skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

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 tomore » 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.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1342328
Report Number(s):
PNNL-SA-115265
Journal ID: ISSN 1932-6203; 47672; KP1601030
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: PLoS ONE; Journal Volume: 11; Journal Issue: 7
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Environmental Molecular Sciences Laboratory

Citation Formats

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., and Mills, Ken. Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. United States: N. p., 2016. Web. doi:10.1371/journal.pone.0155839.
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. Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. United States. doi:10.1371/journal.pone.0155839.
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., and Mills, Ken. Tue . "Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla". United States. doi:10.1371/journal.pone.0155839.
@article{osti_1342328,
title = {Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla},
author = {Waltman, Peter H. and Guo, Jian and Reistetter, Emily Nahas and Purvine, Samuel and Ansong, Charles K. and van Baren, Marijke J. and Wong, Chee-Hong and Wei, Chia-Lin and Smith, Richard D. and Callister, Stephen J. and Stuart, Joshua M. and Worden, Alexandra Z. and Mills, Ken},
abstractNote = {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.},
doi = {10.1371/journal.pone.0155839},
journal = {PLoS ONE},
number = 7,
volume = 11,
place = {United States},
year = {Tue Jul 19 00:00:00 EDT 2016},
month = {Tue Jul 19 00:00:00 EDT 2016}
}