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Photosystem I and the ETC

Photosystem I and the ETC


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In the light reactions of photosynthesis, Photosystem I receives electrons from the ETC after Photosystem II sends them to the ETC. Then, when Photosystem I receives light, the electron becomes excited and passes the electron back to the ETC. This leads me to my question: In the following question, are both $B$ and $E$ correct?

Which of the following are directly associated with photosystem I?

$A)$ harvesting of light energy by ATP

$B)$ receiving electrons from the thylakoid membrane electron transport chain

$C)$ generation of molecular oxygen

$D)$ extraction of hydrogen electrons from the splitting of water

$E)$ passing electrons to the thylakoid membrane electron transport chain


It appears the author of the question is trying to use "thylakoid electron transport chain" in an overly specific way. The chain from which PS I receives electrons has far more components and is different from the shorter chain to which PS I passes its electrons. But according to my copy of Biology, Campbell & Reece 7th edition, both are called "electron transport chains" and both reside in, or on, the thylakoid membrane. Perhaps the "directly" in the question refers to the fact that PS I's electron is first captured by a "primary receptor" before being passed to ferredixon, the first member of the chain to which PS I passes electrons. But, again according to Campbell, this primary acceptor is considered part of the photosystem.

I used to teach this stuff. I'd toss out the question.


17. Photosynthesis I

PSI is also known as the cyclic pathway since the excited electron runs through a closed circuit of the ETC to regenerate the lost electron. This closed circuit also generates a proton gradient through powering of a proton pump but does not lead to the reduction of NADPH. As with the ETC-powered proton pump in mitochondria, the proton gradient is used to power ATP-synthase in producing ATP molecules.

Absorbance spectra of the two most prominent pigments found in plants. Credit: Daniele Pugliesi,M0tty [CC-BY-SA 3.0]




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What is Photosystem 1

PS I is the collection of pigments of chlorophyll, absorbing mostly the wavelength of light at 700 nm. The final stage of the light reaction is catalyzed by PS I. The reaction center of PS I consists of chlorophyll A-700. The core of the PS I is made up of psaA and psaB subunits. Core subunits of the PS I are larger than the core subunits of PS II. PS I is made up of chlorophyll A-670, Chlorophyll A-680, chlorophyll A-695, chlorophyll A-700, chlorophyll B and carotenoids. Photons from light are absorbed by accessory pigments and passed into the reaction center. Reaction center itself is capable of absorbing photons. The energy of absorbed photons is released from the reaction center as high energy electrons. These electrons are transferred through series of electron carriers and finally taken up by NADP + reductase. The enzyme, NADP+ reductase produces NADPH from these electrons. A schematic diagram of a photosystem is shown in figure 1.

Figure 1: A photosystem
1 – Sunlight, 2 – Pigments, 3 – Reaction center, 4 – high energy electron flow, 5 – photosystem


Chloroplasts

13.5.1.1 Charge Separation

Photosystems are pigment-containing protein complexes that contain reaction centers ( Clayton, 1962 Reed and Clayton, 1968 Reed, 1969 Clayton and Wang, 1971 Feher, 1971 Gisriel et al., 2017 ) that convert radiant energy (h ν ) into chemical energy. On excitation, the pigment (P) becomes a strong reducing agent (P + ) that allows it to pass an electron to a primary acceptor (A), which then becomes reduced (A − ). This process, which takes place within the reaction center, is known as charge separation ( Kluyver and van Niel, 1956 ) and is represented in the following reaction:

This reaction is irreversible as a consequence of the rapid rereduction of P + , which occurs as a result of the acquisition of an electron from an electron donor, as well as the rapid reoxidation of A − that results from the reduction of the next electron acceptor. Both PS I and PS II are oriented in the thylakoid membrane such that the excited electron in the reaction center moves from the lumen side of the membrane to the stromal side of the membrane in an electrogenic manner.


Photosynthesis – Electron Transport Chain and Calvin Cycle

Light Dependent Reactions , or Electron Transport Chain
– Occurs in chloroplasts’ thylakoids, only operates under exposure to sunlight
– Thylakoids are flat, thus aiming for maximum surface area in order to capture most sunlight
* During Electron Transport Chain, the aim is the create ATP

Procedures:
1.1. Sunlight energy (photons) hits the reaction center of the chlorophyll Photosystem II, it excites electron and thus it moves to electron-carrier protein, while Water-Splitting Enzyme splits the water (2 H2O -> 4H+ + O2 + 4e-), using the electrons from the split water to replace the excited electron in Photosystem II the oxygen diffuses out of cell
2. Moving along the electron-carrier protein, it reaches the first proton pump and releases energy to pump a hydrogen ion into the thylakoid, then the electron moves into another electron-carrier protein
3. Here, the electron from first Photosystem II replaces the electron that Photosystem I releases after hit by photons, to which Photosystem I’s electron moves into another electron-carrier protein and bonds to NADP and a hydrogen ion in NADP Reductase enzyme.
NADP + H+ + e- -> NADPH, energy rich molecule
1.2. Meanwhile NADPH’s line of reactions occurs, the hydrogen ions from splitting water and from proton pump will stack up inside the thylakoid, thus building potential energy inside and thus, utilizing the potential energy, ATP Synthase enzyme allows hydrogen ions to exist while using their energy to combine ADP + P -> ATP

H+ concentration change:
– Increases inside thylakoid with Photosystem II & proton pump
– Decreases outside thylakoid with proton pump and NADP Reductase (it uses H+ from outside)

Light Independent Reactions , or Calvin Cycle
– Occurs in chloroplasts’ storma
– Series of reactions to take energy from ATP and NADPH, transfer them into sugar, carbohydrates, etc.

Procedures (counting with 3 RuBp)
1. Rubisco (enzyme) fixes 3 CO2’s carbon onto 3 RuBp (5 carbon molecule) to form an unstable 6-carbon molecule
2. Then 6-carbon molecules (3 in quantity) breaks down into 6 G3P (3 carbon molecule) while 6 ATP and 6 NADPH are used on G3P (now has 1 phosphate group attached) here 1 G3P leaves the cycle
3. The rest (5) G3P gets recycled to make 3 RuBp using 3 ATP
2 G3P (modified by ATP and NADPH) are required to make one glucose (6 carbon) molecule

Total of 9 ATP and 6 NADPH used for one cycle starting with 3 RuBp, ADPs and NADPs goes back to Light Dependent Reaction


Photosystem I and the ETC - Biology

Use of our material:
This activity was created by Kell y Riedell for students in Biology class at Brookings High School . We have worked very hard on activities, Powerpoints/games/worksheets, etc to make this a resource for our students. If you are using our materials, please give us credit for our efforts by listing us as a source with links to our site.
Any questions, comments, or corrections can be directed to us at

THINGS YOU WILL NEED:
Roll of Velcro with adhesive on back
yarn
hole puncher
Flashlight

AHEAD OF TIME
P HOTOSYNTHESIS THEATER CARDS BY AUDRA WARD BROWN
1. Copy off the role play cards onto cardstock or colored paper and laminate them.
2. Cut apart the e - , P, H + , and CO2 cards.

3. Use a paper punch to put holes in the following cards and attach string so card can be worn around the neck. (Photosystem I & II, ATP synthase, Stroma, Thylakoid space, ETC, NADP + , Adenosine P P , O, Calvin cycle)

5. Do the sam e with the NADP + and the H + cards.

6 . Do the same with the O card to make places to
attach 2 H + to make a H 2 O molecule.

MINIMUM # OF CARDS YOU WILL NEED:

ACT IT OUT: LIGHT DEPENDENT REACTIONS

Students wear appropriate name tags and line up in correct position.
Photosystem II, ETC, ETC, ETC, Photosystem I, ETC, ATP synthase stand in a line
Sun stands to side of PS II.
2 Stroma people stand in front of line holding baskets
2 Thylakoid space people stand behind line holding baskets
Water stands next to thylakoid space people.
ADP stands near ATP synthase
NADP + stands near ATP synthase and last ETC

Roles:
Sun: Holds flashlight and shines it on Photosystems
PS II: passes e - cards to first ETC
ETC: Passes e - cards along line and pumps H + cards over shoulder to thylakoid space
PS I: Passes e - cards to LAST ETC
WATER: Each starts wearing an O card with 2 H's attached and holds 2 e- cards.
Removes H + from O name card & gives to thylakoid space Passes e- cards to PS II 2 O's join arms and leave room
STROMA: Passes H + cards to ETC Receive H cards from ATP SYNTHASE Pass H + cards to last ETC
THYLAKOID SPACE: Receives H + cards from ETC and passes H + cards to ATP synthase
ATP SYNTHASE: receives H + cards from thylakoid space and passes them to stroma holds P cards and attaches them to ADP.
LAST ETC: collects all e - cards as they come down line, receives H + from stroma and gives 2 e - cards and attaches an H + to NADP +

ACT OUT ETC first. Where is this happening? What are the jobs? Where do electrons come from to replace those lost from PS II? Where are ATP and NADPH made? Where does H + build up? Where do ATP and NADPH go next?

A ct it out, then have students change jobs.

As water is split, the H + cards are detached and are passed to the THYLAKOID SPACE.
The 2 e- cards pass to PS II, and the leftover O holds hands and joins with another O to become O2 and leaves the chloroplast (room).

Actors:
12 students each hold 1 CO2 card, ATP and NADPH from light reactions

CO2, ATP and NADPH travel to CALVIN CYCLE.
ATP removes its P, NADPH removes its H + and passes it and 2 e - cards to CALVIN CYCLE.
CO2's hand their cards to CALVIN CYCLE.

CALVIN CYCLE takes 2 e - and H + from NADPH, and energy and P from ATP and
CO2's hold their cards and CALVIN CYCLE links their arms to form a 6 person ring*
OR they can all form a ring and hold their CO2 cards together in the middle.

* If you want to get technical . . . it should be a 5 person ring with one "flag" C

image from http://www.nofretete-page.de/gemischtNeu/TN_plant_grow_w.JPG


Structure and energy transfer pathways of the plant photosystem I-LHCI supercomplex

Overall structure of plant PSI-LHCI supercomplex reported recently was reviewed.

Energy transfer pathways from LHCI to the PSI core were discussed.

Possible model for the xanthophyll cycle in PSI-LHCI was suggested.

Photosystem I (PSI) is one of the two photosystems in oxygenic photosynthesis, and absorbs light energy to generate reducing power for the reduction of NADP + to NADPH with a quantum efficiency close to 100%. The plant PSI core forms a supercomplex with light-harvesting complex I (LHCI) with a total molecular weight of over 600 kDa. Recent X-ray structure analysis of the PSI-LHCI membrane-protein supercomplex has revealed detailed arrangement of the light-harvesting pigments and other cofactors especially within LHCI. Here we introduce the overall structure of the PSI-LHCI supercomplex, and then focus on the excited energy transfer (EET) pathways from LHCI to the PSI core and photoprotection mechanisms based on the structure obtained.


Definition

A reaction centre is the active site of the organisms that carry out photosynthesis by converting light energy into chemical one via the association of ascesary pigment proteins or antenna molecules. The photosynthetic organisms use either of the two photosystems (PS-I or PS-II) or both to carry out the light absorption, energy transfer and transfer of electrons. Photosystem is the basic component of the light reaction:

  • In plants and algae, the photosystems are located inside the chloroplasts.
  • In photosynthetic bacteria, the photosystem is found in the cytoplasmic membrane.

A reaction centre lies within the photosystems, whose function is to reduce the carrier molecules by using the light energy. Light-harvesting pigments surround the RC, which is altogether called as antenna complex that mediates the absorption of light and transfer of photons to charge the reaction centre. In a photosystem, two kinds of RCs generally exist.

  • Type I RCs: It includes PS-I (P700) and green-sulphur bacteria.
  • Type II RCs: It includes PS-II (P680) and non-sulphur purple bacteria.

Mechanism of Capturing Light Energy

The arrangement of the reaction centre facilitates capturing of photon molecules through light-harvesting pigment molecules. Firstly the light energy is captured by the pigment molecules, and then the antenna molecules transfer the light energy to the reaction centre via resonance transfer.

As the light energy reaches the RC, it passes 2e – into the ETC. Here, the light is considered as the form of energy because it is composed of small bunches of energy termed as photons. The photons from the light energy of a specific wavelength help in the excitation of an electron to a higher energy level.

Electrons are most stable at their ground state. In-ground state an electron possess the least amount of energy in its orbit. The excited electrons return to the photosyntem, by releasing some kind energy that later harnessed by the cell in the dark reaction. Thus, this is the mechanism of a photosynthetic reaction centre.

Reaction Centre of PS-I and PS-II

As we know, the reaction centre plays a significant role in photosynthesis of bacteria, cyanobacteria and higher plants. The photosynthesis occurs in two ways, namely oxygenic and non-oxygenic photophosphorylation.

Cyanobacteria and higher plants carry out oxygenic photosynthesis by using both photosystems I and II. Photosynthetic bacteria undergoes non-oxygenic photosynthesis, and uses only one photosystem (either PS-I or PS-II).

The mechanism of photosynthetic RC involves three consecutive stages:

Light absorption: The photopigments of the RC first absorb the light of specific wavelength.

Energy transfer: Auxillary antenna pigments then passes the photons to the reaction centre, where the photochemical reaction occurs.

Electron excitation: The charged reaction centre releases the high energy electrons by exciting the electrons from a ground to a higher energy state. The high energy electron is accepted by the primary cofactors like plastoquinone or ferredoxin and then goes through a series of the chemical reaction. At last, these electrons are either goes back to the antenna molecules (cyclic photophosphorylation) or may enter to the PS-I (Noncyclic photophosphorylation).

Structure

A reaction centre possesses a multisubunit complex (containing >24 or >33 protein subunits). The RC in photosynthetic bacterial photosynthetic acts as a model organism to research the mechanism of capturing light energy.

Hartmut Michel, Johann Deisenhofer and Robert Huber were the scientists who proposed the crystal structure of RC. On further study, it was found that different subunits and few accessory molecules participate in the photosynthetic reaction centre.

Subunits: A bacterial photosynthetic RC comprises the following distinct subunits.

  1. L and M subunits: These are associated with the cell membrane, both are structurally identical, and each possesses 5 transmembrane polypeptide helices. The ferrous ions are associated with these subunits.
  2. H subunit: It is associated with the cytoplasmic side of the cell membrane.
  3. Cytochrome subunit: It is associated with the periplasmic space of the cell membrane, and comprising four c-type hemes.

Pigment molecules: A bacterial photosynthetic RC comprises the following pigment proteins.

    1. Four bacteriochlorophyll b (BChl-b) molecules: It is the primary protein pigment that facilitates energy transfer via photon absorption. Bacteriochlorophyll roughly resembles the plant chlorophyll.
    2. Two bacteriopheophytin b molecules (BPh) molecules: BPh possesses a more or less same structure as BChl-b, only the central Mg 2+ is replaced by the 2H + .
    3. Two quinones (QA and QB) are the cofactor protein molecules.

    Types of Reaction Centre

    There are six kinds of photosynthetic RCs, depending on the following factors:

    • Size and nature of the light harvesting pigment
    • The associated photosystem
    • Strength of the reaction centre pigment to excite an electron

    The six classes of RC can categorize into two groups:

    Type-I reaction centre: Heliobacteria, green sulfur bacteria, and photosystem-I possesses type-I RC. In this group, the iron-sulfur clusters function as the electron acceptors.

    Type-II reaction centre: Purple bacteria, green filamentous bacteria, and photosystem-II possess type-II RC. In this group, quinones act as the primary electron acceptors.

    In a photosynthetic reaction, the reaction centre functions as a primary donor that passes the electron to the cofactors accepting an electron. The electron donors generally comprise of Tyr residue (TyrZ), which comprises:

    • Cluster of 4 manganese ions for PSII
    • Plastocyanin molecule for PSI
    • Cytochrome-c for the bacterial RCs

    The structure and arrangement of the antenna pigments, associated with the RC differs variably in different photosynthetic organisms. The RC of heliobacteria possess a simple organization by having a single protein complex (contains 40 chlorophyll g pigments) that lacks auxiliary peripheral antenna proteins.

    The RC of photosystem-I and green sulfur bacteria comprises light-harvesting pigments (around 100), while the RC of purple bacteria and photosystem-II comprises around six to eight pigment proteins that possesses C2 symmetry.


    Thinking twice about the evolution of photosynthesis

    Sam Granick opened his seminal 1957 paper titled ‘Speculations on the origins and evolution of photosynthesis’ with the assertion that there is a constant urge in human beings to seek beginnings (I concur). This urge has led to an incessant stream of speculative ideas and debates on the evolution of photosynthesis that started in the first half of the twentieth century and shows no signs of abating. Some of these speculative ideas have become commonplace, are taken as fact, but find little support. Here, I review and scrutinize three widely accepted ideas that underpin the current study of the evolution of photosynthesis: first, that the photochemical reaction centres used in anoxygenic photosynthesis are more primitive than those in oxygenic photosynthesis second, that the probability of acquiring photosynthesis via horizontal gene transfer is greater than the probability of losing photosynthesis and third, and most important, that the origin of anoxygenic photosynthesis pre-dates the origin of oxygenic photosynthesis. I shall attempt to demonstrate that these three ideas are often grounded in incorrect assumptions built on more assumptions with no experimental or observational support. I hope that this brief review will not only serve as a cautionary tale but also that it will open new avenues of research aimed at disentangling the complex evolution of photosynthesis and its impact on the early history of life and the planet.

    1. The study of the evolution of photosynthesis

    Anoxygenic photosynthesis pre-dates the origin of oxygenic photosynthesis [1]. After the emergence of the earliest forms of anoxygenic phototrophic bacteria, the capacity scattered across a few groups of bacteria via horizontal gene transfer [2,3]. Oxygenic photosynthesis originated in an ancestor of Cyanobacteria when an anoxygenic photosystem gave rise to a water-splitting photosystem [4]. These three basic premises currently underlie the study of the evolution of photosynthesis and would hardly make anyone raise a sceptical eyebrow.

    Up for debate are the mechanisms by which Cyanobacteria obtained two distinct photochemical reaction centres linked in series, Photosystem I and Photosystem II, the hallmark of oxygenic photosynthesis. Was the origin of Photosystem I and Photosystem II triggered by a gene duplication event occurring before phototrophy scattered across the tree of life [5–7]? Or were these distinct photosystems acquired via horizontal gene transfer from lineages of anoxygenic phototrophs into a non-photosynthetic ancestor of Cyanobacteria right before the great oxidation event (GOE) [8,9]? We can therefore debate how long it took for anoxygenic photosynthesis to emerge after the origin of life, and how long it took for oxygenic photosynthesis to emerge after the origin of anoxygenic photosynthesis. We could also debate the identity of the earliest phototrophs, the oldest type of photosystem, and whether this ancestral photosystem used chlorophyll, bacteriochlorophyll or a mixture of both.

    By 2007, when the discovery of phototrophic Acidobacteria was first published [10], all groups of phototrophs then known had been proposed as the innovators of phototrophy, a wide-range of bacterial cell fusion and horizontal gene transfer combinations had been suggested for the birth of Cyanobacteria, and almost every possible scenario for the nature of the earliest photochemical reaction centre had already been put forward. I reviewed this briefly before [11] (but see also [12]). It is only proof that the study of the evolution of photosynthesis is fascinating it exerts an almost irresistible force on the curious mind that marvels at the origin of things and drives us to speculate. I have not been able to resist this force despite my best efforts [13] I have certainly not been the first [14] and will undoubtedly not be the last [15].

    This long history of speculation on the evolution of photosynthesis has blurred the line between what is assumed to be true and the facts as supported by rigorous evidence. In this essay, I shall demonstrate that several core ideas in the study of the evolution of photosynthesis are based on unsupported—sometimes incorrect—assumptions. A comprehensive critical assessment of the molecular evolution of photosynthesis would require more space than I have here, for that reason I will only focus on these three basic premises: (i) that anoxygenic reaction centres are more ‘primitive’ than those in oxygenic photosynthesis, (ii) that the horizontal transfer of photosynthesis is more likely than the loss of photosynthesis, but above all (iii) that anoxygenic photosynthesis pre-dates oxygenic photosynthesis.

    2. Primitive photosynthesis

    It is widely believed that the photochemical reaction centres used in anoxygenic photosynthesis are more primitive than those used in oxygenic photosynthesis. Ten years ago, when I was still a PhD student and a few years before the study of the evolution of photosynthesis became my full-time job, I came across an interesting and very memorable analogy: that the anoxygenic Type II reaction centre of phototrophic Proteobacteria and Chloroflexi is like a Ford Model T car, and in comparison Photosystem II, the water-oxidizing enzyme, is like a Formula 1 racing car, implying that the former gave rise to the latter [16]. The logic behind the premise that anoxygenic photosynthesis is primitive goes like this: Water oxidation to oxygen is a difficult chemical reaction that requires great complexity. Photosystem II is more complex than anoxygenic Type II reaction centres so surely, the anoxygenic reaction centre is more primitive and must have given rise to the oxygenic one.

    This assumption is not new and its roots can be traced back to speculative commentary emerging from the early comparative biochemistry of anoxygenic and oxygenic photosynthesis, starting more than 80 years ago [17–19]. For example, H. F. Blum in 1937 reasoned that because oxygenic photosynthesis used four quanta of light to complete a catalytic reaction, unlike anoxygenic photosynthesis, the latter must have been more primitive [19]. Then, this idea was reworked, cemented and popularized by Olson [20], whose insight into the evolution of photosynthesis is as influential today as it was back then [21]. It should be noted that this idea became popular well before we had a comprehensive understanding of the photosynthetic processes and long before we had access to sequences or structures of the reaction centres to put it to the test. Now this assumption has taken the appearance of almost undisputable fact.

    While at first glance it seems quite reasonable, the flaw is found in the incorrect presupposition that the complexity of oxygenic photosynthesis, and by extension of Photosystem II, evolved before the origin of water oxidation photochemistry. Perhaps it is not too counterintuitive to think that the origin of water oxidation should be considered the trigger that led to an increase in complexity, because the increased complexity exists for the sole purpose of supporting water oxidation. After the origin of water oxidation greater complexity was evolved to make catalysis more robust and efficient [22,23], to incorporate protection mechanisms against the formation of reactive oxygen species and to diminish the risk of damage [24,25]. Increased damage caused by reactive oxygen species led to the evolution of a more complex repair and assembly process [26,27]. An increase in structural and functional complexity also led to the evolution of more sophisticated regulatory processes acting from picoseconds to weeks and ranging from fine-tuning of electron transfer [28–30] to long-term chromatic adaptation [31]. The bottom line is that an apparent lack of complexity is not a definitive measure of primitiveness, yet that apparent complexity of Photosystem II disappears when the core reaction centre proteins are compared with each other (figures 1 and 2).

    Figure 1. Structural comparisons. (a) The reaction centre core subunits. PSII stands for cyanobacterial Photosystem II, PbRC for proteobacterial reaction centre, HbRC for heliobacterial reaction centre and PSI for cyanobacterial Photosystem I. (b) The core subunits are shown transparently to highlight the photochemical pigments. Type II reaction centres are characterized by a quinone/non-heme Fe 2+ /quinone electron acceptor system. Type I reaction centres are characterized by a Fe4S4 cluster electron acceptor system. ChlZD1 and ChlZD2 are a pair of peripheral chlorophylls bound to the core, but functionally associated with the antenna domain. These are conserved in PSII and other Type I reaction centres and are absent in anoxygenic Type II. (c) The antenna domains: CP43 and CP47 are the antenna of PSII, PshA of the HbRC and PsaA/PsaB of PSI. In Type I reaction centres, the core and the antenna make a single protein. In PSII, the core and the antenna are separate proteins. Anoxygenic Type II reaction centres (PbRC) lack antenna domains, but have independently evolved a new light-harvesting complex. The Mn4CaO5 cluster is bound by D1 and CP43. In the HbRC, a Ca is found at a similar position and it is bound by the core and the antenna as in PSII. (d) A global top view of all the (bacterio)chlorophyll light-harvesting pigments. ChlZD1 and ChlZD2, and their equivalent in Type I reaction centres, are shown in orange. The other antenna pigments are shown in blue. Which of these structures is the most primitive? PDB ID: PSII, 3wu2 PbRC, 5y5 s HbRC, 5v8 k PSI, 1jb0.

    Figure 2. Heterodimerization of Type II reaction centres. The core of Photosystem II has retained more symmetry than anoxygenic Type II reaction centres. (a) A comparison of some structural elements between Photosystem II and the proteobacterial anoxygenic Type II reaction centre (PbRC). Only the first two transmembrane helices of the core subunits are shown. The N-terminus is marked with a grey and an orange arrow: there is noticeably more symmetry at the N-terminus between D1 and D2 than between L and M. More symmetry in Photosystem II is also observed around the overlap of the 4th transmembrane helix, and the C-terminus. In the PbRC, the bacteriochlorophyll peripheral pigment BchlM interacts with an asymmetrically located carotenoid. This is not found in the reaction centre of the Chloroflexi, instead a ‘third’ pheophytin takes the position of BchlM conserving the pigment asymmetry. In Photosystem II, strictly conserved redox-active Tyr-His pairs are found on D1 and D2 at the donor side. In the PbRC, an Arg takes the position of Tyr. In M, R164 provides a hydrogen-bond to Y193, which is substituted by Phe in the L subunit. (b) A comparison of symmetry at the quinone/non-heme Fe 2+ /quinone electron acceptor system. In Photosystem II, the non-heme Fe 2+ is coordinated by bicarbonate, which is symmetrically bound by strictly conserved Tyr residues. In the PbRC, the non-heme Fe 2+ is coordinated by a Glu residue in the M subunit showing that the PbRC electron acceptor side cannot have retained the ancestral state. (c) Overlap of D1 and D2 (left) and L and M (right). The root-mean-square deviation of atomic positions (RMSD) is a measurement of average distance between overlapped atoms of the backbone's alpha carbons. Between D1 and D2 the RMSD is 2.32 Å over 320 residues, while between L and M is 4.37 Å over 232 residues. The greater the symmetry, the better the overlap and the smaller the RMSD over a greater number of residues.

    The assumption that anoxygenic reaction centres are more primitive than those used in oxygenic photosystems is not supported by phylogenetic and structural evidence [11,32]. Of note is the fact that the heterodimeric core of Photosystem II, made up of D1 and D2, originated from an unambiguous gene duplication event distinct to that which led to the heterodimeric core of the anoxygenic Type II reaction centres, made of L and M [11]. The reason why this is unambiguous lies in the fact that D1 and D2 share much greater sequence and structural identity with each other than with L and M and vice versa. While all Type II reaction centre proteins share common ancestry, the known anoxygenic Type II reaction centres are not direct ancestors of Photosystem II. They cannot be described as more primitive and they do not make any better models for what ancestral photosystems looked like than Photosystem II. The assumption that the ancestral Type II reaction centre before L, M, D1 and D2, was more like those found in Proteobacteria and Chloroflexi than those in Cyanobacteria, carries a wealth of unproven assumptions: for example, that L and M retained more ancestral traits than D1 and D2, or that L and M are evolving at a significantly slower rate than D1 and D2.

    The case for Type I reaction centres is similar. Anoxygenic Type I reaction centres are homodimeric, while Photosystem I in oxygenic photosynthesis is heterodimeric. Undoubtedly, the homodimeric state is the ancestral state, but that does not necessarily imply that Photosystem I in oxygenic photosynthesis directly originated from the reaction centre of any of the known groups of anoxygenic phototrophs. The phylogeny of Type I reaction centres indicates that all anoxygenic Type I homodimers share a more recent common ancestor to the exclusion of Photosystem I core subunits [11], which is also a reflection of the greater sequence and structural identity among homodimeric Type I reaction centres [33]. It is indeed correct to say that a heterodimeric core is a novel trait relative to the ancestral state, but it would be incorrect to say that PshA or PscA, the reaction centre core subunits of phototrophic Firmicutes, Chlorobi and Acidobacteria, gave rise to the ancestral core subunit of cyanobacterial Photosystem I.

    Cardona et al. recently showed that the core subunits of the anoxygenic Type II reaction centres are evolving on average about five times faster than the core subunits of the water-oxidizing enzyme [34]. They have probably done so for most of their evolutionary history. That D1 and D2 are evolving significantly slower has two major implications: (i) that the duplication of the oxygenic core that led to D1 and D2 is older than the duplication that led to L and M and (ii) that Photosystem II has retained more ancestral traits than its anoxygenic cousin. This is clearly seen in the structures of the photosystems, as Photosystem II has retained not only greater sequence and structural symmetry at the core but also greater structural identity with Type I reaction centres (figures 1 and 2). In a manner similar to Type II reaction centres, by studying the rates of evolution I have also found that the gene duplication leading to the heterodimeric core of cyanobacterial Photosystem I has a pretty good chance of having occurred before the diversification event leading to the different groups of phototrophs with homodimeric Type I reaction centres known today [35].

    In conclusion, the assumption that anoxygenic reaction centres are more primitive than those used in oxygenic photosynthesis is, at best, unsupported by their molecular evolution at worst, it is incorrect.

    3. Easy transfer

    Arguably there is no topic more controversial in the study of the evolution of photosynthesis than whether the scattered distribution of phototrophy is largely due to widespread horizontal gene transfer or multiple losses across the tree of life. But why is this important? If horizontal transfer of photosynthesis is a relatively easy process, then one could argue that oxygenic photosynthesis could have emerged at a late stage in the evolutionary history of life from the transfer of anoxygenic photosynthesis into a non-photosynthetic ancestor of Cyanobacteria, for example. If, on the other hand, the transfer of photosynthesis is a more difficult process then it may be more likely that the emergence of two distinct photosystems was the result of a gene duplication event, which occurred in a deep but direct ancestor of Cyanobacteria. Certainly, gains and losses of photosynthesis across geological time are not mutually exclusive, and there is evidence that both have occurred.

    This leads to the next popular assumption in the study of the evolution of photosynthesis: the idea that the probability of a non-photosynthetic organism gaining photosynthesis via horizontal gene transfer is greater than that of a photosynthetic organism losing photosynthesis. Given this assumption, if a clade of photosynthetic bacteria shares a more recent common ancestor with a non-photosynthetic clade, it is assumed that the ancestral state is more likely to be non-photosynthetic [2,3]. The recent discovery of early-branching non-photosynthetic Cyanobacteria, the Melainabacteria [36] and the Sericytochromatia [9], has lent credence to the hypothesis that oxygenic photosynthesis was invented after horizontal transfer of anoxygenic photosynthesis. This hypothesis relies on the assumption that the ancestral state was non-photosynthetic.

    To the best of my knowledge, there are no published studies that have attempted to determine the likelihood of gain versus loss of photosynthesis across the tree of life.

    There is only one case of a group of non-photosynthetic bacteria obtaining photosynthesis via horizontal gene transfer. That is the phototrophic Gemmatimonadetes. Zeng et al. demonstrated that this peculiar group of bacteria obtained a photosynthesis gene cluster from a gammaproteobacterium [37]. Any other case of potential gains of photosynthesis in bacteria is ambiguous. The other (more spectacular) case of gain of photosynthesis are the photosynthetic eukaryotes. Horizontal gene transfer occurred from a cyanobacterium endosymbiont into the host nuclear genome of a non-photosynthetic unicellular eukaryote [38,39]. Nevertheless, after more than a billion years of evolution and the transfer of hundreds, if not thousands [40], of cyanobacterial genes into the eukaryotic nuclear genome, the core subunits of the photosystems have remained encoded in the plastid genome.

    There are many clear cases of horizontal gene transfer of photosynthesis components between phototorphs. Several studies have shown, for example, that the marine Synechococcus and Prochlorococcus strains obtained protochlorophyllide reductase from Gammaproteobacteria [5,41]. Their genes are distinctly and undoubtedly proteobacterial as they cluster specifically within Proteobacteria. Another peculiar case is the transfer of protochlorophyllide and chlorophyllide reductases between a stem-group phototrophic Chlorobi and a stem-group phototrophic Chloroflexi [42], but the direction of transfer is ambiguous.

    Recently, it was suggested that it was not merely Cyanobacteria which obtained photosynthesis via horizontal gene transfer: a compelling case has been made for phototrophic Chloroflexi evolving via the transfer of photosynthesis as early as approximately 900 Ma [43,44]. Gisriel et al. also proposed that Heliobacteria, the only known phototrophic Firmicutes, also obtained phototrophy via horizontal transfer justified by the presence of a photosynthesis gene cluster [45]. It is noteworthy that Cyanobacteria and Chloroflexi show phylogenetic affinity in many phylogenomic analyses appearing in many instances as each other's closest relatives [46–50]. One has reasons to argue that the most recent common ancestor (mrca) of these two phyla had Type II reaction centres. Indeed, the large phylogenetic distance between the core subunits of the anoxygenic Type II reaction centre and Photosystem II would be consistent with such a scenario. Similar kind of reasoning can be presented against the hypothesis that Heliobacteria obtained phototrophy via horizontal gene transfer. For example, Mix et al. noted that the evolution of Type I reaction centres is consistent with vertical descent [51], and if recent phylogenomic trees of prokaryotes have any resemblance to reality only a single gain of horizontal gene transfer of photosynthesis between phyla of bacteria can be identified [52]: phototrophic Gemmatimonadetes, the exception that proves the rule (figure 3).

    Figure 3. Loss of photosynthesis or horizontal gene transfer? Maximum-likelihood trees of Type I reaction centre proteins, Type II reaction centre proteins, protochlorophyllide reductase subunit L (ChlL), oxygen-dependent Mg-protoporphyrin IX monomethyl ester cyclase (AcsF) and a tree of concatenated ribosomal proteins reported before [52]. The different phototrophic clades are coloured at phylum level. The topology of the trees of photosynthetic components matches closely the tree of ribosomal proteins subtracting non-phototorphic clades and accounting for duplication events (stars). The grey arrow represents the position of the root of the tree as calculated in [52]. The orange circle marks the most recent common ancestor of Cyanobacteria capable of oxygenic photosynthesis (Oxyphotobacteria). The duplications leading to PsaA and PsaB, and to D1 and D2 are highlighted with a red star, and these duplications must pre-date the diversification of described Cyanobacteria. Similarly, the duplication leading to L and M (purple star) must pre-date the origin of phototrophic Chloroflexi and Proteobacteria. The asterisk marks a ChlL subunit from an uncharacterized group of phototrophs. Scale bar represents substitutions per site. All photosynthesis proteins are plotted at the same scale.

    An often-cited piece of evidence in favour of horizontal gene transfer scenarios is the fact that in some anoxygenic phototrophs most of the genes required to support phototrophy are encoded in a single gene cluster. Recently, Brinkmann et al. showed that within the family Rhodospirilaceae of Alphaproteobacteria the transfer of complete photosynthesis gene clusters has occurred [53]. The authors calculated that even in the most stringent scenarios at least seven transfer events and eight loss events were needed to reconcile the species tree with the tree of the gene cluster. If these numbers are accurate that would make losses slightly more probable than gains, at least within the Rhodospirilaceae. However, from these seven transfers at least five can be better described as replacements of a native gene cluster with that from a very closely related strain rather than true de novo gains of phototrophy, making the probability of losses substantially greater than gains. It should be noted however, than in none of these transfer cases the photosynthesis gene cluster originated from outside the Rhodospirilaceae. Thus, it could be argued that the greater the phylogenetic distance between the donor and the recipient strain, the less likely it will be that a non-phototroph will successfully integrate and express an entire photosynthesis gene cluster.

    We can now wonder if the reason why phototrophic Gemmatimonadetes managed to successfully integrate a photosynthesis gene cluster from Proteobacteria is because the phylum may have been ancestrally phototrophic to begin with, given that Gemmatimonadetes and Chlorobi show strong phylogenetic affinity [50,52]. This seems unlikely if one is biased towards thinking that lack of photosynthesis is a more plausible ancestral state. A relevant example of these exchange processes was recently reported in the dinoflagellate Lepidodinium. It was shown that its ancestor lost photosynthesis, discarded the entire pathway for the synthesis of chlorophyll a, then regained photosynthesis by acquiring a new algal endosymbiont, and finally rebuilt the chlorophyll synthesis pathway with genes transferred from multiple sources, rather than from the new endosymbiont itself [54].

    There are many examples of losses of oxygenic photosynthesis in Cyanobacteria and eukaryotes. One fascinating case is the loss of all Photosystem II-encoding genes in Atelocyanobacterium thalassa (UCYN-A), along with the loss of roughly 75% of the original genome content [55] in only 100 Myr [56]. Another interesting case of loss of photosystem genes is that of the cyanobacterium endosymbiont of rhopalodiacean diatoms [57]. In photosynthetic eukaryotes we find the well-known case of parasitic apicomplexa [58], multiple losses in dinoflagellates [59], chrysophytes [60], free-living green algae [61,62] and holoparasitic angiosperms [63], among probably many others. Within flowering plants, about 10 independent losses of photosynthetic capacity have already been documented [64]. One could argue that it is much more likely to lose a single anoxygenic photosynthesis gene cluster than to lose the entire complexity of oxygenic photosynthesis.

    Not a single case of horizontal gene transfer of oxygenic photosynthesis between bacteria has been documented. Unlike anoxygenic photosynthesis, the numerous genes now required to support oxygenic photosynthesis are scattered across the cyanobacterial genomes [6] making the probability of a non-photosynthetic bacterium acquiring oxygenic photosynthesis via horizontal gene transfer nil. In contrast, and as we saw in the previous paragraph, the probability of loss of oxygenic photosynthesis is certainly above zero and can occur within less than 100 Ma. Therefore, if the probability of loss of photosynthesis is just slightly greater than gain, it is expected that over billions of years the number of lineages of anoxygenic and, in particular, of oxygenic phototrophs, has decreased. This not only explains the scattered distribution of photosynthesis in bacteria but also the large phylogenetic distance between phototrophic lineages, a distance that is matched by that of their photosynthetic machinery (figure 3): an aspect that is always overlooked and unaccounted for in horizontal gene transfer scenarios.

    This line of thought reveals another assumption on the study of the evolution of photosynthesis not based on any piece of scientific evidence, but nonetheless taken for granted: that Cyanobacteria are the only group of bacteria alive today to have descended from oxygenic phototrophs. In fact, it takes a very simple mental exercise to demonstrate that most of the diversity of oxygenic phototrophs that have existed in the history of the planet probably pre-dates the mrca of Cyanobacteria.

    All Cyanobacteria share an mrca that was capable of oxygenic photosynthesis [4] in the same way that birds originated from an mrca that had already evolved feathers [65,66]. All Cyanobacteria share an mrca that had already evolved Photosystem I with a heterodimeric core. This is a trait that has been retained by all oxygenic phototrophs. A heterodimeric Photosystem I is a distinctive and exclusive characteristic of oxygenic photosynthesis and it is widely accepted that the heterodimerization of the core was an adaptation to oxygenic photosynthesis [29,67,68]. PsaA and PsaB, the core subunits of Photosystem I share about 43% sequence identity: this is true across the entire diversity of oxygenic phototrophs from the earliest-branching Cyanobacteria to the most exotic variety of avocado, which implies that the mrca of Cyanobacteria inherited a heterodimeric Photosystem I that had PsaA and PsaB with about 43% identity. In other words, at the time of the mrca of Cyanobacteria, PsaA and PsaB had already changed by 57%. If we compare the change of sequence identity of PsaA across all oxygenic phototrophs, the maximum level of change is not greater than about 30%, and between all photosynthetic eukaryotes not greater than 20%. It is exactly the same for PsaB. Therefore, most of the sequence change of the core subunits of Photosystem I occurred between the time of the duplication leading to PsaA and PsaB and the mrca of Cyanobacteria [35]. Given that the rates of evolution of complex molecular systems is slow relative to speciation rates [69], that distance between PsaA and PsaB, that amount of change, must have been matched by a substantial biodiversity.

    Such a simple exercise exposes the inherent naivety of every proposed evolutionary scenario for the evolution of photosynthesis (including my very own), since it is impossible not to severely underestimate the biodiversity of anoxygenic and oxygenic phototrophic bacteria that have existed through geological time [70]. With all of this in mind, and based on the current state of knowledge, the assumption that multiple losses of photosynthesis across the tree of life is less parsimonious than gains via horizontal transfer is far from proven, and might just as well not stand up to scrutiny.

    4. Let there be light

    The chief unproven assumption in the evolution of photosynthesis is that the origin of anoxygenic photosynthesis pre-dates the origin of oxygenic photosynthesis. This assumption can be understood at two fundamental levels: (i) that oxygenic phototrophs evolved from anoxygenic phototrophs or (ii) that Photosystem II evolved from an anoxygenic photosystem. The first fundamental level leads to the obvious question of when Cyanobacteria originated, but the question itself is problematic. Only one point in time in the evolution of oxygenic photosynthesis can be clearly defined and accessed through phylogenies of species trees: that is, the mrca of Cyanobacteria (figure 4). A broad range of ages for this ancestor have been provided using molecular clocks ranging from 1.5 to 3.5 billion years [8,72–75]. Yet, in the same way that determining when the mrca of birds occurred cannot tell us when or how feathers originated, determining when the mrca of Cyanobacteria occurred cannot tell us when or how photochemical water oxidation to oxygen originated. And, in the same way that having feathers does not make Tyrannosaurus a modern bird, there is a very real possibility that the origin of photochemical water oxidation to oxygen does not necessarily fall in a lineage that was the immediate ancestor of the known diversity of Cyanobacteria.

    Figure 4. Schematic of the evolution of photosynthesis. Two key transitional points are highlighted: the divergence of Type II and Type I reaction centres, marked 1 and the duplication leading to D1 and D2, marked 2. We can then define two periods of time: one starts with the duplication of D1 and D2 and ends with the emergence of standard Photosystem II (ΔT1), which was inherited by the mrca of Cyanobacteria and the other one starts with the Type II/Type I divergence and ends with the duplication of D1 and D2 (ΔT2). Cardona et al. determined that ΔT1 could comfortably be 1 billion years or more [34]. The main reason for this is the very slow rates of evolution of Photosystem II in Cyanobacteria and photosynthetic eukaryotes. Even when ΔT1 is 1 billion years the rate of evolution at the moment of duplication is calculated to be about 40 times greater than any rate observed in Cyanobacteria or photosynthetic eukaryotes. It also requires an exponential decrease in the rates approaching current rates before the Archaean/Proterozoic transition. Furthermore, due to the exponential decrease in the rates, ΔT2 can be well under 200 million years. It is worth comparing to the evolution of ATP synthases as both display indistinguishable evolutionary trends, both showing similar rates of evolution and a high degree of sequence conservation across distant taxa. The duplication leading to AtpA and AtpB, marked 3, is known to have occurred in the LUCA. At the moment of duplication, the sequence identity between these two was 100%. Today and across all life (including Cyanobacteria), the level of sequence identity of AtpA and AtpB is about 20%. It stands to reason that the span of time between the AtpA/AtpB duplication and the F-type ATP synthase of the mrca of Cyanobacteria is in the order of a billion years or more. In fact, an exponential decrease in the rates of evolution of the same magnitude as in Photosystem II is required for that span of time to be as large. In Photosystem II, the level of sequence identity between D1 and D2 is about 29% and that between CP43 and CP47 is about 18%. Now, if ΔT1 is proposed to be very small, that would require faster rates at the moment of duplication than any rate reported for these types of highly conserved and very slow evolving complexes. If ΔT1 is 100 million years the rate at the duplication would need to be almost 300 times greater than any observed rate: that is twice as fast as the rate of evolution of short peptide toxins of poisonous animals [71], which are usually less than 20 residues long and are among the fastest evolving proteins in biology. In comparison, the ‘simplest’ reaction centre [45], that of Heliobacteria, has a core protein 608 residues long. This ‘simplest’ of reaction centres is made up of 4 interacting protein subunits, 54 (bacterio)chlorophyll pigments, two carotenoids, a Fe4S4 cluster, 4 calcium ions and a bunch of lipid molecules. Due to the structural complexity of the bioenergetics machinery, including the photosystems and ATP synthase, it is likely that they have maintained relatively slow rates of evolution across their entire evolutionary history.

    A more precise line of enquiry is to determine for how long water oxidation existed before the mrca of Cyanobacteria. Contrary to what may appear at a first glance, the answer to this question does not depend on the exact timing of the mrca of Cyanobacteria or whether this ancestor existed before or after the GOE, but instead it is strongly linked to when the earliest stages in the evolution of Photosystem II occurred. For example, the duplication leading to the alpha and beta subunit of ATP synthase is known to have occurred before the last universal common ancestor (LUCA) [76–78]. It follows then that the initial stages in the evolution of ATP synthases is in no way dependent on the time of origin of any particular group of prokaryotes (e.g. Cyanobacteria, Firmicutes, Asgardarchaeota, Euryarchaeota), but it only depends on the molecular events at play during the emergence of the protein complex itself, including the duplication leading to the alpha and beta subunits: an event that pre-dates the divergence of the domains Bacteria and Archaea, and the divergence of F-type and V-type ATP synthases.

    This is also the case for oxygenic photosynthesis (figure 4). The two duplication events, which resulted in the evolution of a heterodimeric Photosystem II, one leading to D1 and D2 and the other to the core antenna subunits, CP43 and CP47, are much more likely to have occurred soon after the origin of the earliest reaction centres than right before the mrca of Cyanobacteria [34,35]. These two duplications together with the duplication leading to the heterodimeric core of Photosystem I are, to the best of our knowledge, exclusive to oxygenic photosynthesis [79–81]. It was suggested before based on conserved symmetrical structural and functional characteristics of Photosystem II that water oxidation started before the duplication leading to heterodimerization [34,80,81]. Cardona et al. recently calculated that the span of time between the duplication leading to D1 and D2 and the mrca of Cyanobacteria could comfortably be more than a billion years even accounting for the large uncertainties inherent to deep-time molecular clocks (figure 4) [34]. We also showed that the photosystem existing before the duplication leading to D1 and D2 had already evolved protective mechanisms to prevent the formation of singlet oxygen [34], such as bicarbonate-mediated redox tuning of electron transfer at the acceptor side (figure 2) [24]. Furthermore, our data also indicated that the span of time from the origin of photosynthesis to well past the point of duplication of D1 and D2 could be less than 200 Ma. In consequence, the only way to find out how and when oxygenic photosynthesis originated is to resolve what happened during the early evolution of photochemical reaction centres, a time in the history of life that in all likelihood considerably pre-dates the appearance of the taxonomic group that today we recognize on a 16S RNA basis as Cyanobacteria.

    The second fundamental level of understanding relies on the assumption that anoxygenic reaction centres are more primitive than Photosystem II: as I discussed before, this assumption is incorrect. And all of a sudden, we find ourselves in a situation in which the fundamentals of the evolution of photosynthesis are based on unproven assumptions built on top of unproven assumptions. For instance, the idea that anoxygenic reaction centres are more primitive leads to the presupposition that primordial reaction centres did not have enough oxidizing power to split water, which then makes it easy to assume that water oxidation could not be an ancestral trait. An assumption that has not been, in any way, validated. Now, these ideas have such a strong grasp on our current understanding of the evolution of life that conceiving a highly oxidizing water-splitting photosystem as the primordial photochemical ancestor, and as part of the bioenergetics toolkit of early life, becomes unthinkable [82], despite the absence of unequivocal data supporting otherwise.

    From a palaeobiological and geochemical perspective, the timing of the origin of oxygenic photosynthesis is far from settled. Rocks older than 2.5 billion years make less than 5% of the surviving rock mass [83]. Stromatolites, microbial mats and bacteria-like fossils ‘are present throughout virtually all of the known geological record’ [84], but anything older than 2.0 billion years cannot confidently be ascribed to any particular type of phototroph, although they have traditionally been described as ‘Cyanobacteria-like’ [84,85]. Of note are the 3.22-billion-year-old fossilized microbial mats of the Barberton Greenstone Belt in South Africa, which in many ways resemble modern cyanobacterial mats [86]. The record of carbon isotopes fractionation extending to the oldest sedimentary rocks is somewhat inconclusive on the matter as rubisco-derived δ 13 C signatures from anoxygenic and oxygenic phototrophs overlap. Nonetheless, and as better said by Nisbet et al. [87], ‘In many cases Archaean carbon isotopic results have been taken to demonstrate that the material is the product of an oxygenic biosphere' (p. 313, citing [88,89]). Furthermore, the interpretation of redox proxies has provided estimates for the origin of oxygenic photosynthesis through the Archaean and down to some of the oldest rocks more than 3.7 billion years old [90–101]. Mass-independent fractionation of sulphur isotopes in sedimentary rock has constrained the concentration of oxygen to below 10 −5 of the present atmospheric level (PAL) until about 2.4 billion years ago [102–104] yet variation in the sulphur isotope record has led researchers to suggest that concentrations of oxygen probably fluctuated greatly across time and space during the Archaean [100,105,106]. To top it all, the biogenicity, indigenousness and syngenicity of the earliest rocks and signs of life have been strongly contested [107]. A perfect and recent example of this is the 3.7-billion-year-old fossilized stromatolites reported by Nutman et al. [108], followed by a rebuttal [109].

    Molecular evolution is equally inconclusive on the timing of the origin of biological oxygen production. For example, reconstructions of the proteome of the LUCA, often pictured as an anaerobe, have retrieved the core subunit of bona fide terminal oxygen reductases [77,110] a result that seems to be supported (not without controversy [111]) by phylogenetic analysis of the same enzymes [112,113]. Reconstructions of the LUCA and phylogenetic analysis also appear to indicate an early origin of superoxide dismutase, rubrerythrin and peroxiredoxin among few other oxygen-using enzymes [77,110,114–116]. Oxygen-tolerant hydrogenases [117] and cytochrome b6f complexes incorporating protective mechanisms against the formation of reactive oxygen species have also been suggested to substantially pre-date the mrca of Cyanobacteria [118]. To top it all, it was recently suggested based on the physico-chemical properties of amino acids that the establishment of the universal genetic code, which should pre-date the LUCA, required ‘biospheric molecular oxygen’ [119]. And this is not meant to be an exhaustive list. One is then forced to either dismiss the above as artefacts of one sort or another [82,110] to accept (rather reluctantly in my personal case) that somehow the vanishingly small traces of oxygen expected from abiotic process alone, up to eight orders of magnitude below 10 −5 PAL [120], played any role at all in the early evolution of life [113,121] or alternatively, one must explain away each observation with a series of rationalizations well suited to each particular case.

    Efforts to time the evolution of prokaryotes or the emergence of the known groups of phototrophs have also generated puzzling results. For example, the most recent common ancestors of phototrophic Firmicutes [49,122], of phototrohic Chlorobi [49,73,123], of phototrophic Chloroflexi [43,49,73] and of phototrophic Proteobacteria [8,47,49,74] have all been timed at about the GOE, but more often than not, after the GOE. What is more, and consistent with the above, my own efforts to understand the evolution of reaction centre proteins as a function of time have suggested that the L and M duplication postdate the D1 and D2 duplication and that the divergence of PshA and PscA postdate the duplication of PsaA and PsaB. Therefore, at the present moment, there is no evidence that clearly demonstrates that anoxygenic photosynthesis ever existed in the absence of oxygenic photosynthesis.

    If neither molecular evolution nor the geochemical record have conclusively proven that anoxygenic photosynthesis pre-dates oxygenic photosynthesis, where does the confidence that this is the case come from? I believe this confidence represents an historical and interpretative bias resulting from early speculation on the evolution of photosynthesis, enduring until this day and blurred into the appearance of facts by the inevitable passage of time [14,17–20,124–127].

    Nevertheless, there is a direct and easy way to demonstrate that the idea that anoxygenic photosynthesis gave rise to oxygenic photosynthesis is based on unproven assumptions. Oxygenic photosynthesis is characterized by the use of a Type II and a Type I reaction centre linked in series. Regardless of whether these two reaction centres got together via an ancient gene duplication or via horizontal gene transfer, all proposed models for the emergence of oxygenic photosynthesis need to fulfil one major requirement. Namely, that at some point in time a transitional photosynthetic stage using an anoxygenic Type II and a Type I reaction centre was favoured over anoxygenic photosynthesis using a single reaction centre. There is no evidence that such a stage in the evolution of anoxygenic photosynthesis ever existed. There are no described anoxygenic phototrophs with genomes encoding both Type I and anoxygenic Type II reaction centre proteins. If towards the evolution of oxygenic photosynthesis such a transitional stage proved advantageous over ‘single-reaction-centre’ anoxygenic photosynthesis, how is it that ‘two-reaction-centre’ anoxygenic photosynthesis has not evolved several times? In theory, it would only require the transfer of a single gene from a bacterium having a homodimeric Type I reaction centre into one having a Type II. That such a type of anoxygenic photosynthesis is not more common than conventional single-reaction-centre anoxygenic photosynthesis is paradoxical considering that horizontal gene transfer of photosynthesis is supposed to be a fairly feasible process, that anoxygenic photosynthesis is supposed to have emerged in the early Archaean, [128–131], and that most groups of anoxygenic phototrophs have cohabited in microbial mats for billions of years [41,132]. One could argue that there is a functional barrier preventing the acquisition and integration of a second anoxygenic photosystem.

    Frankly, observations from the natural world do not match the expectations derived from current models on the evolution of photosynthesis. Consequently, to prove that anoxygenic indeed pre-dates oxygenic photosynthesis one must first demonstrate that ‘two-reaction-centre’ anoxygenic photosynthesis can provide a competitive advantage or increased fitness over ‘single-reaction-centre’ anoxygenic photosynthesis. If one can prove that, then one must explain why this two-reaction-centre anoxygenic photosynthesis did not outcompete and supersede the only known form of anoxygenic photosynthesis across all photic ecosystems. This has not been done yet.

    There is one way out of this paradox: that photochemical water oxidation originated before or at the divergence of Type I and Type II reaction centres.

    Three basic observations from the natural world straightforwardly indicate that the origin of reaction centres was intimately linked to the origin of photochemical water oxidation. These are: (i) that oxygenic photosynthesis is the only process that exclusively uses both reaction centres (ii) that anoxygenic photosynthesis using both reaction centres does not exist and (iii) that Photosystem II, the water oxidizing enzyme, is a chimeric photosystem made of a Type II core bound to a Type I antenna with both parts needed for the coordination of the Mn4CaO5 cluster [133]. Given these three observations, a better starting hypothesis in the study of evolution of photosynthesis is that the origin of photochemical reaction centres was linked to the origin of water oxidation to oxygen, rather than to the origin of a speculative form of anoxygenic photosynthesis.

    There is a fourth observation that had until recently remained unnoticed, yet it is straightforward nonetheless: that Photosystem II is the slowest evolving of all photosystems, evolving at a fifth of the rate of anoxygenic Type II reaction centres [34], and about a third of the rate of Type I reaction centres [35]. That means that Photosystem II is the most likely photosystem to have retained traits once found in the most ancestral reaction centre (figures 1 and 2). Strong support for this superior starting hypothesis was revealed in the recent structure of the homodimeric Type I reaction centre from Heliobacteria [45]. It showed a calcium bound at the electron donor site of the core with unmistakable structural parallels to the Mn4CaO5 cluster of Photosystem II (figure 1) [134]. These structural parallels indicate that the ancestral reaction centre before Type II and Type I had, at the very least, all of the structural elements already in place for the evolution of the Mn4CaO5 cluster. This is because the most recent common ancestor of Photosystem II and the homodimeric Type I reaction centres is the most recent common ancestor of all reaction centres.

    5. Final words

    The study of the origin and evolution of photosynthesis has fascinated scientists for decades and will continue to capture the imagination of the scientific community and the public for decades to come. It is too soon to claim that we understand how photosynthesis originated, let alone to claim that we understand the photochemistry of the earliest reaction centres to ascertain that the origin of anoxygenic photosynthesis pre-dates the origin of oxygenic photosynthesis. For the field to move forward unhindered, more critical, cautious, yet open thought is required. The temptation to speculate will always be too sweet to resist nonetheless, we should strive to keep the lines between assumptions, hypotheses, predictions and facts well delimited. Only then we can lay new foundations upon which to build a modern framework for the study of the evolution of photosynthesis.


    Key Differences Between Cyclic and Noncyclic Photophosphorylation

    1. Cyclic and noncyclic photophosphorylation is the light-dependent photosynthetic pathways that generate ATP by following cyclic and noncyclic electron transport chain, respectively.
    2. Cyclic photophosphorylation follows anoxygenic photosynthesis that predominantly occurs in photosynthetic bacteria like green sulfur and nonsulfur bacteria, purple bacteria etc. Oppositely noncyclic photophosphorylation follows oxygenic photosynthesis that commonly takes place in autotrophic green plants, algae and cyanobacteria.
    3. In cyclic phosphorylation, electrons flow in a cyclic or circular pattern, as it expels out of the PS-I and returns back into it. The electrons flow linearly in a zig-zag pattern in noncyclic phosphorylation, by going out of the PS-II, entering into the PS-I, and finally to the NADP+.
    4. In cyclic phosphorylation, water do not lyse to give protons and oxygen. Oppositely, in noncyclic phosphorylation water molecule photolyses to liberate oxygen into the atmosphere.
    5. Diuron function as an inhibitory agent that is commonly used as herbicide and algaecide that generally inhibits the noncyclic phosphorylation.

    Similarities

    • Both cyclic and noncyclic photophosphorylation is the light-dependent photosynthetic reaction.
    • Cyclic and noncyclic photophosphorylation processes are the part of ETS that carry out phosphorylation (addition of phosphate group) or ATP formation.

    Conclusion

    Therefore, we can conclude that the cyclic and noncyclic photophosphorylation are the light-dependent photosynthetic pathways that carry out phosphorylation to produce ATP. This ATP is then used by the cells of micro and macroorganisms to perform various activities for their growth and survival.


    Watch the video: What are Photosystems? Difference between Photosystem I and Photosystem II PS I vs PS II (June 2022).


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