Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.
Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (<2 μm diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expressi...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4951065?pdf=render |
| _version_ | 1811202925704249344 |
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| author | Peter H Waltman Jian Guo Emily Nahas Reistetter Samuel Purvine Charles K Ansong Marijke J van Baren Chee-Hong Wong Chia-Lin Wei Richard D Smith Stephen J Callister Joshua M Stuart Alexandra Z Worden |
| author_facet | Peter H Waltman Jian Guo Emily Nahas Reistetter Samuel Purvine Charles K Ansong Marijke J van Baren Chee-Hong Wong Chia-Lin Wei Richard D Smith Stephen J Callister Joshua M Stuart Alexandra Z Worden |
| author_sort | Peter H Waltman |
| collection | DOAJ |
| description | Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (<2 μm diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced 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 we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3' UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas. |
| first_indexed | 2024-04-12T02:47:11Z |
| format | Article |
| id | doaj.art-2584346cad1842d9bc0f7c2bc0019081 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T02:47:11Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-2584346cad1842d9bc0f7c2bc00190812022-12-22T03:51:07ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01117e015583910.1371/journal.pone.0155839Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.Peter H WaltmanJian GuoEmily Nahas ReistetterSamuel PurvineCharles K AnsongMarijke J van BarenChee-Hong WongChia-Lin WeiRichard D SmithStephen J CallisterJoshua M StuartAlexandra Z WordenMicromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (<2 μm diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced 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 we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3' UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.http://europepmc.org/articles/PMC4951065?pdf=render |
| spellingShingle | Peter H Waltman Jian Guo Emily Nahas Reistetter Samuel Purvine Charles K Ansong Marijke J van Baren Chee-Hong Wong Chia-Lin Wei Richard D Smith Stephen J Callister Joshua M Stuart Alexandra Z Worden Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. PLoS ONE |
| title | Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. |
| title_full | Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. |
| title_fullStr | Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. |
| title_full_unstemmed | Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. |
| title_short | Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. |
| title_sort | identifying aspects of the post transcriptional program governing the proteome of the green alga micromonas pusilla |
| url | http://europepmc.org/articles/PMC4951065?pdf=render |
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