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ABSTRACT:
PROVIDER: PRJNA1287306 | ENA |
REPOSITORIES: ENA
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Project description:We examine how the transcriptome of Prochlorococcus strain NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002. Significant changes in the Prochlorococcus transcriptome were evident within six hours of co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48-hour experiment, indicating that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely correspond to reduced stress conditions within Prochlorococcus, as inferred from decreases in relative abundance for transcripts encoding DNA repair enzymes and many members of the âhigh-light inducibleâ family of stress response proteins. Notable changes were also seen in transcripts encoding components of the photosynthetic apparatus (particularly an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains. At each of 7 timepoints, samples from 3 biological replicate co-cultures are compared to 3 biological replicate axenic Prochlorococcus cultures that serve as a control.
2016-06-10 | E-GEOD-73511 | biostudies-arrayexpress
Project description:We examine how the transcriptome of Prochlorococcus strain NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002. Significant changes in the Prochlorococcus transcriptome were evident within six hours of co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48-hour experiment, indicating that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely correspond to reduced stress conditions within Prochlorococcus, as inferred from decreases in relative abundance for transcripts encoding DNA repair enzymes and many members of the ‘high-light inducible’ family of stress response proteins. Notable changes were also seen in transcripts encoding components of the photosynthetic apparatus (particularly an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains.
2016-06-10 | GSE73511 | GEO
Project description:The DOM-A complex regulates cell growth and proliferation in Drosophila. Analogous to the mammalian Tip60–p400 complex, DOM-A integrates two epigenetic effectors: a SWR1-type ATPase (Domino-A) that mediates histone exchange and the Tip60/KAT5 acetyltransferase. We identified Xbp1, a conserved transcriptional regulator of the unfolded protein response (UPR), as a tight interactor of the immunopurified DOM-A complex and explored the functional consequences of this association. Integrative analysis of Xbp1 and DOM-A occupancy in proliferating cells, together with reciprocal protein depletion, revealed two distinct modes of Xbp1 chromatin binding. In a sequence-specific mode, Xbp1 recruits DOM-A to motif-bearing promoters of UPR genes. In a second, motif-independent mode, Xbp1 localizes to hundreds of high-confidence DOM-A binding sites that lack Xbp1 recognition motifs; these interactions depend on DOM-A, consistent with a “reverse targeting” mechanism. Consistent with functional coupling, depletion of DOM-A reduces Xbp1 protein abundance without affecting Xbp1 mRNA levels, suggesting post-translational stabilization of Xbp1 upon association with DOM-A. Together, these findings indicate that the genome-wide interplay between Xbp1 and DOM-A may integrate UPR signaling with the broader, DOM-mediated regulation of cell growth and proliferation.
2025-10-20 | E-MTAB-15796 | biostudies-arrayexpress
Project description:We examine how the transcriptome of Prochlorococcus strain NATL2A changes in response to extended light deprivation, both when grown alone and in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002.
2018-05-01 | GSE93197 | GEO
Project description:Prochlorococcus is an obligate marine microorganism which are dominant autotroph in tropical and subtropical central oceans. However, what is the low salinity boundary and how Prochlorococcus would response to low salinity exposure is still unknown. In this study, we first tested the growing salinity range of two Prochlorococcus strains, NATL1A and MED4, and then compared the global transcriptome of their low salinity acclimated cells and cells growing in normal seawater salinity. We found that MED4 could be acclimated in the lowest salinity of 25% and NATL1A could be acclimated in the lowest salinity of 28%. Measurement of the effective quantum yield of PSII photochemistry (Fv/Fm) indicated that both strains were stressed when growing in salinity lower than 34%. The transcriptomic response of NATL1A and MED4 were approximately different, with much more genes having changed transcript abundance in NATL1A than in MED4. To cope with low salinity, NATL1A downregulated the transcript of most genes involved in translation, ribosomal structure and biogenesis, while MED4 upregulated those genes. Moreover, low salinity acclimated NATL1A cells suppressed ATP-producing genes and induced the expression of photosynthesis related genes, while low salinity acclimated MED4 upregulated ATP-producing genes and downregulated photosynthesis related genes. These results indicate that the response to low salinity stress of different Prochlorococcus strains could be distinct. The study provided the first glimpse into the growing salinity range of Prochlorococcus cells and their global gene expression changes due to low salinity stress.
2022-02-02 | GSE195946 | GEO
Project description:Prochlorococcus contributes significantly to ocean primary productivity. The link between primary productivity and iron in specific ocean regions is well established and iron limitation of Prochlorococcus cell division rates in these regions has been shown. However, the extent of ecotypic variation in iron metabolism among Prochlorococcus and the molecular basis for differences is not understood. Here, we examine the growth and transcriptional response of Prochlorococcus strains, MED4 and MIT9313, to changing iron concentrations. During steady state, MIT9313 sustains growth at an order-of-magnitude lower iron concentration than MED4. To explore this difference, we measured the whole-genome transcriptional response of each strain to abrupt iron starvation and rescue. Only four of the 1159 orthologs of MED4 and MIT9313 were differentially expressed in response to iron in both strains. However, in each strain, the expression of over a hundred additional genes changed, many of which are in labile genomic regions, suggesting a role for lateral gene transfer in establishing diversity of iron metabolism among Prochlorococcus. Furthermore, we found that MED4 lacks three genes near the iron-deficiency-induced gene (idiA) that are present and induced by iron stress in MIT9313. These genes are interesting targets for studying the adaptation of natural Prochlorococcus assemblages to local iron conditions as they show more diversity than other genomic regions in environmental metagenomic databases.
2011-01-11 | GSE26533 | GEO
Project description:Prochlorococcus is a cyanobacterium of abundance in open ocean environments and little is known of its iron requirements or iron metabolism. We used microarrays to measure the whole-genome expression response of Prochlorococcus MED4 and MIT9313 to iron stress and recovery from iron stress.
2011-01-11 | E-GEOD-26533 | biostudies-arrayexpress