scholarly journals Circadian protein regulation in the green lineage I. A phospho-dawn anticipates light onset before proteins peak in daytime

2018 ◽  
Author(s):  
Zeenat B. Noordally ◽  
Matthew M. Hindle ◽  
Sarah F. Martin ◽  
Daniel D. Seaton ◽  
T. Ian Simpson ◽  
...  
Keyword(s):  
Phosphorylation Sites ◽  
Transcriptome Data ◽  
Light Onset ◽  
Free Living ◽  
Dynamic Regulation ◽  
Protein Levels ◽  
Ostreococcus Tauri ◽  
Shotgun Mass Spectrometry ◽  
Limited Change ◽  
Green Lineage

AbstractDaily light-dark cycles (LD) drive dynamic regulation of plant and algal transcriptomesviaphotoreceptor pathways and 24-hour, circadian rhythms. Diel regulation of protein levels and modifications has been less studied.Ostreococcus tauri, the smallest free-living eukaryote, provides a minimal model proteome for the green lineage. Here, we compare transcriptome data under LD to the algal proteome and phosphoproteome, assayed using shotgun mass-spectrometry. Under 10% of 855 quantified proteins were rhythmic but two-thirds of 860 phosphoproteins showed rhythmic modification(s). Most rhythmic proteins peaked in the daytime. Model simulations showed that light-stimulated protein synthesis largely accounts for this distribution of protein peaks. Prompted by apparently dark-stable proteins, we sampled during prolonged dark adaptation, where stable RNAs and very limited change to the proteome suggested a quiescent, cellular “dark state”. In LD, acid-directed and proline-directed protein phosphorylation sites were regulated in antiphase. Strikingly, 39% of rhythmic phospho-sites reached peak levels just before dawn. This anticipatory phosphorylation is distinct from light-responsive translation but consistent with plant phosphoprotein profiles, suggesting that a clock-regulated phospho-dawn prepares green cells for daytime functions.

scholarly journals The aphelid-like phagotrophic origins of fungi

2017 ◽  
Author(s):  
Guifre Torruella ◽  
Xavier Grau-Bove ◽  
David Moreira ◽  
Sergey A Karpov ◽  
John Burns ◽  
...  
Keyword(s):  
Cell Wall ◽  
Metabolic Pathways ◽  
Phylogenetic Analyses ◽  
Algal Cell ◽  
Rrna Genes ◽  
Transcriptome Data ◽  
Free Living ◽  
Statistical Support ◽  
Phylogenomic Analyses ◽  
Protein Datasets

Aphelids are poorly known phagotrophic parasites of algae whose life cycle and morphology resemble those of the widely diverse parasitic rozellids (Cryptomycota, Rozellomycota). In previous phylogenetic analyses of RNA polymerase and rRNA genes, aphelids and rozellids formed a monophyletic group together with the extremely reduced parasitic Microsporidia, named Opisthosporidia, which was sister to Fungi. However, the statistical support for that group was always moderate. We generated the first transcriptome data for one aphelid species, Paraphelidium tribonemae. In-depth multi-gene phylogenomic analyses using various protein datasets place aphelids as the closest relatives of Fungi to the exclusion of rozellids and Microsporidia. In contrast with the comparatively reduced Rozella allomycis genome, we infer a rich, free-living-like aphelid proteome, including cellulases likely involved in algal cell-wall penetration, enzymes involved in chitin biosynthesis and several metabolic pathways. Our results suggest that Fungi evolved from a complex aphelid-like ancestor that lost phagotrophy and became osmotrophic.

scholarly journals Optimizing bioreactor growth of the smallest eukaryote

2018 ◽  
Author(s):  
Chuck R. Smallwood ◽  
Eric A. Hill ◽  
William Chrisler ◽  
Jory Brookreson ◽  
James E. Evans
Keyword(s):  
Growth Conditions ◽  
Energy Resources ◽  
Total Biomass ◽  
Nutrient Requirements ◽  
Free Living ◽  
Nutrient Pools ◽  
Photosynthetic Organisms ◽  
Ostreococcus Tauri ◽  
Phototrophic Growth ◽  
Doubling Times

AbstractPhotosynthetic organisms are adept at circumventing nutrient deprivation. Microalgae in particular present novel adaptations to nutrient and light starvation since they can scavenge external and internal nutrient pools to redistribute energy resources for survival. In this report, a turbidostatic photobioreactor was used to characterize environmental conditions and nutrient requirements for cultures of the smallest free-living eukaryote Ostreococcus tauri. Optimized growth conditions were identified that enable 4-times faster phototrophic growth-rates while increasing total biomass 10-fold. By achieving phototrophic doubling times shorter than 6 hours, these results highlight the potential of this smallest eukaryote for future industrial bioproduct applications.

scholarly journals Integrated systems biology and imaging of the smallest free-living eukaryote Ostreococcus tauri

2018 ◽  
Author(s):  
Chuck R. Smallwood ◽  
Jian-Hua Chen ◽  
Neeraj Kumar ◽  
William Chrisler ◽  
Samuel O. Purvine ◽  
...  
Keyword(s):  
Biochemical Analysis ◽  
Starch Granule ◽  
Stimulated Raman Scattering ◽  
Nitrogen Depletion ◽  
Free Living ◽  
X Ray ◽  
Cellular Energy ◽  
Ostreococcus Tauri ◽  
Significant Expression ◽  
Long Chain

AbstractOstreococcus tauri is an ancient phototrophic microalgae that possesses favorable genetic and cellular characteristics for reductionist studies probing biosystem design and dynamics. Here multimodal bioimaging and multi-omics techniques were combined to interrogate O. tauri cellular changes in response to variations in bioavailable nitrogen and carbon ratios. Confocal microscopy, stimulated Raman scattering, and cryo-soft x-ray tomography revealed whole cell ultrastructural dynamics and composition while proteomic and lipidomic profiling captured changes at the molecular and macromolecular scale.Despite several energy dense long-chain triacylglycerol lipids showing more than 40-fold higher abundance under N deprivation, only a few proteins directly associated with lipid biogenesis showed significant expression changes. However, the entire pathway for starch granule biosynthesis was highly upregulated suggesting much of the cellular energy is preferentially directed towards starch over lipid accumulation. Additionally, three of the five most downregulated and five of the ten most upregulated proteins during severe nitrogen depletion were unnamed protein products that warrant additional biochemical analysis and functional annotation to control carbon transformation dynamics in this smallest eukaryote.

scholarly journals A Quantitative Proteome Map of the Human Body

2019 ◽  
Author(s):  
Lihua Jiang ◽  
Meng Wang ◽  
Shin Lin ◽  
Ruiqi Jian ◽  
Xiao Li ◽  
...  
Keyword(s):  
Protein Detection ◽  
Integrated Analysis ◽  
Protein Signaling ◽  
Transcriptome Data ◽  
Tissue Specific ◽  
Protein Levels ◽  
Metabolism Regulation ◽  
Regulatory Processes ◽  
Specific Proteins ◽  
Normal Human

AbstractDetermining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from 12,627 genes across 32 normal human tissue types prepared by the GTEx project. Known and new tissue specific or enriched proteins (5,499) were identified and compared to transcriptome data. Many ubiquitous transcripts are found to encode highly tissue specific proteins. Discordance in the sites of RNA expression and protein detection also revealed potential sites of synthesis and action of protein signaling molecules. Overall, these results provide an extraordinary resource, and demonstrate that understanding protein levels can provide insights into metabolism, regulation, secretome, and human diseases.SummaryQuantitative proteome study of 32 human tissues and integrated analysis with transcriptome data revealed that understanding protein levels could provide in-depth knowledge to post transcriptional or translational regulations, human metabolism, secretome, and diseases.

scholarly journals Delayed Protein Changes During Seed Germination

2021 ◽  
Vol 12 ◽  
Author(s):  
Bing Bai ◽  
Niels van der Horst ◽  
Jan H. Cordewener ◽  
Antoine H. P. America ◽  
Harm Nijveen ◽  
...  
Keyword(s):  
Seed Germination ◽  
Mrna Translation ◽  
Protein Abundance ◽  
Transcriptome Data ◽  
Protein Levels ◽  
Polysomal Mrna ◽  
Mrna Length ◽  
Germinating Seeds ◽  
Important Physiological Process ◽  
Time Point

Over the past decade, ample transcriptome data have been generated at different stages during seed germination; however, far less is known about protein synthesis during this important physiological process. Generally, the correlation between transcript levels and protein abundance is low, which strongly limits the use of transcriptome data to accurately estimate protein expression. Polysomal profiling has emerged as a tool to identify mRNAs that are actively translated. The association of the mRNA to the polysome, also referred to as translatome, provides a proxy for mRNA translation. In this study, the correlation between the changes in total mRNA, polysome-associated mRNA, and protein levels across seed germination was investigated. The direct correlation between polysomal mRNA and protein abundance at a single time-point during seed germination is low. However, once the polysomal mRNA of a time-point is compared to the proteome of the next time-point, the correlation is much higher. 35% of the investigated proteome has delayed changes at the protein level. Genes have been classified based on their delayed protein changes, and specific motifs in these genes have been identified. Moreover, mRNA and protein stability and mRNA length have been found as important predictors for changes in protein abundance. In conclusion, polysome association and/or dissociation predicts future changes in protein abundance in germinating seeds.

scholarly journals Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

2006 ◽  
Vol 103 (31) ◽  
pp. 11647-11652 ◽  
Author(s):  
E. Derelle ◽  
C. Ferraz ◽  
S. Rombauts ◽  
P. Rouze ◽  
A. Z. Worden ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Free Living ◽  
Ostreococcus Tauri

scholarly journals MUTYH Deficiency Is Associated with Attenuated Pulmonary Fibrosis in a Bleomycin-Induced Model

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Qingmin Sun ◽  
Jingwen Chen ◽  
Lizhi Xu ◽  
Jiaqi Kang ◽  
Xin Wu ◽  
...  
Keyword(s):  
Pulmonary Fibrosis ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Unknown Etiology ◽  
Mitochondrial Dynamic ◽  
Pulmonary Tissue ◽  
Dynamic Regulation ◽  
Protein Levels ◽  
Age Related ◽  
Mutyh Gene

Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible lung disease of unknown etiology with limited survival. IPF incidence and prevalence increase significantly with aging, which is associated with an age-related accumulation of oxidative DNA damage. The Mutyh gene is involved in the base excision repair (BER) system, which is critical for repairing the misincorporated adenine that is opposite to the oxidized guanine base, 8-oxoguanine, and maintaining the fidelity of DNA replication. We used Mutyh knockout mice and a bleomycin-induced pulmonary fibrosis model to test the effect of MUTYH deficiency on lesion progression. Unexpectedly, a much less severe lesion of pulmonary fibrosis was observed in Mutyh-/- than in Mutyh+/+mice, which was supported by assay on protein levels of TGF-β1 and both fibrotic markers, α-SMA and Vimentin, in pulmonary tissues of the model animals. Mechanically, MUTYH deficiency prevented the genomic DNA of pulmonary tissue cells from the buildup of single-strand breaks (SSBs) of DNA and maintained the integrity of mtDNA. Furthermore, increased mitochondrial dynamic regulation and mitophagy were detected in pulmonary tissues of the bleomycin-induced Mutyh-/- model mice, which could reduce the pulmonary epithelial cell apoptosis. Our results suggested that MUTYH deficiency could even induce protective responses of pulmonary tissue under severe oxidative stress.

scholarly journals Dynamic regulation of small RNAs in anthocyanin accumulation during blueberry fruit maturation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaobai Li ◽  
Yan Hong ◽  
Aaron Jackson ◽  
Fangqi Guo
Keyword(s):  
Transcriptional Regulation ◽  
Small Rnas ◽  
Indole Acetic Acid ◽  
Target Genes ◽  
Anthocyanin Biosynthesis ◽  
Fruit Maturation ◽  
Dynamic Regulation ◽  
Protein Levels ◽  
Post Transcriptional Regulation ◽  
Insight Into

AbstractBlueberry is rich in anthocyanins which accumulate during fruit maturation. Previous studies mostly focus on their translational/transcriptional regulation, but usually underestimate their post-transcriptional regulation, e.g. small RNAs. This study aimed to identify sRNAs and their potential pathways associated with anthocyanin biosynthesis. During three typical phases of fruit maturation (green, pink, and blue), we investigated dynamic changes of sRNA by deep sequencing sRNA and examined the interaction of sRNAs with their target genes by degradome and RLM-PCR. During maturation, up-regulation of VcmiRNA156 and VcmiR393 resulted in down-regulation of VcSPLs and VcTIR1/AFBs, respectively. An important gene of anthocyanin biosynthesis, VcDFR, was substantially down-regulated at both the mRNA and protein levels, and potentially responded to regulation of VcSPLs and VcTIR1/AFBs. Additionally, indole acetic acid (IAA) and abscisic acid (ABA) were involved in the regulation of anthocyanin biosynthesis by interacting with VcmiR393-TIR1/AFBs and VcmiRNA319-VcMYBs respectively. This information provides another insight into blueberry anthocyanin biosynthesis.

scholarly journals Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage

2019 ◽  
Vol 37 (3) ◽  
pp. 651-659 ◽  
Author(s):  
Naoji Yubuki ◽  
Luis Javier Galindo ◽  
Guillaume Reboul ◽  
Purificación López-García ◽  
Matthew W Brown ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Transcriptome Data ◽  
Free Living ◽  
Functional Impact ◽  
Common Process ◽  
Early Acquisition ◽  
Bacterial Genes

Abstract Lateral gene transfer is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes, and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those lateral gene transfers most likely facilitated the adaptation of the free-living ancestor of the Opalinidae–Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.

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