| Texto completo | |
| Autor(es): Mostrar menos - |
Lorenzetti, Alan P. R.
;
Kusebauch, Ulrike
;
Zaramela, Livia S.
;
Wu, Wei-Ju
;
de Almeida, Joao P. P.
;
Turkarslan, Serdar
;
L. G. de Lomana, Adrian
;
Gomes-Filho, Jose V.
;
Vencio, Ricardo Z. N.
;
Moritz, Robert L.
;
Koide, Tie
;
Baliga, Nitin S.
Número total de Autores: 12
|
| Tipo de documento: | Artigo Científico |
| Fonte: | MSYSTEMS; v. 8, n. 2, p. 22-pg., 2023-03-13. |
| Resumo | |
The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net).IMPORTANCE While the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we collected and integrated omics data from multiple sources and technologies to infer post -transcriptionally regulated genes and the putative mechanisms modulating their expression at the protein level in Halobacterium salinarum NRC-1. The results suggest that post-transcriptional regulation may drive environmental acclimation by regulating hallmark biological processes. To foster discoveries by other research groups interested in the topic, we extended our integrated data to the public in the form of an interactive atlas (https://halodata.systemsbiology.net). (AU) | |
| Processo FAPESP: | 17/03052-2 - RNAs não codificantes derivados de sequências de inserção na arqueia halófila Halobacterium salinarum NRC-1 |
| Beneficiário: | Alan Péricles Rodrigues Lorenzetti |
| Modalidade de apoio: | Bolsas no Brasil - Doutorado |
| Processo FAPESP: | 15/21038-1 - O transcritoma antisense da archaea halofílica Halobacterium salinarum |
| Beneficiário: | Tie Koide |
| Modalidade de apoio: | Auxílio à Pesquisa - Regular |
| Processo FAPESP: | 11/07487-7 - Identificação e caracterização de RNAs não codificantes ligantes a Lsm no extremófilo Halobacterium salinarum |
| Beneficiário: | Lívia Soares Zaramela |
| Modalidade de apoio: | Bolsas no Brasil - Doutorado |
| Processo FAPESP: | 19/13440-5 - Detecção de transposases codificadas por Sequências de Inserção usando dados de proteômica |
| Beneficiário: | Alan Péricles Rodrigues Lorenzetti |
| Modalidade de apoio: | Bolsas no Exterior - Estágio de Pesquisa - Doutorado |
| Processo FAPESP: | 13/21522-5 - Caracterização funcional de RNAs não-codificantes associados a transposons IS1341 em Halobacterium salinarum |
| Beneficiário: | José Vicente Gomes Filho |
| Modalidade de apoio: | Bolsas no Brasil - Doutorado Direto |
| Processo FAPESP: | 09/09532-0 - Biologia sistêmica do extremófilo Halobacterium salinarum: contribuição dos RNAs não-codificantes ao modelo global de regulação gênica |
| Beneficiário: | Tie Koide |
| Modalidade de apoio: | Auxílio à Pesquisa - Jovens Pesquisadores |