title: Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.
abstract: 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.
authors.affiliation: University of California at Santa Cruz, Baskin School of Engineering, Santa Cruz, California, 95064, United States of America.
authors.forename: Peter H
authors.initials: PH
authors.lastname: Waltman
authors.affiliation: Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America.
authors.forename: Jian
authors.initials: J
authors.lastname: Guo
authors.affiliation: Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America.
authors.forename: Emily Nahas
authors.initials: EN
authors.lastname: Reistetter
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
authors.forename: Samuel
authors.initials: S
authors.lastname: Purvine
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
authors.forename: Charles K
authors.initials: CK
authors.lastname: Ansong
authors.affiliation: Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America.
authors.forename: Marijke J
authors.initials: MJ
authors.lastname: van Baren
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, 94598, United States of America.
authors.forename: Chee-Hong
authors.initials: CH
authors.lastname: Wong
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, 94598, United States of America.
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Callister
authors.affiliation: University of California at Santa Cruz, Baskin School of Engineering, Santa Cruz, California, 95064, United States of America.
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Stuart
authors.affiliation: Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America.|University of California Santa Cruz, Department of Ocean Sciences, Santa Cruz, California, 95064, United States of America.|Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, Canada, M5G 1Z8.
authors.forename: Alexandra Z
authors.initials: AZ
authors.lastname: Worden
mesh_terms: D020413:3' Untranslated Regions; D020418:Algal Proteins / Q000235:genetics* / Q000378:metabolism; D000460:Chlorophyta / Q000235:genetics* / Q000378:metabolism; D003062:Codon; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D058977:Molecular Sequence Annotation; D017440:Photoperiod; D010788:Photosynthesis / Q000235:genetics; D014176:Protein Biosynthesis; D040901:Proteomics; D048030:RNA, Algal / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D020413:3' Untranslated Regions; D020418:Algal Proteins; D003062:Codon; D048030:RNA, Algal; D012333:RNA, Messenger