Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria
- Published
- Accepted
- Subject Areas
- Ecology, Marine Biology, Microbiology
- Keywords
- Microbiology, proteomics, exponential growth, marine bacteria, growth phase, stationary phase, signature metabolism, heterotrophs, copiotrophs
- Copyright
- © 2016 Muthusamy et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria. PeerJ Preprints 4:e1804v1 https://doi.org/10.7287/peerj.preprints.1804v1
Abstract
Exponentially growing bacteria are rarely found in nature. Instead, bacteria spend most of their lifetime in a slow- or non-proliferating state, a state that is occasionally interrupted by an increase in accessible nutrients. To successfully compete for pulses of nutrients, copiotrophic marine bacteria have adaptations that allow them to change their metabolism to support exponential growth in response to nutrients and to return to stationary phase when nutrients return to normal scarcity. The molecular details of these adaptations can be observed through proteome profiles, i.e. relative abundances of proteins in cells, and how they change between different conditions. We developed proteome profiles during exponential and stationary phase conditions for three model organisms representing major marine bacterioplankton lineages. 22500-3000 proteins per isolate were detected, representing large proportions of each proteome (67-87%). A shift from protein synthesis and other processes typically associated with active growth, to proteins essential for nutrient scavenging, was observed during transition into stationary phase. The three isolates differed in magnitude of their responses and in how enzymes of different metabolisms responded. Some of the differences can be seen as differences in implementation of a shared strategy, such as an increase in enzymes involved in carbon storage, while other differences are best described as differences in strategy. We thus observed the proteome reflection of “signature metabolisms” in the three isolates – distinct metabolic adaptations to environmental circumstances. These findings have direct implications for the interpretation of proteomic and genetic data from microbes in natural environments.
Author Comment
This is the first version of the manuscript made publically available.
Supplemental Information
Figure 1: Growth curves of three phylogenetically distinct representatives of marine bacterioplankton in nutrient rich marine broth medium
Cells were harvested for proteomic analysis at the time points indicated by arrows for exponential phase (solid arrows) and stationary phase (hatched arrows) respectively. Error bars denote the standard deviation of three biological replicates. If not visible, error bars are within symbols.
Figure 2: Overall growth phase-associated changes in proteomes
(A, C, E) Relative abundances of detected proteins grouped into top level SEED categories: (A) MED92, (C) MED193 and (E) MED134. The three replicates are shown for exponential phase (open circles) and stationary phase (filled circles). Note the log scale on Y-axes. (B, D, F) Counts (y-axis) of increasing (right-pointing triangles), stable (circles) and decreasing proteins (left-pointing triangles) and relative abundances (size of symbols): (B) MED92, (D) MED193 and (F) MED134. Proteins that belong in more than one category were counted in all. Note that y-axes have been cut at 200; categories that exceed 200 were inserted at 200 with a label denoting the proper count.
Figure 3: Top 50 most abundant significantly differentially expressed proteins
Relative abundance and log2 fold changes for the top 50 most abundant significantly differentially expressed proteins. (A, C and E) proteins decreasing from exponential growth to stationary phase. (B, D and F) proteins increasing from exponential growth to stationary phase. (A, B) MED92; (C, D) MED193; and (E, F) MED134. Color codes denote the different functional categories in the SEED classification, Blue: Protein metabolism, Green: Membrane transporters, Orange: Stress response, Purple: Carbon metabolism, Grey: Amino acids and derivatives and Yellow: Respiration.
Figure 4: Changes in relative proportions of membrane transporter categories across growth phases
(A, C, E) Exponential phase in (A) MED92, (C) MED193 and (E) MED134. (B, D, F) Stationary phase in (B) MED92, (D) MED193 and (F) MED134. The areas of rectangles are proportional to relative abundances of categories at the three levels of the TC classification. Top-level categories are denoted with colored rectangles and labels in bold; second level categories are normal font labels spanning several rectangles; and third level categories have labels inside rectangles. Transporter identification according to TC categories.
Figure 5: Carbon metabolisms
(A, C, E) Relative abundances, averaged over triplicates for each growth phase, for enzymes in five important carbon metabolisms in (A) MED92, (C) MED193 and (E) MED134. Significantly differentially abundant proteins have names in bold font. (B, D, F) Glycolysis (EMP), TCA cycle and glyoxylate shunt BioCyc pathways in (B) MED92, (D) MED193 and (F) MED134. Heatmap indicating log2 fold changes of stationary phase in relation to exponential phase. Grey arrows indicate stable, i.e. not significantly differentially abundant proteins. Thin black arrows indicate non detected proteins.
Figure 6: Phosphorus metabolism in all three isolates
List of significantly increasing and decreasing proteins in the SEED category phosphorus metabolism during transition into stationary phase. (A) MED92; (B) MED193; (C) MED134.
Individual protein abundances in MED92
Identified proteins with estimated fold change (FC and log2FC columns), false discovery rate (localfdr), readings per sample (exp1-3 for exponential phase; stat1-3 for stationary phase) and various other statistics. Green shades in the log2FC column indicate higher abundance in stationary phase, yellow shades indicate lower; the stronger the color, the larger the difference between growth phases. False discovery rates less than 5% are indicated with green color, above with red.
Individual protein abundances in MED193
Identified proteins with estimated fold change (FC and log2FC columns), false discovery rate (localfdr), readings per sample (exp1-3 for exponential phase; stat1-3 for stationary phase) and various other statistics. Green shades in the log2FC column indicate higher abundance in stationary phase, yellow shades indicate lower; the stronger the color, the larger the difference between growth phases. False discovery rates less than 5% are indicated with green color, above with red.
Individual protein abundances in MED134
Identified proteins with estimated fold change (FC and log2FC columns), false discovery rate (localfdr), readings per sample (exp1-3 for exponential phase; stat1-3 for stationary phase) and various other statistics. Green shades in the log2FC column indicate higher abundance in stationary phase, yellow shades indicate lower; the stronger the color, the larger the difference between growth phases. False discovery rates less than 5% are indicated with green color, above with red.
Top SEED category summaries
Approximate (order of magnitude precision) relative abundances of proteins summed over top categories of the SEED classification. Proteins classified in more than one category were counted in all categories. The calculation of relative 54abundances counted each protein only once. Log2 fold changes (log2fc) calculated as the ratio between means in stationary phase divided by means in exponential phase. Counts and abundances of the three protein groups, increasing (“Up”), stable and decreasing (“Down”) in the three isolates.
Relative protein abundances summed over second level SEED categories
Approximate (order of magnitude precision) relative abundances of proteins summed over second level categories of the SEED classification. Proteins classified in more than one category were counted in all categories. The calculation of relative abundances counted each protein only once. Log2 fold changes (log2fc) calculated as the ratio between means in stationary phase divided by means in exponential phase.
Relative protein abundances summed over third level SEED categories
Approximate (order of magnitude precision) relative abundances of proteins summed over third level categories of the SEED classification. Proteins classified in more than one category were counted in all categories. The calculation of relative abundances counted each protein only once. Log2 fold changes (log2fc) calculated as the ratio between means in stationary phase divided by means in exponential phase.
Summary of transporter families
Number of detected and differentially abundant protein in the three strains per TCDB transporter family.
Proteins detected in MED92 with their TCDB classifications
The trsphierarchy field describes each protein's place in the TCDB hierarchy. See the TCDB website for explanations (http://www.tcdb.org/superfamily.php). All the other fields, except trspfamily, were taken from the corresponding MED92 SAM table (S1).
Proteins detected in MED193 with their TCDB classifications
The trsphierarchy field describes each protein's place in the TCDB hierarchy. See the TCDB website for explanations (http://www.tcdb.org/superfamily.php). All the other fields, except trspfamily, were taken from the corresponding MED193 SAM table (S2).
Proteins detected in MED134 with their TCDB classifications
The trsphierarchy field describes each protein's place in the TCDB hierarchy. See the TCDB website for explanations (http://www.tcdb.org/superfamily.php). All the other fields, except trspfamily, were taken from the corresponding MED134 SAM table (S3).