Open Access
International Journal of Molecular Sciences, volume 23, issue 20, pages 12293
Flow-Seq Evaluation of Translation Driven by a Set of Natural Escherichia coli 5′-UTR of Variable Length
Komarova Ekaterina S
1
,
Slesarchuk Anna N
2
,
Rubtsova Maria P
2
,
Osterman Ilya A.
3
,
Tupikin Alexey E
4
,
Пышный Д. В.
4
,
Dontsova Olga A.
2, 3, 5, 6
,
Sergiev Petr V.
1, 2, 3, 6
Publication type: Journal Article
Publication date: 2022-10-14
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 5.6
ISSN: 16616596, 14220067
PubMed ID:
36293163
Catalysis
Organic Chemistry
Inorganic Chemistry
Physical and Theoretical Chemistry
Computer Science Applications
Spectroscopy
Molecular Biology
General Medicine
Abstract
Flow-seq is a method that combines fluorescently activated cell sorting and next-generation sequencing to deduce a large amount of data about translation efficiency from a single experiment. Here, we constructed a library of fluorescent protein-based reporters preceded by a set of 648 natural 5′-untranslated regions (5′-UTRs) of Escherichia coli genes. Usually, Flow-seq libraries are constructed using uniform-length sequence elements, in contrast to natural situations, where functional elements are of heterogenous lengths. Here, we demonstrated that a 5′-UTR library of variable length could be created and analyzed with Flow-seq. In line with previous Flow-seq experiments with randomized 5′-UTRs, we observed the influence of an RNA secondary structure and Shine–Dalgarno sequences on translation efficiency; however, the variability of these parameters for natural 5′-UTRs in our library was smaller in comparison with randomized libraries. In line with this, we only observed a 30-fold difference in translation efficiency between the best and worst bins sorted with this factor. The results correlated with those obtained with ribosome profiling.
Citations by journals
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Acta Naturae
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Acta Naturae, 1, 100%
Acta Naturae
1 publication, 100%
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Citations by publishers
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Acta Naturae Ltd
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Acta Naturae Ltd, 1, 100%
Acta Naturae Ltd
1 publication, 100%
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Komarova E. S. et al. Flow-Seq Evaluation of Translation Driven by a Set of Natural Escherichia coli 5′-UTR of Variable Length // International Journal of Molecular Sciences. 2022. Vol. 23. No. 20. p. 12293.
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Komarova E. S., Slesarchuk A. N., Rubtsova M. P., Osterman I. A., Tupikin A. E., Пышный Д. В., Dontsova O. A., Kabilov M. R., Sergiev P. V. Flow-Seq Evaluation of Translation Driven by a Set of Natural Escherichia coli 5′-UTR of Variable Length // International Journal of Molecular Sciences. 2022. Vol. 23. No. 20. p. 12293.
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TY - JOUR
DO - 10.3390/ijms232012293
UR - https://doi.org/10.3390%2Fijms232012293
TI - Flow-Seq Evaluation of Translation Driven by a Set of Natural Escherichia coli 5′-UTR of Variable Length
T2 - International Journal of Molecular Sciences
AU - Slesarchuk, Anna N
AU - Rubtsova, Maria P
AU - Osterman, Ilya A.
AU - Tupikin, Alexey E
AU - Пышный, Д. В.
AU - Dontsova, Olga A.
AU - Kabilov, Marsel R.
AU - Sergiev, Petr V.
AU - Komarova, Ekaterina S
PY - 2022
DA - 2022/10/14 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 12293
IS - 20
VL - 23
PMID - 36293163
SN - 1661-6596
SN - 1422-0067
ER -
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BibTex
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@article{2022_Komarova,
author = {Anna N Slesarchuk and Maria P Rubtsova and Ilya A. Osterman and Alexey E Tupikin and Д. В. Пышный and Olga A. Dontsova and Marsel R. Kabilov and Petr V. Sergiev and Ekaterina S Komarova},
title = {Flow-Seq Evaluation of Translation Driven by a Set of Natural Escherichia coli 5′-UTR of Variable Length},
journal = {International Journal of Molecular Sciences},
year = {2022},
volume = {23},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {oct},
url = {https://doi.org/10.3390%2Fijms232012293},
number = {20},
pages = {12293},
doi = {10.3390/ijms232012293}
}
Cite this
MLA
Copy
Komarova, Ekaterina S., et al. “Flow-Seq Evaluation of Translation Driven by a Set of Natural Escherichia coli 5′-UTR of Variable Length.” International Journal of Molecular Sciences, vol. 23, no. 20, Oct. 2022, p. 12293. https://doi.org/10.3390%2Fijms232012293.