Transcriptome remodeling associated with chronological aging in the dinoflagellate, Karenia brevis

Johnson, Jillian G.; Morey, Jeanine S.; Neely, Marion G.; Ryan, James C.; Dolah, Frances M. Van

doi:10.1016/j.margen.2011.08.005

Cited by 34 publications

(28 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…, ), consistent with a secondary metabolite, the PKSs are among a large set of transcripts downregulated during stationary phase, which is consistent with a role in primary, rather than secondary metabolism (Johnson et al. ). There were no differences observed in PKS transcript levels expressed in a toxic isolate of K. brevis as compared to a nontoxic isolate when analyzed by microarray or qPCR.…”

Section: Discussionsupporting

confidence: 63%

Subcellular localization of dinoflagellate polyketide synthases and fatty acid synthase activity

Dolah

Zippay

Pezzolesi

et al. 2013

Journal of Phycology

Self Cite

View full text Add to dashboard Cite

Dinoflagellates are prolific producers of polyketide secondary metabolites. Dinoflagellate polyketide synthases (PKSs) have sequence similarity to Type I PKSs, megasynthases that encode all catalytic domains on a single polypeptide. However, in dinoflagellate PKSs identified to date, each catalytic domain resides on a separate transcript, suggesting multiprotein complexes similar to Type II PKSs. Here, we provide evidence through coimmunoprecipitation that single-domain ketosynthase and ketoreductase proteins interact, suggesting a predicted multiprotein complex. In Karenia brevis (C.C. Davis) Gert Hansen & Ø. Moestrup, previously observed chloroplast localization of PKSs suggested that brevetoxin biosynthesis may take place in the chloroplast. Here, we report that PKSs are present in both cytosol and chloroplast. Furthermore, brevetoxin is not present in isolated chloroplasts, raising the question of what chloroplast-localized PKS enzymes might be doing. Antibodies to K. brevis PKSs recognize cytosolic and chloroplast proteins in Ostreopsis cf. ovata Fukuyo, and Coolia monotis Meunier, which produce different suites of polyketide toxins, suggesting that these PKSs may share common pathways. Since PKSs are closely related to fatty acid synthases (FAS), we sought to determine if fatty acid biosynthesis colocalizes with either chloroplast or cytosolic PKSs. [(3) H]acetate labeling showed fatty acids are synthesized in the cytosol, with little incorporation in chloroplasts, consistent with a Type I FAS system. However, although 29 sequences in a K. brevis expressed sequence tag database have similarity (BLASTx e-value <10(-10) ) to PKSs, no transcripts for either Type I (cytosolic) or Type II (chloroplast) FAS are present. Further characterization of the FAS complexes may help to elucidate the functions of the PKS enzymes identified in dinoflagellates.

show abstract

Section: Discussionsupporting

confidence: 63%

Subcellular localization of dinoflagellate polyketide synthases and fatty acid synthase activity

Dolah

Zippay

Pezzolesi

et al. 2013

Journal of Phycology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Percentages of gene responses ranged from 1.1% to 29% (Okamoto and Hastings, 2003;Moustafa et al, 2010;Morey et al, 2011;Johnson et al, 2012). The present study revealed that 8.6% of genes responded to CuSO 4 .…”

Section: Transcriptomic Responses In Dinoflagellatesmentioning

confidence: 46%

“…With modern technological advances, recent molecular methods (e.g., microarray and next generation sequencing) could allow analyses of the genomes and transcriptomes of dinoflagellates (Okamoto and Hastings, 2003;Moustafa et al, 2010;Toulza et al, 2010;Yang et al, 2011;Johnson et al, 2012;Shoguchi et al, 2013;Zhang et al, 2014a,c;Lin et al, 2015;Xiang et al, 2015). This has increased our understanding of the extraordinary genomic features of dinoflagellates, particularly the evolution of the eukaryotic genome.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of transcription and photosynthesis inhibition in the harmful dinoflagellate Prorocentrum minimum in response to the biocide copper sulfate

Guo

Lim

2016

Harmful Algae

View full text Add to dashboard Cite

“…Using massively parallel signature sequencing (MPSS), Moustafa et al [19] found 73% of the transcriptome of Alexandrium tamarense unchanged under a variety of conditions. A similar magnitude of transcriptome restructuring is found concurrent with the entry into stationary phase in K. brevis (29%) [20] and Alexandrium minutum (36%) [21]. However, microarray and MPSS cannot determine what mechanism(s) are responsible for the measured changes in transcript abundance.…”

Section: Introductionmentioning

confidence: 85%

Global Analysis of mRNA Half-Lives and de novo Transcription in a Dinoflagellate, Karenia brevis

Morey

Dolah

2013

PLoS ONE

Self Cite

View full text Add to dashboard Cite

Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the roles of differential mRNA stability and de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. These isolated fractions were then used for analysis of global mRNA stability and de novo transcription by hybridization to a K. brevis microarray. Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed to pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer). Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 144 h, with a median of 33 hours. Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages. Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes. One such family of proteins involved in post-transcriptional regulation in chloroplasts and mitochondria, the pentatricopeptide repeat (PPR) proteins, had dramatically shorter half-lives when compared to the arrayed transcriptome. As transcript abundances for PPR proteins were previously observed to rapidly increase in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of increases in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.

show abstract

Transcriptome remodeling associated with chronological aging in the dinoflagellate, Karenia brevis

Cited by 34 publications

References 74 publications

Subcellular localization of dinoflagellate polyketide synthases and fatty acid synthase activity

Subcellular localization of dinoflagellate polyketide synthases and fatty acid synthase activity

Genome-wide analysis of transcription and photosynthesis inhibition in the harmful dinoflagellate Prorocentrum minimum in response to the biocide copper sulfate

Global Analysis of mRNA Half-Lives and de novo Transcription in a Dinoflagellate, Karenia brevis

Contact Info

Product

Resources

About