Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique.
Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative ferroxidase rubrerythrin transcripts increased to a lesser extent. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome. Thus, we propose sfuC as a marker gene for indicating iron limitation in marine metatranscriptomic and metaproteomic ecological surveys. The marked proteome reduction was not directly correlated to changes in the transcriptome, implicating post-transcriptional regulatory mechanisms as modulators of protein expression. Two RNA-binding proteins, CspE and CspL, correlated well with iron availability, suggesting that they may contribute to the observed differences between the transcriptome and proteome. We propose a model in which the RNA-binding activity of CspE and CspL selectively enables protein synthesis of the iron acquisition protein SfuC during transient growth-limiting episodes of iron scarcity.
Smith
Daniel P
DP
Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America.
Kitner
Joshua B
JB
Norbeck
Angela D
AD
Clauss
Therese R
TR
Lipton
Mary S
MS
Schwalbach
Michael S
MS
Steindler
Laura
L
Nicora
Carrie D
CD
Smith
Richard D
RD
Giovannoni
Stephen J
SJ
D020561:Alphaproteobacteria / Q000166:cytology / Q000187:drug effects* / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D049109:Cell Proliferation / Q000187:drug effects; D003080:Cold Temperature; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D005798:Genes, Bacterial / Q000235:genetics; D007501:Iron / Q000494:pharmacology; D000090463:Iron Deficiencies; D020411:Oligonucleotide Array Sequence Analysis; D014176:Protein Biosynthesis / Q000187:drug effects; D040901:Proteomics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012623:Seawater / Q000382:microbiology*; D017262:Siderophores / Q000378:metabolism; D014158:Transcription, Genetic / Q000187:drug effects
D001426:Bacterial Proteins; D012333:RNA, Messenger; D017262:Siderophores; D007501:Iron
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