Document Type

Article

Publication Date

12-2019

DOI

10.1038/s41597-019-0308-y

Publication Title

Scientific Data

Volume

6

Pages

303 (1-6)

Abstract

The heterotrophic marine bacterium, Ruegeria pomeroyi, was experimentally cultured under environmentally realistic carbon conditions and with a tracer-level addition of 13C-labeled leucine to track bacterial protein biosynthesis through growth phases. A combination of methods allowed observation of real-time bacterial protein production to understand metabolic priorities through the different growth phases. Over 2000 proteins were identified in each experimental culture from exponential and stationary growth phases. Within two hours of the 13C-labeled leucine addition, R. pomeroyi significantly assimilated the newly encountered substrate into new proteins. This dataset provides a fundamental baseline for understanding growth phase differences in molecular physiology of a cosmopolitan marine bacterium.

Rights

© The Author(s) 2019

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files associated with this article.

Data Availability

Article states:

"Data Records

Figshare File 117: Calculations used to derive the amount of 13C-labeled leucine incorporated into cells. File is in .docx format.

Figshare File 417: Proteomics data from the growth experiment (the proteomics without 13C label). The first column contains the protein identifer (Uniprot accession), followed by the protein length, then the total number of unique peptides detected for that protein across all biological and technical replicates (‘No. Unique Peptides Across All Replicates). The subsequent columns contain the total spectral counts and Normalized Spectral Abundance Factor values for each mass spectrometry analysis, (e.g., Early Exp 1, the frst technical replicate for early exponential stage). Table is in .xlsx format.

Figshare File 517: Proteomics data from the 13C-labeled leucine experiment. The data are arranged similarly to Figshare File 4, except the last 4 columns are indicators of label incorporation into the protein. An asterisk in the column indicates that a peptide with a 13C label was detected for that protein. Table is in .xlsx format.

Figshare File 617: Raw proteomics mass spectrometry fles record. Files were deposited in the online repository PRIDE under the ProteomExchange with identifer PXD00866127. The frst column of the table contains the file name, the second column is the file format, third is how the file was produced, and fourth is the growth stage the data are derived from. Table is in .xlsx format."

Code Availability

"Figshare File 217: Parameters file used for Comet searches of mass spectrometry data. File is in .docx format.

Figshare File 317: Parameters file used for Abacus analysis of Comet search results. File is in .docx format."

Data location as cited in reference 17 is: https://doi.org/10.6084/m9.figshare.c.4675310.v1.

Data location as cited in reference 27 is: https://identifiers.org/pride.project:PXD008661.

Original Publication Citation

Krayushkina, D., Timmins-Schiffman, E., Faux, J., May, D. H., Riffle, M., Harvey, H. R., & Nunn, B. L. (2019). Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi. Scientific Data, 6, 303. doi:10.1038/s41597-019-0308-y

ORCID

0000-0001-7746-7758 (Harvey)

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