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| Status |
Public on Oct 10, 2016 |
| Title |
Global gene expression profiles of Mycobacterium smegmatis under shock and mild nutrient starvation |
| Organism |
Mycolicibacterium smegmatis MC2 155 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Mycobacteria are known to be non-spore forming but very hardy: the bacilli can for instance survive starvation in zero-nutrient saline in a non-replicating state. Recently we reported that mycobacteria in fact can undergo cellular differentiation when exposed to different starvation conditions. The presence of traces of nutrients triggers the development of a new, ‘small resting cell’ form (SMRCs). Saline shock-starved large resting cells (LARCs), which did not show cell size or surface changes when observed by scanning electron microscopy, remodeled their internal structure to the septated, multi-nucleoided cells seen during differentiation to SMRCs. Here we conduct RNA-seq to gain greater insights into whether starvation elicited a distinct developmental pathway. Comparative transcriptome analysis of SMRC and LARC development revealed largely overlapping sets of differentially expressed regulatory and metabolic genes. These transcriptome data are consistent with a mycobacterial starvation-induced differentiation program in which at first septated, multi-nuceloided cells are generated. Under zero-nutrient conditions bacteria terminate development at this stage as LARCs. In the presence of traces of a carbon source, these multi-nucleoided cells continue differentiation into mono-nuleoided SMRCs.
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| Overall design |
Exponentially growing M. smegmatis in rich 7H9 medium (0h sample, baseline) was transferred to PBS or PBS-Tween80 and RNA was sampled and sequenced after 1h and 3h to capture immediate responses, and after 24h when LARC formation in PBS cultures and SMRC formation in PBS-Tween80 culture are completed. In addition we sampled 14d old starved cultures to determine long term gene expression changes.
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| Contributor(s) |
Wu M, Gengenbacher M, Chung JC, Chen SL, Mollenkopf H, Kaufmann SH, Dick T |
| Citation(s) |
27784279 |
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| Submission date |
Jun 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Dick |
| E-mail(s) |
thomas_dick@nuhs.edu.sg
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| Phone |
+65 6601 1018
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| Organization name |
National University of Singapore
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| Department |
Microbiology
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| Lab |
Antibacterial Drug Discovery Laboratory
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| Street address |
Centre for Translational Medicine, Block MD6, 15-01, 14 Medical Drive
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| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
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| Platforms (1) |
| GPL20580 |
Illumina HiSeq 1500 (Mycobacterium smegmatis str. MC2 155) |
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| Samples (30)
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| GSM1715079 |
SMRCs 1h, biological rep1 |
| GSM1715080 |
SMRCs 1h, biological rep2 |
| GSM1715081 |
SMRCs 1h, biological rep3 |
| GSM1715082 |
SMRCs 3h, biological rep1 |
| GSM1715083 |
SMRCs 3h, biological rep2 |
| GSM1715084 |
SMRCs 3h, biological rep3 |
| GSM1715085 |
SMRCs 24h, biological rep1 |
| GSM1715086 |
SMRCs 24h, biological rep2 |
| GSM1715087 |
SMRCs 24h, biological rep3 |
| GSM1715088 |
SMRCs 14d, biological rep1 |
| GSM1715089 |
SMRCs 14d, biological rep2 |
| GSM1715090 |
SMRCs 14d, biological rep3 |
| GSM1715091 |
LARCs 0h, biological rep1 |
| GSM1715092 |
LARCs 0h, biological rep2 |
| GSM1715093 |
LARCs 0h, biological rep3 |
| GSM1715094 |
LARCs 1h, biological rep1 |
| GSM1715095 |
LARCs 1h, biological rep2 |
| GSM1715096 |
LARCs 1h, biological rep3 |
| GSM1715097 |
LARCs 3h, biological rep1 |
| GSM1715098 |
LARCs 3h, biological rep2 |
| GSM1715099 |
LARCs 3h, biological rep3 |
| GSM1715100 |
LARCs 24h, biological rep1 |
| GSM1715101 |
LARCs 24h, biological rep2 |
| GSM1715102 |
LARCs 24h, biological rep3 |
| GSM1715103 |
LARCs 14d, biological rep1 |
| GSM1715104 |
LARCs 14d, biological rep2 |
| GSM1715105 |
LARCs 14d, biological rep3 |
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| Relations |
| BioProject |
PRJNA287328 |
| SRA |
SRP059625 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE69983_Differential_expression_analyses_LARCs_14d.txt.gz |
210.4 Kb |
(ftp)(http) |
TXT |
| GSE69983_Differential_expression_analyses_LARCs_1h.txt.gz |
209.2 Kb |
(ftp)(http) |
TXT |
| GSE69983_Differential_expression_analyses_LARCs_24h.txt.gz |
209.1 Kb |
(ftp)(http) |
TXT |
| GSE69983_Differential_expression_analyses_LARCs_3h.txt.gz |
209.6 Kb |
(ftp)(http) |
TXT |
| GSE69983_Differential_expression_analyses_SMRCs_14d.txt.gz |
212.0 Kb |
(ftp)(http) |
TXT |
| GSE69983_Differential_expression_analyses_SMRCs_1h.txt.gz |
208.9 Kb |
(ftp)(http) |
TXT |
| GSE69983_Differential_expression_analyses_SMRCs_24h.txt.gz |
211.4 Kb |
(ftp)(http) |
TXT |
| GSE69983_Differential_expression_analyses_SMRCs_3h.txt.gz |
209.6 Kb |
(ftp)(http) |
TXT |
| GSE69983_Normalised_counts_LARCs_14d.txt.gz |
253.1 Kb |
(ftp)(http) |
TXT |
| GSE69983_Normalised_counts_LARCs_1h.txt.gz |
252.8 Kb |
(ftp)(http) |
TXT |
| GSE69983_Normalised_counts_LARCs_24h.txt.gz |
250.8 Kb |
(ftp)(http) |
TXT |
| GSE69983_Normalised_counts_LARCs_3h.txt.gz |
252.8 Kb |
(ftp)(http) |
TXT |
| GSE69983_Normalised_counts_SMRCs_14d.txt.gz |
254.7 Kb |
(ftp)(http) |
TXT |
| GSE69983_Normalised_counts_SMRCs_1h.txt.gz |
252.6 Kb |
(ftp)(http) |
TXT |
| GSE69983_Normalised_counts_SMRCs_24h.txt.gz |
255.4 Kb |
(ftp)(http) |
TXT |
| GSE69983_Normalised_counts_SMRCs_3h.txt.gz |
254.3 Kb |
(ftp)(http) |
TXT |
| GSE69983_Raw_counts.txt.gz |
289.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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