RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process
Abstract
:1. Introduction
2. Materials and Methods
2.1. Growth and Harvesting of Bacterial Cultures
2.2. Extraction of RNA from Bacterial Cells
2.3. Preparation and Sequencing of Directional RNA-Seq Library
2.4. Mapping of Reads to the Genome Sequence and Analysis of Differential Expression
2.5. Verification of RNA-Seq Data by Quantitative RT-PCR
3. Results and Discussion
3.1. New Information on the Transcriptome under N2-Fixing Conditions Provided by RNA-Seq Compared to Previous Microarray-Based Transcriptome Analyses
3.2. The Higher Sensitivity of RNA-Seq Confirms Known Regulation Patterns
3.3. The Quest for Alternative Nitrogen Sources during Nitrogen Fixation
3.4. Motility Fostered by N2-Deplete Environment–Search for More Favourable Niches?
3.5. Increased Energy Requirements under Diazotrophic Reflected in Transcriptome
3.6. Suppression of Vitamin Biosynthesis during N2-Fixation
3.7. Down-Regulation of Ribosomal Genes Corresponding to Decreased Growth Rates
3.8. Differential Expression of Transcriptional Regulators
3.9. Preparing for Sustained N Starvation
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
Abbreviations
BNF | Biological nitrogen fixation |
COGs | Cluster of orthologous groups |
DEGs | Differentially expressed genes |
EMP | Embden–Meyerhof–Parnas pathway |
GTP | Guanosine triphosphate |
nif-cluster | Nitrogen fixation gene cluster |
ORFs | Open reading frames |
padj | Benjamini–Hochberg adjusted p-value |
PHB | poly-ß-hydroxybutyrate |
PPP | Pentose Phosphate Pathway |
PRPP | 5-phosphoribosyl 1-pyrophosphate |
RPKM | Reads Per Kilobase per Million mapped reads |
SM | Synthetic malate |
T2SS | Type 2 protein secretion system |
T6SS | Type 6 protein secretion system |
TCA | Tricarboxylic acid cycle |
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Solaiyappan Mani, S.; Reinhold-Hurek, B. RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process. Microorganisms 2021, 9, 1888. https://doi.org/10.3390/microorganisms9091888
Solaiyappan Mani S, Reinhold-Hurek B. RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process. Microorganisms. 2021; 9(9):1888. https://doi.org/10.3390/microorganisms9091888
Chicago/Turabian StyleSolaiyappan Mani, Shanmugam, and Barbara Reinhold-Hurek. 2021. "RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process" Microorganisms 9, no. 9: 1888. https://doi.org/10.3390/microorganisms9091888