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Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria.

Meyer P, Cecchi G, Stolovitzky G - BMC Syst Biol (2014)

Bottom Line: We found that out of 857 globular enzymes, at least 219 have a discrete punctuate localization in the cytoplasm and catalyze the first or the last reaction in 60% of biosynthetic pathways.A Gene Ontology analysis of these enzymes reveals an enrichment of terms related to essential metabolic functions in growing cells.We conclude that active biochemical pathways inside the cytoplasm are organized spatially following a rule where their first or their last enzymes localize to effectively connect the different active pathways and thus could reflect the activity state of the cell's metabolic network.

View Article: PubMed Central - PubMed

Affiliation: IBM Computational Biology Center, Yorktown Heights, NY, USA. pmeyerr@us.ibm.com.

ABSTRACT

Background: Although much is understood about the enzymatic cascades that underlie cellular biosynthesis, comparatively little is known about the rules that determine their cellular organization. We performed a detailed analysis of the localization of E.coli GFP-tagged enzymes for cells growing exponentially.

Results: We found that out of 857 globular enzymes, at least 219 have a discrete punctuate localization in the cytoplasm and catalyze the first or the last reaction in 60% of biosynthetic pathways. A graph-theoretic analysis of E.coli's metabolic network shows that localized enzymes, in contrast to non-localized ones, form a tree-like hierarchical structure, have a higher within-group connectivity, and are traversed by a higher number of feed-forward and feedback loops than their non-localized counterparts. A Gene Ontology analysis of these enzymes reveals an enrichment of terms related to essential metabolic functions in growing cells. Given that these findings suggest a distinct metabolic role for localization, we studied the dynamics of cellular localization of the cell wall synthesizing enzymes in B. subtilis and found that enzymes localize during exponential growth but not during stationary growth.

Conclusions: We conclude that active biochemical pathways inside the cytoplasm are organized spatially following a rule where their first or their last enzymes localize to effectively connect the different active pathways and thus could reflect the activity state of the cell's metabolic network.

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Localized enzymes form a tree-like loop-dense network A matrix representing the connectivity of the 1214 different biochemical reactions of E.coli was constructed (see Additional file 1: Figure S1B). A. Left Diagram illustrating the clustering (cls) and within-group connectivity (wgc) of localized (green) and non-localized (blue) enzymes. Red edges represent inter-group connections. Dotted arrows represent pathways 1 & 2 connected via localized reactions. Right Diagram illustrates the distribution of randomly selected nodes constructed to compare mean loop density with nodes from localized enzymes. B. Left. Associated p-values of the KS-test for higher number of loops in nodes derived from localized enzymes compared to non- localized ones. Right. Four plots showing the Log-scale distributions of the number of loops for each node in localized (green) and non-localized (blue) enzymes. The type of loop is indicated top right. C. Table shows the associated p-values for higher number of loops per connection in nodes derived from localized enzymes compared to nodes chosen randomly.
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Fig3: Localized enzymes form a tree-like loop-dense network A matrix representing the connectivity of the 1214 different biochemical reactions of E.coli was constructed (see Additional file 1: Figure S1B). A. Left Diagram illustrating the clustering (cls) and within-group connectivity (wgc) of localized (green) and non-localized (blue) enzymes. Red edges represent inter-group connections. Dotted arrows represent pathways 1 & 2 connected via localized reactions. Right Diagram illustrates the distribution of randomly selected nodes constructed to compare mean loop density with nodes from localized enzymes. B. Left. Associated p-values of the KS-test for higher number of loops in nodes derived from localized enzymes compared to non- localized ones. Right. Four plots showing the Log-scale distributions of the number of loops for each node in localized (green) and non-localized (blue) enzymes. The type of loop is indicated top right. C. Table shows the associated p-values for higher number of loops per connection in nodes derived from localized enzymes compared to nodes chosen randomly.

Mentions: Enzyme localization is present in most pathways of the E.coli metabolic network (Figure 1B & Additional file 1: Figure S1) and is prevalent in the first and last position (Figure 2D). In order to explore the properties of these localized enzymes when considering the complete E.coli set of metabolic reactions, we constructed a metabolic network using the KEGG definitions of compounds, reactions and enzymes (see Methods). The metabolic network is described by an asymmetric Boolean square matrix Mij of 1214 unique reactions where each reaction is associated to an enzyme and a non-zero matrix value mij = 1 indicates that the reaction i feeds into reaction j by producing a compound used by reaction j (see Additional file 4: Figure S2A). While trying to differentiate nodes of 189 reactions catalyzed by localized enzymes from 1025 others, we plotted for each node the number of outcoming reactions against the number of incoming reactions (Additional file 4: Figure S2B). Localized enzymes were found at low and high-connected nodes varying from 1 to 50, but no significant differences were found in the distributions of incoming or outcoming reactions, nor in length of shortest paths, when considering localized and non-localized enzymes (Additional file 4: Figure S2B insets). However, when the two classes where considered separately (Figure 3A left & Additional file 4: Figure S2B green and blue), we observed that localized reactions have a significantly higher probability to establish within-group connections (wgc) than non-localized ones have (0.0177 vs 0.0076 t-test z-score = 9.32 for a distribution choosing random nodes as shown in the right diagram of Figure 3A). Interestingly, this higher within-group connectivity does not result in higher within-group structure as localized reactions form less triangulations among themselves than localized ones, hence displaying a more tree-like hierarchical structure of connections (see green nodes left diagram Figure 3A and Additional file 4: Figure S2A). Triangulations were measured by the clustering coefficient, yielding 0.36 vs 0.5 for localized and non-localized reactions respectively (Kolmogorov-Smirnov, KS test. p-value < 1E-12, see Methods for details on scaffold triangulations for clustering coefficient).Figure 3


Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria.

Meyer P, Cecchi G, Stolovitzky G - BMC Syst Biol (2014)

Localized enzymes form a tree-like loop-dense network A matrix representing the connectivity of the 1214 different biochemical reactions of E.coli was constructed (see Additional file 1: Figure S1B). A. Left Diagram illustrating the clustering (cls) and within-group connectivity (wgc) of localized (green) and non-localized (blue) enzymes. Red edges represent inter-group connections. Dotted arrows represent pathways 1 & 2 connected via localized reactions. Right Diagram illustrates the distribution of randomly selected nodes constructed to compare mean loop density with nodes from localized enzymes. B. Left. Associated p-values of the KS-test for higher number of loops in nodes derived from localized enzymes compared to non- localized ones. Right. Four plots showing the Log-scale distributions of the number of loops for each node in localized (green) and non-localized (blue) enzymes. The type of loop is indicated top right. C. Table shows the associated p-values for higher number of loops per connection in nodes derived from localized enzymes compared to nodes chosen randomly.
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Fig3: Localized enzymes form a tree-like loop-dense network A matrix representing the connectivity of the 1214 different biochemical reactions of E.coli was constructed (see Additional file 1: Figure S1B). A. Left Diagram illustrating the clustering (cls) and within-group connectivity (wgc) of localized (green) and non-localized (blue) enzymes. Red edges represent inter-group connections. Dotted arrows represent pathways 1 & 2 connected via localized reactions. Right Diagram illustrates the distribution of randomly selected nodes constructed to compare mean loop density with nodes from localized enzymes. B. Left. Associated p-values of the KS-test for higher number of loops in nodes derived from localized enzymes compared to non- localized ones. Right. Four plots showing the Log-scale distributions of the number of loops for each node in localized (green) and non-localized (blue) enzymes. The type of loop is indicated top right. C. Table shows the associated p-values for higher number of loops per connection in nodes derived from localized enzymes compared to nodes chosen randomly.
Mentions: Enzyme localization is present in most pathways of the E.coli metabolic network (Figure 1B & Additional file 1: Figure S1) and is prevalent in the first and last position (Figure 2D). In order to explore the properties of these localized enzymes when considering the complete E.coli set of metabolic reactions, we constructed a metabolic network using the KEGG definitions of compounds, reactions and enzymes (see Methods). The metabolic network is described by an asymmetric Boolean square matrix Mij of 1214 unique reactions where each reaction is associated to an enzyme and a non-zero matrix value mij = 1 indicates that the reaction i feeds into reaction j by producing a compound used by reaction j (see Additional file 4: Figure S2A). While trying to differentiate nodes of 189 reactions catalyzed by localized enzymes from 1025 others, we plotted for each node the number of outcoming reactions against the number of incoming reactions (Additional file 4: Figure S2B). Localized enzymes were found at low and high-connected nodes varying from 1 to 50, but no significant differences were found in the distributions of incoming or outcoming reactions, nor in length of shortest paths, when considering localized and non-localized enzymes (Additional file 4: Figure S2B insets). However, when the two classes where considered separately (Figure 3A left & Additional file 4: Figure S2B green and blue), we observed that localized reactions have a significantly higher probability to establish within-group connections (wgc) than non-localized ones have (0.0177 vs 0.0076 t-test z-score = 9.32 for a distribution choosing random nodes as shown in the right diagram of Figure 3A). Interestingly, this higher within-group connectivity does not result in higher within-group structure as localized reactions form less triangulations among themselves than localized ones, hence displaying a more tree-like hierarchical structure of connections (see green nodes left diagram Figure 3A and Additional file 4: Figure S2A). Triangulations were measured by the clustering coefficient, yielding 0.36 vs 0.5 for localized and non-localized reactions respectively (Kolmogorov-Smirnov, KS test. p-value < 1E-12, see Methods for details on scaffold triangulations for clustering coefficient).Figure 3

Bottom Line: We found that out of 857 globular enzymes, at least 219 have a discrete punctuate localization in the cytoplasm and catalyze the first or the last reaction in 60% of biosynthetic pathways.A Gene Ontology analysis of these enzymes reveals an enrichment of terms related to essential metabolic functions in growing cells.We conclude that active biochemical pathways inside the cytoplasm are organized spatially following a rule where their first or their last enzymes localize to effectively connect the different active pathways and thus could reflect the activity state of the cell's metabolic network.

View Article: PubMed Central - PubMed

Affiliation: IBM Computational Biology Center, Yorktown Heights, NY, USA. pmeyerr@us.ibm.com.

ABSTRACT

Background: Although much is understood about the enzymatic cascades that underlie cellular biosynthesis, comparatively little is known about the rules that determine their cellular organization. We performed a detailed analysis of the localization of E.coli GFP-tagged enzymes for cells growing exponentially.

Results: We found that out of 857 globular enzymes, at least 219 have a discrete punctuate localization in the cytoplasm and catalyze the first or the last reaction in 60% of biosynthetic pathways. A graph-theoretic analysis of E.coli's metabolic network shows that localized enzymes, in contrast to non-localized ones, form a tree-like hierarchical structure, have a higher within-group connectivity, and are traversed by a higher number of feed-forward and feedback loops than their non-localized counterparts. A Gene Ontology analysis of these enzymes reveals an enrichment of terms related to essential metabolic functions in growing cells. Given that these findings suggest a distinct metabolic role for localization, we studied the dynamics of cellular localization of the cell wall synthesizing enzymes in B. subtilis and found that enzymes localize during exponential growth but not during stationary growth.

Conclusions: We conclude that active biochemical pathways inside the cytoplasm are organized spatially following a rule where their first or their last enzymes localize to effectively connect the different active pathways and thus could reflect the activity state of the cell's metabolic network.

Show MeSH