Universally high transcript error rates in bacteria
Abstract
Errors can occur at any level during the replication and transcription of genetic information. Genetic mutations derived mainly from replication errors have been extensively studied. However, fundamental details of transcript errors, such as their rate, molecular spectrum, and functional effects, remain largely unknown. To globally identify transcript errors, we applied an adapted rolling-circle sequencing approach to Escherichia coli, Bacillus subtilis, Agrobacterium tumefaciens, and Mesoplasma florum, revealing transcript-error rates 3 to 4 orders of magnitude higher than the corresponding genetic mutation rates. The majority of detected errors would result in amino-acid changes, if translated. With errors identified from 9929 loci, the molecular spectrum and distribution of errors were uncovered in great detail. A G→A substitution bias was observed in M. florum, which apparently has an error-prone RNA polymerase. Surprisingly, an increased frequency of nonsense errors towards the 3' end of mRNAs was observed, suggesting a Nonsense-Mediated Decay-like quality-control mechanism in prokaryotes.
- Authors:
-
[1];
[2]
- Indiana Univ., Bloomington, IN (United States)
- Indiana Univ., Bloomington, IN (United States); Arizona State Univ., Tempe, AZ (United States)
- Publication Date:
- Research Org.:
- SLAC National Accelerator Lab., Menlo Park, CA (United States)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH); US Army Research Office (ARO)
- OSTI Identifier:
- 1638082
- Grant/Contract Number:
- AC02-76SF00515; R01-GM036827; R35-GM122566; W911NF-09-1-0444; W911NF-14-1-0411
- Resource Type:
- Accepted Manuscript
- Journal Name:
- eLife
- Additional Journal Information:
- Journal Volume: 9; Journal ID: ISSN 2050-084X
- Publisher:
- eLife Sciences Publications, Ltd.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Li, Weiyi, and Lynch, Michael. Universally high transcript error rates in bacteria. United States: N. p., 2020.
Web. doi:10.7554/elife.54898.
Li, Weiyi, & Lynch, Michael. Universally high transcript error rates in bacteria. United States. https://doi.org/10.7554/elife.54898
Li, Weiyi, and Lynch, Michael. Fri .
"Universally high transcript error rates in bacteria". United States. https://doi.org/10.7554/elife.54898. https://www.osti.gov/servlets/purl/1638082.
@article{osti_1638082,
title = {Universally high transcript error rates in bacteria},
author = {Li, Weiyi and Lynch, Michael},
abstractNote = {Errors can occur at any level during the replication and transcription of genetic information. Genetic mutations derived mainly from replication errors have been extensively studied. However, fundamental details of transcript errors, such as their rate, molecular spectrum, and functional effects, remain largely unknown. To globally identify transcript errors, we applied an adapted rolling-circle sequencing approach to Escherichia coli, Bacillus subtilis, Agrobacterium tumefaciens, and Mesoplasma florum, revealing transcript-error rates 3 to 4 orders of magnitude higher than the corresponding genetic mutation rates. The majority of detected errors would result in amino-acid changes, if translated. With errors identified from 9929 loci, the molecular spectrum and distribution of errors were uncovered in great detail. A G→A substitution bias was observed in M. florum, which apparently has an error-prone RNA polymerase. Surprisingly, an increased frequency of nonsense errors towards the 3' end of mRNAs was observed, suggesting a Nonsense-Mediated Decay-like quality-control mechanism in prokaryotes.},
doi = {10.7554/elife.54898},
journal = {eLife},
number = ,
volume = 9,
place = {United States},
year = {2020},
month = {5}
}
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Figure 1: The distribution of transcript errors across the whole transcriptomes of E. coli, B. subtilis, A. tumefaciens, and M. florum. The first nucleotide of the circular chromosome starts at the 12 o’clock position. For A. tumefaciens, chromosomes and plasmids are arranged from the largest to smallest size in amore »
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