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Genome-wide transcription responses during transition from exponential growth to stationary phase in the Archaeon Sulfolobus solfataricus
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Transition from exponential phase to stationary phase has been extensively studied in bacteria, which brings in-depth knowledge about bacterial cell adaptation, stress response, and transcriptional regulation network, such as stationary specific σ factors and (p)ppGpp mediated stringent response, etc. However, little is known for archaeal in this field. To shed light on archaeal phase adaptation and metabolic responses during growth phase transitions, global gene expression during growth of S. solfataricus were studied. Total RNAs from cells that were collected at 4 time points, representing exponential growth, the transition stage, early stationary phase and late stationary phase were extracted and sequenced. RNA-seq analysis identified a total of 1067 differentially expressed genes during phase transition, which included 456 induced genes most of which are related to transposases, stress response, and transcription factors, 464 repressed genes most of them involved in translation, basic transcriptional apparatus, DNA replication, cell division, amino acids metabolism and defense mechanisms, and 147 genes with fluctuated profile including transporters, oxidation-reduction process related genes and few metabolic genes. This study not only provide an overview of gene expression profiles of S. solfataricus during growth phase transition, but also provide a rich repository for further studies by the archaea community.

Keywords [en]
Archaea
National Category
Microbiology
Research subject
Molecular Bioscience
Identifiers
URN: urn:nbn:se:su:diva-153922OAI: oai:DiVA.org:su-153922DiVA, id: diva2:1188945
Available from: 2018-03-08 Created: 2018-03-08 Last updated: 2018-03-20Bibliographically approved
In thesis
1. Transcription regulation and growth phase transition in hyperthermoacidophilic archaea
Open this publication in new window or tab >>Transcription regulation and growth phase transition in hyperthermoacidophilic archaea
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Organisms from the domain Archaea are ubiquitously represented on our planet and encompass diverse fascinating organisms. The genus Sulfolobus belonging to the phylum Crenarchaeota including hyperthermoacidophilic strains that grow optimally at 65-85°C and pH 2-3. These organisms have been used as model organisms for thermophiles to investigate archaeal DNA replication, transcription, translation, cell cycle, etc.

The focus of this thesis is on the study of archaeal specific transcription factors (TFs) as well as transcriptome changes during growth phase transition of the hyperthermoacidophilic archaeons Sulfolobus acidocaldarius and Sulfolobus solfataricus, respectively, to expand our knowledge on archaeal transcription regulation and growth phase adaptation.

In paper 1, we studied the genome-wide binding sites of BarR, which is a β-alanine responsive Lrp family TF that activates the expression of β-alanine aminotransferase located in a divergent operon in S. acidocaldarius. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) revealed 21 binding regions, including previously characterized barR/Saci_2137 intergenic region. However, only one additional operon containing two glutamine synthase genes (Saci_2320 and Saci_2321) was found to be under activation of BarR. This operon is a common target of LyM and Sa-Lrp, which indicates a regulatory network between different Lrp-like regulators. In paper 2, we showed that a TetR family transcription repressor FadRSa regulates fatty acid metabolism in S. acidocaldarius. FadRSa rests in a gene cluster, Saci_1103-Saci_1126, that mainly contains lipid degradation and fatty acid metabolism genes. ChIP-seq revealed four binding sites within the gene cluster and RNA-seq further confirmed that the entire gene cluster is repressed by FadRSa. FadRSa binds DNA at a 16-base pair motif with dyad symmetry, and binding of medium- to long-chain acyl-CoA molecules resulted in dissociation of FadRSa from the DNA. Although FadRSa is similar to its bacterial counterparts functionally and structurally, fundamentally different ligand binding mode has been observed.

In paper 3, transcriptome data of S. solfataricus at four time points during growth, including early exponential phase, late exponential phase, early stationary phase and late stationary phase, has been studied and revealed a massive change in gene expressions during growth phase transition. 1067 out of a total of 2978 (35.8%) protein coding genes were identified as differentially expressed, which included 456 induced genes most of which were related to transposase, metabolism and stress response, 464 repressed genes most of them involved in translation, basic transcription, DNA replication, amino acids metabolism and defence mechanisms, and 147 genes with fluctuated profile including transporters, oxidation-reduction process related genes and few metabolic genes.

In summary, the studies of two metabolic related TFs in S. acidocaldarius, BarR and FadRSa, shed light on their function and regulatory mechanisms. In addition, the transcriptome data of S. solfataricus not only reveals genome-wide alteration of gene expression during growth phase transition, but also provide a rich source of information for further studies by the archaea research community.

Place, publisher, year, edition, pages
Stockholm: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 2018. p. 51
Keywords
Archaea, Sulfolobus, Transcription regulation, Lrp, TetR, BarR, ChIP-seq, RNA-seq, Transcriptome, growth phase transition
National Category
Natural Sciences
Research subject
Molecular Bioscience
Identifiers
urn:nbn:se:su:diva-153538 (URN)978-91-7797-189-4 (ISBN)978-91-7797-190-0 (ISBN)
Public defence
2018-04-27, Högbomsalen, Geovetenskapens Hus, Svante Arrhenius väg 12, Stockholm, 10:00 (English)
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Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.

Available from: 2018-04-04 Created: 2018-03-09 Last updated: 2018-03-22Bibliographically approved

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