|
| Status |
Public on Dec 24, 2015 |
| Title |
Transcriptome signatures for robustness of Lactococcus lactis IL1403 |
| Platform organism |
Lactococcus lactis |
| Sample organism |
Lactococcus lactis subsp. lactis Il1403 |
| Experiment type |
Expression profiling by array
|
| Summary |
Recently, we demonstrated that fermentation conditions strongly impact on subsequent survival of Lactococcus lactis strain MG1363 during heat and oxidative stress, two important parameters during spray drying. Moreover, employment of a transcriptome-phenotype matching approach revealed groups of genes associated with robustness towards heat and/or oxidative stress. To investigate if other strains have similar or distinct transcriptome signatures for robustness, we applied a similar transcriptome-robustness phenotype matching approach on the L. lactis strains IL1403, KF147 and SK11. These strains were employed in an identical fermentation regime as was performed earlier for strain MG1363 which consisted of twelve conditions, varying in the presence of salt and/or oxygen, as well as fermentation temperature and pH. In the exponential phase of growth, cells were harvested for transcriptome analysis and assessment of heat and oxidative stress survival phenotypes. The variation in fermentation conditions resulted in differences in heat and oxidative stress survival up to five 10-log units. Effects of the fermentation conditions on stress survival of the L. lactis strains were typically strain-dependent, although the fermentation conditions had mainly similar effects on the growth characteristics of the different strains. Association of transcriptomes and robustness phenotypes identified highly strain-specific transcriptome signatures for robustness, indicating that multiple mechanism exist to increase robustness and, as a consequence, robustness of each strain requires individual optimization. However, a relatively small overlap in the transcriptome responses of the strains was also identified and this generic transcriptome signature included genes previously associated with stress (ctsR and lplL) and novel genes, including nanE and genes encoding transport proteins. The transcript levels of these genes can function as indicators of robustness and could aid in selection of fermentation parameters, potentially resulting in more optimal robustness during spray drying.
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| Overall design |
two connected loops, both containing samples derived on a single day (sample 1-6, sample 7-13)
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| |
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| Contributor(s) |
Dijkstra AR, Alkema W, Starrenburg MJ, Hugenholtz J, van Hijum SA, Bron PA |
| Citation(s) |
27973578 |
| |
| Submission date |
Aug 13, 2015 |
| Last update date |
Dec 22, 2016 |
| Contact name |
Annereinou Dijkstra |
| E-mail(s) |
annereinou.dijkstra@nizo.com
|
| Organization name |
NIZO food research
|
| Street address |
Kernhemseweg 2
|
| City |
Ede |
| ZIP/Postal code |
6718 ZB |
| Country |
Netherlands |
| |
|
| Platforms (1) |
| GPL20800 |
NIZO food research Lactococcus lactis IL1403 60-mer array |
|
| Samples (32)
|
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| This SubSeries is part of SuperSeries: |
| GSE72045 |
Transcriptome signatures for robustness of Lactococcus lactis |
|
| Relations |
| BioProject |
PRJNA292813 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE72042_253132110002-1_1.txt.gz |
445.5 Kb |
(ftp)(http) |
TXT |
| GSE72042_253132110002-1_2.txt.gz |
449.1 Kb |
(ftp)(http) |
TXT |
| GSE72042_253132110002-2_1.txt.gz |
449.0 Kb |
(ftp)(http) |
TXT |
| GSE72042_253132110002-2_2.txt.gz |
448.8 Kb |
(ftp)(http) |
TXT |
| GSE72042_253132110002-3_1.txt.gz |
445.3 Kb |
(ftp)(http) |
TXT |
| GSE72042_253132110002-3_2.txt.gz |
432.3 Kb |
(ftp)(http) |
TXT |
| GSE72042_253132110002-4_1.txt.gz |
432.5 Kb |
(ftp)(http) |
TXT |
| GSE72042_253132110002-4_2.txt.gz |
432.3 Kb |
(ftp)(http) |
TXT |
| GSE72042_253432110001-1_1.txt.gz |
438.4 Kb |
(ftp)(http) |
TXT |
| GSE72042_253432110001-1_2.txt.gz |
431.1 Kb |
(ftp)(http) |
TXT |
| GSE72042_253432110001-2_1.txt.gz |
438.1 Kb |
(ftp)(http) |
TXT |
| GSE72042_253432110001-2_2.txt.gz |
443.1 Kb |
(ftp)(http) |
TXT |
| GSE72042_253432110001-3_1.txt.gz |
441.2 Kb |
(ftp)(http) |
TXT |
| GSE72042_253432110001-3_2.txt.gz |
438.4 Kb |
(ftp)(http) |
TXT |
| GSE72042_253432110001-4_1.txt.gz |
434.8 Kb |
(ftp)(http) |
TXT |
| GSE72042_253432110001-4_2.txt.gz |
434.1 Kb |
(ftp)(http) |
TXT |
| GSE72042_IL_intensity_data.txt.gz |
251.5 Kb |
(ftp)(http) |
TXT |
| GSE72042_RAW.tar |
430.0 Kb |
(http)(custom) |
TAR |
| Processed data are available on Series record |
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