Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla

Waltman, Peter H.; Guo, Jian; Reistetter, Emily Nahas; Purvine, Samuel; Ansong, Charles K.; van Baren, Marijke J.; Wong, Chee-Hong; Wei, Chia-Lin; Smith, Richard D.; Callister, Stephen J.; Stuart, Joshua M.; Worden, Alexandra Z.; Mills, Ken

doi:10.1371/journal.pone.0155839

Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla

Journal Article · Tue Jul 19 00:00:00 EDT 2016 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0155839· OSTI ID:1342328

Waltman, Peter H. ^[1]; Guo, Jian ^[2]; Reistetter, Emily Nahas ^[2]; Purvine, Samuel ^[3]; Ansong, Charles K. ^[3]; van Baren, Marijke J. ^[2]; Wong, Chee-Hong ^[4]; Wei, Chia-Lin ^[4]; Smith, Richard D. ^[3]; Callister, Stephen J. ^[3]; Stuart, Joshua M. ^[1]; Worden, Alexandra Z. ^[5]; Mills, Ken ^[6]

Univ. of California, Santa Cruz, CA (United States)
Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States); Univ. of California, Santa Cruz, CA (United States); Canadian Inst. for Advanced Research, Toronto (Canada)
Queen's Univ., Belfast, Northern Ireland (United Kingdom)

Micromonas is a unicellular green alga that belongs to the prasinophytes, a sister lineage to land plants. This picoeukaryotic (<2 μm diameter) alga is widespread in the marine environment but still not understood at the cellular level. Here, we examine the mRNA and protein level changes that take place over the course of the day-night cycle using mid-exponential nutrient replete cultures of Micromonas pusilla CCMP1545 grown and analyzed in biological triplicate. During the experiment, samples were collected at key transition points during the diel for evaluation using high-throughput LC-MS proteomics. We also sequenced matched mRNA samples from the same time points, using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels using both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including the codon usage and the length of the 3’ UTR. Collectively, our studies provide insights into the regulation of the proteome over a diel as relationships between the transcriptional and translational programs in the widespread marine green alga Micromonas.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1342328

Report Number(s):: PNNL-SA--115265; 47672; KP1601030

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 7 Vol. 11; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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