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| Status |
Public on Oct 24, 2013 |
| Title |
Systems-level analysis of N-starvation induced modifications of carbon metabolism in a Chlamydomonas starchless mutant |
| Organism |
Chlamydomonas reinhardtii |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To understand the molecular basis underlying increased triacylglycerol accumulation in starchless Chlamydomonas mutants, we undertook comparative time course transcriptomics of sta6 (CC-4348), a cw strain purported to represent the parental STA6 strain (CC-4349), and 3 independent STA6 strains (STA6-C2, STA6-C4 and STA6-C6, generated by complementation of sta6, CC-4565, –4566 and –4567) in the context of nitrogen deprivation. Despite the N starvation induced dramatic remodeling of the transcriptome, there are relatively few differences (5 x 102) between sta6 and STA6, the most dramatic of which are in the abundance of transcripts encoding key regulated or rate-limiting steps in central carbon metabolism, specifically ICL1, MAS1, TAL1, FBP1 and PCK1, suggestive of increased carbon movement towards hexosephosphate in sta6 by up-regulation of the glyoxylate pathway and gluconeogenesis. Enzyme assays validated the increase in isocitrate lyase and malate synthase activities. Targeted metabolite analysis indicates increased succinate and malate, increased Glc-6-P and decreased fructose-1,6-bisphosphate, which documents the impact of these changes. Comparisons of the independent datasets in multiple strains allowed the delineation of a sequence of events in a global N-starvation response in Chlamydomonas, starting within minutes with up-regulation of alternative N assimilation routes and carbohydrate synthesis and subsequently a more gradual up-regulation of genes encoding enzymes of TAG synthesis. Finally, genome re-sequencing analysis indicated that i) the deletion in sta6 extends into the neighboring gene, RBO1, and ii) a commonly-used STA6 strain (CC-4349) as well as the sequenced reference (CC-503) are not congenic with respect to sta6 (CC-4348), underscoring the importance of using complemented strains for more rigorous assignment of phenotype to genotype.
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| Overall design |
The transcriptomes of five different Chlamydomonas strains (wild type CC-4349, sta6 mutant (CC-4348),and three indepdent STA6 strains (STA6-C2, STA6-C4 and STA6-C6) are profiled by RNA-Seq in timecourse experiments after the transition to minus nitrogen
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| Contributor(s) |
Blaby I, Glaesener A, Mettler T, Fitz-Gibbon S, Gallaher S, Liu B, Boyle N, Kropat J, Stitt M, Johnson S, Benning C, Pellegrini M, Casero D, Merchant S |
| Citation(s) |
24280389 |
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| Submission date |
Oct 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabeeha Merchant |
| E-mail(s) |
merchant@chem.ucla.edu
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| Phone |
310-825-8300
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| Organization name |
University of California Los Angeles
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| Department |
Department of Chemistry and Biochemistry
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| Street address |
607 Charles E. Young Drive East
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095-1569 |
| Country |
USA |
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| Platforms (2) |
| GPL15083 |
Illumina Genome Analyzer IIx (Chlamydomonas reinhardtii) |
| GPL17828 |
Illumina HiSeq 1000 (Chlamydomonas reinhardtii) |
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| Samples (31)
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| GSM1249022 |
Chlamydomonas reinhardtii CC-4349 minus N 0h SMNBcwN0.TS |
| GSM1249023 |
Chlamydomonas reinhardtii CC-4349 minus N 0.5h SMNBcwN05.TS |
| GSM1249024 |
Chlamydomonas reinhardtii CC-4349 minus N 2h SMNBcwN2.TS |
| GSM1249025 |
Chlamydomonas reinhardtii CC-4349 minus N 4h SMNBcwN4.TS |
| GSM1249026 |
Chlamydomonas reinhardtii CC-4349 minus N 8h SMNBcwN8.TS |
| GSM1249027 |
Chlamydomonas reinhardtii CC-4349 minus N 12h SMNBcwN12TS |
| GSM1249028 |
Chlamydomonas reinhardtii CC-4349 minus N 24h SMNBcwN24TS |
| GSM1249029 |
Chlamydomonas reinhardtii CC-4349 minus N 48h SMNBcwN48TS |
| GSM1249030 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 0h SMNBs6N0.TS |
| GSM1249031 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 0.5h SMNBs6N05TS |
| GSM1249032 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 2h SMNBs6N2.TS |
| GSM1249033 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 4h SMNBs6N4.TS |
| GSM1249034 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 8h SMNBs6N8.TS |
| GSM1249035 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 12h SMNBs6N12TS |
| GSM1249036 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 24h SMNBs6N24TS |
| GSM1249037 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 48h SMNBs6N48TS |
| GSM1249038 |
Chlamydomonas reinhardtii CC-4349 minus N 0.5h SMIBcwN05.TP1 |
| GSM1249039 |
Chlamydomonas reinhardtii CC-4349 minus N 4h SMIBcwN4.TP1 |
| GSM1249040 |
Chlamydomonas reinhardtii CC-4349 minus N 48h SMIBcwN48TP1 |
| GSM1249041 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 0.5h SMIBs6N05.TP1 |
| GSM1249042 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 4h SMIBs6N4.TP1 |
| GSM1249043 |
Chlamydomonas reinhardtii CC-4348 sta6 minus N 48h SMIBs6N48TP1 |
| GSM1249044 |
Chlamydomonas reinhardtii CC-4565 STA6 minus N 0.5h SMIBC2N05.TP1 |
| GSM1249045 |
Chlamydomonas reinhardtii CC-4565 STA6 minus N 4h SMIBC2N4.TP1 |
| GSM1249046 |
Chlamydomonas reinhardtii CC-4565 STA6 minus N 48h SMIBC2N48TP1 |
| GSM1249047 |
Chlamydomonas reinhardtii CC-4566 STA6 minus N 0.5h SMIBC4N05.TP1 |
| GSM1249048 |
Chlamydomonas reinhardtii CC-4566 STA6 minus N 4h SMIBC4N4.TP1 |
| GSM1249049 |
Chlamydomonas reinhardtii CC-4566 STA6 minus N 48h SMIBC4N48TP1 |
| GSM1249050 |
Chlamydomonas reinhardtii CC-4567 STA6 minus N 0.5h SMIBC6N05.TP1 |
| GSM1249051 |
Chlamydomonas reinhardtii CC-4567 STA6 minus N 4h SMIBC6N4.TP1 |
| GSM1249052 |
Chlamydomonas reinhardtii CC-4567 STA6 minus N 48h SMIBC6N48TP1 |
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| Relations |
| BioProject |
PRJNA223676 |
| SRA |
SRP031856 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE51602_ssmerchant_Expression_GEO_2013Oct.txt.gz |
3.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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