 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 04, 2024 |
| Title |
Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium |
| Organism |
Chlamydomonas reinhardtii |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short- and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition.
|
| |
|
| Overall design |
Sampling of Chlamydomonas CC-4532 cells cultivated photoheterotrophically (TAP) under Fe-starvation condition (0 uM Fe-EDTA). Samples were collected at multiple timepoints from biological duplicate cultures after washing in TAP medium lacking Fe. Two time courses were collected. A short time course with t=0 (pre-wash), 0 (post-wash), 5, 10, 15, 30, 60, 120, and 240 min. A long time course with t= 0, 0.5, 1, 2, 4, 8, 12, 24 and 48 hours.
Please note that, for long time course, the GSE44611/PRJNA190650 samples were re-used/re-analyzed together with the short time course data:
GSM1087792 C.reinhardtii_Fe_Long_0_hours SRX245324 SAMN01924672
GSM1087793 C.reinhardtii_Fe_Long_0.5_hours SRX245325 SAMN01924673
GSM1087794 C.reinhardtii_Fe_Long_1_hours SRX245326 SAMN01924674
GSM1087795 C.reinhardtii_Fe_Long_2_hours SRX245327 SAMN01924675
GSM1087796 C.reinhardtii_Fe_Long_4_hours SRX245328 SAMN01924676
GSM1087797 C.reinhardtii_Fe_Long_8_hours SRX245329 SAMN01924677
GSM1087798 C.reinhardtii_Fe_Long_12_hours SRX245330 SAMN01924678
GSM1087799 C.reinhardtii_Fe_Long_24_hours SRX245331 SAMN01924679
GSM1087800 C.reinhardtii_Fe_Long_48_hours SRX245332 SAMN01924680
|
| |
|
| Contributor(s) |
Liu HW, Urzica EI, Gallaher SD, Merchant SS |
| Citation(s) |
23983122 |
| |
| Submission date |
Apr 04, 2024 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Sean D. Gallaher |
| Organization name |
UC Berkeley
|
| Department |
California Institute for Quantitative Biosciences
|
| Lab |
Sabeeha Merchant
|
| Street address |
176 Stanley Hall, room 408
|
| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL15922 |
Illumina HiSeq 2000 (Chlamydomonas reinhardtii) |
|
| Samples (18)
|
| GSM8187517 |
C.reinhardtii, short Fe timecourse, 0 min pre-wash, rep 1 |
| GSM8187518 |
C.reinhardtii, short Fe timecourse, 0 min pre-wash, rep 2 |
| GSM8187519 |
C.reinhardtii, short Fe timecourse, 0 min post-wash, rep 1 |
| GSM8187520 |
C.reinhardtii, short Fe timecourse, 0 min post-wash, rep 2 |
| GSM8187521 |
C.reinhardtii, short Fe timecourse, 5 min, rep 1 |
| GSM8187522 |
C.reinhardtii, short Fe timecourse, 5 min, rep 2 |
| GSM8187523 |
C.reinhardtii, short Fe timecourse, 10 min, rep 1 |
| GSM8187524 |
C.reinhardtii, short Fe timecourse, 10 min, rep 2 |
| GSM8187525 |
C.reinhardtii, short Fe timecourse, 15 min, rep 1 |
| GSM8187526 |
C.reinhardtii, short Fe timecourse, 15 min, rep 2 |
| GSM8187527 |
C.reinhardtii, short Fe timecourse, 30 min, rep 1 |
| GSM8187528 |
C.reinhardtii, short Fe timecourse, 30 min, rep 2 |
| GSM8187529 |
C.reinhardtii, short Fe timecourse, 60 min, rep 1 |
| GSM8187530 |
C.reinhardtii, short Fe timecourse, 60 min, rep 2 |
| GSM8187531 |
C.reinhardtii, short Fe timecourse, 120 min, rep 1 |
| GSM8187532 |
C.reinhardtii, short Fe timecourse, 120 min, rep 2 |
| GSM8187533 |
C.reinhardtii, short Fe timecourse, 240 min, rep 1 |
| GSM8187534 |
C.reinhardtii, short Fe timecourse, 240 min, rep 2 |
|
| Relations |
| Reanalysis of |
GSM1087792 |
| Reanalysis of |
GSM1087793 |
| Reanalysis of |
GSM1087794 |
| Reanalysis of |
GSM1087795 |
| Reanalysis of |
GSM1087796 |
| Reanalysis of |
GSM1087797 |
| Reanalysis of |
GSM1087798 |
| Reanalysis of |
GSM1087799 |
| Reanalysis of |
GSM1087800 |
| BioProject |
PRJNA1096253 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE263199_Fe_timecourses.FPKMs.tsv.gz |
1.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...