Limits...
Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique.

Smith DP, Kitner JB, Norbeck AD, Clauss TR, Lipton MS, Schwalbach MS, Steindler L, Nicora CD, Smith RD, Giovannoni SJ - PLoS ONE (2010)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America.

ABSTRACT
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.

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Genes transcribed during iron limitation were different from stationary phase genes.The four clusters indicate up-regulation of similar condition-specific mRNA. Symbols for each microarray sample (open circles) were manually positioned on a circle according to each sample's iron availability and growth rate. Genes were “attracted” to the samples in which they were most abundant. Larger points indicate genes with larger condition-to-condition variation; a key for the 10 largest points in each cluster is provided. The complete list of gene locations for this graph can be found in Supplementary Table S1.
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pone-0010487-g002: Genes transcribed during iron limitation were different from stationary phase genes.The four clusters indicate up-regulation of similar condition-specific mRNA. Symbols for each microarray sample (open circles) were manually positioned on a circle according to each sample's iron availability and growth rate. Genes were “attracted” to the samples in which they were most abundant. Larger points indicate genes with larger condition-to-condition variation; a key for the 10 largest points in each cluster is provided. The complete list of gene locations for this graph can be found in Supplementary Table S1.

Mentions: Seventy-eight percent of these genes are found in Figure 2's early and late iron stress clusters. Bullet points in the first column indicate contiguous loci.


Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique.

Smith DP, Kitner JB, Norbeck AD, Clauss TR, Lipton MS, Schwalbach MS, Steindler L, Nicora CD, Smith RD, Giovannoni SJ - PLoS ONE (2010)

Genes transcribed during iron limitation were different from stationary phase genes.The four clusters indicate up-regulation of similar condition-specific mRNA. Symbols for each microarray sample (open circles) were manually positioned on a circle according to each sample's iron availability and growth rate. Genes were “attracted” to the samples in which they were most abundant. Larger points indicate genes with larger condition-to-condition variation; a key for the 10 largest points in each cluster is provided. The complete list of gene locations for this graph can be found in Supplementary Table S1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2864753&req=5

pone-0010487-g002: Genes transcribed during iron limitation were different from stationary phase genes.The four clusters indicate up-regulation of similar condition-specific mRNA. Symbols for each microarray sample (open circles) were manually positioned on a circle according to each sample's iron availability and growth rate. Genes were “attracted” to the samples in which they were most abundant. Larger points indicate genes with larger condition-to-condition variation; a key for the 10 largest points in each cluster is provided. The complete list of gene locations for this graph can be found in Supplementary Table S1.
Mentions: Seventy-eight percent of these genes are found in Figure 2's early and late iron stress clusters. Bullet points in the first column indicate contiguous loci.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America.

ABSTRACT
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.

Show MeSH