Thinking twice about the evolution of photosynthesis

Boundaries of photosynthesis: adaptations of carbon fixation in extreme environments

Extreme environments challenge fundamental pillars of photosynthesis: light capture and carbon fixation. Organisms thriving in extreme conditions, such as high and low temperatures, extreme pH levels, and high salinity, have evolved remarkable adaptive mechanisms allowing them to sustain photosynthesis. Research into these adaptations has expanded our understanding of the limits and evolution of photosynthesis, while also providing promising biotechnological applications. In this review, we explore the adaptations that tolerant and extremophilic photosynthetic organisms have evolved, overcoming these environmental challenges while maintaining photosynthetic functionality. These adaptations include modifications in photosystems and electron transport chain components, the development of photoprotective mechanisms, the use of unique CO2-concentrating mechanisms (CCMs), and fine-tuning of Rubisco's kinetic properties and concentration. Our aim is to provide the basis for future research in extremophile biology while highlighting its applications in biotechnology.

Non-Respiratory Extracellular Electron Transfer Competes with Nitrogenase for Electrons in Rhodopseudomonas Palustris

Biological nitrogen fixation (BNF) is a pivotal process that reduces nitrogen to ammonium within the nitrogen cycle. Extracellular electron transfer (EET) between diazotrophs and the extracellular environment influences the occurrence and efficiency of BNF. Although extracellular electron acceptors can function as a component of the electron transport chain, providing energy for chemotrophic nitrogen fixation via extracellular respiration, the function and mechanism of outward EET in photosynthetic diazotrophs remain unclear. Here, using Rhodopseudomonas palustris TIE-1, a photosynthetic bioelectrochemical nitrogen fixation system is established for simultaneous nitrogen fixation and current generation, to dissect the complex interaction between these two processes. Outward EET functions are found to maintain redox balance, rather than serving as an extracellular respiration pathway. It significantly suppresses BNF by competing with nitrogenase for electrons. Lumichrome serves as the primary electron shuttle for indirect electron transfer, while cytochromes play an important role in direct electron transfer. Notably, the pio operon participates in outward EET. This study reveals the interaction mechanism between photosynthetic BNF and outward EET, providing new insight into the regulatory mechanisms of nitrogen fixation in anoxygenic phototrophs across diverse environmental conditions.

Evolution of far-red light photoacclimation in cyanobacteria

Cyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of ∼20 genes and involves the synthesis of red-shifted chlorophylls d and f, together with paralogs of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups, but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to help clarify this issue: sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 51 new gene clusters. These data enable high-resolution phylogenetics and-by relying on multiple gene trees, together with gene arrangement conservation-support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and we hypothesize that the process was associated with the formation of microbial mats and stromatolites in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing features that have been maintained for billions of years. Overall, far-red-light-driven oxygenic photosynthesis may have played a significant role in Earth's early history.

Diversity and abundance of filamentous and non-filamentous "Leptothrix" in global wastewater treatment plants

Species belonging to the genus Leptothrix are widely distributed in the environment and in activated sludge (AS) wastewater treatment plants (WWTPs). They are commonly found in iron-rich environments and reported to cause filamentous bulking in WWTPs. In this study, the diversity, distribution, and metabolic potential of the most prevalent Leptothrix spp. found in AS worldwide were studied. Our 16S rRNA amplicon survey showed that Leptothrix belongs to the general core community of AS worldwide, comprising 32 species with four species being most commonly found. Their taxonomic classification was re-evaluated based on both 16S rRNA gene and genome-based phylogenetic analysis showing that three of the most abundant "Leptothrix" species represented species in three other genera, Rubrivivax, Ideonella, and the novel genus, Ca. Intricatilinea. New fluorescence in situ hybridization (FISH) probes revealed rod-shaped morphology for the novel Ca. Rubrivivax defluviihabitans and Ca. Ideonella esbjergensis, while filamentous morphology was found only for Ca. Intricatilinea gracilis. Analysis of high-quality metagenome-assembled genomes revealed metabolic potential for aerobic growth, fermentation, storage of intracellular polymers, partial denitrification, photosynthesis, and iron reduction. FISH in combination with Raman microspectroscopy confirmed the in situ presence of chlorophyll and carotenoids in Ca. Rubrivivax defluviihabitans and Ca. Intricatilinea gracilis. This study resolves the taxonomy of abundant but poorly classified "Leptothrix" species, providing important insights into their diversity, morphology, and function in global AS wastewater treatment systems.IMPORTANCEThe genus Leptothrix has been extensively studied and described since the 1880s, with six species currently described but with the majority uncultured and undescribed. Some species are assumed to have a filamentous morphology and can cause settling problems in wastewater treatment plants (WWTPs). Here, we revised the classification of the most abundant Leptothrix spp. present in WWTPs across the world, showing that most belong to other genera, such as Rubrivivax and Ideonella. Furthermore, most do not have a filamentous morphology and are not problematic in WWTPs as previously believed. Metabolic reconstruction, including some traits validated in situ by the application of new fluorescence in situ hybridization probes and Raman microspectroscopy, provided additional insights into their metabolism. The study has contributed to a better understanding of the diversity, morphology, and function of "Leptothrix," which belong to the abundant core community across global activated sludge WWTPs.

Spatiotemporal Characteristics Determining the Multifaceted Nature of Reactive Oxygen, Nitrogen, and Sulfur Species in Relation to Proton Homeostasis

Significance: Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) act as signaling molecules, regulating gene expression, enzyme activity, and physiological responses. However, excessive amounts of these molecular species can lead to deleterious effects, causing cellular damage and death. This dual nature of ROS, RNS, and RSS presents an intriguing conundrum that calls for a new paradigm. Recent Advances: Recent advancements in the study of photosynthesis have offered significant insights at the molecular level and with high temporal resolution into how the photosystem II oxygen-evolving complex manages to prevent harmful ROS production during the water-splitting process. These findings suggest that a dynamic spatiotemporal arrangement of redox reactions, coupled with strict regulation of proton transfer, is crucial for minimizing unnecessary ROS formation. Critical Issues: To better understand the multifaceted nature of these reactive molecular species in biology, it is worth considering a more holistic view that combines ecological and evolutionary perspectives on ROS, RNS, and RSS. By integrating spatiotemporal perspectives into global, cellular, and biochemical events, we discuss local pH or proton availability as a critical determinant associated with the generation and action of ROS, RNS, and RSS in biological systems. Future Directions: The concept of localized proton availability will not only help explain the multifaceted nature of these ubiquitous simple molecules in diverse systems but also provide a basis for new therapeutic strategies to manage and manipulate these reactive species in neural disorders, pathogenic diseases, and antiaging efforts.

Solid-State NMR Analysis of the Dynamics of Cofactors: Comparison of Heliobacterial and Purple Bacterial Reaction Centers

Photosynthetic reaction centers (RCs) serve as natural engines converting solar energy to chemical energy. Understanding the principles of efficient charge separation and light-induced electron transfer (ET) between the chlorophyll-type pigments might guide the synthesis for artificial photosynthetic systems. We present detailed insight into the dynamics at the atomic level using solid-state NMR techniques applied to the RCs of Heliobacillus (Hb.) mobilis (HbRCs) and the purple bacterium Rhodobacter (R.) sphaeroides (PbRCs). It is assumed that heliobacteria were among the first phototrophic organisms; therefore, their RC can be regarded as ancient. They are constructed homodimerically with perfect C2 symmetry, enabling ET over both branches of cofactors. Modern RCs of R. sphaeroides wild-type (WT) have higher redox power and are functionally highly asymmetric. The dynamics of the cofactors in both RCs has been explored using nuclear hyperpolarization, induced by the solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) effect. Based on the individual incorporation of 13C positions of the cofactors (through supplementation by 13C-δ-aminolevulinic acid), photo-CIDNP magic-angle spinning (MAS) NMR experiments provide access to the local dynamics of the cofactors along the ET path over a broad range of time scales. Theoretical analysis of the dynamic deformation of these macrocycles is also discussed in terms of function. The dynamics observed in HbRCs appears to be correlated to ET. The cofactors in PbRC are significantly less dynamic than those in the HbRC. Relevance for efficiency and redox properties are discussed.

Redesign of the Chlamydomonas reinhardtii QB binding niche reveals photosynthesis works in the absence of a driving force for QA-QB electron transfer

An in silico redesign of the secondary quinone electron acceptor (QB) binding pocket of the D1 protein of Photosystem II (PSII) suggested that mutations of the F265 residue would affect atrazine binding. Chlamydomonas reinhardtii mutants F265T and F265S were produced to obtain atrazine-hypersensitive strains for biosensor applications, and the mutants were indeed found to be more atrazine-sensitive than the reference strain IL. Fluorescence and thermoluminescence data agree with a weak driving force and confirm slow electron transfer but cannot exclude an additional effect on protonation of the secondary quinone. Both mutants grow autotrophically, indicating that PSII requires strong light for optimal function, as was the case in the ancestral homodimeric reaction center.

Reconstructing Early Microbial Life

For more than 3.5 billion years, life experienced dramatic environmental extremes on Earth. These include shifts from oxygen-less to overoxygenated atmospheres and cycling between hothouse conditions and global glaciations. Meanwhile, an ecological revolution took place. Earth evolved from one dominated by microbial life to one containing the plants and animals that are most familiar today. Many key cellular features evolved early in the history of life, collectively defining the nature of our biosphere and underpinning human survival. Recent advances in molecular biology and bioinformatics have greatly improved our understanding of microbial evolution across deep time. However, the incorporation of molecular genetics, population biology, and evolutionary biology approaches into the study of Precambrian biota remains a significant challenge. This review synthesizes our current knowledge of early microbial life with an emphasis on ancient metabolisms. It also outlines the foundations of an emerging interdisciplinary area that integrates microbiology, paleobiology, and evolutionary synthetic biology to reconstruct ancient biological innovations.

Exploring the Origins and Evolution of Oxygenic and Anoxygenic Photosynthesis in Deeply Branched Cyanobacteriota

Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, vesicle-inducing protein in plastids 1 (Vipp1). Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven AnoxyP by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre

Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified1,2. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes3 and bacteriochlorophylls4 related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.

Molecular diversity and evolution of far-red light-acclimated photosystem I

The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.

Stromatolite-like Structures Within Microbially Laminated Sandstones of the Paleoarchean Moodies Group, Barberton Greenstone Belt, South Africa

We report abundant small calcareous mounds associated with fossilized kerogenous microbial mats in tidal-facies sandstones of the predominantly siliciclastic Moodies Group (ca. 3.22 Ga) of the Barberton Greenstone Belt (BGB), South Africa and Eswatini. Most of the bulbous, internally microlaminated mounds are several centimeters in diameter and formed at the sediment-water interface contemporaneously with sedimentation. They originally consisted of Fe-Mg-Mn carbonate, which is now largely silicified; subtle internal compositional laminations are composed of organic matter and sericite. Their presence for >6 km along strike, their restriction to the inferred photic zone, and the internal structure suggest that mineral precipitation was induced by photosynthetic microorganisms. Similar calcareous mounds in this unit also occur within and on top of fluid-escape conduits, suggesting that carbonate precipitation may either have occurred abiogenically or involved chemotrophic metabolism(s) utilizing the oxidation of organic matter, methane, or hydrogen, the latter possibly generated by serpentinization of underlying ultramafic rocks. Alternatively or additionally, carbonate may have precipitated abiotically where heated subsurface fluids, sourced by the intrusion of a major Moodies-age sill, reached the tidal flats. In summary, precipitation mechanisms may have been variable; the calcareous mounds may represent "hybrid carbonates" that may have originated from the small-scale overlap of bioinduced and abiotic processes in space and time. Significantly, the widespread occurrence of these stromatolite-like structures in a fully siliciclastic, high-energy tidal setting broadens search criteria in the search for life on Mars while their possible hybrid origin challenges our ability to unambiguously identify a biogenic component.

Solar energy conversion by photosystem II: principles and structures

Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.

A New Ecological and Evolutionary Perspective on the Emergence of Oxygenic Photosynthesis

In this hypothesis article, we propose that the timing of the evolution of oxygenic photosynthesis and the diversification of cyanobacteria is firmly tied to the geological evolution of Earth in the Mesoarchean to Neoarchean. Specifically, the diversification of species capable of oxygenic photosynthesis is tied to the growth of subaerial (above sea-level/terrestrial) continental crust, which provided niches for their diversification. Moreover, we suggest that some formerly aerobic bacterial lineages evolved to become anoxygenic photosynthetic as a result of changes in selection following the reintroduction of ferruginous conditions in the oceans at 1.88 GYa. Both conclusions are fully compatible with phylogenetic evidence. The hypothesis carries with it a predictive component-at least for terrestrial organisms-that the development and expansion of photosynthesis species was dependent on the geological evolution of Earth.

Cryo-EM structure of the whole photosynthetic reaction center apparatus from the green sulfur bacterium Chlorobaculum tepidum

Light energy absorption and transfer are very important processes in photosynthesis. In green sulfur bacteria light is absorbed primarily by the chlorosomes and its energy is transferred via the Fenna-Matthews-Olson (FMO) proteins to a homodimeric reaction center (RC). Here, we report the cryogenic electron microscopic structure of the intact FMO-RC apparatus from Chlorobaculum tepidum at 2.5 Å resolution. The FMO-RC apparatus presents an asymmetric architecture and contains two FMO trimers that show different interaction patterns with the RC core. Furthermore, the two permanently bound transmembrane subunits PscC, which donate electrons to the special pair, interact only with the two large PscA subunits. This structure fills an important gap in our understanding of the transfer of energy from antenna to the electron transport chain of this RC and the transfer of electrons from reduced sulfur compounds to the special pair.

Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c

Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 Fe₄S₄ clusters, 12 lipids, 2 Ca²⁺ ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs.

Genes encoding the photosystem II proteins are under purifying selection: an insight into the early evolution of oxygenic photosynthesis

The molecular evolution concerns coding sequences (CDSs) of genes and may affect the structure and function of proteins. Non-uniform use of synonymous codons during translation, known as codon usage bias (CUB), depends on the balance between mutations bias and natural selection. We estimated different CUB indices, i.e. the effective number of codons (ENC), G + C content in the 3rd codon positions (GC₃), and codon adaptation index for CDSs of intrinsic proteins of photosystem II (PSII), such as psbA (D1), psbD (D2), psbB (CP47), psbC (CP43), and CDSs of the extrinsic protein psbO (PsbO). These genes occur in all organisms that perform oxygenic photosynthesis (OP) on Earth: cyanobacteria, algae and plants. Comparatively, a similar analysis of codon bias for CDSs of L and M subunits that constitute the core proteins of the type II reaction centre (RCII) in anoxygenic bacteria was performed. Analysis of CUB indices and determination of the number of synonymous (d_S) and nonsynonymous substitutions (d_N) in all analysed CDSs indicated that the crucial PSII and RCII proteins were under strong purifying (negative) selection in course of evolution. Purifying selection was also estimated for CDSs of atpA, the α subunit of ATP synthase, an enzyme that was most likely already present in the last universal common ancestor (LUCA). The data obtained point to an ancient origin of OP, even in the earliest stages of the evolution of life on Earth.

Phylogenomic Evidence for the Origin of Obligate Anaerobic Anammox Bacteria Around the Great Oxidation Event

The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32-2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.

Origin of cyanobacterial thylakoids via a non-vesicular glycolipid phase transition and their impact on the Great Oxygenation Event

The appearance of oxygenic photosynthesis in cyanobacteria is a major event in evolution. It had an irreversible impact on the Earth, promoting the Great Oxygenation Event (GOE) ~2.4 billion years ago. Ancient cyanobacteria predating the GOE were Gloeobacter-type cells lacking thylakoids, which hosted photosystems in their cytoplasmic membrane. The driver of the GOE was proposed to be the transition from unicellular to filamentous cyanobacteria. However, the appearance of thylakoids expanded the photosynthetic surface to such an extent that it introduced a multiplier effect, which would be more coherent with an impact on the atmosphere. Primitive thylakoids self-organize as concentric parietal uninterrupted multilayers. There is no robust evidence for an origin of thylakoids via a vesicular-based scenario. This review reports studies supporting that hexagonal II-forming glucolipids and galactolipids at the periphery of the cytosolic membrane could be turned, within nanoseconds and without any external source of energy, into membrane multilayers. Comparison of lipid biosynthetic pathways shows that ancient cyanobacteria contained only one anionic lamellar-forming lipid, phosphatidylglycerol. The acquisition of sulfoquinovosyldiacylglycerol biosynthesis correlates with thylakoid emergence, possibly enabling sufficient provision of anionic lipids to trigger a hexagonal II-to-lamellar phase transition. With this non-vesicular lipid-phase transition, a framework is also available to re-examine the role of companion proteins in thylakoid biogenesis.

From manganese oxidation to water oxidation: assembly and evolution of the water-splitting complex in photosystem II

The manganese cluster of photosystem II has been the focus of intense research aiming to understand the mechanism of H₂O-oxidation. Great effort has also been applied to investigating its oxidative photoassembly process, termed photoactivation that involves the light-driven incorporation of metal ions into the active Mn₄CaO₅ cluster. The knowledge gained on these topics has fundamental scientific significance, but may also provide the blueprints for the development of biomimetic devices capable of splitting water for solar energy applications. Accordingly, synthetic chemical approaches inspired by the native Mn cluster are actively being explored, for which the native catalyst is a useful benchmark. For both the natural and artificial catalysts, the assembly process of incorporating Mn ions into catalytically active Mn oxide complexes is an oxidative process. In both cases this process appears to share certain chemical features, such as producing an optimal fraction of open coordination sites on the metals to facilitate the binding of substrate water, as well as the involvement of alkali metals (e.g., Ca²⁺) to facilitate assembly and activate water-splitting catalysis. This review discusses the structure and formation of the metal cluster of the PSII H₂O-oxidizing complex in the context of what is known about the formation and chemical properties of different Mn oxides. Additionally, the evolutionary origin of the Mn₄CaO₅ is considered in light of hypotheses that soluble Mn²⁺ was an ancient source of reductant for some early photosynthetic reaction centers ('photomanganotrophy'), and recent evidence that PSII can form Mn oxides with structural resemblance to the geologically abundant birnessite class of minerals. A new functional role for Ca²⁺ to facilitate sustained Mn²⁺ oxidation during photomanganotrophy is proposed, which may explain proposed physiological intermediates during the likely evolutionary transition from anoxygenic to oxygenic photosynthesis.

In Silico Identification and Characterization of a Hypothetical Protein From Rhodobacter capsulatus Revealing S-Adenosylmethionine-Dependent Methyltransferase Activity

Rhodobacter capsulatus is a purple non-sulfur bacteria widely used as a model organism to study bacterial photosynthesis. It exhibits extensive metabolic activities and demonstrates other distinctive characteristics such as pleomorphism and nitrogen-fixing capability. It can act as a gene transfer agent (GTA). The commercial importance relies on producing polyester polyhydroxyalkanoate (PHA), extracellular nucleic acids, and commercially critical single-cell proteins. These diverse features make the organism an exciting and environmentally and industrially important one to study. This study was aimed to characterize, model, and annotate the function of a hypothetical protein (Accession no. CAA71016.1) of R capsulatus through computational analysis. The urf7 gene encodes the protein. The tertiary structure was predicted through MODELLER and energy minimization and refinement by YASARA Energy Minimization Server and GalaxyRefine tools. Analysis of sequence similarity, evolutionary relationship, and exploration of domain, family, and superfamily inferred that the protein has S-adenosylmethionine (SAM)-dependent methyltransferase activity. This was further verified by active site prediction by CASTp server and molecular docking analysis through Autodock Vina tool and PatchDock server of the predicted tertiary structure of the protein with its ligands (SAM and SAH). Normally, as a part of the gene product of photosynthetic gene cluster (PGC), the established roles of SAM-dependent methyltransferases are bacteriochlorophyll and carotenoid biosynthesis. But the STRING database unveiled its association with NADH-ubiquinone oxidoreductase (Complex I). The assembly and regulation of this Complex I is mediated by the gene products of the nuo operon. As a part of this operon, the urf7 gene encodes SAM-dependent methyltransferase. As a consequence of these findings, it is reasonable to propose that the hypothetical protein of interest in this study is a SAM-dependent methyltransferase associated with bacterial NADH-ubiquinone oxidoreductase assembly. Due to conservation of Complex I from prokaryotes to eukaryotes, R capsulatus can be a model organism of study to understand the common disorders which are linked to the dysfunctions of complex I.

Probing the Role of Cysteine Thiyl Radicals in Biology: Eminently Dangerous, Difficult to Scavenge

Thiyl radicals are exceptionally interesting reactive sulfur species (RSS), but rather rarely considered in a biological or medical context. We here review the reactivity of protein thiyl radicals in aqueous and lipid phases and provide an overview of their most relevant reaction partners in biological systems. We deduce that polyunsaturated fatty acids (PUFAs) are their preferred reaction substrates in lipid phases, whereas protein side chains arguably prevail in aqueous phases. In both cellular compartments, a single, dominating thiyl radical-specific antioxidant does not seem to exist. This conclusion is rationalized by the high reaction rate constants of thiyl radicals with several highly concentrated substrates in the cell, precluding effective interception by antioxidants, especially in lipid bilayers. The intractable reactivity of thiyl radicals may account for a series of long-standing, but still startling biochemical observations surrounding the amino acid cysteine: (i) its global underrepresentation on protein surfaces, (ii) its selective avoidance in aerobic lipid bilayers, especially the inner mitochondrial membrane, (iii) the inverse correlation between cysteine usage and longevity in animals, (iv) the mitochondrial synthesis and translational incorporation of cysteine persulfide, and potentially (v) the ex post introduction of selenocysteine into the genetic code.

Phylum Gemmatimonadota and Its Role in the Environment

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

ORPER: A Workflow for Constrained SSU rRNA Phylogenies

The continuous increase in sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects ever more complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow “ORPER”, for “ORganism PlacER”, containerized in Singularity, which allows the determination the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants

The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants

The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.

The role of carotenoids in proton-pumping rhodopsin as a primitive solar energy conversion system

Rhodopsin and carotenoids are two molecules that certain bacteria use to absorb and utilize light. Type I rhodopsin, the simplest active proton transporter, converts light energy into an electrochemical potential. Light produces a proton gradient, which is known as the proton motive force across the cell membrane. Some carotenoids are involved in light absorbance and transfer of absorbed energy to chlorophyll during photosynthesis. A previous study in Salinibacter ruber has shown that carotenoids act as antennae to harvest light and transfer energy to retinal in xanthorhodopsin (XR). Here, we describe the role of canthaxanthin (CAN), a carotenoid, as an antenna for Gloeobacter rhodopsin (GR). The non-covalent complex formed by the interaction between CAN and GR doubled the proton pumping speed and improved the pumping capacity by 1.5-fold. The complex also tripled the proton pumping speed and improved the pumping capacity by 5-fold in the presence of strong and weak light, respectively. Interestingly, when canthaxanthin was bound to Gloeobacter rhodopsin, it showed a 126-fold increase in heat resistance, and it survived better under drought conditions than Gloeobacter rhodopsin. The results suggest direct complementation of Gloeobacter rhodopsin with a carotenoid for primitive solar energy harvesting in cyanobacteria.

Time-resolved comparative molecular evolution of oxygenic photosynthesis

Oxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that the origin of oxygenic photosynthesis is a late innovation relative to the origin of life and bioenergetics. However, when exactly water oxidation originated remains an unanswered question. Here we use phylogenetic analysis to study a gene duplication event that is unique to photosystem II: the duplication that led to the evolution of the core antenna subunits CP43 and CP47. We compare the changes in the rates of evolution of this duplication with those of some of the oldest well-described events in the history of life: namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of Cyanobacteria-specific FtsH metalloprotease subunits and the radiation leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on phylogenetic or phylogenomic species trees alone.

Cysteine, glutathione and a new genetic code: biochemical adaptations of the primordial cells that spread into open water and survived biospheric oxygenation

Life most likely developed under hyperthermic and anaerobic conditions in close vicinity to a stable geochemical source of energy. Epitomizing this conception, the first cells may have arisen in submarine hydrothermal vents in the middle of a gradient established by the hot and alkaline hydrothermal fluid and the cooler and more acidic water of the ocean. To enable their escape from this energy-providing gradient layer, the early cells must have overcome a whole series of obstacles. Beyond the loss of their energy source, the early cells had to adapt to a loss of external iron-sulfur catalysis as well as to a formidable temperature drop. The developed solutions to these two problems seem to have followed the principle of maximum parsimony: Cysteine was introduced into the genetic code to anchor iron-sulfur clusters, and fatty acid unsaturation was installed to maintain lipid bilayer viscosity. Unfortunately, both solutions turned out to be detrimental when the biosphere became more oxidizing after the evolution of oxygenic photosynthesis. To render cysteine thiol groups and fatty acid unsaturation compatible with life under oxygen, numerous counter-adaptations were required including the advent of glutathione and the addition of the four latest amino acids (methionine, tyrosine, tryptophan, selenocysteine) to the genetic code. In view of the continued diversification of derived antioxidant mechanisms, it appears that modern life still struggles with the initially developed strategies to escape from its hydrothermal birthplace. Only archaea may have found a more durable solution by entirely exchanging their lipid bilayer components and rigorously restricting cysteine usage.

Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes

Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes' epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments.IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.

Complex Evolution of Light-Dependent Protochlorophyllide Oxidoreductases in Aerobic Anoxygenic Phototrophs: Origin, Phylogeny, and Function

Light-dependent protochlorophyllide oxidoreductase (LPOR) and dark-operative protochlorophyllide oxidoreductase are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis that LPORs are only present in oxygenic phototrophs, we recently identified a functional LPOR in the aerobic anoxygenic phototrophic bacterium (AAPB) Dinoroseobacter shibae and attributed its presence to a single horizontal gene transfer event from cyanobacteria. Here, we provide evidence for the more widespread presence of genuine LPOR enzymes in AAPBs. An exhaustive bioinformatics search identified 36 putative LPORs outside of oxygenic phototrophic bacteria (cyanobacteria) with the majority being AAPBs. Using in vitro and in vivo assays, we show that the large majority of the tested AAPB enzymes are genuine LPORs. Solution structural analyses, performed for two of the AAPB LPORs, revealed a globally conserved structure when compared with a well-characterized cyanobacterial LPOR. Phylogenetic analyses suggest that LPORs were transferred not only from cyanobacteria but also subsequently between proteobacteria and from proteobacteria to Gemmatimonadetes. Our study thus provides another interesting example for the complex evolutionary processes that govern the evolution of bacteria, involving multiple horizontal gene transfer events that likely occurred at different time points and involved different donors.

Engineering Photosynthetic Bioprocesses for Sustainable Chemical Production: A Review

Microbial production of chemicals using renewable feedstocks such as glucose has emerged as a green alternative to conventional chemical production processes that rely primarily on petroleum-based feedstocks. The carbon footprint of such processes can further be reduced by using engineered cells that harness solar energy to consume feedstocks traditionally considered to be wastes as their carbon sources. Photosynthetic bacteria utilize sophisticated photosystems to capture the energy from photons to generate reduction potential with such rapidity and abundance that cells often cannot use it fast enough and much of it is lost as heat and light. Engineering photosynthetic organisms could enable us to take advantage of this energy surplus by redirecting it toward the synthesis of commercially important products such as biofuels, bioplastics, commodity chemicals, and terpenoids. In this work, we review photosynthetic pathways in aerobic and anaerobic bacteria to better understand how these organisms have naturally evolved to harness solar energy. We also discuss more recent attempts at engineering both the photosystems and downstream reactions that transfer reducing power to improve target chemical production. Further, we discuss different methods for the optimization of photosynthetic bioprocess including the immobilization of cells and the optimization of light delivery. We anticipate this review will serve as an important resource for future efforts to engineer and harness photosynthetic bacteria for chemical production.

Primordial bioenergy sources: The two facets of adenosine triphosphate

Life requires energy to exist, to reproduce and to survive. Two major hypotheses have been put forward concerning the source of this energy at the very early stages of life evolution: (i) abiotic organics either brought to Earth by comets and/or meteorites, or produced at its atmosphere, and (ii) mineral surface-dependent bioinorganic catalytic reactions. Considering the latter possibility, I propose that, besides being a precursor of nucleic acids, adenosine triphosphate (ATP), which probably was used very early to improve the fidelity of nucleic acid polymerization, played an essential role in the transition between mineral-bound protocells and their free counterparts. Indeed, phosphorylation by ATP renders carboxylate groups electrophilic enough to react with nucleophiles such as amines, an effect that, thanks to their Lewis acid character, also have dehydrated metal ions on mineral surfaces. Early ATP synthesis for metabolic processes most likely depended on substrate level phosphorylation. However, the exaptation of a hexameric helicase-like ATPase and a transmembrane H⁺ pump (which evolved to counteract the acidity caused by fermentation reactions within the protocell) generated a much more efficient membrane-bound ATP synthase that uses chemiosmosis to make ATP.

International conference on "Photosynthesis and Hydrogen Energy Research for Sustainability-2019": in honor of Tingyun Kuang, Anthony Larkum, Cesare Marchetti, and Kimiyuki Satoh

The 10th International Conference on «Photosynthesis and Hydrogen Energy Research for Sustainability-2019» was held in honor of Tingyun Kuang (China), Anthony Larkum (Australia), Cesare Marchetti (Italy), and Kimiyuki Satoh (Japan), in St. Petersburg (Russia) during June 23-28, 2019. The official conference organizers from the Russian side were from the Institute of Basic Biological Problems of the Russian Academy of Sciences (IBBP RAS), Russian Society for Photobiology (RSP), and the Komarov Botanical Institute of the Russian Academy of Sciences ([K]BIN RAS). This conference was organized with the help of Monomax Company, a member of the International Congress Convention Association (ICCA), and was supported by the Ministry of Education and Science of the Russian Federation. Here, we provide a brief description of the conference, its scientific program, as well as a brief introduction and key contributions of the four honored scientists. Further, we emphasize the recognition given, at this conference, to several outstanding young researchers, from around the World, for their research in the area of our conference. A special feature of this paper is the inclusion of photographs provided by one of us (Tatsuya Tomo). Lastly, we urge the readers to watch for information on the next 11th conference on "Photosynthesis and Hydrogen Energy Research for Sustainability-2021," to be held in Bulgaria in 2021.

On the origin of oxygenic photosynthesis and Cyanobacteria

Oxygenic phototrophs have played a fundamental role in Earth's history by enabling the rise of atmospheric oxygen (O₂ ) and paving the way for animal evolution. Understanding the origins of oxygenic photosynthesis and Cyanobacteria is key when piecing together the events around Earth's oxygenation. It is likely that photosynthesis evolved within bacterial lineages that are not extant, so it can be challenging when studying the early history of photosynthesis. Recent genomic and molecular evolution studies have transformed our understanding about the evolution of photosynthetic reaction centres and the evolution of Cyanobacteria. The evidence reviewed here highlights some of the most recent advances on the origin of photosynthesis both at the genomic and gene family levels.

Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I

Photosynthetic organisms capture light energy to drive their energy metabolism, and employ the chemical reducing power to convert carbon dioxide (CO2) into organic molecules. Photorespiration, however, significantly reduces the photosynthetic yields. To survive under low CO2 concentrations, cyanobacteria evolved unique carbon-concentration mechanisms that enhance the efficiency of photosynthetic CO2 fixation, for which the molecular principles have remained unknown. We show here how modular adaptations enabled the cyanobacterial photosynthetic complex I to concentrate CO2 using a redox-driven proton-pumping machinery. Our cryo-electron microscopy structure at 3.2 Å resolution shows a catalytic carbonic anhydrase module that harbours a Zn2+ active site, with connectivity to proton-pumping subunits that are activated by electron transfer from photosystem I. Our findings illustrate molecular principles in the photosynthetic complex I machinery that enabled cyanobacteria to survive in drastically changing CO2 conditions.

Evolution of Photochemical Reaction Centres: More Twists?

One of the earliest events in the molecular evolution of photosynthesis is the structural and functional specialisation of type I (ferredoxin-reducing) and type II (quinone-reducing) reaction centres. In this opinion article we point out that the homodimeric type I reaction centre of heliobacteria has a calcium-binding site with striking structural similarities to the Mn₄CaO₅ cluster of photosystem II. These similarities indicate that most of the structural elements required to evolve water oxidation chemistry were present in the earliest reaction centres. We suggest that the divergence of type I and type II reaction centres was made possible by a drastic structural shift linked to a change in redox properties that coincided with or facilitated the origin of photosynthetic water oxidation.