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(A) Scatter plot of best BLASTP hit score of Chlamydomonas proteins to Arabidopsis proteins versus best BLASTP hit score of Chlamydomonas proteins to human proteins. Functional or genomic groupings are colored [see inset key in (A)]: Chlamydomonas flagellar proteome (42) high confidence set (chlamyFPhc); CiliaCut; Arabidopsis stroma plastid proteome (stromaPP); Arabidopsis thylakoid plastid proteome (thylakoidPP); eyespot proteome; GreenCut; remaining proteins are gray. (B) Chlamydomonas protein paralogs were grouped into families together with their homologs from human and Arabidopsis. The outer circle represents the proteins in Chlamydomonas, 7476 (out of 15,143 total), that fall into 6968 families. Another 7937 proteins cannot be placed in families. Counts of families (and the numbers of proteins from each species in them) with proteins from Chlamydomonas and human only, Chlamydomonas and Arabidopsis only, and Chlamydomonas and human and Arabidopsis, are shown in the inner circles and the overlap between the two inner circles, respectively. Cre, Chlamydomonas; Hsa, human; Ath, Arabidopsis.
Source publication
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying
chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were
inherited from the common ancestor of plants and animals, but lost in...
Context in source publication
Context 1
... comparison of CiliaCut proteins with proteins encoded by the Physcomitrella genome indi- cates that Physcomitrella has lost five of the outer dynein arm proteins ( Fig. 1, table S14). However, Physcomitrella contains inner dynein arm subunits IDA4 and DHC2, as well as subunits of the central microtubules, the radial spokes, and the dynein reg- ulatory complex (table S14). From this we conclude that Physcomitrella sperm flagella have a "9+2" axoneme containing inner dynein arms, central microtubules, and radial ...
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Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in...
The unicellular green alga Chlamydomonas reinhardtii is a biflagellated cell with two actin genes: one encoding a conventional actin (IDA5) and the other encoding a divergent novel actin-like protein (NAP1). Here, we probe how actin redundancy contributes to flagellar assembly. Disrupting a single actin allows complete flagellar assembly. However,...
Citations
... plantbiology.msu.edu/), and for Chlorella variabilis and Chara braunii from the NCBI database (https://www.ncbi.nlm.nih.gov/). Additionally, we downloaded genome data for Chlamydomonas reinhardtii (Merchant et al., 2007), Volvox carteri (Prochnik et al., 2010), Ostreococcus lucimarinus (Palenik et al., 2007), Amborella trichopoda (Project et al., 2013), P. patens (Lang et al., 2018), Selaginella moellendorfii (Banks et al., 2011), maize (Hirsch et al., 2016), sorghum (Sorghum bicolor) (McCormick et al., 2018) and foxtail millet (Bennetzen et al., 2012) in the JGI database (https://genome. jgi.doe.gov/). ...
The NODULE-INCEPTION-like protein (NLP) family is a plant-specific transcription factor (TF) family involved in nitrate transport and assimilation in plants, which are essential for improving plant nitrogen use efficiency. Currently, the molecular nature and evolutionary trajectory of NLP genes in the C4 model crop foxtail millet are unknown. Therefore, we performed a comprehensive analysis of NLP and molecular evolution in foxtail millet by scanning the genomes of foxtail millet and representative species of the plant kingdom. We identified seven NLP genes in the foxtail millet genome, all of which are individually and separately distributed on different chromosomes. They were not structurally identical to each other and were mainly expressed on root tissues. We unearthed two key genes (Si5G004100.1 and Si6G248300.1) with a variety of excellent characteristics. Regarding its molecular evolution, we found that NLP genes in Gramineae mainly underwent dispersed duplication, but maize NLP genes were mainly generated via WGD events. Other factors such as base mutations and natural selection have combined to promote the evolution of NLP genes. Intriguingly, the family in plants showed a gradual expansion during evolution with more duplications than losses, contrary to most gene families. In conclusion, this study advances the use of NLP genetic resources and the understanding of molecular evolution in cereals.
... Using C. rheinhardtii as a neutrophilic relative reference for polar organisms, and based on current DNA sequencing analysis, it is the most likely ancestral species that evolved from single-celled to multicellular groups. So we selected these most representative species for our next comparative genomics analysis (Merchant et al., 2007), G. pectorale and V. carteri, along with the current genome, enabled us to analyze the evolutionary relationships of species within the Volvocales family using OrthoFinder software (Figure 2A) (Emms and Kelly, 2015). This provides a reference for inferring the genome content and structure of the most recent common ancestor of all extant Volvocales, thereby improving our understanding of their origins and evolution. ...
Dunaliella salina is by far the most salt-tolerant organism and contains many active substances, including β-carotene, glycerol, proteins, and vitamins, using in the production of dried biomass or cell extracts for the biofuels, pharmaceutical formulations, food additives, and fine chemicals, especially β-carotene. We report a high-quality genome sequence of D. Salina FACHB435, which has a 472 Mb genome size, with a contig N50 of 458 Kb. A total of 30,752 protein-coding genes were predicted. The annotation results evaluated by BUSCO was shown that completeness was 91.0% and replication was 53.1%. The fragments were 6.3% and the deletions were 2.6%. Phylogenomic and comparative genomic analyses revealed that A. thaliana diverged from Volvocales about 448 million years ago, then Volvocales C. eustigma, D. salina, and other species diverged about 250 million years ago. High light could promote the accumulation of β-carotene in D. salina at a 13 d stage of culture. The enrichment of DEGs in KEGG, it notes that the predicted up-regulated genes of carotenoid metabolic pathway include DsCrtB, DsPDS, DsZ-ISO, DsZDS, DsCRTISO, DsLUT5, DsCrtL-B, and DsCCD8, while the predicted down-regulated genes include DsCrtF, and DsLUT1. The four genes that were both up-regulated and down-regulated were DsZEP, DsCrtR-b, DsCruA/P and DsCrtZ 4. The research results can provide scientific basis for the industrialization practice of D. salina.
... Studying this organism offers great opportunities to look into how flagella coordinate with each other and how such coordination helps facilitate targeted steering. C. reinhardtii has a symmetric cell body and two near-identical flagella inherited from the common ancestors of land plants and animals (Merchant et al., 2007). It swims by beating its two flagella synchronously and is capable of photo-and chemotaxis (Rüffer and Nultsch, 1991;Choi et al., 2016). ...
Eukaryotes swim with coordinated flagellar (ciliary) beating and steer by fine-tuning the coordination. The model organism for studying flagellate motility, Chlamydomonas reinhardtii, employs synchronous, breaststroke-like flagellar beating to swim, and it modulates the beating amplitudes differentially to steer. This strategy hinges on both inherent flagellar asymmetries (e.g. different response to chemical messengers) and such asymmetries being effectively coordinated in the synchronous beating. In C. reinhardtii, the synchrony of beating is known to be supported by a mechanical connection between flagella; however, how flagellar asymmetries persist in the synchrony remains elusive. For example, it has been speculated for decades that one flagellum leads the beating, as its dynamic properties (i.e. frequency, waveform, etc.) appear to be copied by the other one. In this study, we combine experiments, computations, and modeling efforts to elucidate the roles played by each flagellum in synchronous beating. With a non-invasive technique to selectively load each flagellum, we show that the coordinated beating essentially only responds to load exerted on the cis flagellum; and that such asymmetry in response derives from a unilateral coupling between the two flagella. Our results highlight a distinct role for each flagellum in coordination and have implication for biflagellates' tactic behaviors. Editor's evaluation This important manuscript investigates how the two flagella of C. reinhardtii, which have inherently different dynamic properties, synchronize their beating. Through careful, non-invasive experiments, the authors help the field to understand the mechanisms responsible for this synchronization, arguing that these mechanisms are due to unilateral coupling between the two flagella. The data are convincing, and the conclusion about unilateral coupling has been strengthened by additional analysis during revision.
... In the past 70 years, this species has been developed into a powerful and widely used model system to study processes such as photosynthesis and cell motility, and it has advanced our understanding of cell organelles like cilia and pyrenoid (Findinier & Grossman, 2023;Salom e & Merchant, 2019;Sasso et al., 2018). Efficient genetic tools including genome editing with CRISPR technology (Akella et al., 2021;Ferenczi et al., 2017;Shin et al., 2016), a large library of mapped mutants (Li et al., 2019), as well as a fully sequenced genome (Craig et al., 2022;Merchant et al., 2007), further enable the successful utilization of this alga for basic and applied research. ...
... Conserved elements with a possible enhancer function were predicted in the intergenic regions of three histone H3/H4 and H2A/H2B gene pairs before a genome sequence was available (Fabry et al., 1995). Since then, 32 H3/H4 histone gene pairs and 27 H2A/H2B gene pairs have been annotated (Craig et al., 2022;Merchant et al., 2007). Together with the expression patterns throughout the cell cycle (Strenkert et al., 2019;Table S1), this genome sequence enables a more reliable identification of activating CREs with conserved sequences and positions relative to the TSS. ...
Regulation of gene expression in eukaryotes is controlled by cis ‐regulatory modules (CRMs). A major class of CRMs are enhancers which are composed of activating cis ‐regulatory elements (CREs) responsible for upregulating transcription. To date, most enhancers and activating CREs have been studied in angiosperms; in contrast, our knowledge about these key regulators of gene expression in green algae is limited. In this study, we aimed at characterizing putative activating CREs/CRMs from the histone genes of the unicellular model alga Chlamydomonas reinhardtii . To test the activity of four candidates, reporter constructs consisting of a tetramerized CRE, an established promoter, and a gene for the mCerulean3 fluorescent protein were incorporated into the nuclear genome of C. reinhardtii , and their activity was quantified by flow cytometry. Two tested candidates, E upstr and E hist cons , significantly upregulated gene expression and were characterized in detail. E upstr , which originates from highly expressed genes of C. reinhardtii , is an orientation‐independent CRE capable of activating both the RBCS2 and β2‐tubulin promoters. E hist cons , which is a CRM from histone genes of angiosperms, upregulates the β2‐tubulin promoter in C. reinhardtii over a distance of at least 1.5 kb. The octamer motif present in E hist cons was identified in C. reinhardtii and the related green algae Chlamydomonas incerta , Chlamydomonas schloesseri , and Edaphochlamys debaryana , demonstrating its high evolutionary conservation. The results of this investigation expand our knowledge about the regulation of gene expression in green algae. Furthermore, the characterized activating CREs/CRMs can be applied as valuable genetic tools.
... The genus Chlamydomonas currently consists of several hundred species, but it is highly polyphyletic [7,8]. Chlamydomonas reinhardtii is a well-established model system for examining photosynthesis, physiology, metabolism and the structure and function of flagella [3,4,9]. However, most contemporary laboratory strains of C. reinhardtii, including those used in the work described here, are derived from a single zygote isolated from a potato field in Massachusetts in 1945 [3,4]. ...
Core chlorophytes possess glycerol-3-phosphate dehydrogenases (GPDs) with an unusual bidomain structure, consisting of a glycerol-3-phosphate phosphatase (GPP) domain fused to canonical GPD domains. These plastid-localized enzymes have been implicated in stress responses, being required for the synthesis of glycerol under high salinity and triacylglycerols under nutrient deprivation. However, their regulation under varying environmental conditions is poorly understood. C. reinhardtii transgenic strains expressing constitutively bidomain GPD2 did not accumulate glycerol or triacylglycerols in the absence of any environmental stress. Although the glycerol contents of both wild type and transgenic strains increased significantly upon exposure to high salinity, cycloheximide, an inhibitor of cytoplasmic protein synthesis, abolished this response in the wild type. In contrast, GPD2 transgenic strains were still capable of glycerol accumulation when cultured in medium containing cycloheximide and NaCl. Thus, the pre-existing GPD2 protein appears to become activated for glycerol synthesis upon salt stress. Interestingly, staurosporine, a non-specific inhibitor of protein kinases, prevented this post-translational GPD2 protein activation. Structural modeling analyses suggested that substantial conformational rearrangements, possibly triggered by high salinity, may characterize an active GPD2 GPP domain. Understanding this mechanism(s) may provide insights into the rapid acclimation responses of microalgae to osmotic/salinity stress.
... Subsequently, we employed the 'chlorella gene model' to train Augustus v. 3.3 [54]. To identify protein-coding genes, we utilized the MAKER2 pipeline [55], which integrated the gene models predicted from GeneMark-ES and Augustus, as well as the protein sequences from four closely related organisms: Chlamydomonas reinhardtii (Gen-Bank accession: GCF_000002595.2) [56], Chlorella variabilis (GCF_000147415.1) [57], Chlorella sorokiniana strain 1602 (GCA_002245835.2) [58], and Micractinium conductrix (GCA_002245815.2) [58]. ...
Background
Centromeres play a crucial and conserved role in cell division, although their composition and evolutionary history in green algae, the evolutionary ancestors of land plants, remains largely unknown.
Results
We constructed near telomere-to-telomere (T2T) assemblies for two Trebouxiophyceae species, Chlorella sorokiniana NS4-2 and Chlorella pyrenoidosa DBH, with chromosome numbers of 12 and 13, and genome sizes of 58.11 Mb and 53.41 Mb, respectively. We identified and validated their centromere sequences using CENH3 ChIP-seq and found that, similar to humans and higher plants, the centromeric CENH3 signals of green algae display a pattern of hypomethylation. Interestingly, the centromeres of both species largely comprised transposable elements, although they differed significantly in their composition. Species within the Chlorella genus display a more diverse centromere composition, with major constituents including members of the LTR/Copia, LINE/L1, and LINE/RTEX families. This is in contrast to green algae including Chlamydomonas reinhardtii, Coccomyxa subellipsoidea, and Chromochloris zofingiensis, in which centromere composition instead has a pronounced single-element composition. Moreover, we observed significant differences in the composition and structure of centromeres among chromosomes with strong collinearity within the Chlorella genus, suggesting that centromeric sequence evolves more rapidly than sequence in non-centromeric regions.
Conclusions
This study not only provides high-quality genome data for comparative genomics of green algae but gives insight into the composition and evolutionary history of centromeres in early plants, laying an important foundation for further research on their evolution.
... Although they encompass both prokaryotes (cyanobacteria) and eukaryotes ("true" microalgae), they will be collectively referred to as microalgae in the present review [6]. Microalgae such as the model Chlamydomonas reinhardtii are widely studied to improve our understanding of key plant functions such as chloroplast-based photosynthesis and nutrient assimilation, and the structure and function of the eukaryotic flagella [7][8][9][10]. In addition, due to their physiology and biochemistry, significant research is focusing on the development of microalgae-based environmental biotechnologies for food and high-value molecules production, biofuels generation, wastewater treatment and nutrient recovery [11][12][13][14]. ...
... With a wide range of applications, these technologies have considerably accelerated the rate of discoveries and provided a leap forward in fundamental and applied research. For example, the sequencing and study of the C. reinhardtii genome in 2007 unraveled the evolution of the eukaryotic flagellum and plastid [7]. In the past decade, ...
... C. reinhardtii is the first microalga to have been sequenced [7]. Consequently, the availability of extensive resources, such as genetic and proteomic databases, mutant collections and the development of protocols for genetic modifications, make it an organism of choice for fundamental research [8]. ...
Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field.
... Genomic resources have been established for several groups of microalgae, notably Chlamydomonas, Nannochloropsis, and diatoms. This availability of genomic data has provided valuable insights into the genetic makeup and molecular mechanisms of these microalgae species (Armbrust et al., 2012;Gong et al., 2020;Merchant et al., 2010). Comparative genomics studies have played a crucial role in investigating the evolutionary connections between different microalgal species, identifying expansions or contractions in gene families, and pinpointing conserved regions shared among diverse microalgal taxa. ...
... Natural diversity in microalgae and optimization techniques of growth and bioproductivity also play an important role in strain improvement towards enhancing stress tolerance and production of high added value compounds. the first to be published in 2004 (Matsuzaki et al., 2004), and although Chlamydomonas reinhardtii, a single-celled flagellate freshwater green alga, is one of the most researched species (Mishra et al., 2019) its genome was published only later in 2007 (Merchant et al., 2010). ...
... Several diatom genes have already been studied in the literature (Kim Tiam et al. 2018;Moisset et al. 2015) and others were selected from the complete sequenced genome of N. palea which was obtained collaboratively. Tests have also been carried out with C. reinhardtii, whose complete genome has been sequenced and is available in databases (Blaby et al. 2014;Merchant et al. 2007). All selected genes could not be studied for both species due to either unavailability in the data banks or to the absence of functional primers. ...
... Both species studied in this work are unicellular algae, but rather far apart in terms of phylogeny. They are indeed from different families: Chlorophyta for the green alga C. reinhardtii (Merchant et al. 2007), while (Bagmet et al. 2020). They also have a number of morphological differences such as size and shape: C. reinhardtii is an ellipsoid of around 3 to 25 µm (Harris 2008), whereas the diatom is a pennate species with length estimated between 12 and 42 µm (Kociolek 2011). ...
Platinum group element levels have increased in natural aquatic environments in the last few decades, in particular as a consequence of the use of automobile catalytic converters on a global scale. Concentrations of Pt over tens of μg L⁻¹ have been observed in rivers and effluents. This raises questions regarding its possible impacts on aquatic ecosystems, as Pt natural background concentrations are extremely low to undetectable. Primary producers, such as microalgae, are of great ecological importance, as they are at the base of the food web. The purpose of this work was to better understand the impact of Pt on a cellular level for freshwater unicellular algae. Two species with different characteristics, a green alga C. reinhardtii and a diatom N. palea, were studied. The bioaccumulation of Pt as well as its effect on growth were quantified. Moreover, the induction or repression factors of 16 specific genes were determined and allowed for the determination of possible intracellular effects and pathways of Pt. Both species seemed to be experiencing copper deficiency as suggested by inductions of genes linked to copper transporters. This is an indication that Pt might be internalized through the Cu(I) metabolic pathway. Moreover, Pt could possibly be excreted using an efflux pump. Other highlights include a concentration-dependent negative impact of Pt on mitochondrial metabolism for C. reinhardtii which is not observed for N. palea. These findings allowed for a better understanding of some of the possible impacts of Pt on freshwater primary producers, and also lay the foundations for the investigation of pathways for Pt entry at the base of the aquatic food web.
Graphical Abstract
... Machin's study thereby effectively refuted the first of the two hypotheses for flagellar beating, a result later confirmed by experiments that culminated in the identification of dynein as the molecular motor responsible for force generation inside these filaments [7][8][9]. The cilium is now known to be a remarkably conserved organelle, found in almost all eukaryotes (Gibbons and Rowe [8], Mitchell [10], Lindemann [11], Merchant et al. [12] and Fig. 1). It is now well-established that ciliary beating is universally driven by distributed activity rather than localised actuation. ...
