Cyanobacterial UV Pigments Evolved to Optimize Photon Dissipation Rather than Photoprotection

Abstract

An ancient repertoire of ultraviolet (UV)-absorbing pigments which survive today in the phylogenetically oldest extant photosynthetic organisms, the cyanobacteria, point to a direction in evolutionary adaptation of the pigments and their associated biota; from largely UV-C absorbing pigments in the Archean to pigments covering ever more of the longer wavelength UV and visible regions in the Phanerozoic. Since photoprotection is not dependent on absorption, such a scenario could imply selection of photon dissipation rather than photoprotection over the evolutionary history of life, consistent with the thermodynamic dissipation theory of the origin and evolution of life which suggests that the most important hallmark of biological evolution has been the covering of Earth’s surface with organic pigment molecules and water to absorb and dissipate ever more completely the prevailing surface solar spectrum. In this article we compare a set of photophysical, photochemical, biosynthetic, and other inherent properties of the two dominant classes of cyanobacterial UV-absorbing pigments, the mycosporine-like amino acids (MAAs) and scytonemins. We show that the many anomalies and paradoxes related to these biological pigments, for example, their exudation into the environment, spectral coverage of the entire high-energy part of surface solar spectrum, their little or null photoprotective effect, their origination at UV-C wavelengths and then spreading to cover the prevailing Earth surface solar spectrum, can be better understood once photodissipation, and not photosynthesis or photoprotection, is considered as being the important variable optimized by nature.

1. Introduction

Considering the non-equilibrium thermodynamic aspects of life, and using the formalism of Prigogine’s “classical irreversible thermodynamics” [1,2] in the non-linear regime, Michaelian [3,4,5] has proposed a theory for life’s origin and evolution as the microscopic self-organized dissipative structuring of organic pigment molecules and the dispersal of these over the entire surface of the Earth as a response to the impressed high energy (from UV-C to visible) solar photon spectrum prevailing at the Earth’s surface. All physicochemical structuring associated with the pigments, such as the photosynthetic organisms primarily, and heterotrophic organisms secondarily, can be regarded as agents for the synthesis, proliferation, and distribution of the pigments [6,7]. The theory suggests that it is the thermodynamic imperative of increasing the entropy production of the Earth in its solar environment through photon dissipation in the biosphere that is behind the vitality of living matter manifest in its ability to proliferate, diversify, and evolve.

The theory explains satisfactorily, for example, why the three major classes of photosynthetic pigments (chlorophylls, carotenoids, and phycobilins) of phototrophic organisms dissipate most of the absorbed photonic energy into heat (a process known as non-photochemical quenching, NPQ) while funneling only a minute fraction into productive photochemistry [8,9,10,11,12,13]. Moreover, these organisms often contain a vast array of other organic pigments in addition to the photosynthetic ones, whose absorption spectra extend outside of the photosynthetically active radiation (PAR) in the visible and into the UV-A, UV-B, and UV-C regions, hence allowing full coverage of the past and present incident surface solar spectra [14,15]. In contradistinction to the thermodynamic dissipation theory, in the biological literature, this phenomenon of full spectral coverage has been explained primarily through invoking the conventional wisdom of photoprotection [16,17,18,19,20,21].

Photoprotective roles have especially been attributed to UV-absorbing biological pigments (e.g., mycosporine-like amino acids and scytonemins in cyanobacteria and algae; flavonoids and anthocyanins in plants, etc.) since they do not seem to contribute to photosynthesis at all [21,22]. These theories usually trace the photoprotective role of UV pigments back to the beginnings of cellular life in the early Archean when UV radiation was a far more important component of the surface solar spectrum than it is today [17,19,23,24,25]. UV-screening ostensibly conferred pigment-containing organisms Darwinian advantages for survival in the harsh Archean environment of intense UV radiation.

However, from a thermodynamic viewpoint, the UV-C is the region of the solar spectrum with an energy per photon sufficient for directly reconfiguring covalent bonds, and it also corresponds to the greatest possible entropy production potential per unit photon dissipated. Therefore, under the high UV ambient conditions of our primitive planet, the non-equilibrium thermodynamic principle of increasing the entropy production of Earth in its solar environment through dissipative structuring was probably the motive force for the dissipative synthesis of these organic pigments [5,26]. The evidence for this inextricable link between UV light and nascent life has been reinforced with the verification of the biogenicity of ~3.5 Ga old euphotic stromatolite formations [27,28,29,30,31,32,33,34] of evidently photosynthetically active, yet UV-C bathed, microbial colonies of cyanobacteria-like organisms [35,36].

Here we discuss how the two major classes of cyanobacterial UV-absorbing pigments, the mycosporine-like amino acids and the scytonemins, whose occurrence in organisms today is regarded as a relic from Archean times [24,37], concur with the type of microscopic dissipative structure which non-equilibrium thermodynamic principles would predict for microscopic dissipative structuring under the Archean Earth conditions.

The aim of this paper is to show that the many anomalies and paradoxes related to biological pigments, for example, the poor efficiency of photosynthesis, the exudation of pigments into the environment, pigment coverage of the entire surface solar spectrum, the little or null photoprotective effect of most pigments, the first pigments being in the UV-C, etc., can be better understood once photodissipation, and not photosynthesis or photoprotection, is considered as being the important variable optimized by nature.

In the following section we separately detail a set of inherent properties of both pigment classes, taken from the literature. In the third section we demonstrate how these properties are consistent with several postulates concerning photon dissipation made in previous work [15]. Also in the third section, we compare the pigments’ optical properties with our previous construct of the most probable Earth surface solar spectrum as a function of time (see [15]).

2. Properties of Cyanobacterial UV-Absorbing Pigments

2.1. Mycosporine-like Amino Acids (MAAs)

MAAs and a related group of organic compounds called mycosporines represent a large family of colorless, low-molecular-weight (<400 u), water-soluble, usually intracellular secondary metabolites widespread in the biological world [38,39,40,41]. The exact number of compounds within this family is yet to be determined, since they have only relatively recently been discovered (for a historical overview, see [42,43]), and novel molecular species are constantly being discovered. Thus far, however, their number is around 70 [44]. The name “mycosporine” refers to them being originally isolated and chemically identified from mycelia of sporulating fungi, where it was thought they played a role in light-induced sporulation [45,46].

2.1.1. Physicochemical Properties of MAAs

Chemically, both MAAs and mycosporines are alicyclic compounds (see Figure 1) sharing a central 5-hydroxy-5-hydroxymethyl-2-methoxycyclohex-2-ene ring with an amino compound substituted at the third C-atom and either an oxo- or an imino-functionality at the first C-atom [44,47,48,49,50]. While most authors do not make a clear chemical distinction between the two groups, several authors (for example [42,51,52,53,54]), when using the term mycosporines, refer only to those molecular species with a central amino-cyclohexenone chromophore (also called oxo-mycosporines), and when using the term MAAs refer only to molecules with a central amino-cyclohexenimine chromophore (also called imino-mycosporines). The N-substitution on C-3 with different amino acids or amino alcohols is what gives the diversity of molecular structures within both groups [55,56,57]. Within the MAA group, the most common amino acid at the C-3 position is glycine, whereas they also have a second amino acid, amino alcohol, or an enaminone system attached at the C-1 position [58].

This unique molecular structuring and bonding underlie their unique spectral properties. MAAs are considered to be one of the strongest UV-A/UV-B-absorbing substances in nature [59], with wavelength absorption maxima (${\lambda }_{max}$) in the 310–362 nm interval and molar attenuation coefficients ($\epsilon$) between 28,100 and 50,000 ${\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1}$ [60,61,62,63].

Their absorption spectra are characterized by a single sharp peak with a width of approximately 20 nm and are only about 2–3 nm away from the ${\lambda }_{max}$ of structurally similar MAAs (see Figure 2, ref. [64] making it very difficult to distinguish these compounds based solely on their absorption spectra [57,65,66].

The values of ${\lambda }_{max}$ and $\epsilon$ are dependent on the degree of derivatization of the central ring and the nature of the nitrogenous side groups (in particular, the presence of additional conjugated double bonds) [67,68].

Smaller, mono-substituted mycosporines (typically oxo-mycosporines) have their ${\lambda }_{max}$ values shifted to shorter wavelengths in the UV-B and usually have lower $\epsilon$ values; whereas MAAs (imino-mycosporines) are normally bi-substituted, with higher $\epsilon$ values and ${\lambda }_{max}$ values shifted to longer wavelengths in the UV-A [69,70].

For example, the direct metabolic precursor of all mycosporines, 4-deoxygadusol (Figure 1), which has the minimal level of derivatization, has ${\lambda }_{max}=268 \mathrm{n}\mathrm{m}$ at acidic pH, and ${\lambda }_{max}=294 \mathrm{n}\mathrm{m}$ at basic pH; mycosporine-glycine (Figure 1), the simplest oxo-mycosporine and direct precursor of all other mycosporines and MAAs, has a ${\lambda }_{max}=310 \mathrm{n}\mathrm{m}$, whereas palythine (Figure 1), a simple mono-substituted MAA (amino-MAA), has ${\lambda }_{max}=320 \mathrm{n}\mathrm{m}$ and $\epsilon =\mathrm{36,200} {\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1}$ [61,62]. Palythene (Figure 1), a bi-substituted MAA with an additional conjugated double bond, has one of the most red-shifted bands of all known MAA species, with ${\lambda }_{max}=360 \mathrm{n}\mathrm{m}$ and $\epsilon =\mathrm{50,000} {\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1}$ [68,71].

The observed red shift in ${\lambda }_{max}$ is a consequence of the degree of resonance delocalization inside the molecules; the more efficient is the electron delocalization (i.e., the stronger the π-conjugation character), the lower is the energy requirement for an electronic transition, and consequently the higher are the ${\lambda }_{max}$ and $\epsilon$ values [57,68].

From a thermodynamic perspective, the fate of the electronic excitation energy is also a very relevant aspect of the absorption event since it is directly linked to the amount of entropy produced by the dissipative microscopic structure (i.e., the pigment molecule). Nonradiative, vibrational relaxation pathways of the excited state lead to more efficient energy dissipation and higher entropy production when compared to the fluorescent or phosphorescent radiative decay channels [4,5,6,7,14,72,73]. In this respect MAAs prove to be very efficient dissipative structures.

Aiming to fully describe their photophysical and photochemical properties and increase the evidence for the assigned UV-photoprotective role, Conde et al. [74,75,76] conducted several in vitro studies on the excited-state properties and photostability of various MAAs in aqueous solution (

Table 1. Comparison between the photophysical properties of the aromatic amino acids and representative compounds of the major classes of cyanobacterial UV-absorbing pigments.

UV Bio-Pigments	${\mathit{\lambda }}_{\mathit{m}\mathit{a}\mathit{x}}$ (nm)	$\mathit{\epsilon }$ (M−1 cm−1)	Excited State Lifetime (ns)	Fluorescence Quantum Yield (${\mathit{\varphi }}_{\mathit{F}}$)
Aromatic amino acids
Phenylalanine a	257	195	7.5	0.024
Tyrosine a	274	1405	2.5	0.14
Tryptophan a	278	5579	3.03	0.13
Mycosporines and MAAs
Gadusol b	296	21,800	/	non-fluorescent
Mycosporine-γ-aminobutyric acid c	310	28,900	/	/
Mycosporine-glutamic acid c	311	20,900	/	/
Palythine b,c	320	36,200	/	non-fluorescent
Shinorine b	333	44,700	0.35	0.002
Porphyra-334 b	334	42,300	0.4	0.0016
Palythene c	360	50,000	/	/
Scytonemins
Scytonemin d,e	212 252 278 300 384	/ / / / 16,200	/	non-fluorescent
Reduced Scytonemin d	246 276 314 378 474 572	30,000 14,000 15,000 22,000 14,000 7600	/	/
Scytonemin-imine f	237 366 437 564	/ / / /	/	/
Dimethoxyscytonemin d	215 316 422	60,354 18,143 23,015	/	/
Tetramethoxy-scytonemin d	212 562	35,928 5944	/	/
Scytonine d	207 225 270	38,948 37,054 22,484	/	/
Other poorly characterized cyanobacterial UV-absorbing pigments
Gloeocapsin g	392	/	/	/
Microcystbiopterins h	~275 ~350	10,000 3500	/	/

^a Berezin and Achilefu [79]; ^b Arbeloa et al. [80]; ^c Wada et al. [68]; ^d Varnali and Edwards [81]; ^e Balskus et al. [82]; ^f Grant and Louda [83]; ^g Storme et al. [84]; ^h Lifshits et al. [85].

). The results showed picosecond excited state lifetimes, very low fluorescence quantum yields (e.g.,${\varphi }_F\left(\mathrm{p}\mathrm{o}\mathrm{r}\mathrm{p}\mathrm{h}\mathrm{y}\mathrm{r}\mathrm{a} 334\right)=0.0016$), very low triplet formation quantum yields (e.g., ${\varphi }_T\left(\mathrm{p}\mathrm{o}\mathrm{r}\mathrm{p}\mathrm{h}\mathrm{y}\mathrm{r}\mathrm{a} 334\right)<0.05$), and very low photodegradation quantum yields (e.g.,${\varphi }_R\left(\mathrm{p}\mathrm{o}\mathrm{r}\mathrm{p}\mathrm{h}\mathrm{y}\mathrm{r}\mathrm{a} 334\right)=2-4\times {10}^{-4}$) for all the MAAs studied. These results are consistent with a very fast internal conversion (IC) process as the main deactivation pathway of the excited states, which was directly quantified by photoacoustic calorimetry experiments showing that ~97% of the absorbed photonic energy is promptly dissipated into the surrounding medium as heat [75,77,78].

A computational study by Sampedro [86] employing palythine as a model compound confirmed these findings. The study indicates that the fast IC processes connecting the $S_2/S_1$ and $S_1/S_0$ states are due to the presence of two energetically accessible conical intersection points that can be reached by small geometrical changes in the atomic coordinates. It is now well established that conical intersections (also known as molecular funnels or diabolic points) play a very important role in fast, non-radiative de-excitation transitions from excited electronic states to ground electronic state of molecules, particularly in many fundamental biological molecules, such as DNA/RNA, amino acids and peptides [15,87]. They enable effective coupling of the electronic degrees of freedom of the molecule to its phonon degrees of freedom, thereby facilitating radiationless decay by vibrational cooling to the ground state (in the process converting the absorbed high-frequency UV photon into many low frequency infrared photons—Figure 3), making them examples of microscopic dissipative structures, formed in response to the impressed photon potential [5,26,73].

2.1.2. MAAs Spatial Distribution Within the Biosphere

MAAs and mycosporines are cosmopolitan substances in “optical” habitats, planktonic, benthic, and terrestrial, with the largest concentrations detected in environments with water exposed to high levels of solar irradiance (Castenholz and Garcia-Pichel [20] and references therein). They are now known to be the most common type of UV-absorbing natural substances, especially among aquatic organisms [41,88].

While mycosporines have been found only in the kingdom Fungi (mycosporine-glycine and mycosporine-taurine are exceptions), MAAs are more extensively distributed among taxonomically diverse organisms [57,89]. These include cyanobacteria; heterotrophic bacteria; dinoflagellates, diatoms, and other protists; red algae; green algae; and various marine animals, especially corals and their associated biota (for a database on the distribution of MAAs, see Sinha et al. [56]). They seem to be completely absent from terrestrial plants and animals but are regularly found in terrestrial cyanobacteria [90,91] and terrestrial algae [92].

An interesting discovery by Ingalls et al. [93] reveals that MAAs represent a considerable portion of the organic matter bound to diatom frustules, accounting for 3–27% of the total carbon and 2–18% of the total nitrogen content of the frustules. Previously established views held that MAAs have mainly an intracellular location in these organisms.

2.1.3. Extant Biosynthesis of MAAs

The cyclohexenone core of MAAs is derived from intermediates of two fundamental anabolic pathways: the shikimate pathway [69,94,95] and the pentose phosphate pathway [96], with the shikimate pathway being the predominant route for UV-induced MAA biosynthesis [97,98].

In MAA/mycosporine biosynthesis both pathways converge at a point where their respective 6-membered cyclic intermediates with similar structures are converted to 4-deoxygadusol (Figure 1), the common precursor of all MAAs and mycosporines, a reaction catalyzed by the key enzyme O-methyltransferase [58,97].

These basic biochemical pathways lie at the heart of carbon metabolism shared by all three domains of life; the shikimate pathway links carbohydrate catabolism to the biosynthesis of the aromatic amino acids and other aromatic biomolecules. Similarly, the pentose phosphate pathway uses glycolysis for the synthesis of pentose sugars, the nucleotide building blocks [99]. Thus, they are considered to have an ancient evolutionary origin, possibly even dating back to prebiotic times [100,101,102].

As mentioned in the previous section, a very interesting trait of MAAs is that they are extremely prevalent natural compounds produced by a variety of taxonomically very distant organisms, from simple bacteria to algae and animals. A natural question arises: how can so evolutionary distant organisms share the same MAA encoding genes?

Several lines of evidence now suggest that the progenitor of the enzymatic machinery for MAA biosynthesis was probably a cyanobacterium or the cyanobacterial ancestor, while endosymbiotic events and prokaryote-to-eukaryote lateral gene transfer events during evolution account for their prevalence among all other biological taxa [67,103,104,105,106,107].

2.1.4. Function of MAAs: Traditional Protective View vs. Thermodynamic View

Since their discovery in the 1960s, authors have struggled to confer specific physiological functions to MAAs. A UV-photoprotective role seemed most conspicuous, largely because of their unique UV-dissipating traits and the fact that their production is stimulated by UV-B light. Later, this theory faced serious challenges, for example, the failure to find a correlation between intracellular MAA accumulation and UV-resistance in certain coral zooxanthellae [108] (Kinzie, 1993), the phytoplankton Phaeocystis antarctica [109], the dinoflagellate Prorocentrum micans [110] (Lesser, 1996), certain cyanobacterial strains [111], the red alga Gracilaria cornea [112], Antarctic sea ice algae [113], the red alga Palmaria palmata [114], and others.

As a response, many researchers in the field came up with their own suggestions for MAA physiological roles, sometimes very different from the sunscreen role, such as osmotic regulation, antioxidants, nitrogen storage, accessory pigments, protection from desiccation, protection from thermal stress, reproductive functions in fungi and marine invertebrates etc., all of which have also been challenged or discredited (for reviews of the different theories of MAA functions and the challenges they face, see Korbee et al. [55]; Oren and Gunde-Cimerman [115]; Rosic and Dove [40]; Zwerger et al. [116]).

From a traditional biological standpoint, this apparent lack of a clear defining physiological function looks extremely perplexing, especially when considering the extraordinary prevalence of these compounds in nature. Darwinian theory, in its strictest traditional formulation with evolution through natural selection operating only at the individual level, categorically dismisses these kinds of phenomena. An organism would not wastefully spend free energy and resources for the synthesis of metabolically expensive nitrogen-containing compounds with no vital physiological function commensurate with their ubiquity and hence no, or little, benefit for its survival and reproduction. According to Darwinian theory, such a biosynthetic pathway, with little or no direct utility to the organism, should have been suppressed or eliminated through natural selection. However, exactly the opposite has happened during evolution; MAA biosynthetic genes have not only survived but have undergone extensive dissemination across numerous taxa through horizontal gene transfer.

We postulate that the shortcoming of Darwinian theory to find a niche for MAAs in its classical “struggle for survival” paradigm may be related to the fact that this theory is not founded on thermodynamic principles (for a discussion on this topic, see Michaelian, [4,6,14,73]). From the perspective of non-equilibrium thermodynamics, MAAs do have a function, and it is a thermodynamic function of energy dissipation, or, more generally, entropy production. This thermodynamic function can be readily inferred from the physicochemical properties related to photon dissipation described above. MAAs can be regarded as typical examples of microscopic dissipative structuring of matter for the sole purpose of entropy production through highly efficient dissipation of high-energy UV photons into heat [3,4,5,26,73]. This may be the reason for their “coming into being” and tendency to proliferate over the surface of the Earth, as it is the fundamental reason for the origin and evolution of life on Earth, and, in fact, the reason for the ubiquity of organic pigments in the neighborhood of stars throughout the universe [73,117].

This irreversible process of photon dissipation that MAAs and other bio-pigments perform then couples to a secondary abiotic irreversible process of the water cycle through increased evaporation from surfaces through the heat of photon dissipation released into the aqueous milieu [14]. Evidence exists that the profusion of life and chromophoric dissolved organic matter (CDOM) in the sea-surface microlayer (SML) causes significant heating of the ocean surface, fomenting evaporation [118,119,120,121,122,123]. The heat of dissipation in the surface layer can even foment another irreversible process, hurricane formation and steering [124].

CDOM is the fraction of dissolved organic matter (DOM) in water that interacts with solar radiation [125,126]. Light energy absorption by CDOM at the surface of the ocean usually exceeds that of phytoplankton pigments; 54 ± 15% of the total light absorption at 440 nm and >70% of the total light absorption at 300 nm is due to CDOM [127,128,129,130]. It is a complex and extremely variable mixture of organic pigments such as pheopigments [129], metal-free porphyrins [131], humic and fulvic acids [132,133], aromatic amino acids [134] and MAAs [135,136,137,138]. While it was previously believed that CDOM in the open ocean is chiefly a byproduct of heterotrophic organisms recycling phytoplankton cell contents [139], more recent observations [140,141] suggest a large contribution from active plankton exudation.

Active secretion of MAAs into the surrounding water during surface blooms was demonstrated for the colonial cyanobacterium Trichodesmium spp. [136,142], the dinoflagellate Lingulodinium polyedrum [135,143], and the dinoflagellate Prorocentrum micans [137]. Interestingly, Tilstone et al. [137] found far greater MAA concentration in the sea-surface microlayer samples when compared to the near-surface (0–2 m) and subsurface (0–110 m) samples. Whitehead and Vernet [135] also concluded that free-floating MAAs contributed up to 10% of the UV absorption of the total DOM pool at 330 nm during the L. polyandrium bloom. This exudation of pigments by organisms into their environment would also seem to have little Darwinian advantage.

The evidence presented above strongly suggests that MAAs are, like most of the other bio-pigments in nature, catalysts for the dissipation of photons into heat at the Earth’s surface and the coupling of this heat to other abiotic entropy producing processes, such as the water cycle, hurricanes, water and wind currents, etc. [14,144].

2.2. Scytonemins

Scytonemin was first described in the 19th century by Swiss botanist Carl Nägeli [145,146] but was not isolated until 1991 when Garcia-Pichel and Castenholz [147] made a more in-depth study of the compound. Proteau et al. [148] elucidated the chemical structure of scytonemin, which proved to be a completely novel indolic-phenolic dimeric structure, unique among all hitherto known natural organic substances. The carbon skeleton of this novel eight-ring homodimeric molecule was given the trivial name “the scytoneman skeleton” [148]. In 1994, another scytoneman-type molecule was isolated from the cyanobacterium Nostoc commune and termed “nostodione A” [149]. Thus far, four additional substances with a scytoneman-type molecular structure, or a structure derived from it, have been isolated from cyanobacteria: dimethoxyscytonemin, tetramethoxy-scytonemin, scytonine [150,151], and scytonemin-imine [83], for which, in this review, we use the colloquial term “scytonemin” or “scytoneman” pigments.

2.2.1. Physicochemical Properties of Scytonemins

Scytonemin (Figure 4), the representative and most common member of this yet poorly explored family of aromatic indole alkaloids, is a relatively small molecule (544 u) built from two identical condensation products of tryptophanyl- and tyrosyl-derived subunits linked through a carbon–carbon bond [148].

Depending on the redox conditions, it can exist in two interconvertible forms: a predominant oxidized yellowish-brown form that is insoluble in water and only fairly soluble in organic solvents, such as pyridine and tetrahydrofuran, and a reduced form (Figure 4) with a bright red color that is slightly more soluble in organic solvents [147,148,152].

Dimethoxy- and tetramethoxy-scytonemin can be considered as derivatives of reduced scytonemin, where one or both ethenyl groups in the molecule have been saturated by two or four methoxy groups, respectively [81,150]. Another moderate degree of modification of the parent scytoneman skeleton can also be seen in scytonemin-3a-imine (a.k.a. scytonemin-imine), where the C-3a atom of scytonemin has been appended with a 2-imino-propyl radical [83].

Only the structure of scytonine deviates substantially from the dimeric scytoneman skeleton, due to the loss of one para-substituted phenol group and ring openings of both cyclopentenones, where successive methoxylation and secondary cyclizations take place [150].

A full, in-depth photophysical and photochemical characterization of scytonemins has yet to be attained; thus far, only their elemental spectroscopic properties are known.

Scytonemin absorbs very strongly and broadly across the UV-C–UV-B–UV-A–violet–blue spectral region [153] (see Figure 2 and Figure 5, with in vivo ${\lambda }_{max}$ at 370 nm and in vitro (tetrahydrofuran) ${\lambda }_{max}$ at 386 and 252 nm, with smaller peaks at 212, 278, and 300 nm [147,153,154,155].

Its observed long-term persistence in cyanobacterial biocrusts or dried mats exposed to intense solar radiation is an indication of exceptionally high photostability [154,156,157,158,159].

Reduced scytonemin has a similar spectroscopic profile, with in vitro (tetrahydrofuran) ${\lambda }_{max}$ (nm) and $\epsilon ({\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1})$ values: 246 (30,000), 276 (14,000), 314 (15,000), 378 (22,000), 474 (14,000), and 572 (broad shoulder 7600) [81].

A comparable absorption spectrum is also exhibited by scytonemin-imine, the mahogany-colored, polar derivative of scytonemin, with slightly different ${\lambda }_{max}$ values when measured in acetone (237, 366, 437, and 564 nm) and in ethanol (248, 305, 364, 440, and 553 nm) [83].

Contrary to these three scytoneman-type molecules, the methoxylated derivatives and scytonine do not absorb strongly in the UV-A region but have very high absorbances in the UV-C region, with in vitro (methanol) ${\lambda }_{max}$(nm) and $\epsilon ({\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1})$ values for dimethoxyscytonemin: 215 (60,354), 316 (18,143), and 422 (23,015); for tetramethoxy-scytonemin: 212 (35,928) and 562 (5944); and for scytonine: 207 (38,948), 225 (37,054), and 270 (22,484) [150,151].

Concerning the monomeric scytoneman-type molecules nostodione A and prenostodione, isolated from natural cyanobacterial blooms, it remains debatable whether they are genuine cyanobacterial pigments or just intermediates in the biosynthesis of scytonemin [160,161].

2.2.2. Scytonemin Spatial Distribution Within the Biosphere

Unlike MAAs, scytonemins are hydrophobic, pigmented molecules, typically confined to terrestrial habitats and produced exclusively by sheathed cyanobacterial strains [162].

All phylogenetic lines of sheathed cyanobacteria contain scytonemins [148]; most notable strains are of the genera Nostoc, Calothrix, Scytonema, Rivularia, Chlorogloeopsis, Lyngbya, Hyella, etc. [163], as well as cyanolichens of the genera Peltula, Collema, and Gonohymenia [164].

The mucilaginous extracellular sheath (matrix) consists of heteroglycans, peptides, proteins, DNA, and different secondary metabolites [165,166], where scytonemins are usually deposited in the outer layers, giving the sheath its distinctive dark yellow to brown color [166,167,168]. Up to 5% of the dry weight of cultured scytonemin-synthesizing cyanobacteria is due to the pigment, but in natural assemblages this value can be even higher [152,169]. Curiously, Abed et al. [170] reported two to six times higher concentrations of scytonemin than chlorophyll a in cyanobacterial cryptobiotic soil crusts in the Oman Desert.

Scytonemin-producing cyanobacteria typically inhabit highly insolated terrestrial, freshwater, and coastal environments such as deserts, exposed rocks, cliffs, marine intertidal flats, shallow oligotrophic fresh waters, hot springs, etc. (Castenholz and Garcia-Pichel [20] and references therein). In microbial mat communities, especially the extremophilic terrestrial and aquatic colonies, these cyanobacteria occupy the uppermost sunlit layers [82]. Scytonemin-imine, for example, was isolated from samples of natural Scytonema hoffmani mats growing under high to intense (300–2000 μmol quanta m⁻² s⁻¹) photon flux density [83]. The methoxyscytonemins and scytonine were isolated alongside scytonemin from colonies of Scytonema sp. growing on exposed granite at the Mitaraka inselberg in French Guyana, a region subjected to intense UVR-insolation [150].

2.2.3. Extant Biosynthesis of Scytonemins

The biochemistry and genetics of cyanobacterial scytonemin biosynthesis have been extensively investigated by Soule et al. [161,171,172], Balskus and Walsh [173,174], Sorrels et al. [175], and Gao et al. [152]. They confirm the assumption by Proteau et al. [148], the discoverers of the scytonemin structure, that the scytoneman molecular scaffold is a condensation product of the aromatic amino acids tryptophan and tyrosine.

Not only do these amino acids absorb in the UV themselves (Michaelian and Simeonov [15] and references therein), but they also serve as biosynthetic precursors for most known aromatic UV-absorbing bio-pigments, including anthocyanins, flavonoids, and phenylpropanoids in plants, melanins in heterotrophic organisms, scytonemins in cyanobacteria, etc. [176,177].

Sorrels et al. [175] proposed an ancient evolutionary origin for the scytonemin biosynthetic pathway based on the combination of facts that this gene cluster is highly conserved among evolutionary diverse strains of cyanobacteria [161,171] and their own phylogenetic analyses, implying the cluster is under strong selection pressure. Intriguingly, Soule et al. [161] observed scytonemin biosynthetic genes even in some cyanobacterial strains incapable of producing the pigment (e.g., Anabaena and Nodularia), and interpreted this as a case of relic genetic information.

2.2.4. Function of Scytonemins: Traditional Protective View vs. Thermodynamic View

Similarly to MAAs, the Darwinian point of view can only describe scytonemin as an efficient protective biomolecule designed to filter out supposedly damaging high-frequency UV radiation while at the same time allowing the transmittance of wavelengths necessary for photosynthesis [178,179].

Within the framework of this traditional “struggle for survival” viewpoint, the majority of authors define scytonemins as an adaptive mechanism of extremophilic cyanobacteria that colonize harsh, inhospitable habitats experiencing high doses of UVR-insolation [163,167,179,180,181,182].

Among the evidence for the accredited photoprotective role is the discovery that up to 90% of incident UV photons are prevented from entering sheathed, scytonemin-producing cyanobacterial cells, thus accomplishing a significant reduction in chlorophyll a photobleaching and maintaining photosynthetic efficiency [147,152,154]. Other authors ascribe, in addition to the sunscreen role, supplementary defensive roles to scytonemin such as protection from oxidative, osmotic, heat, and desiccation stress [152,183,184].

Additionally, scytonemin’s superior UV-C-absorbing capabilities in vivo, experimentally proven by treating cyanobacterial colonies with 0.5–1.0 Wm⁻² UV-C radiation added to natural solar irradiance [185], have led many authors to consider modern cyanobacterial production of scytonemins as a relic UV-protection mechanism from the pre-Great Oxygenation Event [24,186,187]. Indeed, Raman spectral biosignatures of scytonemins, carotenoids, and porphyrins were unambiguously identified in ~3.5 Ga old fossilized sedimentary geological specimens [188,189]. Extracellular pigments, presumably scytonemins, also seem to occur in ~2.0 Ga old cyanobacterial microfossils preserved in silicified stromatolites that grew in tidal or shallow subtidal waters [190,191,192,193].

Although it is beyond doubt that the efficient UV absorption and dissipation properties of the scytoneman pigments provide, to some extent, a beneficiary effect for the survival of sheathed cyanobacterial cells, the opinion that this is the primary reason for the biological production of these pigments may be erroneous. The following are examples of serious challenges and inconsistencies that the photoprotection paradigm faces:

• Inability to explain the strong visible absorption bands of scytonemin-imine, where photosynthetic pigments absorb. The question is raised by Grant and Louda [83].
  “The absorption spectrum ($\lambda$_max 237, 366, 437, 564 nm in vitro), extending from the ultraviolet (UVB & UVA) into the blue and green of the visible, appears to indicate a photoprotective role beyond shielding only UVR. That is, going on the premise that evolution generates and retains only advantageous secondary metabolites, then what is the role of the visible bands in this case?”
• Inability to explain the production of the strongly UV-C/UV-B-absorbing methoxyscytonemins and scytonine, in spite of the absence of UV-C wavelengths and the low intensity of UV-B in today’s surface solar spectrum. The question is raised by Varnali and Edwards [81].
  “The realization that scytonemin is the parent molecule of perhaps a whole family of related molecules is important in that an analytical challenge is generated to detect these family members in admixture and in the presence of each other naturally, and also the question is raised about the role of these molecules in the survival strategy processes involving scytonemin; what subtle changes to the radiation absorption process require molecular modification of what apparently is already a highly successful radiation protectant, especially when the molecular syntheses are accomplished in energy-poor situations?”
• Inability to explain why many species of cyanobacteria do not synthesize scytonemins or MAAs but, nevertheless, successfully cope with UV-induced cellular damage by employing only metabolic repair mechanisms [111,194,195].
• Soule et al. [171] developed a scytoneminless mutant of the cyanobacterium Nostoc punctiforme, which proved to have an indistinguishable growth rate from the wild type after both were subjected to UV-A irradiation. The conclusion of the authors was that other photoprotective mechanisms can fully accommodate the absence of scytonemin in the mutant.

Finally, very efficient absorption and dissipation of high-energy photons is not a prerequisite for photoprotection, but it is for dynamical dissipative structuring of material under an external generalized chemical potential. Nature has a simpler way of creating photoprotective molecules, if this was really nature’s intention: making them either highly reflective or transparent to UV wavelengths [73].

These problems and paradoxes arising when attempting to explain scytonemins from within the Darwinian photoprotection paradigm can be resolved by viewing the situation from established non-equilibrium thermodynamic principles. In this context, we first address the questions raised by Grant and Louda [83] and Varnali and Edwards [81], and then, based on all the evidence presented, we assign a thermodynamic dissipative role to scytonemins.

The seemingly paradoxical absorption spectra of scytonemin-imine, the methoxyscytonemins, and scytonine, which extend outside of the photoprotectively relevant part of the spectrum, make sense only when these bio-pigments are understood as microscopic dissipative structures obeying non-equilibrium thermodynamic directives related to increasing the global solar photon dissipation rate [4,5,15,26,73,196]. Under these directives, one of the several ways to increase the global solar photon dissipation rate is by evolving (inventing) novel molecular structures (pigments) that cover ever more completely the prevailing surface solar spectrum [15].

This is precisely what is observed in the absorption spectra of the different scytoneman pigments. The strong visible absorption peaks of scytonemin-imine at 437 nm (violet) and 564 nm (green/yellow), of tetramethoxy-scytonemin at 562 nm (green/yellow), of dimethoxyscytonemin at 422 nm (violet), and the strong near-UV-C/UV-B absorption peaks of scytonine (270 nm) and dimethoxyscytonemin (316 nm) is exactly where the photosynthetic pigments do not peak in absorption (see, for example, Rowan [197]). It is because of this rich assortment of diverse pigment molecules with complementary absorption bands that cyanobacterial biofilms, mats, and soil crusts in nature tend to have high absorptivity, low albedo, and appear almost black in color [198].

These facts lead us to an important conclusion on the thermodynamic function of the scytoneman pigments. We believe that it is most reasonable to consider the photon dissipation role of scytonemins as the terrestrial analogue of the function that MAAs perform in the open aquatic environment. This assertion may be justified by their hydrophobic character and their inextricable connection to the extracellular polymeric substances (EPSs) of the cyanobacterial sheaths. Ekebergh et al. [178] indicate that scytonemins have the greatest photostability in vivo, where they are embedded in their natural extracellular matrix milieu. These extracellular polymeric substances may therefore be playing the role of dissipators after photon excitation of the pigment, bringing the system rapidly to the ground state and ready to absorb another photon [199].

In wet terrestrial regions of the planet, the thermodynamic role of photon dissipation coupled to the water cycle is performed mainly by the plant cover, but in arid and semiarid lands, where vegetation is severely restricted, this function is allotted to microscopic assemblages of cyanobacteria, heterotrophic bacteria, algae, and fungi known as biological soil crusts or biocrusts [200,201,202]. It is theorized that these types of microbial communities were pioneers on dry land and were the dominant ecosystem on the continents up until the advent of land plants and animals in the Early Devonian [203,204] brought on by the microbial retainment of water on the continents and the concomitant extension of the water cycle to regions far inland from the coasts.

Michaelian [196] postulated that bio-pigments are generally found in association with water because they use the high-frequency vibrational modes of water molecules to facilitate their de-excitation. In this context, we emphasize the fact that cyanobacteria isolated from dry regions display a very high capacity to excrete large amounts of EPSs [205,206,207,208,209], which are the main constituent of the biofilm matrix and, together with microbial filaments, play a key structural role in forming the biocrusts [210,211]. The unique hydrophilic/hydrophobic nature of the EPSs enables highly efficient water capture and water storage within the biocrust by allowing the creation of moistened microenvironments where water dynamics are intricately regulated (Colica et al. [212] and references therein). Hence, crust-covered soils are very hygroscopic and always exhibit higher water content compared to bare neighboring surfaces [213]. This phenomenon is in accordance with our postulate that life’s fundamental role is that of dispersing organic pigments and water over the entire surface of the Earth [4,5,7,14,73,196].

A very conspicuous analogy between these terrestrial macroscopic and microscopic photon-dissipating biological “carpets” can be drawn. In the same manner as ecological succession of plant coverage leads to old climax forests with higher pigment content and lower albedos [214,215,216], ecological succession in biocrusts leads to an increase in biomass of the late-stage scytonemin-producing cyanobacteria, and consequently accumulation of scytonemins in the matrix, an effect macroscopically observed as darkening of the biocrusted soil (i.e., decrease in albedo) [217].

During dry periods in deserts when water availability is very limited, the heat generated from scytonemin’s photon dissipation is expected to go predominantly into sensible heat of the biocrusts instead of into the latent heat of vaporization of water, and this is exactly what Couradeau et al. [217] found when they measured ~10 °C higher temperature of biocrust-covered, dark soils in comparison to bare soils. Dark soils absorb and dissipate photons, producing more entropy than bare soils, which predominantly reflect the incident light.

3. Discussion

In a previous work (Michaelian and Simeonov [15]) we posited five basic tendencies that organic pigment evolution on Earth would have followed: (1) increases in the photon absorption cross section with respect to the pigment physical size, (2) decreases in the electronic excited-state lifetimes of the pigments, (3) quenching of the radiative de-excitation channels (e.g., fluorescence), (4) greater coverage of the surface solar spectrum, and (5) pigment proliferation and dispersion over an ever greater surface area of Earth.

To examine whether these five tendencies are satisfied with the evolutionary invention of MAAs and scytonemins, we compare their properties to those of the aromatic amino acids (AAAs) (see Table 1), which are also fundamental pigments [218].

AAAs are most likely the precursors of MAAs since (1) they are considered to be among the earliest chromophoric organic molecules used by life with a prebiotic origin [15,219] and (2) both MAAs and scytonemins are derived from intermediates of the shikimate pathway for AAA biosynthesis, so they most likely appeared later in evolution compared to the AAAs, probably when the biosynthetic machinery for the synthesis of the AAAs was already robust, an event that most likely long predated 3.4 Ga, considering that Busch et al. [220] demonstrated that the ancestral tryptophan synthase of the last universal common ancestor (LUCA) was already a highly sophisticated enzyme at 3.4 Ga.

Based on all the data presented in previous sections on the spectral coverage and biological and geographical ubiquity of these pigments, we can state with a high degree of certainty that the fourth and fifth requirements are satisfied with the evolutionary inventions of MAAs and scytonemins.

With respect to the first to third strategies for augmenting photon dissipation, in addition to the previously discussed material, we offer the data presented in Table 1, which has been collected from the available literature up to 2025. All compounds listed are representative members of their respective chemical groups. Gadusol is used instead of the more relevant compound 4-deoxygadusol because of a lack of available data on 4-deoxygadusol and because of their chemical relatedness with similar spectroscopic properties [221,222]. The ${\lambda }_{max}$ and $\epsilon$ values of gadusol in water are pH-dependent: 268 nm at pH 2 and 296 nm at pH 7 [80,221]. In Table 1 we use the values for neutral pH 7 since the Archean seawater was probably slightly acidic with pH ~ 6.5 [223,224].

All absorption peaks and attenuation coefficients below about 205 nm, we believe, are due to the ionization of the molecules, a process which could destroy them. Photon dissipation is not quenching through a conical intersection at these very short wavelengths, and this is why they are omitted from Table 1 and Figure 6.

It is our hope that future experiments and studies into the nature and properties of these bio-pigments will help complete the data missing from the table. However, even with the limited data available and presented in this article, a trend compatible with our conjecture of increasing photon dissipation is evident.

Another conjecture made in Michaelian and Simeonov [15] states that the surface solar spectrum wavelength region from approximately 285 to 310 nm has never reached the surface of the Earth during its entire geologic history, because during the Hadean and Archean eons these wavelengths were probably absorbed by atmospheric aldehydes [23] and from the end of the Archean onwards gradual accumulation of oxygen and stratospheric ozone was responsible for their attenuation [225,226]. In this earlier paper we also demonstrated how numerous fundamental molecules of life, common to all three domains of life, have strong absorbances across the UV-C and UV-A regions but little in the UV-B region (280–315 nm), consistent with the thermodynamic dissipation theory of the origin and evolution of life [3,4,14].

The same appears to apply to the cyanobacterial UV-absorbing pigments scytonemins and MAAs, which can be considered as evolutionary successors to the primordial pigments of life, specifically the AAAs. Indeed, the absorption spectrum of scytonemin (Figure 5) seems to adhere to this pattern. Although it is continuous from ~220 to ~700 nm, there is a dip in the ~275 to ~325 nm interval, and two large maxima at ~250 nm and ~380 nm. This is exactly the kind of shape that would be expected if the selective force for the evolution of this pigment was the Archean surface solar spectrum [15].

Combining these crucial facts on scytonemin, it is tempting to speculate that this class of pigment had a key role in photon dissipation during the Archean, being capable of dissipating almost the entire Archean surface solar spectrum (see Figure 6). The evolutionary invention of scytonemin’s derivatives, as well as the mycosporines, the MAAs, and still many other extinct and extant biological pigments, most likely resulted from the necessity to complement scytonemin’s absorption with pigments that absorbed wavelengths reaching Earth’s surface but were poorly absorbed by scytonemin itself. This kind of spectral complementary relationship between scytonemin and MAAs has been well documented by several authors (e.g., Ehling-Schulz and Scherer [168]; Ferroni et al. [227]; Castenholz and Garcia-Pichel [20]) and is illustrated in Figure 2.

While some MAAs and scytonemins have large molar absorption coefficients in the UV-C and UV-B, for example, scytonemins (278 nm, 16,200 ${\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1}$), and gadusols (296 nm, 21,800 ${\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1}$-Arbeloa et al. [80]), most have maximum absorption in the UV-A (315–400 nm), and some absorb in the visible, e.g., dimethoxyscytonemin (422 nm, 23,015 ${\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1}$) and tetramethoxy-scytonemin (562 nm, 5944 ${\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1}$). They all have low yields of fluorescence, photodecomposition, and intersystem crossing, which are a consequence of the very short lifetimes of the excited singlet states due to their rapid internal conversion, possibly through conical intersections [80].

The molar absorption coefficients of chlorophyll in the UV-B, due to an absorption tail extending from the Soret band, are less than 1000 ${\mathrm{M}}^{-1} {\mathrm{c}\mathrm{m}}^{-1}$. However, chlorophyll can indeed be degraded by UV-B light, but this is usually due to the UV creation of reactive oxygen species (ROS). Photolysis of water to form •OH is significant with UV-C (<280 nm), where the energy is sufficient to break H₂O bonds (requires ~5 eV, corresponding to ~248 nm). The presence of dissolved organic matter, nitrates, or metal ions enhances ROS production. For example, studies on aquatic systems show that UV-B exposure (280–315 nm) generates measurable amounts of •OH and H₂O₂ [228].

From the above it can be concluded that since chlorophyll only absorbs weakly in the UV-B and that most of the delerious effects on chlorophyll attributed to UV-B light are due to the generation of ROS, the MAAs which absorb in the UV-B could certainly help reduce oxidation, but those absorbing in the UV-A and visible would not help. If the latter instead act as antioxidants, as is generally believed, then there would be no need for their strong photon absorption.

Our perspective is that all pigments, MAAs, scytonemins, and chlorophylls, as well as many others, are first and foremost dissipative pigments, carrying out the thermodynamic imperative of entropy production through photon dissipation. Their secondary functions may be (but not always are) photosynthetic, photoprotective, or antioxidant.

4. Conclusions

The available data on the ubiquity of pigments covering the region from the UV-C to the infrared, many exuded into the environment by the organisms that produce them, make it questionable to assign to them a protective or antenna role within the Darwinian paradigm of the optimization of photosynthesis benefiting the organism. We believe that sense can only be made of this by shifting the paradigm from one of “photoprotection” of the organism to the thermodynamic optimization of photon dissipation.

A number of contemporary pigment lines, most notably scytonemins and the mycosporine-like amino acids (MAAs), appear to harbor relics of ancient biosynthetic production routes based on the most ancient of the amino acids, the aromatics [219]. The aromatic amino acids have known affinities to their RNA anticodons [229,230] and were perhaps the first antenna pigments for photon dissipation in the UV-C at the beginnings of life [4,218].

These pigment lines absorb and dissipate efficiently in the UV-C and UV-A, as well as somewhat in the UV-B and the visible. Some of these pigments are exuded into the environment, which excludes the possibility of assigning them a role in photoprotection. Their strong absorption and dissipation in regions out of the photosynthetically active radiation (PAR) has been perplexing to adherents of the Darwinian paradigm since these pigments appear to have little utility to the organisms themselves. In fact, they absorb exactly where the photosynthetic pigments do not (and where water does not). They appear to have completely covered the prevailing Archean surface solar spectrum and do the same today.

It should be emphasized that our current knowledge of the diversity of cyanobacterial, algal, and plant pigments and the thermodynamic function they perform is incomplete. For example, there are several indications of even richer diversity of UV-absorbing pigments in cyanobacteria than those hitherto characterized and classified into the two groups, mycosporines, and scytonemins. The chemical structure and other elemental properties of one of these poorly investigated pigments, named gloeocapsin, have yet to be determined, but initial results suggest that it is chemically unrelated to both MAAs and scytonemins [84,231]. Still other chemically distinct UV-absorbing cyanobacterial pigments, with a unique pterin structure, have been reported elsewhere [85,232]. The wavelengths of maximum absorption of these two ill-defined groups of cyanobacterial pigments are listed in Table 1 and are plotted in Figure 6. As with the mycosporines and the scytonemins, their absorption properties are consistent with the optimization of dissipation of the prevailing photon spectrum at the Earth’s surface.

Taken as a whole, these data seem to indicate that, rather than photosynthesis being optimized under a Darwinian “survival of the fittest” paradigm, the origin and evolution of life is driven by photon dissipation, with the net effect of covering the Earth’s entire surface with pigments and water, reducing the albedo and the effective black-body temperature at which Earth radiates into space, thereby increasing the entropy production of the biosphere. It is our hope that this article will incite further investigation into the proposition that photon dissipation efficacy has been the fundamental driver of biological evolution on Earth.