Meta-analysis reveals host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia

AbstractThe metabolic symbiosis with photosynthetic algae of the genus Symbiodinium allows corals to thrive in the oligotrophic environments of tropical seas. Many aspects of this relationship have been investigated using transcriptomic analyses in the emerging model organism Aiptasia. However, previous studies identified thousands of putatively symbiosis-related genes, making it difficult to disentangle symbiosis-induced responses from undesired experimental parameters. Using a meta-analysis approach, we identified a core set of 731 high-confidence symbiosis-associated genes that reveal host-dependent recycling of waste ammonium and amino acid synthesis as central processes in this relationship. Combining transcriptomic and metabolomic analyses, we show that symbiont-derived carbon enables host recycling of ammonium into nonessential amino acids. We propose that this provides a regulatory mechanism to control symbiont growth through a carbon-dependent negative feedback of nitrogen availability to the symbiont. The dependence of this mechanism on symbiont-derived carbon highlights the susceptibility of this symbiosis to changes in carbon translocation, as imposed by environmental stress.

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Essential amino acid synthesis and nitrogen recycling in an alga-invertebrate symbiosis

Marine Biology ◽

10.1007/s002270050619 ◽

1999 ◽

Vol 135 (2) ◽

pp. 219-222 ◽

Cited By ~ 72

Author(s):

J. T. Wang ◽

A. E. Douglas

Keyword(s):

Amino Acid ◽

Essential Amino Acid ◽

Acid Synthesis ◽

Nitrogen Recycling ◽

Amino Acid Synthesis

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Integrative meta-analysis reveals that most yeast proteins are very stable

10.1101/165290 ◽

2017 ◽

Cited By ~ 2

Author(s):

Keira Wiechecki ◽

Sandhya Manohar ◽

Gustavo Silva ◽

Konstantine Tchourine ◽

Samson Jacob ◽

...

Keyword(s):

Protein Stability ◽

Exponential Decay ◽

Ribosomal Proteins ◽

Ribosome Biogenesis ◽

Doubling Time ◽

Meta Analysis ◽

Acid Synthesis ◽

Subtle Difference ◽

Amino Acid Synthesis ◽

Doubling Times

AbstractMeasurements for protein half-lives in yeast Saccharomyces cerevisiae reported large discrepancies, with median values between minutes to several hours. We present a unifying analysis that provides a consistent half-life estimate, based on our re-analysis of three published and one new dataset of cells grown under similar conditions. We found that degradation of many proteins can be approximated by exponential decay. Protein disappearance was primarily driven by dilution due to cell division, with cell doubling times ranging from ∼2 to 3.5 hours across the four experiments. After adjusting for doubling time, protein half-lives increased to median values between ∼7.5 to ∼40 hours. Half-lives correlated with cell doubling time even after adjustment, implying that slow growth also slows protein degradation. All estimates were validated by multiple means and were robust to different analysis methods. Overall, protein stability correlated with abundance and showed weak enrichment for degradation signals such as degrons and disordered regions. Long-lived proteins often functioned in oxidation-reduction and amino acid synthesis. Short-lived proteins often functioned in ribosome biogenesis. Despite some overall differences in behavior, all methods were able to resolve subtle difference in half-lives of ribosomal proteins, e.g. the short lifespan of RPL10. Finally, our results help the design of future experiments: time series measurements need to cover at least two to three cell doubling times for accurate estimates, exponential decay provides a reasonable proxy for protein stability, and it can be sufficiently estimated with four measurement points.

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Influence of increased nutrient supply on Microcystis aeruginosa at cellular and proteomic levels

Aquatic Microbial Ecology ◽

10.3354/ame01939 ◽

2020 ◽

Vol 85 ◽

pp. 47-58

Author(s):

Y Jiang ◽

Y Liu

Keyword(s):

Microcystis Aeruginosa ◽

Regulatory Protein ◽

Acid Synthesis ◽

Nutrient Supply ◽

Nitrogen Supply ◽

Nitrogen And Phosphorus ◽

Comprehensive Description ◽

Amino Acid Synthesis ◽

High Nutrient ◽

Proteomic Responses

Various studies have observed that increased nutrient supply promotes the growth of bloom-forming cyanobacteria, but only a limited number of studies have investigated the influence of increased nutrient supply on bloom-forming cyanobacteria at the proteomic level. We investigated the cellular and proteomic responses of Microcystis aeruginosa to elevated nitrogen and phosphorus supply. Increased supply of both nutrients significantly promoted the growth of M. aeruginosa and the synthesis of chlorophyll a, protein, and microcystins. The release of microcystins and the synthesis of polysaccharides negatively correlated with the growth of M. aeruginosa under high nutrient levels. Overexpressed proteins related to photosynthesis, and amino acid synthesis, were responsible for the stimulatory effects of increased nutrient supply in M. aeruginosa. Increased nitrogen supply directly promoted cyanobacterial growth by inducing the overexpression of the cell division regulatory protein FtsZ. NtcA, that regulates gene transcription related to both nitrogen assimilation and microcystin synthesis, was overexpressed under the high nitrogen condition, which consequently induced overexpression of 2 microcystin synthetases (McyC and McyF) and promoted microcystin synthesis. Elevated nitrogen supply induced the overexpression of proteins involved in gas vesicle organization (GvpC and GvpW), which may increase the buoyancy of M. aeruginosa. Increased phosphorus level indirectly affected growth and the synthesis of cellular substances in M. aeruginosa through the mediation of differentially expressed proteins related to carbon and phosphorus metabolism. This study provides a comprehensive description of changes in the proteome of M. aeruginosa in response to an increased supply of 2 key nutrients.

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Faculty Opinions recommendation of Photoredox activation of carbon dioxide for amino acid synthesis in continuous flow.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727212076.793527478 ◽

2017 ◽

Author(s):

Donald Pinto ◽

Kumar Pabbisetty ◽

Vladimir Ladziata

Keyword(s):

Carbon Dioxide ◽

Amino Acid ◽

Continuous Flow ◽

Acid Synthesis ◽

Amino Acid Synthesis

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O-AcylTEMPOs, a Modified and Fundamental, but Unexplored Carboxylic Derivative: Recent Progress in Synthetic Applications

Current Organic Chemistry ◽

10.2174/1385272823666191019102511 ◽

2019 ◽

Vol 23 (19) ◽

pp. 2102-2121

Author(s):

Hiroyuki Kawafuchi ◽

Lijian Ma ◽

Md Imran Hossain ◽

Tsutomu Inokuchi

Keyword(s):

Organic Synthesis ◽

Recent Progress ◽

Knoevenagel Condensation ◽

Acid Synthesis ◽

Amino Acid Synthesis ◽

Electrophilic Amination ◽

Weinreb Amides ◽

Anionic Species ◽

Diastereoselective Addition ◽

Carbonyl Function

O-Acylated 2,2,6,6-tetramethylpiperidine-N-oxyls (abbr. O-AcylTEMPOs) are easily available and stable carboxylic derivatives, but their utility in organic synthesis is unexplored in contrast to analogues, such as the N-methoxy-N-methylamides, known as Weinreb amides. Especially, the O–N unit of the O-acylTEMPOs dictates a fairly electronwithdrawing character for the carbonyl function. This enhances the reactivity and stability of the resulting enolate ions. Accordingly, O-acylTEMPOs allow various transformations and this review encompasses seven topics: (1) Reactivity of O-acylTEMPOs towards nucleophiles and chemoselective transformations, (2) Reactivity of anionic species derived from O-acylTEMPOs, (3) E-Selective Knoevenagel condensation of acetoacetylTEMPOs and synthesis of furans, (4) Electrocyclization of 2,4-dienones derived from acetoacetic derivatives and 2-substituted enals, (5) Diastereoselective addition of amide anion to O-(2-alkenoyl)TEMPOs and β-amino acid synthesis, (6) Thermolysis of O-acylTEMPOs, and (7) Applications for Umpolung reactions using O-benzoylTEMPOs, useful for the electrophilic amination of alkenes and alkynes.

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Petasis vs. Strecker Amino Acid Synthesis: Convergence, Divergence and Opportunities in Organic Synthesis

Molecules ◽

10.3390/molecules26061707 ◽

2021 ◽

Vol 26 (6) ◽

pp. 1707

Author(s):

Wayiza Masamba

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Organic Synthesis ◽

Acid Synthesis ◽

Physical Sciences ◽

Amino Acid Synthesis

α-Amino acids find widespread applications in various areas of life and physical sciences. Their syntheses are carried out by a multitude of protocols, of which Petasis and Strecker reactions have emerged as the most straightforward and most widely used. Both reactions are three-component reactions using the same starting materials, except the nucleophilic species. The differences and similarities between these two important reactions are highlighted in this review.

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