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X Demographics
Mendeley readers
Attention Score in Context
| Title |
Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)
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|---|---|
| Published in |
BMC Genomics, February 2016
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| DOI | 10.1186/s12864-016-2456-1 |
| Pubmed ID | |
| Authors |
Klaus Neuhaus, Richard Landstorfer, Lea Fellner, Svenja Simon, Andrea Schafferhans, Tatyana Goldberg, Harald Marx, Olga N. Ozoline, Burkhard Rost, Bernhard Kuster, Daniel A. Keim, Siegfried Scherer |
| Abstract |
Genomes of E. coli, including that of the human pathogen Escherichia coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which, apparently, have escaped annotation due to their small size and non-essential function. To find such genes, global gene expression of EHEC EDL933 was examined, using strand-specific RNAseq (transcriptome), ribosomal footprinting (translatome) and mass spectrometry (proteome). Using the above methods, 72 short, non-annotated protein-coding genes were detected. All of these showed signals in the ribosomal footprinting assay indicating mRNA translation. Seven were verified by mass spectrometry. Fifty-seven genes are annotated in other enterobacteriaceae, mainly as hypothetical genes; the remaining 15 genes constitute novel discoveries. In addition, protein structure and function were predicted computationally and compared between EHEC-encoded proteins and 100-times randomly shuffled proteins. Based on this comparison, 61 of the 72 novel proteins exhibit predicted structural and functional features similar to those of annotated proteins. Many of the novel genes show differential transcription when grown under eleven diverse growth conditions suggesting environmental regulation. Three genes were found to confer a phenotype in previous studies, e.g., decreased cattle colonization. These findings demonstrate that ribosomal footprinting can be used to detect novel protein coding genes, contributing to the growing body of evidence that hypothetical genes are not annotation artifacts and opening an additional way to study their functionality. All 72 genes are taxonomically restricted and, therefore, appear to have evolved relatively recently de novo. |
X Demographics
The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Canada | 1 | 33% |
| Unknown | 2 | 67% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 2 | 67% |
| Scientists | 1 | 33% |
Mendeley readers
The data shown below were compiled from readership statistics for 51 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Iran, Islamic Republic of | 1 | 2% |
| Germany | 1 | 2% |
| Unknown | 49 | 96% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 13 | 25% |
| Researcher | 12 | 24% |
| Student > Master | 8 | 16% |
| Student > Bachelor | 4 | 8% |
| Student > Postgraduate | 3 | 6% |
| Other | 8 | 16% |
| Unknown | 3 | 6% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 23 | 45% |
| Agricultural and Biological Sciences | 13 | 25% |
| Veterinary Science and Veterinary Medicine | 2 | 4% |
| Business, Management and Accounting | 2 | 4% |
| Environmental Science | 1 | 2% |
| Other | 7 | 14% |
| Unknown | 3 | 6% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. 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 26 February 2016.
All research outputs
#15,361,255
of 22,851,489 outputs
Outputs from BMC Genomics
#6,694
of 10,658 outputs
Outputs of similar age
#177,011
of 298,866 outputs
Outputs of similar age from BMC Genomics
#171
of 234 outputs
Altmetric has tracked 22,851,489 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,658 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 29th percentile – i.e., 29% of its peers scored the same or lower than it.
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We're also able to compare this research output to 234 others from the same source and published within six weeks on either side of this one. This one is in the 18th percentile – i.e., 18% of its contemporaries scored the same or lower than it.