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Halovirus HF2 Intergenic Repeat Sequences Carry Promoters

Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were...

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Autores principales: Russ, Brendan, Pfeiffer, Friedhelm, Dyall-Smith, Mike
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8707807/
https://www.ncbi.nlm.nih.gov/pubmed/34960657
http://dx.doi.org/10.3390/v13122388
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author Russ, Brendan
Pfeiffer, Friedhelm
Dyall-Smith, Mike
author_facet Russ, Brendan
Pfeiffer, Friedhelm
Dyall-Smith, Mike
author_sort Russ, Brendan
collection PubMed
description Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present study, nine IRs were cloned upstream of the bgaH reporter gene, and all displayed promoter activity, providing experimental evidence for the previous conjecture. Comparative genomics showed that IR sequences and their relative genomic positions were strongly conserved among other members of the same virus genus. The transcription of HF2 was also examined by the reverse-transcriptase-PCR (RT-PCR) method, which demonstrated very long transcripts were produced that together covered most of the genome, and from both strands. The presence of long counter transcripts suggests a regulatory role or possibly unrecognized coding potential.
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spelling pubmed-87078072021-12-25 Halovirus HF2 Intergenic Repeat Sequences Carry Promoters Russ, Brendan Pfeiffer, Friedhelm Dyall-Smith, Mike Viruses Article Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present study, nine IRs were cloned upstream of the bgaH reporter gene, and all displayed promoter activity, providing experimental evidence for the previous conjecture. Comparative genomics showed that IR sequences and their relative genomic positions were strongly conserved among other members of the same virus genus. The transcription of HF2 was also examined by the reverse-transcriptase-PCR (RT-PCR) method, which demonstrated very long transcripts were produced that together covered most of the genome, and from both strands. The presence of long counter transcripts suggests a regulatory role or possibly unrecognized coding potential. MDPI 2021-11-29 /pmc/articles/PMC8707807/ /pubmed/34960657 http://dx.doi.org/10.3390/v13122388 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Russ, Brendan
Pfeiffer, Friedhelm
Dyall-Smith, Mike
Halovirus HF2 Intergenic Repeat Sequences Carry Promoters
title Halovirus HF2 Intergenic Repeat Sequences Carry Promoters
title_full Halovirus HF2 Intergenic Repeat Sequences Carry Promoters
title_fullStr Halovirus HF2 Intergenic Repeat Sequences Carry Promoters
title_full_unstemmed Halovirus HF2 Intergenic Repeat Sequences Carry Promoters
title_short Halovirus HF2 Intergenic Repeat Sequences Carry Promoters
title_sort halovirus hf2 intergenic repeat sequences carry promoters
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8707807/
https://www.ncbi.nlm.nih.gov/pubmed/34960657
http://dx.doi.org/10.3390/v13122388
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