Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in <i>Halobacterium salinarum</i>
<i>Halobacterium salinarum</i> NRC-1 is an extremophile that grows optimally at 4.3 M NaCl concentration. In spite of being an established model microorganism for the archaea domain, direct comparisons between its proteome and transcriptome during osmotic stress are still not available....
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| Format: | Article |
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MDPI AG
2022-12-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/12/2442 |
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| author | Evelyn Ayumi Onga Ricardo Z. N. Vêncio Tie Koide |
| author_facet | Evelyn Ayumi Onga Ricardo Z. N. Vêncio Tie Koide |
| author_sort | Evelyn Ayumi Onga |
| collection | DOAJ |
| description | <i>Halobacterium salinarum</i> NRC-1 is an extremophile that grows optimally at 4.3 M NaCl concentration. In spite of being an established model microorganism for the archaea domain, direct comparisons between its proteome and transcriptome during osmotic stress are still not available. Through RNA-seq-based transcriptomics, we compared a low salt (2.6 M NaCl) stress condition with 4.3 M of NaCl and found 283 differentially expressed <i>loci</i>. The more commonly found classes of genes were: ABC-type transporters and transcription factors. Similarities, and most importantly, differences between our findings and previously published datasets in similar experimental conditions are discussed. We validated three important biological processes differentially expressed: gas vesicles production (due to down-regulation of <i>gvpA1b</i>, <i>gvpC1b</i>, <i>gvpN1b</i>, and <i>gvpO1b</i>); archaellum formation (due to down-regulation of <i>arlI</i>, <i>arlB1</i>, <i>arlB2</i>, and <i>arlB3</i>); and glycerol metabolism (due to up-regulation of <i>glpA1</i>, <i>glpB</i>, and <i>glpC</i>). Direct comparison between transcriptomics and proteomics showed 58% agreement between mRNA and protein level changes, pointing to post-transcriptional regulation candidates. From those genes, we highlight <i>rpl15e</i>, encoding for the 50S ribosomal protein L15e, for which we hypothesize an ionic strength-dependent conformational change that guides post-transcriptional processing of its mRNA and, thus, possible salt-dependent regulation of the translation machinery. |
| first_indexed | 2024-03-09T16:04:11Z |
| format | Article |
| id | doaj.art-5a002e004c244e2694f137eaf07e286c |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T16:04:11Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-5a002e004c244e2694f137eaf07e286c2023-11-24T16:49:10ZengMDPI AGMicroorganisms2076-26072022-12-011012244210.3390/microorganisms10122442Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in <i>Halobacterium salinarum</i>Evelyn Ayumi Onga0Ricardo Z. N. Vêncio1Tie Koide2Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, BrazilDepartment of Computation and Mathematics, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, BrazilDepartment of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil<i>Halobacterium salinarum</i> NRC-1 is an extremophile that grows optimally at 4.3 M NaCl concentration. In spite of being an established model microorganism for the archaea domain, direct comparisons between its proteome and transcriptome during osmotic stress are still not available. Through RNA-seq-based transcriptomics, we compared a low salt (2.6 M NaCl) stress condition with 4.3 M of NaCl and found 283 differentially expressed <i>loci</i>. The more commonly found classes of genes were: ABC-type transporters and transcription factors. Similarities, and most importantly, differences between our findings and previously published datasets in similar experimental conditions are discussed. We validated three important biological processes differentially expressed: gas vesicles production (due to down-regulation of <i>gvpA1b</i>, <i>gvpC1b</i>, <i>gvpN1b</i>, and <i>gvpO1b</i>); archaellum formation (due to down-regulation of <i>arlI</i>, <i>arlB1</i>, <i>arlB2</i>, and <i>arlB3</i>); and glycerol metabolism (due to up-regulation of <i>glpA1</i>, <i>glpB</i>, and <i>glpC</i>). Direct comparison between transcriptomics and proteomics showed 58% agreement between mRNA and protein level changes, pointing to post-transcriptional regulation candidates. From those genes, we highlight <i>rpl15e</i>, encoding for the 50S ribosomal protein L15e, for which we hypothesize an ionic strength-dependent conformational change that guides post-transcriptional processing of its mRNA and, thus, possible salt-dependent regulation of the translation machinery.https://www.mdpi.com/2076-2607/10/12/2442salt stress response<i>Halobacterium salinarum</i> NRC-1transcriptome proteome comparisonlow salt |
| spellingShingle | Evelyn Ayumi Onga Ricardo Z. N. Vêncio Tie Koide Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in <i>Halobacterium salinarum</i> Microorganisms salt stress response <i>Halobacterium salinarum</i> NRC-1 transcriptome proteome comparison low salt |
| title | Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in <i>Halobacterium salinarum</i> |
| title_full | Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in <i>Halobacterium salinarum</i> |
| title_fullStr | Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in <i>Halobacterium salinarum</i> |
| title_full_unstemmed | Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in <i>Halobacterium salinarum</i> |
| title_short | Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in <i>Halobacterium salinarum</i> |
| title_sort | low salt influences archaellum based motility glycerol metabolism and gas vesicles biogenesis in i halobacterium salinarum i |
| topic | salt stress response <i>Halobacterium salinarum</i> NRC-1 transcriptome proteome comparison low salt |
| url | https://www.mdpi.com/2076-2607/10/12/2442 |
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