Streptophyte Terrestrialization in Light of Plastid Evolution

Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae

BACKGROUND

Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred.

RESULTS

Our ancestral-state reconstructions, show that multicellularity arose independently twice in the volvocine algae. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae.

CONCLUSIONS

Large molecular datasets and robust phylogenetic methods are bringing the evolutionary history of the volvocine algae more sharply into focus. Mounting evidence suggests that extant species in this group are the result of two independent origins of multicellularity and multiple independent origins of cell differentiation. Also, the origin of the Tetrabaenaceae-Goniaceae-Volvocaceae clade may be much older than previously thought. Finally, the possibility of cryptic species in the Tetrabaenaceae provides an exciting opportunity to study the recent divergence of lineages adapted to live in very different thermal environments.

Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages

The gain and loss of genes fluctuate over evolutionary time in major eukaryotic clades. However, the full profile of these macroevolutionary trajectories is still missing. To give a more inclusive view on the changes in genome complexity across the tree of life, here we recovered the evolutionary dynamics of gene family gain and loss ranging from the ancestor of cellular organisms to 352 eukaryotic species. We show that in all considered lineages the gene family content follows a common evolutionary pattern, where the number of gene families reaches the highest value at a major evolutionary and ecological transition, and then gradually decreases towards extant organisms. This supports theoretical predictions and suggests that the genome complexity is often decoupled from commonly perceived organismal complexity. We conclude that simplification by gene family loss is a dominant force in Phanerozoic genomes of various lineages, probably underpinned by intense ecological specializations and functional outsourcing.

The Ethyl Acetate Extract of Caulerpa microphysa Promotes Collagen Homeostasis and Inhibits Inflammation in the Skin

Inflammation and collagen-degrading enzymes' overexpression promote collagen decomposition, which affects the structural integrity of the extracellular matrix. The polysaccharide and peptide extracts of the green alga Caulerpa microphysa (C. microphysa) have been proven to have anti-inflammatory, wound healing, and antioxidant effects in vivo and in vitro. However, the biological properties of the non-water-soluble components of C. microphysa are still unknown. In the present study, we demonstrated the higher effective anti-inflammatory functions of C. microphysa ethyl acetate (EA) extract than water extract up to 16-30% in LPS-induced HaCaT cells, including reducing the production of interleukin (IL)-1β, IL-6, IL-8, and tumor necrosis factor-α (TNF-α). Furthermore, the excellent collagen homeostasis effects from C. microphysa were proven by suppressing the matrix metalloproteinase-1 (MMP-1) secretion, enhancing type 1 procollagen and collagen expressions dose-dependently in WS1 cells. Moreover, using UHPLC-QTOF-MS analysis, four terpenoids, siphonaxanthin, caulerpenyne, caulerpal A, and caulerpal B, were identified and may be involved in the superior collagen homeostasis and anti-inflammatory effects of the C. microphysa EA extract.

Zygospore development of Spirogyra (Charophyta) investigated by serial block-face scanning electron microscopy and 3D reconstructions

Sexual reproduction of Zygnematophyceae by conjugation is a less investigated topic due to the difficulties of the induction of this process and zygospore ripening under laboratory conditions. For this study, we collected field sampled zygospores of Spirogyra mirabilis and three additional Spirogyra strains in Austria and Greece. Serial block-face scanning electron microscopy was performed on high pressure frozen and freeze substituted zygospores and 3D reconstructions were generated, allowing a comprehensive insight into the process of zygospore maturation, involving storage compound and organelle rearrangements. Chloroplasts are drastically changed, while young stages contain both parental chloroplasts, the male chloroplasts are aborted and reorganised as 'secondary vacuoles' which initially contain plastoglobules and remnants of thylakoid membranes. The originally large pyrenoids and the volume of starch granules is significantly reduced during maturation (young: 8 ± 5 µm³, mature: 0.2 ± 0.2 µm³). In contrast, lipid droplets (LDs) increase significantly in number upon zygospore maturation, while simultaneously getting smaller (young: 21 ± 18 µm³, mature: 0.1 ± 0.2 and 0.5 ± 0.9 µm³). Only in S. mirabilis the LD volume increases (34 ± 29 µm³), occupying ~50% of the zygospore volume. Mature zygospores contain barite crystals as confirmed by Raman spectroscopy with a size of 0.02 - 0.05 µm³. The initially thin zygospore cell wall (~0.5 µm endospore, ~0.8 µm exospore) increases in thickness and develops a distinct, electron dense mesospore, which has a reticulate appearance (~1.4 µm) in Spirogyra sp. from Greece. The exo- and endospore show cellulose microfibrils in a helicoidal pattern. In the denser endospore, pitch angles of the microfibril layers were calculated: ~18 ± 3° in S. mirabilis, ~20 ± 3° in Spirogyra sp. from Austria and ~38 ± 8° in Spirogyra sp. from Greece. Overall this study gives new insights into Spirogyra sp. zygospore development, crucial for survival during dry periods and dispersal of this genus.

Structure of the multi-subunit chloroplast RNA polymerase

Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression.

SCAB1 coordinates sequential Ca2+ and ABA signals during osmotic stress induced stomatal closure in Arabidopsis

Hyperosmotic stress caused by drought is a detrimental threat to plant growth and agricultural productivity due to limited water availability. Stomata are gateways of transpiration and gas exchange, the swift adjustment of stomatal aperture has a strong influence on plant drought resistance. Despite intensive investigations of stomatal closure during drought stress in past decades, little is known about how sequential signals are integrated during complete processes. Here, we discovered that the rapid Ca2+ signaling and subsequent abscisic acid (ABA) signaling contribute to the kinetics of both F-actin reorganizations and stomatal closure in Arabidopsis thaliana, while STOMATAL CLOSURE-RELATED ACTIN BINDING PROTEIN1 (SCAB1) is the molecular switch for this entire process. During the early stage of osmotic shock responses, swift elevated calcium signaling promotes SCAB1 phosphorylation through calcium sensors CALCIUM DEPENDENT PROTEIN KINASE3 (CPK3) and CPK6. The phosphorylation restrained the microfilament binding affinity of SCAB1, which bring about the F-actin disassembly and stomatal closure initiation. As the osmotic stress signal continued, both the kinase activity of CPK3 and the phosphorylation level of SCAB1 attenuated significantly. We further found that ABA signaling is indispensable for these attenuations, which presumably contributed to the actin filament reassembly process as well as completion of stomatal closure. Notably, the dynamic changes of SCAB1 phosphorylation status are crucial for the kinetics of stomatal closure. Taken together, our results support a model in which SCAB1 works as a molecular switch, and directs the microfilament rearrangement through integrating the sequentially generated Ca2+ and ABA signals during osmotic stress induced stomatal closure.

The extracellular matrix of green algae

Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.

Membrane-anchored calpains - hidden regulators of growth and development beyond plants?

Calpains are modulatory proteases that modify diverse cellular substrates and play essential roles in eukaryots. The best studied are animal cytosolic calpains. Here, we focus on enigmatic membrane-anchored calpains, their structural and functional features as well as phylogenetic distribution. Based on domain composition, we identified four types of membrane-anchored calpains. Type 1 and 2 show broad phylogenetic distribution among unicellular protists and streptophytes suggesting their ancient evolutionary origin. Type 3 and 4 diversified early and are present in brown algae and oomycetes. The plant DEK1 protein is the only representative of membrane-anchored calpains that has been functionally studied. Here, we present up to date knowledge about its structural features, putative regulation, posttranslational modifications, and biological role. Finally, we discuss potential model organisms and available tools for functional studies of membrane-anchored calpains with yet unknown biological role. Mechanistic understanding of membrane-anchored calpains may provide important insights into fundamental principles of cell polarization, cell fate control, and morphogenesis beyond plants.

Genome-wide identification and evolutionary view of ALOG gene family in Solanaceae

The ALOG gene family, which was named after its earliest identified members ( Arabidopsis LSH1 and Oryza G1), encodes a class of transcription factors (TF) characterized by the presence of a highly conserved ALOG domain. These proteins are found in various plant species playing regulatory roles in plant growth, development, and morphological diversification of inflorescence. The functional characterization of these genes in some plant species has demonstrated their involvement in floral architecture. In this study, we used a genome-wide and phylogenetic approach to gain insights into plants' origin, diversification, and functional aspects of the ALOG gene family. In total, 648 ALOG homologous genes were identified in 77 Viridiplantae species, and their evolutionary relationships were inferred using maximum likelihood phylogenetic analyses. Our results suggested that the ALOG gene family underwent several rounds of gene duplication and diversification during angiosperm evolution. Furthermore, we found three functional orthologous groups in Solanaceae species. The study provides insights into the evolutionary history and functional diversification of the ALOG gene family, which could aid in understanding the mechanisms underlying floral architecture in angiosperms.

Acquisition of Desiccation Tolerance Unveiled: Polar Lipid Profiles of Streptophyte Algae Offer Insights

Terrestrialization by photosynthetic eukaryotes took place in the two branches of green microalgae: Chlorophyta and Charophyta. Within the latter, the paraphyletic streptophytic algae divide into two clades. These are named Klebsormidiophyceae-Chlorokybophyceae-Mesostigmatophyceae (KCM), which is the oldest, and Zygnematophyceae-Coleochaetophyceae-Charophyceae (ZCC), which contains the closest relatives of vascular plants. Terrestrialization required the emergence of adaptations in response to new challenges, such as irradiance, temperature oscillations and water deprivation. In this study, we evaluated lipid composition in species representative of distinct phylogenetic clusters within Charophyta and Chlorophyta. We aim to study whether the inherent thylakoid lipid composition, as well as its adaptability in response to desiccation, were fundamental factors for the evolutionary history of terrestrial plants. The results showed that the lipid composition was similar to that found in flowering land plants, differing only in betaine lipids. Likewise, the largest constitutive pool of oligogalactolipids (OGL) was found only in the fully desiccation-tolerant species Klebsormidium nitens. After desiccation, the content of polar lipids decreased in all species. Conversely, the content of OGL increased, particularly trigalactosyldiacylglycerol and tetragalactosyldiacylglycerol in the ZCC clade. The analysis of the molecular species composition of the newly formed OGL may suggest a different biosynthetic route for the KCM and ZCC clades. We speculate that the appearance of a new OGL synthesis pathway, which eventually arose during the streptophyte evolutionary process, endowed algae with a much more dynamic regulation of thylakoid composition in response to stress, which ultimately contributed to the colonization of terrestrial habitats.

3D-reconstructions of zygospores in Zygnema vaginatum (Charophyta) reveal details of cell wall formation, suggesting adaptations to extreme habitats

The streptophyte green algal class Zygnematophyceae is the immediate sister lineage to land plants. Their special form of sexual reproduction via conjugation might have played a key role during terrestrialization. Thus, studying Zygnematophyceae and conjugation is crucial for understanding the conquest of land. Moreover, sexual reproduction features are important for species determination. We present a phylogenetic analysis of a field-sampled Zygnema strain and analyze its conjugation process and zygospore morphology, both at the micro- and nanoscale, including 3D-reconstructions of the zygospore architecture. Vegetative filament size (26.18 ± 1.07 μm) and reproductive features allowed morphological determination of Zygnema vaginatum, which was combined with molecular analyses based on rbcL sequencing. Transmission electron microscopy (TEM) depicted a thin cell wall in young zygospores, while mature cells exhibited a tripartite wall, including a massive and sculptured mesospore. During development, cytological reorganizations were visualized by focused ion beam scanning electron microscopy (FIB-SEM). Pyrenoids were reorganized, and the gyroid cubic central thylakoid membranes, as well as the surrounding starch granules, degraded (starch granule volume: 3.58 ± 2.35 μm3 in young cells; 0.68 ± 0.74 μm3 at an intermediate stage of zygospore maturation). Additionally, lipid droplets (LDs) changed drastically in shape and abundance during zygospore maturation (LD/cell volume: 11.77% in young cells; 8.79% in intermediate cells, 19.45% in old cells). In summary, we provide the first TEM images and 3D-reconstructions of Zygnema zygospores, giving insights into the physiological processes involved in their maturation. These observations help to understand mechanisms that facilitated the transition from water to land in Zygnematophyceae.

Green land: Multiple perspectives on green algal evolution and the earliest land plants

Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute the primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades of green plants have independently made the transition from fully aquatic to subaerial habitats many times throughout Earth's history. The transition, from unicells or simple filaments to complex multicellular plant bodies with functionally differentiated tissues and organs, was accompanied by innovations built upon a genetic and phenotypic toolkit that have served aquatic green phototrophs successfully for at least a billion years. These innovations opened an enormous array of new, drier places to live on the planet and resulted in a huge diversity of land plants that have dominated terrestrial ecosystems over the past 500 million years. This review examines the greening of the land from several perspectives, from paleontology to phylogenomics, to water stress responses and the genetic toolkit shared by green algae and plants, to the genomic evolution of the sporophyte generation. We summarize advances on disparate fronts in elucidating this important event in the evolution of the biosphere and the lacunae in our understanding of it. We present the process not as a step-by-step advancement from primitive green cells to an inevitable success of embryophytes, but rather as a process of adaptations and exaptations that allowed multiple clades of green plants, with various combinations of morphological and physiological terrestrialized traits, to become diverse and successful inhabitants of the land habitats of Earth.

Plastids: diving into their diversity, their functions, and their role in plant development

Plastids are a group of essential, heterogenous semi-autonomous organelles characteristic of plants that perform photosynthesis and a diversity of metabolic pathways that impact growth and development. Plastids are remarkably dynamic and can interconvert in response to specific developmental and environmental cues, functioning as a central metabolic hub in plant cells. By far the best studied plastid is the chloroplast, but in recent years the combination of modern techniques and genetic analyses has expanded our current understanding of plastid morphological and functional diversity in both model and non-model plants. These studies have provided evidence of an unexpected diversity of plastid subtypes with specific characteristics. In this review, we describe recent findings that provide insights into the characteristics of these specialized plastids and their functions. We concentrate on the emerging evidence that supports the model that signals derived from particular plastid types play pivotal roles in plant development, environmental, and defense responses. Furthermore, we provide examples of how new technologies are illuminating the functions of these specialized plastids and the overall complexity of their differentiation processes. Finally, we discuss future research directions such as the use of ectopic plastid differentiation as a valuable tool to characterize factors involved in plastid differentiation. Collectively, we highlight important advances in the field that can also impact future agricultural and biotechnological improvement in plants.

What can hornworts teach us?

The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

Crossroads in the evolution of plant specialized metabolism

The monophyletic group of embryophytes (land plants) stands out among photosynthetic eukaryotes: they are the sole constituents of the macroscopic flora on land. In their entirety, embryophytes account for the majority of the biomass on land and constitute an astounding biodiversity. What allowed for the massive radiation of this particular lineage? One of the defining features of all land plants is the production of an array of specialized metabolites. The compounds that the specialized metabolic pathways of embryophytes produce have diverse functions, ranging from superabundant structural polymers and compounds that ward off abiotic and biotic challenges, to signaling molecules whose abundance is measured at the nanomolar scale. These specialized metabolites govern the growth, development, and physiology of land plants-including their response to the environment. Hence, specialized metabolites define the biology of land plants as we know it. And they were likely a foundation for their success. It is thus intriguing to find that the closest algal relatives of land plants, freshwater organisms from the grade of streptophyte algae, possess homologs for key enzymes of specialized metabolic pathways known from land plants. Indeed, some studies suggest that signature metabolites emerging from these pathways can be found in streptophyte algae. Here we synthesize the current understanding of which routes of the specialized metabolism of embryophytes can be traced to a time before plants had conquered land.

A MYB Transcription Factor Atlas Provides Insights into the Evolution of Environmental Adaptations in Plants

The MYB transcription factor superfamily includes key regulators of plant development and responses to environmental changes. The diversity of lifestyles and morphological characteristics exhibited by plants are potentially associated with the genomic dynamics of the MYB superfamily. With the release of the plant genomes, a comprehensive phylogenomic analysis of the MYB superfamily across Viridiplantae is allowed. The present study performed phylogenetic, phylogenomic, syntenic, horizontal gene transfer, and neo/sub-functionalization analysis of the MYB superfamily to explore the evolutionary contributions of MYB members to species diversification, trait formation, and environmental adaptation in 437 different plant species. We identified major changes in copy number variation and genomic context within subclades across lineages. Multiple MYB subclades showed highly conserved copy number patterns and synteny across flowering plants, whereas others were more dynamic and showed lineage-specific patterns. As examples of lineage-specific morphological divergence, we hypothesize that the gain of a MYB orthogroup associated with flower development and environmental responses and an orthogroup associated with auxin and wax biosynthesis in angiosperms were correlated with the emergence of flowering plants, unbiased neo-/sub-functionalization of gene duplicates contributed to environmental adaptation, and species-specific neo-/sub-functionalization contributed to phenotype divergence between species. Transposable element insertion in promoter regions may have facilitated the sub-/neo-functionalization of MYB genes and likely played a tissue-specific role contributing to sub-/neo-functionalization in plant root tissues. This study provides new insights into the evolutionary divergence of the MYB superfamily across major flowering and non-flowering lineages and emphasizes the need for lineage-/tissue-specific characterization to further understand trait variability and environmental adaptation.

Zygospores of the green alga Spirogyra: new insights from structural and chemical imaging

Zygnematophyceae, a class of streptophyte green algae and sister group to land plants (Embryophytes) live in aquatic to semi-terrestrial habitats. The transition from aquatic to terrestrial environments requires adaptations in the physiology of vegetative cells and in the structural properties of their cell walls. Sexual reproduction occurs in Zygnematophyceae by conjugation and results in the formation of zygospores, possessing unique multi-layered cell walls, which might have been crucial in terrestrialization. We investigated the structure and chemical composition of field sampled Spirogyra sp. zygospore cell walls by multiple microscopical and spectral imaging techniques: light microscopy, confocal laser scanning microscopy, transmission electron microscopy following high pressure freeze fixation/freeze substitution, Raman spectroscopy and atomic force microscopy. This comprehensive analysis allowed the detection of the subcellular organization and showed three main layers of the zygospore wall, termed endo-, meso- and exospore. The endo- and exospore are composed of polysaccharides with different ultrastructural appearance, whereas the electron dense middle layer contains aromatic compounds as further characterized by Raman spectroscopy. The possible chemical composition remains elusive, but algaenan or a sporopollenin-like material is suggested. Similar compounds with a non-hydrolysable character can be found in moss spores and pollen of higher plants, suggesting a protective function against desiccation stress and high irradiation. While the tripartite differentiation of the zygospore wall is well established in Zygnematopyhceae, Spirogyra showed cellulose fibrils arranged in a helicoidal pattern in the endo- and exospore. Initial incorporation of lipid bodies during early zygospore wall formation was also observed, suggesting a key role of lipids in zygospore wall synthesis. Multimodal imaging revealed that the cell wall of the sexually formed zygospores possess a highly complex internal structure as well as aromatics, likely acting as protective compounds and leading to impregnation. Both, the newly discovered special three-dimensional arrangement of microfibrils and the integration of highly resistant components in the cell wall are not found in the vegetative state. The variety of methods gave a comprehensive view on the intricate zygospore cell wall and its potential key role in the terrestrial colonization and plant evolution is discussed.

The colonization of land was a likely driving force for the evolution of mitochondrial retrograde signalling in plants

Most retrograde signalling research in plants was performed using Arabidopsis, so an evolutionary perspective on mitochondrial retrograde regulation (MRR) is largely missing. Here, we used phylogenetics to track the evolutionary origins of factors involved in plant MRR. In all cases, the gene families can be traced to ancestral green algae or earlier. However, the specific subfamilies containing factors involved in plant MRR in many cases arose during the transition to land. NAC transcription factors with C-terminal transmembrane domains, as observed in the key regulator ANAC017, can first be observed in non-vascular mosses, and close homologs to ANAC017 can be found in seed plants. Cyclin-dependent kinases (CDKs) are common to eukaryotes, but E-type CDKs that control MRR also diverged in conjunction with plant colonization of land. AtWRKY15 can be traced to the earliest land plants, while AtWRKY40 only arose in angiosperms and AtWRKY63 even more recently in Brassicaceae. Apetala 2 (AP2) transcription factors are traceable to algae, but the ABI4 type again only appeared in seed plants. This strongly suggests that the transition to land was a major driver for developing plant MRR pathways, while additional fine-tuning events have appeared in seed plants or later. Finally, we discuss how MRR may have contributed to meeting the specific challenges that early land plants faced during terrestrialization.

Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT

Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na⁺/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.

The cell biology of charophytes: Exploring the past and models for the future

Charophytes (Streptophyta) represent a diverse assemblage of extant green algae that are the sister lineage to land plants. About 500-600+ million years ago, a charophyte progenitor successfully colonized land and subsequently gave rise to land plants. Charophytes have diverse but relatively simple body plans that make them highly attractive organisms for many areas of biological research. At the cellular level, many charophytes have been used for deciphering cytoskeletal networks and their dynamics, membrane trafficking, extracellular matrix secretion, and cell division mechanisms. Some charophytes live in challenging habitats and have become excellent models for elucidating the cellular and molecular effects of various abiotic stressors on plant cells. Recent sequencing of several charophyte genomes has also opened doors for the dissection of biosynthetic and signaling pathways. While we are only in an infancy stage of elucidating the cell biology of charophytes, the future application of novel analytical methodologies in charophyte studies that include a broader survey of inclusive taxa will enhance our understanding of plant evolution and cell dynamics.

Temperature- and light stress adaptations in Zygnematophyceae: The challenges of a semi-terrestrial lifestyle

Streptophyte green algae comprise the origin of land plants and therefore life on earth as we know it today. While terrestrialization opened new habitats, leaving the aquatic environment brought additional abiotic stresses. More-drastic temperature shifts and high light levels are major abiotic stresses in semi-terrestrial habitats, in addition to desiccation, which has been reviewed elsewhere. Zygnematophyceae, a species-rich class of streptophyte green algae, is considered a sister-group to embryophytes. They have developed a variety of avoidance and adaptation mechanisms to protect against temperature extremes and high radiation in the form of photosynthetically active and ultraviolet radiation (UV) radiation occurring on land. Recently, knowledge of transcriptomic and metabolomic changes as consequences of these stresses has become available. Land-plant stress-signaling pathways producing homologs of key enzymes have been described in Zygnematophyceae. An efficient adaptation strategy is their mat-like growth habit, which provides self-shading and protects lower layers from harmful radiation. Additionally, Zygnematophyceae possess phenolic compounds with UV-screening ability. Resting stages such as vegetative pre-akinetes tolerate freezing to a much higher extent than do young cells. Sexual reproduction occurs by conjugation without the formation of flagellated male gametes, which can be seen as an advantage in water-deficient habitats. The resulting zygospores possess a multilayer cell wall, contributing to their resistance to terrestrial conditions. Especially in the context of global change, understanding temperature and light tolerance is crucial.

PAP8/pTAC6 Is Part of a Nuclear Protein Complex and Displays RNA Recognition Motifs of Viral Origin

Chloroplast biogenesis depends on a complex transcriptional program involving coordinated expression of plastid and nuclear genes. In particular, photosynthesis-associated plastid genes are expressed by the plastid-encoded polymerase (PEP) that undergoes a structural rearrangement during chloroplast formation. The prokaryotic-type core enzyme is rebuilt into a larger complex by the addition of nuclear-encoded PEP-associated proteins (PAP1 to PAP12). Among the PAPs, some have been detected in the nucleus (PAP5 and PAP8), where they could serve a nuclear function required for efficient chloroplast biogenesis. Here, we detected PAP8 in a large nuclear subcomplex that may include other subunits of the plastid-encoded RNA polymerase. We have made use of PAP8 recombinant proteins in Arabidopsis thaliana to decouple its nucleus- and chloroplast-associated functions and found hypomorphic mutants pointing at essential amino acids. While the origin of the PAP8 gene remained elusive, we have found in its sequence a micro-homologous domain located within a large structural homology with a rhinoviral RNA-dependent RNA polymerase, highlighting potential RNA recognition motifs in PAP8. PAP8 in vitro RNA binding activity suggests that this domain is functional. Hence, we propose that the acquisition of PAPs may have occurred during evolution by different routes, including lateral gene transfer.

Looking at mechanobiology through an evolutionary lens

Mechanical forces were arguably among the first stimuli to be perceived by cells, and they continue to shape the evolution of all organisms. Great strides have been made in recent years in the field of plant cell and molecular mechanobiology, in part owing to focused efforts on key model systems. Here, we propose to enrich such work through evolutionary mechanobiology, or 'evo-mechano', and describe three major themes that could drive research in this area. We use plastid evo-mechano as a case study, describing how plastids from different lineages perceive their mechanical environments, how their mechanical properties vary across lineages, and their distinct roles in graviperception. Finally, we argue that future research into the biomechanical properties and mechanobiological signaling mechanisms that have been elaborated by green species over the past 1.5 billion years will help us understand both the universal and the unique adaptations of plants to their physical environment.

Origin and adaptive evolution of UV RESISTANCE LOCUS 8-mediated signaling during plant terrestrialization

UV RESISTANCE LOCUS 8 (UVR8) mediates photomorphogenic responses and acclimation to UV-B radiation by regulating the transcription of a series of transcription factors (TFs). However, the origin and evolution of UVR8-mediated signaling pathways remain largely unknown. In this study, we investigated the origin and evolution of the major components of the UVR8-mediated signaling pathway (UVR8, REPRESSOR OF UV-B PHOTOMORPHOGENESIS [RUP], BRI1-EMS-SUPPRESSOR1 [BES1], BES1-INTERACTING MYC-LIKE 1 (BIM1), WRKY DNA-BINDING PROTEIN 36 (WRKY36), MYB DOMAIN PROTEIN 73/77/13 [MYB73/MYB77/MYB13], and PHYTOCHROME INTERACTING FACTOR 4/5 [PIF4 and PIF5]) using comparative genomics and phylogenetic approaches. We showed that the central regulator UVR8 presented a conservative evolutionary route during plant evolution, and the evolutionary history of downstream negative regulators and TFs was different from that of green plant phylogeny. The canonical UVR8-CONSTITUTIVELY PHOTOMORPHOGENIC 1(COP1)/SUPPRESSOR OF PHYA-105 (SPA)-ELONGATED HYPOCOTYL 5 (HY5)-RUP signaling pathway originated in chlorophytes and conferred green algae the additional ability to cope with UV-B radiation. Moreover, the emergence of multiple UVR8-mediated signaling pathways in charophytes laid the foundations for the cross-talk between UV-B signals and endogenous hormone responses. Importantly, we observed signatures that reflect plant adaptations to high UV-B irradiance in subaerial/terrestrial environments, including positive selection in UVR8 and RUPs and increased copy number of some vital TFs. These results revealed that green plants not only experienced adaptive modifications in the canonical UVR8-COP1/SPA-HY5-RUP signaling pathway, but also diversified their UV-B signal transduction mechanisms through increasing cross-talk with other pathways, such as those associated with brassinosteroids and auxin. This study greatly expands our understanding of molecular evolution and adaptive mechanisms underlying plant UV-B acclimation.

Chloroplast Genome Traits Correlate With Organismal Complexity and Ecological Traits in Chlorophyta

A positive relationship between cell size and chloroplast genome size within chloroplast-bearing protists has been hypothesized in the past and shown in some case studies, but other factors influencing chloroplast genome size during the evolution of chlorophyte algae have been less studied. We study chloroplast genome size and GC content as a function of habitats and cell size of chlorophyte algae. The chloroplast genome size of green algae in freshwater, marine and terrestrial habitats was differed significantly, with terrestrial algae having larger chloroplast genome sizes in general. The most important contributor to these enlarged genomes in terrestrial species was the length of intergenic regions. There was no clear difference in the GC content of chloroplast genomes from the three habitats categories. Functional morphological categories also showed differences in chloroplast genome size, with filamentous algae having substantially larger genomes than other forms of algae, and foliose algae had lower GC content than other groups. Chloroplast genome size showed no significant differences among the classes Ulvophyceae, Trebouxiophyceae, and Chlorophyceae, but the GC content of Chlorophyceae chloroplast genomes was significantly lower than that of Ulvophyceae and Trebouxiophyceae. There was a certain positive relationship between chloroplast genome size and cell size for the Chlorophyta as a whole and within each of three major classes. Our data also confirmed previous reports that ancestral quadripartite architecture had been lost many times independently in Chlorophyta. Finally, the comparison of the phenotype of chlorophytes algae harboring plastids uncovered that most of the investigated Chlorophyta algae housed a single plastid per cell.

An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?

Microsatellites (SSRs) are tandem repeat sequences in eukaryote genomes, including plant cytoplasmic genomes. The mitochondrial genome (mtDNA) has been shown to vary in size, number, and distribution of SSRs among different plant groups. Thus, SSRs contribute with genomic diversity in mtDNAs. However, the abundance, distribution, and evolutionary significance of SSRs in mtDNA from a wide range of algae and plants have not been explored. In this study, the mtDNAs of 204 plant and algal species were investigated related to the presence of SSRs. The number of SSRs was positively correlated with genome size. Its distribution is dependent on plant and algal groups analyzed, although the cluster analysis indicates the conservation of some common motifs in algal and terrestrial plants that reflect common ancestry of groups. Many SSRs in coding and non-coding regions can be useful for molecular markers. Moreover, mitochondrial SSRs are highly abundant, representing an important source for natural or induced genetic variation, i.e., for biotechnological approaches that can modulate mtDNA gene regulation. Thus, this comparative study increases the understanding of the plant and algal SSR evolution and brings perspectives for further studies.

Different Metabolic Roles for Alternative Oxidase in Leaves of Palustrine and Terrestrial Species

The alternative oxidase pathway (AOP) is associated with excess energy dissipation in leaves of terrestrial plants. To address whether this association is less important in palustrine plants, we compared the role of AOP in balancing energy and carbon metabolism in palustrine and terrestrial environments by identifying metabolic relationships between primary carbon metabolites and AOP in each habitat. We measured oxygen isotope discrimination during respiration, gas exchange, and metabolite profiles in aerial leaves of ten fern and angiosperm species belonging to five families organized as pairs of palustrine and terrestrial species. We performed a partial least square model combined with variable importance for projection to reveal relationships between the electron partitioning to the AOP (τa) and metabolite levels. Terrestrial plants showed higher values of net photosynthesis (AN) and τa, together with stronger metabolic relationships between τa and sugars, important for water conservation. Palustrine plants showed relationships between τa and metabolites related to the shikimate pathway and the GABA shunt, to be important for heterophylly. Excess energy dissipation via AOX is less crucial in palustrine environments than on land. The basis of this difference resides in the contrasting photosynthetic performance observed in each environment, thus reinforcing the importance of AOP for photosynthesis.

Reassessing the evolution of the 1-deoxy-D-xylulose 5-phosphate synthase family suggests a possible novel function for the DXS class 3 proteins

The methylerythritol 4-phosphate (MEP) pathway is of paramount importance for generating plastidial isoprenoids. The first enzyme of the MEP pathway, 1-deoxy-D-xylulose-5-phosphate synthase (DXS), catalyzes a flux-controlling step. In plants the DXS gene family is composed of three distinct classes with non-redundant functions. Although the DXS1 and DXS2 subfamilies have been well characterized, the DXS3 subfamily has been considerably understudied. Here, we carried out in silico and functional analyses to better understand the DXS3 class. Our phylogenetic analysis showed high variation in copy number among the different DXS classes, with the apparent absence of DXS1 class in some species. We found that DXS3 subfamily emerged later than DXS1 and DXS2 and it is under less intense purifying selection. Furthermore, in the DXS3 subfamily critical amino acids positions in the thiamine pyrophosphate binding pocket are not conserved. We demonstrated that the DXS3 proteins from Arabidopsis, Maize, and Rice lack functional DXS activity. Moreover, the Arabidopsis DXS3 protein displayed distinctive sub-organellar chloroplast localization not observed in any DXS1 or DXS2 proteins. Co-expression analysis of the DXS3 from Arabidopsis showed that, unlike DXS1 and DXS2 proteins, it co-expresses with genes related to post-embryonic development and reproduction and not with primary metabolism and isoprenoid synthesis.

N,N-dimethyl-hexadecylamine modulates Arabidopsis root growth through modifying the balance between stem cell niche and jasmonic acid-dependent gene expression

N,N-dimethyl-hexadecylamine (DMHDA) is released as part of volatile blends emitted by plant probiotic bacteria and affects root architecture, defense and nutrition of plants. Here, we investigated the changes in gene expression of transcription factors responsible of maintenance of the root stem cell niche and jasmonic acid signaling in Arabidopsis seedlings in response to this volatile. Concentrations of DMHDA that repress primary root growth were found to alter cell size and division augmenting cell tissue layers in the meristem and causing root widening. DMHDA triggered the division of quiescent center cells, which correlated with repression of SHORT ROOT (SHR), SCARECROW (SCR), and PLETHORA 1 (PLT1) proteins and induction of WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor. Interestingly, an activation of the expression of the jasmonic acid-related reporter genes JAZ1/TIFY10A-GFP and JAZ10pro::JAZ10-GFP suggests that the halted growth of the primary root inversely correlated with expression patterns underlying the defense reaction, which may be of adaptive importance to protect roots against biotic stress. Our data help to unravel the gene expression signatures upon sensing of a highly active bacterial volatile in Arabidopsis seedlings.

Characterization of Two Zygnema Strains (Zygnema circumcarinatum SAG 698-1a and SAG 698-1b) and a Rapid Method to Estimate Nuclear Genome Size of Zygnematophycean Green Algae

Zygnematophyceae green algae (ZGA) have been shown to be the closest relatives of land plants. Three nuclear genomes (Spirogloea muscicola, Mesotaenium endlicherianum, and Penium margaritaceum) of ZGA have been recently published, and more genomes are underway. Here we analyzed two Zygnema circumcarinatum strains SAG 698-1a (mating +) and SAG 698-1b (mating -) and found distinct cell sizes and other morphological differences. The molecular identities of the two strains were further investigated by sequencing their 18S rRNA, psaA and rbcL genes. These marker genes of SAG 698-1a were surprisingly much more similar to Z. cylindricum (SAG 698-2) than to SAG 698-1b. Phylogenies of these marker genes also showed that SAG 698-1a and SAG 698-1b were well separated into two different Zygnema clades, where SAG 698-1a was clustered with Z. cylindricum, while SAG 698-1b was clustered with Z. tunetanum. Additionally, physiological parameters like ETRmax values differed between SAG 698-1a and SAG 698-1b after 2 months of cultivation. The de-epoxidation state (DEPS) of the xanthophyll cycle pigments also showed significant differences. Surprisingly, the two strains could not conjugate, and significantly differed in the thickness of the mucilage layer. Additionally, ZGA cell walls are highly enriched with sticky and acidic polysaccharides, and therefore the widely used plant nuclear extraction protocols do not work well in ZGA. Here, we also report a fast and simple method, by mechanical chopping, for efficient nuclear extraction in the two SAG strains. More importantly, the extracted nuclei were further used for nuclear genome size estimation of the two SAG strains by flow cytometry (FC). To confirm the FC result, we have also used other experimental methods for nuclear genome size estimation of the two strains. Interestingly, the two strains were found to have very distinct nuclear genome sizes (313.2 ± 2.0 Mb in SAG 698-1a vs. 63.5 ± 0.5 Mb in SAG 698-1b). Our multiple lines of evidence strongly indicate that SAG 698-1a possibly had been confused with SAG 698-2 prior to 2005, and most likely represents Z. cylindricum or a closely related species.

Evolutionary Origins of Drought Tolerance in Spermatophytes

It is commonly known that drought stress is a major constraint limiting crop production. Drought stress and associated drought tolerance mechanisms are therefore under intense investigation with the view to future production of drought tolerant crops. With an ever-growing population and variable climate, novel approaches need to be considered to sustainably feed future generations. In this context, definitions of drought tolerance are highly variable, which poses a major challenge for the systematic assessment of this trait across the plant kingdom. Furthermore, drought tolerance is a polygenic trait and understanding the evolution of this complex trait may inform us about patterns of gene gain and loss in relation to diverse drought adaptations. We look at the transition of plants from water to land, and the role of drought tolerance in enabling this transition, before discussing the first drought tolerant plant and common drought responses amongst vascular plants. We reviewed the distribution of a combined "drought tolerance" trait in very broad terms to encompass different experimental systems and definitions used in the current literature and assigned a binary trait "tolerance vs. sensitivity" in 178 extant plant species. By simplifying drought responses of plants into this "binary" trait we were able to explore the evolution of drought tolerance across the wider plant kingdom, compared to previous studies. We show how this binary "drought tolerance/sensitivity" trait has evolved and discuss how incorporating this information into an evolutionary genomics framework could provide insights into the molecular mechanisms underlying extreme drought adaptations.

Cryogenian Glacial Habitats as a Plant Terrestrialisation Cradle - The Origin of the Anydrophytes and Zygnematophyceae Split

For tens of millions of years (Ma), the terrestrial habitats of Snowball Earth during the Cryogenian period (between 720 and 635 Ma before present-Neoproterozoic Era) were possibly dominated by global snow and ice cover up to the equatorial sublimative desert. The most recent time-calibrated phylogenies calibrated not only on plants but on a comprehensive set of eukaryotes indicate that within the Streptophyta, multicellular charophytes (Phragmoplastophyta) evolved in the Mesoproterozoic to the early Neoproterozoic. At the same time, Cryogenian is the time of the likely origin of the common ancestor of Zygnematophyceae and Embryophyta and later, also of the Zygnematophyceae-Embryophyta split. This common ancestor is proposed to be called Anydrophyta; here, we use anydrophytes. Based on the combination of published phylogenomic studies and estimated diversification time comparisons, we deem it highly likely that anydrophytes evolved in response to Cryogenian cooling. Also, later in the Cryogenian, secondary simplification of multicellular anydrophytes and loss of flagella resulted in Zygnematophyceae diversification as an adaptation to the extended cold glacial environment. We propose that the Marinoan geochemically documented expansion of first terrestrial flora has been represented not only by Chlorophyta but also by Streptophyta, including the anydrophytes, and later by Zygnematophyceae, thriving on glacial surfaces until today. It is possible that multicellular early Embryophyta survived in less abundant (possibly relatively warmer) refugia, relying more on mineral substrates, allowing the retention of flagella-based sexuality. The loss of flagella and sexual reproduction by conjugation evolved in Zygnematophyceae and zygomycetous fungi during the Cryogenian in a remarkably convergent way. Thus, we support the concept that the important basal cellular adaptations to terrestrial environments were exapted in streptophyte algae for terrestrialization and propose that this was stimulated by the adaptation to glacial habitats dominating the Cryogenian Snowball Earth. Including the glacial lifestyle when considering the rise of land plants increases the parsimony of connecting different ecological, phylogenetic, and physiological puzzles of the journey from aquatic algae to terrestrial floras.

The chloroplast NADH dehydrogenase-like complex influences the photosynthetic activity of the moss Physcomitrella patens

Alternative electron pathways contribute to regulation of photosynthetic light reactions to adjust to metabolic demands in dynamic environments. The chloroplast NADH dehydrogenase-like (NDH) complex mediates the cyclic electron transport pathway around PSI in different cyanobacteria, algae, and plant species, but it is not fully conserved in all photosynthetic organisms. In order to assess how the physiological role of this complex changed during plant evolution, we isolated Physcomitrella patens lines knocked out for the NDHM gene that encodes a subunit fundamental for the activity of the complex. ndhm knockout mosses indicated high PSI acceptor side limitation upon abrupt changes in illumination. In P. patens, pseudo-cyclic electron transport mediated by flavodiiron proteins (FLVs) was also shown to prevent PSI over-reduction in plants exposed to light fluctuations. flva ndhm double knockout mosses had altered photosynthetic performance and growth defects under fluctuating light compared with the wild type and single knockout mutants. The results showed that while the contribution of NDH to electron transport is minor compared with FLV, NDH still participates in modulating photosynthetic activity, and it is critical to avoid PSI photoinhibition, especially when FLVs are inactive. The functional overlap between NDH- and FLV-dependent electron transport supports PSI activity and prevents its photoinhibition under light variations.

Heat stress response in the closest algal relatives of land plants reveals conserved stress signaling circuits

All land plants (embryophytes) share a common ancestor that likely evolved from a filamentous freshwater alga. Elucidating the transition from algae to embryophytes - and the eventual conquering of Earth's surface - is one of the most fundamental questions in plant evolutionary biology. Here, we investigated one of the organismal properties that might have enabled this transition: resistance to drastic temperature shifts. We explored the effect of heat stress in Mougeotia and Spirogyra, two representatives of Zygnematophyceae - the closest known algal sister lineage to land plants. Heat stress induced pronounced phenotypic alterations in their plastids, and high-performance liquid chromatography-tandem mass spectroscopy-based profiling of 565 transitions for the analysis of main central metabolites revealed significant shifts in 43 compounds. We also analyzed the global differential gene expression responses triggered by heat, generating 92.8 Gbp of sequence data and assembling a combined set of 8905 well-expressed genes. Each organism had its own distinct gene expression profile; less than one-half of their shared genes showed concordant gene expression trends. We nevertheless detected common signature responses to heat such as elevated transcript levels for molecular chaperones, thylakoid components, and - corroborating our metabolomic data - amino acid metabolism. We also uncovered the heat-stress responsiveness of genes for phosphorelay-based signal transduction that links environmental cues, calcium signatures and plastid biology. Our data allow us to infer the molecular heat stress response that the earliest land plants might have used when facing the rapidly shifting temperature conditions of the terrestrial habitat.

Evo-physio: on stress responses and the earliest land plants

Embryophytes (land plants) can be found in almost any habitat on the Earth's surface. All of this ecologically diverse embryophytic flora arose from algae through a singular evolutionary event. Traits that were, by their nature, indispensable for the singular conquest of land by plants were those that are key for overcoming terrestrial stressors. Not surprisingly, the biology of land plant cells is shaped by a core signaling network that connects environmental cues, such as stressors, to the appropriate responses-which, thus, modulate growth and physiology. When did this network emerge? Was it already present when plant terrestrialization was in its infancy? A comparative approach between land plants and their algal relatives, the streptophyte algae, allows us to tackle such questions and resolve parts of the biology of the earliest land plants. Exploring the biology of the earliest land plants might shed light on exactly how they overcame the challenges of terrestrialization. Here, we outline the approaches and rationale underlying comparative analyses towards inferring the genetic toolkit for the stress response that aided the earliest land plants in their conquest of land.

Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants

The 1,000 Plants (1KP) initiative was the first large-scale effort to collect next-generation sequencing (NGS) data across a phylogenetically representative sampling of species for a major clade of life, in this case theViridiplantae, or green plants. As an international multidisciplinary consortium, we focused on plant evolution and its practical implications. Among the major outcomes were the inference of a reference species tree for green plants by phylotranscriptomic analysis of low-copy genes, a survey of paleopolyploidy (whole-genome duplications) across the Viridiplantae, the inferred evolutionary histories for many gene families and biological processes, the discovery of novel light-sensitive proteins for optogenetic studies in mammalian neuroscience, and elucidation of the genetic network for a complex trait (C₄ photosynthesis). Altogether, 1KP demonstrated how value can be extracted from a phylodiverse sequencing data set, providing a template for future projects that aim to generate even more data, including complete de novo genomes, across the tree of life.

Origins, function, and regulation of the TOC-TIC general protein import machinery of plastids

The evolution of chloroplasts from the original endosymbiont involved the transfer of thousands of genes from the ancestral bacterial genome to the host nucleus, thereby combining the two genetic systems to facilitate coordination of gene expression and achieve integration of host and organelle functions. A key element of successful endosymbiosis was the evolution of a unique protein import system to selectively and efficiently target nuclear-encoded proteins to their site of function within the chloroplast after synthesis in the cytoplasm. The chloroplast TOC-TIC (translocon at the outer chloroplast envelope-translocon at the inner chloroplast envelope) general protein import system is conserved across the plant kingdom, and is a system of hybrid origin, with core membrane transport components adapted from bacterial protein targeting systems, and additional components adapted from host genes to confer the specificity and directionality of import. In vascular plants, the TOC-TIC system has diversified to mediate the import of specific, functionally related classes of plastid proteins. This functional diversification occurred as the plastid family expanded to fulfill cell- and tissue-specific functions in terrestrial plants. In addition, there is growing evidence that direct regulation of TOC-TIC activities plays an essential role in the dynamic remodeling of the organelle proteome that is required to coordinate plastid biogenesis with developmental and physiological events.

Major Changes in Plastid Protein Import and the Origin of the Chloroplastida

Core components of plastid protein import and the principle of using N-terminal targeting sequences are conserved across the Archaeplastida, but lineage-specific differences exist. Here we compare, in light of plastid protein import, the response to high-light stress from representatives of the three archaeplastidal groups. Similar to land plants, Chlamydomonas reinhardtii displays a broad response to high-light stress, not observed to the same degree in the glaucophyte Cyanophora paradoxa or the rhodophyte Porphyridium purpureum. We find that only the Chloroplastida encode both Toc75 and Oep80 in parallel and suggest that elaborate high-light stress response is supported by changes in plastid protein import. We propose the origin of a phenylalanine-independent import pathway via Toc75 allowed higher import rates to rapidly service high-light stress, but with the cost of reduced specificity. Changes in plastid protein import define the origin of the green lineage, whose greatest evolutionary success was arguably the colonization of land.

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Chloroplastida evolved a dual system, Toc75/Oep80, for high throughput protein import

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Loss of F-based targeting led to dual organelle targeting using a single ambiguous NTS

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Relaxation of functional constraints allowed a wider Toc/Tic modification

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A broad response to high-light stress appears unique to Chloroplastida

The Arctic Cylindrocystis (Zygnematophyceae, Streptophyta) Green Algae are Genetically and Morphologically Diverse and Exhibit Effective Accumulation of Polyphosphate

The green algal genus Cylindrocystis is widespread in various types of environments, including extreme habitats. However, very little is known about its diversity, especially in polar regions. In the present study, we isolated seven new Cylindrocystis-like strains from terrestrial and freshwater habitats in Svalbard (High Arctic). We aimed to compare the new isolates on a molecular (rbcL and 18S rDNA), morphological (light and confocal laser scanning microscopy), and cytological (Raman microscopy) basis. Our results demonstrated that the Arctic Cylindrocystis were not of a monophyletic origin and that the studied strains clustered within two clades (tentatively named the soil and freshwater/glacier clades) and four separate lineages. Morphological data (cell size, shape, and chloroplast morphology) supported the presence of several distinct taxa among the new isolates. Moreover, the results showed that the Arctic Cylindrocystis strains were closely related to strains originating from the temperate zone, indicating high ecological versatility and successful long-distance dispersal of the genus. Large amounts of inorganic polyphosphate (polyP) grains were detected within the chloroplasts of the cultured Arctic Cylindrocystis strains, suggesting effective luxury uptake of phosphorus. Additionally, various intracellular structures were identified using Raman microscopy and cytochemical and fluorescent staining. This study represents the first attempt to combine molecular, morphological, ecological, and biogeographical data for Arctic Cylindrocystis. Our novel cytological observations partially explain the success of Cylindrocystis-like microalgae in polar regions.

Genomes of early-diverging streptophyte algae shed light on plant terrestrialization

Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.

Plant Evolution: Assembling Land Plants

Traditional evolutionary scenarios posit that land plants emerged from land plant-like relatives, the charophytes. New phylogenies suggest a closer affinity to simpler pond scum relatives, and evidence the gradual assembly of the land plant genome, revealing a phenotypic simplification from the complex ancestors envisaged by traditional scenarios.

Organellar protein multi-functionality and phenotypic plasticity in plants

With the increasing impact of climate instability on agricultural and ecological systems has come a heightened sense of urgency to understand plant adaptation mechanisms in more detail. Plant species have a remarkable ability to disperse their progeny to a wide range of environments, demonstrating extraordinary resiliency mechanisms that incorporate epigenetics and transgenerational stability. Surprisingly, some of the underlying versatility of plants to adapt to abiotic and biotic stress emerges from the neofunctionalization of organelles and organellar proteins. We describe evidence of possible plastid specialization and multi-functional organellar protein features that serve to enhance plant phenotypic plasticity. These features appear to rely on, for example, spatio-temporal regulation of plastid composition, and unusual interorganellar protein targeting and retrograde signalling features that facilitate multi-functionalization. Although we report in detail on three such specializations, involving MSH1, WHIRLY1 and CUE1 proteins in Arabidopsis, there is ample reason to believe that these represent only a fraction of what is yet to be discovered as we begin to elaborate cross-species diversity. Recent observations suggest that plant proteins previously defined in one context may soon be rediscovered in new roles and that much more detailed investigation of proteins that show subcellular multi-targeting may be warranted.

This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.

The conjugating green alga Zygnema sp. (Zygnematophyceae) from the Arctic shows high frost tolerance in mature cells (pre-akinetes)

Green algae of the genus Zygnema form extensive mats and produce large amounts of biomass in shallow freshwater habitats. Environmental stresses including freezing may perturb these mats, which usually have only annual character. To estimate the limits of survival at subzero temperatures, freezing resistance of young Zygnema sp. (strain MP2011Skan) cells and pre-akinetes was investigated. Young, 2-week-old cultures were exposed to temperatures of 0 to - 14 °C at 2-K steps, whereas 8-month-old cultures were frozen from - 10 to - 70 °C at 10-K intervals. Cell viability after freezing was determined by 0.1% auramine O vital fluorescence staining and measurements of the effective quantum yield of photosystem II (Ф_PSII). At - 8 °C, the young vegetative cells were unable to recover from severe frost damage. But temperatures even slightly below zero (- 2 °C) negatively affected the cells' physiology. Single pre-akinetes could survive even at - 70 °C, but their LT₅₀ value was - 26.2 °C. Severe freezing cytorrhysis was observed via cryo-microscopy at - 10 °C, a temperature found to be lethal for young cells. The ultrastructure of young cells appeared unchanged at - 2 °C, but severe damage to biomembranes and formation of small foamy vacuoles was observed at - 10 °C. Pre-akinetes did not show ultrastructural changes at - 20 °C; however, vacuolization increased, and gas bubbles appeared at - 70 °C. Our results demonstrate that the formation of pre-akinetes increases freezing resistance. This adaptation is crucial for surviving the harsh temperature conditions prevailing in the High Arctic in winter and a key feature in seasonal dynamics of Zygnema sp.

Adaptation to life on land at high O2 via transition from ferredoxin-to NADH-dependent redox balance

Pyruvate : ferredoxin oxidoreductase (PFO) and iron only hydrogenase ([Fe]-HYD) are common enzymes among eukaryotic microbes that inhabit anaerobic niches. Their function is to maintain redox balance by donating electrons from food oxidation via ferredoxin (Fd) to protons, generating H₂ as a waste product. Operating in series, they constitute a soluble electron transport chain of one-electron transfers between FeS clusters. They fulfil the same function—redox balance—served by two electron-transfers in the NADH- and O₂-dependent respiratory chains of mitochondria. Although they possess O₂-sensitive FeS clusters, PFO, Fd and [Fe]-HYD are also present among numerous algae that produce O₂. The evolutionary persistence of these enzymes among eukaryotic aerobes is traditionally explained as adaptation to facultative anaerobic growth. Here, we show that algae express enzymes of anaerobic energy metabolism at ambient O₂ levels (21% v/v), Chlamydomonas reinhardtii expresses them with diurnal regulation. High O₂ environments arose on Earth only approximately 450 million years ago. Gene presence/absence and gene expression data indicate that during the transition to high O₂ environments and terrestrialization, diverse algal lineages retained enzymes of Fd-dependent one-electron-based redox balance, while the land plant and land animal lineages underwent irreversible specialization to redox balance involving the O₂-insensitive two-electron carrier NADH.

The evolution of the plastid phosphate translocator family

The plastid phosphate translocators evolved in algae but diversified into several groups, which adopted different physiological functions by extensive gene duplications and losses in Streptophyta. The plastid phosphate translocators (pPT) are a family of transporters involved in the exchange of metabolites and inorganic phosphate between stroma and cytosol. Based on their substrate specificities, they were divided into four subfamilies named TPT, PPT, GPT and XPT. To analyse the occurrence of these transporters in different algae and land plant species, we identified 652 pPT genes in 101 sequenced genomes for phylogenetic analysis. The first three subfamilies are found in all species and evolved before the split of red and green algae while the XPTs were derived from the duplication of a GPT gene at the base of Streptophyta. The analysis of the intron-exon structures of the pPTs corroborated these findings. While the number and positions of introns are conserved within each subfamily, they differ between the subfamilies suggesting an insertion of the introns shortly after the three subfamilies evolved. During angiosperm evolution, the subfamilies further split into different groups (TPT1-2, PPT1-3, GPT1-6). Angiosperm species differ significantly in the total number of pPTs, with many species having only a few, while several plants, especially crops, have a higher number, pointing to the importance of these transporters for improved source-sink strength and yield. The differences in the number of pPTs can be explained by several small-scale gene duplications and losses in plant families or single species, but also by whole genome duplications, for example, in grasses. This work could be the basis for a comprehensive analysis of the molecular and physiological functions of this important family of transporters.

Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium?

Photosynthetic eukaryotes are the product of an endosymbiotic event between a eukaryotic host and a cyanobacterium that became today's plastid. A new phylogenomic study suggests that the closest relative of plastids among extant cyanobacteria is the recently discovered freshwater-dwelling Gloeomargarita lithophora.

Origin and Evolution of Core Components Responsible for Monitoring Light Environment Changes during Plant Terrestrialization

Light serves as the source of energy as well as an information signal for photosynthetic plants. During evolution, plants have acquired the ability to monitor environmental light radiation and adjust their developmental patterns to optimally utilize light energy for photosynthesis. The mechanisms of light perception and signal transduction have been comprehensively studied in past decades, mostly in a few model plants, including Arabidopsis thaliana. However, systematic analyses of the origin and evolution of core components involved in light perception and signaling are still lacking. In this study, we took advantage of the recently sequenced genomes and transcriptomes covering all the main Archaeplastida clades in the public domain to identify orthologous genes of core components involved in light perception and signaling and to reconstruct their evolutionary history. Our analyses suggested that acclimation to different distribution of light quality in new environments led to the origination of specific light signaling pathways in plants. The UVR8 (UV Resistance Locus 8) signaling pathway originated during the movement of plants from the deeper sea to shallow water and enabled plants to deal with ultraviolet B light (UV-B). After acquisition of UV-B adaptation, origination of the phytochrome signaling pathway helped plants to colonize water surface where red light became the prominent light energy source. The seedling emergence pathway, which is mediated by a combination of light and phytohormone signals that orchestrate plant growth pattern transitions, originated before the emergence of seed plants. Although cryptochromes and some key components of E3 ubiquitin ligase systems already existed before the divergence of the plant and animal kingdoms, the coevolution and optimization of light perception and downstream signal transduction components, including key transcription factors and E3 ubiquitin ligase systems, are evident during plant terrestrialization.

Glacier Algae: A Dark Past and a Darker Future

"Glacier algae" grow on melting glacier and ice sheet surfaces across the cryosphere, causing the ice to absorb more solar energy and consequently melt faster, while also turning over carbon and nutrients. This makes glacier algal assemblages, which are typically dominated by just three main species, a potentially important yet under-researched component of the global biosphere, carbon, and water cycles. This review synthesizes current knowledge on glacier algae phylogenetics, physiology, and ecology. We discuss their significance for the evolution of early land plants and highlight their impacts on the physical and chemical supraglacial environment including their role as drivers of positive feedbacks to climate warming, thereby demonstrating their influence on Earth's past and future. Four complementary research priorities are identified, which will facilitate broad advances in glacier algae research, including establishment of reliable culture collections, sequencing of glacier algae genomes, development of diagnostic biosignatures for remote sensing, and improved predictive modeling of glacier algae biological-albedo effects.

Darkening of the Greenland Ice Sheet: Fungal Abundance and Diversity Are Associated With Algal Bloom

Recent studies have highlighted the importance of ice-algal blooms in driving darkening and therefore surface melt of the Greenland Ice Sheet (GrIS). However, the contribution of fungal and bacterial communities to this microbially driven albedo reduction remains unconstrained. To address this significant knowledge gap, fungi were isolated from key GrIS surface habitats (surface ice containing varying abundance of ice algae, supraglacial water, cryoconite holes, and snow), and a combination of cultivation and sequencing methods utilized to characterize the algal-associated fungal and bacterial diversity and abundance. Six hundred and ninety-seven taxa of fungi were obtained by amplicon sequencing and more than 200 fungal cultures belonging to 46 different species were isolated through cultivation approaches. Basidiomycota dominated in surface ice and water samples, and Ascomycota in snow samples. Amplicon sequencing revealed that bacteria were characterized by a higher diversity (883 taxa detected). Results from cultivation as well as ergosterol analyses suggested that surface ice dominated by ice algae and cryoconite holes supported the highest fungal biomass (104-105 CFU/100 ml) and that many fungal taxa recognized as endophytes and plant pathogens were associated with dark ice characterized by a high abundance of ice algae. This paper significantly advances this field of research by investigating for the first time the fungal abundance and diversity associated with algal blooms causing the darkening of the GrIS. There is a strong association between the abundance and diversity of fungal species and the blooming of algae on the surface ice of the Greenland Ice Sheet.