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Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum

Overview of attention for article published in Biotechnology for Biofuels, June 2015
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  • Above-average Attention Score compared to outputs of the same age (51st percentile)
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Mentioned by

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3 tweeters

Citations

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22 Dimensions

Readers on

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57 Mendeley
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Title
Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum
Published in
Biotechnology for Biofuels, June 2015
DOI 10.1186/s13068-015-0260-9
Pubmed ID
Authors

Keerthi P. Venkataramanan, Lie Min, Shuyu Hou, Shawn W. Jones, Matthew T. Ralston, Kelvin H. Lee, E. Terry Papoutsakis

Abstract

Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production. The organism is exposed to its own toxic metabolites butyrate and butanol, which trigger an adaptive stress response. Integrative analysis of proteomic and RNAseq data may provide novel insights into post-transcriptional regulation. The identified iTRAQ-based quantitative stress proteome is made up of 616 proteins with a 15 % genome coverage. The differentially expressed proteome correlated poorly with the corresponding differential RNAseq transcriptome. Up to 31 % of the differentially expressed proteins under stress displayed patterns opposite to those of the transcriptome, thus suggesting significant post-transcriptional regulation. The differential proteome of the translation machinery suggests that cells employ a different subset of ribosomal proteins under stress. Several highly upregulated proteins but with low mRNA levels possessed mRNAs with long 5'UTRs and strong RBS scores, thus supporting the argument that regulatory elements on the long 5'UTRs control their translation. For example, the oxidative stress response rubrerythrin was upregulated only at the protein level up to 40-fold without significant mRNA changes. We also identified many leaderless transcripts, several displaying different transcriptional start sites, thus suggesting mRNA-trimming mechanisms under stress. Downregulation of Rho and partner proteins pointed to changes in transcriptional elongation and termination under stress. The integrative proteomic-transcriptomic analysis demonstrated complex expression patterns of a large fraction of the proteome. Such patterns could not have been detected with one or the other omic analyses. Our analysis proposes the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the observed complex stress response.

Twitter Demographics

The data shown below were collected from the profiles of 3 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 57 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Mexico 1 2%
United States 1 2%
Germany 1 2%
Unknown 54 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 14 25%
Researcher 8 14%
Student > Bachelor 8 14%
Student > Master 6 11%
Student > Doctoral Student 5 9%
Other 10 18%
Unknown 6 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 22 39%
Biochemistry, Genetics and Molecular Biology 13 23%
Immunology and Microbiology 4 7%
Engineering 4 7%
Chemical Engineering 3 5%
Other 5 9%
Unknown 6 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 14 August 2015.
All research outputs
#2,532,258
of 5,482,709 outputs
Outputs from Biotechnology for Biofuels
#200
of 473 outputs
Outputs of similar age
#86,357
of 192,039 outputs
Outputs of similar age from Biotechnology for Biofuels
#10
of 23 outputs
Altmetric has tracked 5,482,709 research outputs across all sources so far. This one has received more attention than most of these and is in the 51st percentile.
So far Altmetric has tracked 473 research outputs from this source. They receive a mean Attention Score of 4.0. This one has gotten more attention than average, scoring higher than 54% 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 192,039 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 51% of its contemporaries.
We're also able to compare this research output to 23 others from the same source and published within six weeks on either side of this one. This one is in the 47th percentile – i.e., 47% of its contemporaries scored the same or lower than it.