. After two cycles of
reduction, two protons are taken up from inside the membrane to form the
doubly reduced dihydroubiquinol in the QB site. Dihydroubiquinol diffuses to
the cytochrome bc1 complex, where it becomes oxidized, regenerating
ubiquinone. The cytochrome bc1 complex employs the protonmotive Q-cycle
and translocates up to two protons per electron across the membrane. The
energy stored in the resulting electrochemical proton gradient is used to
synthesize ATP via the membrane-bound ATP synthase complex. The
cytochrome bc1 complex completes the cycle by transferring the electron
back to the primary donor via the soluble carrier protein cytochrome c.
Green Sulfur Bacteria
Green sulfur bacteria such as Chlorobium tepidum and Chlorobium
vibrioforme belong to the phyla Chlorobi and are strictly anaerobic
photoautotrophs. They use reduced sulfur compounds as their electron
donors and fix carbon using the reverse TCA cycle. Unlike purple bacteria,
light-induced electron transfer is noncyclic in green sulfur bacteria; hence
NADPH is generated. These bacteria live in sulfur-rich environments that have
characteristically low light intensities. They employ a unique antenna complex
termed the chlorosome, which comprises BChl c, BChl d, and BChl e. It is the
largest known antenna structure in biology, with each chlorosome containing
200 000 BChl molecules. The habitats of green sulfur bacteria necessitate such
an extensive antenna system, requiring a very large optical cross section to
capture the few available photons. The light energy is transferred to a
homodimeric Type I reaction center via the BChl a containing the Fenna–
Matthews–Olsen (FMO) protein. The FMO protein is soluble in water, and was
the first chlorophyll-containing protein to have its threedimensional structure
solved. The reaction center core is a homodimer of PscA, and it contains most
of the redox cofactors. Electron transfer begins at P840, a special pair of BChl
a molecules, and proceeds through the primary acceptor, a Chl a molecule
monomer, and three [4Fe–4S] clusters FX, FA, and FB. It is uncertain whether
a quinone functions as an intermediate electron transfer cofactor between A0
and FX. FA and FB are bound to a protein named PscB, which has an unusually
long N-terminal segment of proline, lysine, and arginine residues. A protein
named PscD is thought to be involved in the docking of soluble ferredoxin and
in the stabilization of the FMO protein. Another protein, PscC, is a tightly
bound cytochrome, c551, which donates electrons to P840.
Heliobacteria
Heliobacteria (e.g., Heliobacterium mobilis and Heliobacterium
modesticaldum) are members of the phylum Firmicutes and are the only
known Gram-positive photosynthetic organisms. They were discovered 25
years ago in soil on the campus of Indiana University, Bloomington.
Heliobacteria are anaerobic photoheterotrophs that fix nitrogen and are
commonly found in rice fields. They can grow on selected organic substrates
like pyruvate, lactate, and butyrate. Heliobacteria do not contain ribulose-1, 5-
bisphosphate or ATP-citrate lyase, the two enzymes commonly used in carbon
fixation, but rather incorporate carbon via an incomplete reductive carboxylic
acid pathway. These bacteria use BChlg as their primary pigment and employ
a simple homodimeric Type I reaction center to perform noncyclic electron
transfer. The components of the electron transfer chain are similar to green
sulfur bacteria except that the pigment used as the special pair (P798) is
BChlg. The reaction center core is a homodimer of PshA, and it contains the
primary donor and acceptor chlorophylls and the FX iron–sulfur cluster. The
FA and FB iron–sulfur clusters are harbored on a low molecular mass
polypeptide termed PshB. Similar to the reaction centers in the phylum
Chlorobi, the participation of a quinone as an electron transfer cofactor
between A0 and FX is still under debate. Little or no structural information is
available on any homodimeric Type I reaction center. Based on analogy with
PS I, it is believed that a bifurcating electron transfer chain with two
equivalent branches of cofactors exists in these reaction centers, but there is
no spectroscopic evidence yet to support this proposal.
Other Photosynthetic Bacteria
Some species of photosynthetic bacteria do not fall under any of the
previously discussed categories. The green gliding bacteria (Chloroflexi), also
known as green filamentous bacteria, can grow photosynthetically under
anaerobic conditions or in the dark by respiration under aerobic conditions.
Like green sulfur bacteria, they harvest light by using chlorosomes, but like
purple bacteria, they employ a Type II reaction center. These poorly studied
organisms fix CO2 via the 3-hydroxypropionate pathway. The most recent
addition to the list of photosynthetic microbes is an acidobacterium, C.
thermophilum, which reportedly synthesizes BChl a and BChl c in aerobic
environments. This organism was isolated from microbial mats at an alkaline
hot spring and is thought to contain chlorosomes and a homodimeric Type I
reaction center. Further studies are needed to determine whether the
photosynthetic apparatus has new and interesting features, or whether it falls
into a typical Type I class.
2.8 Experimental History
Although some of the steps in photosynthesis are still not completely
understood, the overall photosynthetic equation has been known since the
19th century. Jan van Helmont began the research of the process in the mid-
17th century when he carefully measured the mass of the soil used by a plant
and the mass of the plant as it grew. After noticing that the soil mass changed
very little, he hypothesized that the mass of the growing plant must come
from the water, the only substance he added to the potted plant. His
hypothesis was partially accurate – much of the gained mass comes from
carbon dioxide as well as water. However, this was a signaling point to the
idea that the bulk of a plant's biomass comes from the inputs of
photosynthesis, not the soil itself. Joseph Priestley, a chemist and minister,
discovered that when he isolated a volume of air under an inverted jar and
burned a candle in it (which gave off CO2), the candle would burn out very
quickly, much before it ran out of wax. He further discovered that a mouse
could similarly "injure" air. He then showed that the air that had been
"injured" by the candle and the mouse could be restored by a plant.
In 1779, Jan Ingenhousz repeated Priestley's experiments. He discovered that
it was the influence of sunlight on the plant that could cause it to revive a
mouse in a matter of hours.
In 1796, Jean Senebier, a Swiss pastor, botanist, and naturalist, demonstrated
that green plants consume carbon dioxide and release oxygen under the
influence of light. Soon afterward, Nicolas-Théodore de Saussure showed that
the increase in mass of the plant as it grows could not be due only to uptake of
CO2 but also to the incorporation of water. Thus, the basic reaction by which
photosynthesis is used to produce food (such as glucose) was outlined.

2.9 Cyanobacteria and the evolution of photosynthesis

The biochemical capacity to use water as the source for electrons in
photosynthesis evolved once, in a common ancestor of extant cyanobacteria
(formerly called blue-green algae), which are the only prokaryotes performing
oxygenic photosynthesis. The geological record indicates that this
transforming event took place early in Earth's history, at least 2450–2320
million years ago (Ma), and, it is speculated, much earlier. Because the Earth's
atmosphere contained almost no oxygen during the estimated development of
photosynthesis, it is believed that the first photosynthetic cyanobacteria did
not generate oxygen. Available evidence from geobiological studies of Archean
(>2500 Ma) sedimentary rocks indicates that life existed 3500 Ma, but the
question of when oxygenic photosynthesis evolved is still unanswered. A clear
paleontological window on cyanobacterial evolution opened about 2000 Ma,
revealing an already-diverse biota of cyanobacteria. Cyanobacteria remained
the principal primary producers of oxygen throughout the Proterozoic Eon
(2500–543 Ma), in part because the redox structure of the oceans favored
photoautotrophs capable of nitrogen fixation. Green algae joined
cyanobacteria as the major primary producers of oxygen on continental
shelves near the end of the Proterozoic, but only with the Mesozoic (251–66
Ma) radiations of dinoflagellates, coccolithophorids, and diatoms did the
primary production of oxygen in marine shelf waters take modern form.
Cyanobacteria remain critical to marine ecosystems as primary producers of
oxygen in oceanic gyres, as agents of biological nitrogen fixation, and, in
modified form, as the plastids of marine algae.
2.10 Factors
There are three main factors affecting photosynthesis and several corollary
factors. The three main are:
 Light irradiance, wavelength and temperature
 Carbon dioxide concentration
Total photosynthesis is limited by a range of environmental factors. These
include the amount of light available, the amount of leaf area a plant has to
capture light (shading by other plants is a major limitation of photosynthesis),
the rate at which carbon dioxide can be supplied to the chloroplasts to
support photosynthesis, the availability of water, and the availability of
suitable temperatures for carrying out photosynthesis.
2.10.1 Light intensity (irradiance), wavelength and temperature
The process of photosynthesis provides the main input of free energy into the
biosphere, and is one of four main ways in which radiation is important for
plant life. The radiation climate within plant communities is extremely
variable, in both time and space. In the early 20th century, Frederick
Blackman and Gabrielle Matthaei investigated the effects of light intensity
(irradiance) and temperature on the rate of carbon assimilation. At constant
temperature, the rate of carbon assimilation varies with irradiance, increasing
as the irradiance increases, but reaching a plateau at higher irradiance. At low
irradiance, increasing the temperature has little influence on the rate of
carbon assimilation. At constant high irradiance, the rate of carbon
assimilation increases as the temperature is increased.
2.10.2 Carbon dioxide levels and photorespiration
As carbon dioxide concentrations rise, the rate at which sugars are made by
the lightindependent reactions increases until limited by other factors.
RuBisCO, the enzyme that captures carbon dioxide in the lightindependent
reactions, has a binding affinity for both carbon dioxide and oxygen. When the
concentration of carbon dioxide is high, RuBisCO will fix carbon dioxide.
However, if the carbon dioxide concentration is low, RuBisCO will bind oxygen
instead of carbon dioxide. This process, called photorespiration, uses energy,
but does not produce sugars.
 CHAPTER 3
3.1 Recommendation

3.2 Conclusion:
The process of photosynthesis originated early in Earth’s history, and
has evolved to its current mechanistic diversity and phylogenetic
distribution by a complex, nonlinear process. Current evidence suggests
that the earliest photosynthetic organisms were anoxygenic, that all
photosynthetic RCs have been derived from a single source, and that
antenna systems and carbon fixation pathways have been invented
multiple times.

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