Prediction, Microarray and Northern Blot Analyses Identify New Intergenic Small RNAs in Aliivibrio salmonicida
Bacterial small RNAs (sRNAs) are trans-encoded regulatory RNAs that typically bind mRNAs by short-sequence complementarities and change the expression of the corresponding proteins. Some of the well-characterized sRNAs serve critical steps in the regulation of important cellular processes, such as q...
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crskarger:10.1159/000345769 2024-09-15T17:56:26+00:00 Prediction, Microarray and Northern Blot Analyses Identify New Intergenic Small RNAs in Aliivibrio salmonicida Ahmad, Rafi Hansen, Geir Åsmund Hansen, Hilde Hjerde, Erik Pedersen, Hege Lynum Paulsen, Steinar M. Nyrud, May Liss Julianne Strauss, Anja Willassen, Nils-Peder Haugen, Peik 2012 http://dx.doi.org/10.1159/000345769 https://www.karger.com/Article/Pdf/345769 en eng S. Karger AG https://www.karger.com/Services/SiteLicenses https://www.karger.com/Services/SiteLicenses Microbial Physiology volume 22, issue 6, page 352-360 ISSN 2673-1665 2673-1673 journal-article 2012 crskarger https://doi.org/10.1159/000345769 2024-07-31T04:07:17Z Bacterial small RNAs (sRNAs) are trans-encoded regulatory RNAs that typically bind mRNAs by short-sequence complementarities and change the expression of the corresponding proteins. Some of the well-characterized sRNAs serve critical steps in the regulation of important cellular processes, such as quorum sensing (Qrr), iron homeostasis (RyhB), oxidative stress (OxyS), and carbon metabolism (Spot 42). However, many sRNAs remain to be identified, and the functional roles of sRNAs are known for only a small fraction. For example, of the hundreds of candidate sRNAs from members of the bacterial family Vibrionaceae, the function is known for only 9. We have in this study significantly contributed to the discovery and verification of new sRNAs in a representative of Vibrionaceae, i.e. the Aliivibrio salmonicida, which causes severe disease in farmed Atlantic salmon and other fishes. A computational search for intergenic non-coding (nc) RNAs in the 4.6-Mb genome identified a total of 252 potential ncRNAs (including 233 putative sRNAs). Depending on the set threshold value for fluorescence signal in our microarray approach, we identified 50–80 putative ncRNAs, 12 of which were verified by Northern blot analysis. In total, we identified 9 new sRNAs. Article in Journal/Newspaper Atlantic salmon Karger Microbial Physiology 22 6 352 360 |
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English |
description |
Bacterial small RNAs (sRNAs) are trans-encoded regulatory RNAs that typically bind mRNAs by short-sequence complementarities and change the expression of the corresponding proteins. Some of the well-characterized sRNAs serve critical steps in the regulation of important cellular processes, such as quorum sensing (Qrr), iron homeostasis (RyhB), oxidative stress (OxyS), and carbon metabolism (Spot 42). However, many sRNAs remain to be identified, and the functional roles of sRNAs are known for only a small fraction. For example, of the hundreds of candidate sRNAs from members of the bacterial family Vibrionaceae, the function is known for only 9. We have in this study significantly contributed to the discovery and verification of new sRNAs in a representative of Vibrionaceae, i.e. the Aliivibrio salmonicida, which causes severe disease in farmed Atlantic salmon and other fishes. A computational search for intergenic non-coding (nc) RNAs in the 4.6-Mb genome identified a total of 252 potential ncRNAs (including 233 putative sRNAs). Depending on the set threshold value for fluorescence signal in our microarray approach, we identified 50–80 putative ncRNAs, 12 of which were verified by Northern blot analysis. In total, we identified 9 new sRNAs. |
format |
Article in Journal/Newspaper |
author |
Ahmad, Rafi Hansen, Geir Åsmund Hansen, Hilde Hjerde, Erik Pedersen, Hege Lynum Paulsen, Steinar M. Nyrud, May Liss Julianne Strauss, Anja Willassen, Nils-Peder Haugen, Peik |
spellingShingle |
Ahmad, Rafi Hansen, Geir Åsmund Hansen, Hilde Hjerde, Erik Pedersen, Hege Lynum Paulsen, Steinar M. Nyrud, May Liss Julianne Strauss, Anja Willassen, Nils-Peder Haugen, Peik Prediction, Microarray and Northern Blot Analyses Identify New Intergenic Small RNAs in Aliivibrio salmonicida |
author_facet |
Ahmad, Rafi Hansen, Geir Åsmund Hansen, Hilde Hjerde, Erik Pedersen, Hege Lynum Paulsen, Steinar M. Nyrud, May Liss Julianne Strauss, Anja Willassen, Nils-Peder Haugen, Peik |
author_sort |
Ahmad, Rafi |
title |
Prediction, Microarray and Northern Blot Analyses Identify New Intergenic Small RNAs in Aliivibrio salmonicida |
title_short |
Prediction, Microarray and Northern Blot Analyses Identify New Intergenic Small RNAs in Aliivibrio salmonicida |
title_full |
Prediction, Microarray and Northern Blot Analyses Identify New Intergenic Small RNAs in Aliivibrio salmonicida |
title_fullStr |
Prediction, Microarray and Northern Blot Analyses Identify New Intergenic Small RNAs in Aliivibrio salmonicida |
title_full_unstemmed |
Prediction, Microarray and Northern Blot Analyses Identify New Intergenic Small RNAs in Aliivibrio salmonicida |
title_sort |
prediction, microarray and northern blot analyses identify new intergenic small rnas in aliivibrio salmonicida |
publisher |
S. Karger AG |
publishDate |
2012 |
url |
http://dx.doi.org/10.1159/000345769 https://www.karger.com/Article/Pdf/345769 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Microbial Physiology volume 22, issue 6, page 352-360 ISSN 2673-1665 2673-1673 |
op_rights |
https://www.karger.com/Services/SiteLicenses https://www.karger.com/Services/SiteLicenses |
op_doi |
https://doi.org/10.1159/000345769 |
container_title |
Microbial Physiology |
container_volume |
22 |
container_issue |
6 |
container_start_page |
352 |
op_container_end_page |
360 |
_version_ |
1810432644184276992 |