A Chlorophyte Alga Utilizes Alternative Electron Transport for Primary Photoprotection
Not Available
Ware, Maxwell A.↗
SEARCH · Search NASA
Results for “Chlorophytes”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Integrating phytoplankton pigment and DNA meta-barcoding observations to determine phytoplankton composition in the coastal ocean
Quantifying phytoplankton composition is critical to predicting marine ecosystem structure and function. DNA meta-barcoding and high-performance liquid chromatography (HPLC) pigment analysis are two widely used methods for assessing phytoplankton composition; however, comparing their performance has been done only rarely. Here, we integrate DNA meta-barcoding and HPLC pigment observations to determine eukaryotic phytoplankton composition in the Santa Barbara Channel, California. We find that both methods identify the same four dominant eukaryotic phytoplankton taxa (diatoms, dinoflagellates, chlorophytes, and prymnesiophytes), but inter- and intra-lineage variability in biomarker pigmentation (associated with both a lack of taxonomic specificity of biomarker pigments and intrinsic differences in accessory pigmentation) drives substantial disagreement between the methods. Covariation network analysis circumvents this disagreement and reveals that diverse assemblages of phytoplankton and other protists covary with distinct suites of biomarker pigments. Our results highlight the strengths and weaknesses of each method in characterizing phytoplankton composition and reveal novel insights into phytoplankton physiology that could only be gained by integrating the two methods. Finally, we suggest a path to monitor eukaryotic plankton communities on unprecedented spatiotemporal scales based on the covariation of unique phytoplankton and protistan assemblages with remotely sensible phytoplankton pigment concentrations.
59 BASIC BIOLOGICAL SCIENCES↗
Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii , Arabidopsis thaliana , and Setaria viridis
Abstract The rapid accumulation of sequenced plant genomes in the past decade has outpaced the still difficult problem of genome‐wide protein‐coding gene annotation. A substantial fraction of protein‐coding genes in all plant genomes are poorly annotated or unannotated and remain functionally uncharacterized. We identified unannotated proteins in three model organisms representing distinct branches of the green lineage (Viridiplantae): Arabidopsis thaliana (eudicot), Setaria viridis (monocot), and Chlamydomonas reinhardtii (Chlorophyte alga). Using similarity searching, we identified a subset of unannotated proteins that were conserved between these species and defined them as Deep Green proteins. Bioinformatic, genomic, and structural predictions were performed to begin classifying Deep Green genes and proteins. Compared to whole proteomes for each species, the Deep Green set was enriched for proteins with predicted chloroplast targeting signals predictive of photosynthetic or plastid functions, a result that was consistent with enrichment for daylight phase diurnal expression patterning. Structural predictions using AlphaFold and comparisons to known structures showed that a significant proportion of Deep Green proteins may possess novel folds. Though only available for three organisms, the Deep Green genes and proteins provide a starting resource of high‐value targets for further investigation of potentially new protein structures and functions conserved across the green lineage.
59 BASIC BIOLOGICAL SCIENCES↗
Chapter 5: Methods for Algal Protein Isolation and Proteome Analysis
Microalgae present promising feedstocks to produce renewable fuel and chemical intermediates, in part due to high storage carbon flux capacity to triacylglycerides or storage carbohydrates upon nutrient deprivation. However, the mechanism(s) governing deprivation-mediated carbon partitioning remain to be fully elucidated, limiting targeted strain engineering strategies in algal biocatalysts. Though genomic and transcriptomic analyses offer key insights into these mechanisms, active post-transcriptional regulatory mechanisms, ubiquitous in many microalgae, necessitate proteomic and post-translational (e.g., phospho- and nitroso-proteomic) analyses to more completely evaluate algal responsiveness to nutrient deprivation. Herein, we describe methods for isolating total algal protein and conducting proteomic, phosphoproteomic, and nitrosoproteomic analyses. We focus on methods deployed for the chlorophyte, Chlorella vulgaris, a model oleaginous alga with high flux to renewable fuel and chemical precursors.
BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗
Co-locality to co-functionality: Eukaryotic gene neighborhoods as a resource for function
Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for non model organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved Proximal Orthologous Gene (POG) pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte-chlorophyte split, 1,000 million years ago. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid (MAA), "sunscreen", neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene (PGK). Mutants of the ArsJ-like transporter and PGK-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.
59 BASIC BIOLOGICAL SCIENCES↗
Antarctic lake phytoplankton and bacteria from near‐surface waters exhibit high sensitivity to climate‐driven disturbance
Abstract The McMurdo Dry Valleys (MDVs), Antarctica, represent a cold, desert ecosystem poised on the threshold of melting and freezing water. The MDVs have experienced dramatic signs of climatic change, most notably a warm austral summer in 2001–2002 that caused widespread flooding, partial ice cover loss and lake level rise. To understand the impact of these climatic disturbances on lake microbial communities, we simulated lake level rise and ice‐cover loss by transplanting dialysis‐bagged communities from selected depths to other locations in the water column or to an open water perimeter moat. Bacteria and eukaryote communities residing in the surface waters (5 m) exhibited shifts in community composition when exposed to either disturbance, while microbial communities from below the surface were largely unaffected by the transplant. We also observed an accumulation of labile dissolved organic carbon in the transplanted surface communities. In addition, there were taxa‐specific sensitivities: cryptophytes and Actinobacteria were highly sensitive particularly to the moat transplant, while chlorophytes and several bacterial taxa increased in relative abundance or were unaffected. Our results reveal that future climate‐driven disturbances will likely undermine the stability and productivity of MDV lake phytoplankton and bacterial communities in the surface waters of this extreme environment.
54 ENVIRONMENTAL SCIENCES↗
The Land–Sea Connection: Insights Into the Plant Lineage from a Green Algal Perspective
The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems—the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages.
Plant Sciences↗
divergence in basal transcriptomes of "Wild Type" Chlamydomonas reinhardtii strains
This is a study to compare the basal transcriptomes of several widely used laboratory strains of the Chlorophyte alga, Chlamydomonas reinhardtii. Given that there is a high degree of genetic diversity among the closely-related laboratory strains, we wished to examine how much variation there is at the transcriptome level. A panel of WT strains (CC-124, CC-125, CC-1009, CC-1690, CC-1691), all believed to be descended from a single zygospore isolated in 1945, were chosen based on their representing the oldest lineages among the standard laboratory strains. Additionally, CC-4532, which was the source for the current (v6) reference assembly, and CC-4533, which is the initial parental strain of the CLiP library collection of mutant strains, were also included in this study based on their significance to the Chlamydomonas community. All strains were grown in liquid cultures under identical, mixotrophic conditions (light + acetate) to mid-log phase before collecting mRNA for RNA-Seq analysis. Overall design: Pre-cultures of each strain (CC-124, CC-125, CC-1009, CC-1690, CC-1691, CC-4532, and CC-4533) were used to innoculate flasks of Tris-Acetate-Phosphate (TAP) media supplemented with Kropat's trace metals at a concentration of 1.5 x 10^4 cells/mL. Flasks were placed on a shaking platform at 180 RPM under 50-70 µmol x m^-2 x s^-1 of light. Cultures were grown until they reached ~2-3 x 10^6 cells/mL, about three days, before total RNA was collected and subjected RNA-Seq analysis.
Source record↗
Gene Expression in Dunaliella salina Bardawil +/- Iron
Dunaliella salina Bardawil (also known as Dunaliella bardawil) is an extremophilic, unicellular green alga from the Chlorophyte lineage. D. salina is found in hypersaline environments where it can tolerate extremes of heat, light, pH, and up to saturating concentrations of salt. The D. salina Bardawil isolate (UTEX LB 2538) was found in a salt pond near the Bardawil Lagoon on the Sinai peninsula in 1976. This isolate of D. salina is the richest natural source of beta-carotene, a highly valuable commercial product. This accession includes an RNA-Seq analysis of D. salina Bardawil cultures grown in iron-replete (1.5 µM) or iron-deficient (0 µM) media.
54 ENVIRONMENTAL SCIENCES↗
Gene Expression in Dunaliella tertiolecta +/- Iron
Dunaliella tertiolecta is an extremophilic, green alga from the Chlorophyte lineage. It is found in coastal marine environments around the world. D. tertiolecta can tolerate extremes of heat, light, pH, and salinity. D. tertiolecta is under development for the production biofuels and other bioproducts because it can produce large quantities of neutral lipids, and it can be grown in open raceway ponds using only the inputs of seawater and sunlight. This isolate of D. tertiolecta (UTEX LB 999) was found in Oslofjord, Norway in 1938. This accession includes an RNA-Seq analysis of D. tertiolecta cultures grown in iron-replete (1.5 µM) or iron-deficient (0 µM) media.
54 ENVIRONMENTAL SCIENCES↗
Genome-Wide Analysis of Sorghum GT47 Family Reveals Functional Divergences of MUR3-Like Genes
Sorghum (Sorghum bicolor) is an important bioenergy crop. Its biomass mainly consists of the cellulosic and non-cellulosic polysaccharides, both which can be converted to biofuels. The biosynthesis of non-cellulosic polysaccharides involves several glycosyltransferases (GT) families including GT47. However, there was no systemic study on GT47 family in sorghum to date. Here, we identified 39 sorghum GT47 family members and showed the functional divergences of MURUS3 (MUR3) homologs. Sorghum GT47 proteins were phylogenetically clustered into four distinct subfamilies. Within each subfamily, gene structure was relatively conserved between the members. Ten gene pairs were identified from the 39 GT47 genes, of which two pairs might be originated from tandem duplication. 25.6% (10/39) of sorghum GT47 genes were homologous to Arabidopsis MUR3, a xyloglucan biosynthesis gene in primary cell walls. SbGT47_2, SbGT47_7, and SbGT47_8, three most homologous genes of MUR3, exhibited different tissue expression patterns and were selected for complementation into Arabidopsis mur3-3. Physiological and cell wall analyses showed that SbGT47_2 and SbGT47_7 may be two functional xyloglucan galactosyltransferases in sorghum. Further studies found that MUR3-like genes are widely present in the seed plants but not in the chlorophytic alga Chlamydomonas reinhardtii. Our results provide novel information for evolutionary analysis and functional dissection of sorghum GT47 family members.
59 BASIC BIOLOGICAL SCIENCES↗
Gamete expression of TALE class HD genes activates the diploid sporophyte program in Marchantia polymorpha
Eukaryotic life cycles alternate between haploid and diploid phases and in phylogenetically diverse unicellular eukaryotes, expression of paralogous homeodomain genes in gametes primes the haploid-to-diploid transition. In the unicellular chlorophyte alga Chlamydomonas, KNOX and BELL TALE-homeodomain genes mediate this transition. We demonstrate that in the liverwort Marchantia polymorpha, paternal (sperm) expression of three of five phylogenetically diverse BELL genes, MpBELL234, and maternal (egg) expression of both MpKNOX1 and MpBELL34 mediate the haploid-to-diploid transition. Loss-of-function alleles of MpKNOX1 result in zygotic arrest, whereas a loss of either maternal or paternal MpBELL234 results in variable zygotic and early embryonic arrest. Expression of MpKNOX1 and MpBELL34 during diploid sporophyte development is consistent with a later role for these genes in patterning the sporophyte. These results indicate that the ancestral mechanism to activate diploid gene expression was retained in early diverging land plants and subsequently co-opted during evolution of the diploid sporophyte body.
59 BASIC BIOLOGICAL SCIENCES↗
Description of a novel extremophile green algae, Chlamydomonas pacifica , and its potential as a biotechnology host
We present the comprehensive characterization of a newly identified microalga, Chlamydomonas pacifica , originally isolated from a soil sample in San Diego, CA, USA. This species showcases remarkable biological versatility, including a broad pH range tolerance (6–11.5), high thermal tolerance (up to 42 °C), and salinity resilience (up to 2 % NaCl). Its amenability to genetic manipulation and sexual reproduction via mating, particularly between the two opposing strains CC-5697 & CC-5699, now publicly available through the Chlamydomonas Resource Center, underscores its potential as a biotechnological chassis. The biological assessment of C. pacifica revealed versatile metabolic capabilities, including diverse nitrogen assimilation capability, motility and phototaxis. Genomic and transcriptomic analyses identified 17,829 genes within a 121 Mb genome, featuring a GC content of 61 %. The codon usage of C. pacifica closely mirrors that of C. reinhardtii , indicating a conserved genetic architecture that supports a trend in codon preference with minor variations. Phylogenetic analyses position C. pacifica within the core-Reinhardtinia clade yet distinct from known Volvocales species. The lipidomic data revealed an abundance of triacylglycerols (TAGs), promising for biofuel applications and lipids for health-related benefits. Our investigation lays the groundwork for exploiting C. pacifica in biotechnological applications, from biofuel generation to synthesizing biodegradable plastics, positioning it as a versatile host for future bioengineering endeavors.
Alkali tolerant↗
From economy to luxury: Copper homeostasis in Chlamydomonas and other algae
Not Available
59 BASIC BIOLOGICAL SCIENCES↗