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Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica

Overview of attention for article published in BMC Genomics, February 2016
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  • Above-average Attention Score compared to outputs of the same age and source (58th percentile)

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7 tweeters

Citations

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31 Dimensions

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76 Mendeley
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Title
Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica
Published in
BMC Genomics, February 2016
DOI 10.1186/s12864-016-2471-2
Pubmed ID
Authors

Kyle R. Pomraning, Young-Mo Kim, Carrie D. Nicora, Rosalie K. Chu, Erin L. Bredeweg, Samuel O. Purvine, Dehong Hu, Thomas O. Metz, Scott E. Baker

Abstract

Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. While the enzymatic pathways responsible for neutral lipid accumulation in Y. lipolytica are well characterized, regulation of these pathways has received little attention. We therefore sought to characterize the response to nitrogen limitation at system-wide levels, including the proteome, phosphoproteome and metabolome, to better understand how this organism regulates and controls lipid metabolism and to identify targets that may be manipulated to improve lipid yield. We found that ribosome structural genes are down-regulated under nitrogen limitation, during which nitrogen containing compounds (alanine, putrescine, spermidine and urea) are depleted and sugar alcohols and TCA cycle intermediates accumulate (citrate, fumarate and malate). We identified 1219 novel phosphorylation sites in Y. lipolytica, 133 of which change in their abundance during nitrogen limitation. Regulatory proteins, including kinases and DNA binding proteins, are particularly enriched for phosphorylation. Within lipid synthesis pathways, we found that ATP-citrate lyase, acetyl-CoA carboxylase and lecithin cholesterol acyl transferase are phosphorylated during nitrogen limitation while many of the proteins involved in β-oxidation are down-regulated, suggesting that storage lipid accumulation may be regulated by phosphorylation of key enzymes. Further, we identified short DNA elements that associate specific transcription factor families with up- and down-regulated genes. Integration of metabolome, proteome and phosphoproteome data identifies lipid accumulation in response to nitrogen limitation as a two-fold result of increased production of acetyl-CoA from excess citrate and decreased capacity for β-oxidation.

Twitter Demographics

The data shown below were collected from the profiles of 7 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 76 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 4%
Sweden 1 1%
Germany 1 1%
France 1 1%
Unknown 70 92%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 30 39%
Student > Master 15 20%
Researcher 10 13%
Student > Bachelor 5 7%
Student > Doctoral Student 4 5%
Other 7 9%
Unknown 5 7%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 26 34%
Agricultural and Biological Sciences 20 26%
Chemical Engineering 5 7%
Chemistry 4 5%
Engineering 3 4%
Other 10 13%
Unknown 8 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 March 2016.
All research outputs
#2,860,104
of 10,682,373 outputs
Outputs from BMC Genomics
#2,163
of 6,721 outputs
Outputs of similar age
#94,596
of 292,426 outputs
Outputs of similar age from BMC Genomics
#92
of 231 outputs
Altmetric has tracked 10,682,373 research outputs across all sources so far. This one has received more attention than most of these and is in the 52nd percentile.
So far Altmetric has tracked 6,721 research outputs from this source. They receive a mean Attention Score of 4.2. This one has gotten more attention than average, scoring higher than 60% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 292,426 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 65% of its contemporaries.
We're also able to compare this research output to 231 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 58% of its contemporaries.