Evidence map›Paper›PMID 26269711›Full record

ArticleBiotechnology for biofuels2015

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

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

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biotechnology for biofuels, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed
4.1field-weighted citation impact, top 6% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

19 citing papers in PubMed, 47 citations in OpenAlex.

  1. Article
  2. Article
  3. Molecular Insights into the Marine GastropodInternational journal of molecular sciences · 2025
    Article
  4. Article
  5. Article
  6. The potential of native and engineered Clostridia for biomass biorefining.Frontiers in bioengineering and biotechnology · 2024
    Review
  7. Review
  8. Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont.Proceedings of the National Academy of Sciences of the United States of America · 2021
    Article
  9. Article
  10. Frontiers in microbiology · 2021
    Article
  11. Review
  12. Article
  13. Article
  14. Review
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 2 institutions in 1 country.

Keerthi P Venkataramanan15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
Lie Min15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
Shuyu Hou15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
Shawn W Jones15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
Matthew T Ralston15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 15 Innovation Way, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711 USA.
Kelvin H Lee15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
E Terry Papoutsakis15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
University of Delaware · USBiotechnology Institute · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundClostridium 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.

resultsThe 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.

conclusionsThe 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.

Indexed as

Integrative analysisiTRAQ proteomeMetabolite stressMicroarrayPost-transcriptional regulationRNAseq

Identifiers

PMID26269711
PMCPMC4533764
OpenAlexW1496200635

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.