Limits...
Whole-Transcriptome Analysis of Verocytotoxigenic Escherichia coli O157:H7 (Sakai) Suggests Plant-Species-Specific Metabolic Responses on Exposure to Spinach and Lettuce Extracts.

Crozier L, Hedley PE, Morris J, Wagstaff C, Andrews SC, Toth I, Jackson RW, Holden NJ - Front Microbiol (2016)

Bottom Line: Plant extracts were used to reduce heterogeneity inherent in plant-microbe interactions and remove the effect of plant immunity.Induction of stress-response genes reflected the apparent physiological status of the bacterial genes in each extract, as a result of glutamate-dependent acid resistance, nutrient stress, or translational stalling.A large proportion of differentially regulated genes are uncharacterized (annotated as hypothetical), which could indicate yet to be described functional roles associated with plant interaction for E. coli O157:H7 Sakai.

View Article: PubMed Central - PubMed

Affiliation: Cell and Molecular Sciences, The James Hutton Institute Dundee, UK.

ABSTRACT
Verocytotoxigenic Escherichia coli (VTEC) can contaminate crop plants, potentially using them as secondary hosts, which can lead to food-borne infection. Currently, little is known about the influence of the specific plant species on the success of bacterial colonization. As such, we compared the ability of the VTEC strain, E. coli O157:H7 'Sakai,' to colonize the roots and leaves of four leafy vegetables: spinach (Spinacia oleracea), lettuce (Lactuca sativa), vining green pea (Pisum sativum), and prickly lettuce (Lactuca serriola), a wild relative of domesticated lettuce. Also, to determine the drivers of the initial response on interaction with plant tissue, the whole transcriptome of E. coli O157:H7 Sakai was analyzed following exposure to plant extracts of varying complexity (spinach leaf lysates or root exudates, and leaf cell wall polysaccharides from spinach or lettuce). Plant extracts were used to reduce heterogeneity inherent in plant-microbe interactions and remove the effect of plant immunity. This dual approach provided information on the initial adaptive response of E. coli O157:H7 Sakai to the plant environment together with the influence of the living plant during bacterial establishment and colonization. Results showed that both the plant tissue type and the plant species strongly influence the short-term (1 h) transcriptional response to extracts as well as longer-term (10 days) plant colonization or persistence. We show that propagation temperature (37 vs. 18°C) has a major impact on the expression profile and therefore pre-adaptation of bacteria to a plant-relevant temperature is necessary to avoid misleading temperature-dependent wholescale gene-expression changes in response to plant material. For each of the plant extracts tested, the largest group of (annotated) differentially regulated genes were associated with metabolism. However, large-scale differences in the metabolic and biosynthetic pathways between treatment types indicate specificity in substrate utilization. Induction of stress-response genes reflected the apparent physiological status of the bacterial genes in each extract, as a result of glutamate-dependent acid resistance, nutrient stress, or translational stalling. A large proportion of differentially regulated genes are uncharacterized (annotated as hypothetical), which could indicate yet to be described functional roles associated with plant interaction for E. coli O157:H7 Sakai.

No MeSH data available.


Related in: MedlinePlus

GO term enrichment for response to plant extracts. GO terms for E. coli O157:H7 (Sakai) genes that were significantly differentially expressed following growth in spinach leaf lysates (A), spinach root exudates (B), CWPS extracts from spinach (C) or lettuce (D), relative to their respective controls. Data was obtained from the Gene Ontology Consortium website. Significantly enriched Biological Processes are shown for induced (blue) and repressed genes (red), using GO-Slim and selected GO-complete categories (indicated by ‘∗’; full list in Supplementary Table S2). The numbers of individual genes are adjacent to each bar on the charts.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4940412&req=5

Figure 3: GO term enrichment for response to plant extracts. GO terms for E. coli O157:H7 (Sakai) genes that were significantly differentially expressed following growth in spinach leaf lysates (A), spinach root exudates (B), CWPS extracts from spinach (C) or lettuce (D), relative to their respective controls. Data was obtained from the Gene Ontology Consortium website. Significantly enriched Biological Processes are shown for induced (blue) and repressed genes (red), using GO-Slim and selected GO-complete categories (indicated by ‘∗’; full list in Supplementary Table S2). The numbers of individual genes are adjacent to each bar on the charts.

Mentions: To determine which groups of genes were affected by exposure to the plant extracts, analysis was performed for genes annotated with GO terms. GO-term enrichment enabled identification of over- or under-represented groups of genes that were differentially expressed by each treatment. Analysis of significantly enriched (p < 0.05) ‘Biological Processes’ were performed on a broad-scale level using GO-Slim terms, and supplemented with GO-Complete for a more a detailed breakdown of smaller classes of genes (Figure 3; Supplementary Table S2). When all of the plant extract treatments are considered together, Metabolic Processes is the category with the largest number (41–510) of affected genes, although there are clear differences between treatments in the ratio and number of up and down-regulated genes, and for different specific metabolic classes (Figure 3). Exposure to spinach leaf lysate resulted in differential expression of 364 genes in metabolic processes (163 induced, 201 repressed). The highest level of enrichment was for induced genes associated with lipid transport (six induced; sevenfold enriched) and there was significant positive enrichment for translation-related processes (translation, rRNA metabolism, regulation of translation) and protein metabolism (48, and 45 induced, respectively). Genes involved in primary metabolism were subject to a high degree of control with 127 genes induced and 162 repressed. Following exposure to spinach root exudates, a large number of genes associated with metabolic processes were down-regulated genes (340), with half as many (170) induced. In general, more down-regulated genes were enriched for the different GO term categories compared to those induced (67 vs. 33% in Figure 3B). The highest level of enrichment for repressed genes was seen for those associated with translation-related processes (translation, rRNA metabolism, regulation of translation), of which 84 were down-regulated and just 12 induced; this pattern is the reverse of that seen above for spinach leaf lysate. The highest enrichment for induced genes (14) was in response to stress. These expression effects thus suggest that exposure to spinach root exudates caused increased stress combined with reduced translation capacity.


Whole-Transcriptome Analysis of Verocytotoxigenic Escherichia coli O157:H7 (Sakai) Suggests Plant-Species-Specific Metabolic Responses on Exposure to Spinach and Lettuce Extracts.

Crozier L, Hedley PE, Morris J, Wagstaff C, Andrews SC, Toth I, Jackson RW, Holden NJ - Front Microbiol (2016)

GO term enrichment for response to plant extracts. GO terms for E. coli O157:H7 (Sakai) genes that were significantly differentially expressed following growth in spinach leaf lysates (A), spinach root exudates (B), CWPS extracts from spinach (C) or lettuce (D), relative to their respective controls. Data was obtained from the Gene Ontology Consortium website. Significantly enriched Biological Processes are shown for induced (blue) and repressed genes (red), using GO-Slim and selected GO-complete categories (indicated by ‘∗’; full list in Supplementary Table S2). The numbers of individual genes are adjacent to each bar on the charts.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940412&req=5

Figure 3: GO term enrichment for response to plant extracts. GO terms for E. coli O157:H7 (Sakai) genes that were significantly differentially expressed following growth in spinach leaf lysates (A), spinach root exudates (B), CWPS extracts from spinach (C) or lettuce (D), relative to their respective controls. Data was obtained from the Gene Ontology Consortium website. Significantly enriched Biological Processes are shown for induced (blue) and repressed genes (red), using GO-Slim and selected GO-complete categories (indicated by ‘∗’; full list in Supplementary Table S2). The numbers of individual genes are adjacent to each bar on the charts.
Mentions: To determine which groups of genes were affected by exposure to the plant extracts, analysis was performed for genes annotated with GO terms. GO-term enrichment enabled identification of over- or under-represented groups of genes that were differentially expressed by each treatment. Analysis of significantly enriched (p < 0.05) ‘Biological Processes’ were performed on a broad-scale level using GO-Slim terms, and supplemented with GO-Complete for a more a detailed breakdown of smaller classes of genes (Figure 3; Supplementary Table S2). When all of the plant extract treatments are considered together, Metabolic Processes is the category with the largest number (41–510) of affected genes, although there are clear differences between treatments in the ratio and number of up and down-regulated genes, and for different specific metabolic classes (Figure 3). Exposure to spinach leaf lysate resulted in differential expression of 364 genes in metabolic processes (163 induced, 201 repressed). The highest level of enrichment was for induced genes associated with lipid transport (six induced; sevenfold enriched) and there was significant positive enrichment for translation-related processes (translation, rRNA metabolism, regulation of translation) and protein metabolism (48, and 45 induced, respectively). Genes involved in primary metabolism were subject to a high degree of control with 127 genes induced and 162 repressed. Following exposure to spinach root exudates, a large number of genes associated with metabolic processes were down-regulated genes (340), with half as many (170) induced. In general, more down-regulated genes were enriched for the different GO term categories compared to those induced (67 vs. 33% in Figure 3B). The highest level of enrichment for repressed genes was seen for those associated with translation-related processes (translation, rRNA metabolism, regulation of translation), of which 84 were down-regulated and just 12 induced; this pattern is the reverse of that seen above for spinach leaf lysate. The highest enrichment for induced genes (14) was in response to stress. These expression effects thus suggest that exposure to spinach root exudates caused increased stress combined with reduced translation capacity.

Bottom Line: Plant extracts were used to reduce heterogeneity inherent in plant-microbe interactions and remove the effect of plant immunity.Induction of stress-response genes reflected the apparent physiological status of the bacterial genes in each extract, as a result of glutamate-dependent acid resistance, nutrient stress, or translational stalling.A large proportion of differentially regulated genes are uncharacterized (annotated as hypothetical), which could indicate yet to be described functional roles associated with plant interaction for E. coli O157:H7 Sakai.

View Article: PubMed Central - PubMed

Affiliation: Cell and Molecular Sciences, The James Hutton Institute Dundee, UK.

ABSTRACT
Verocytotoxigenic Escherichia coli (VTEC) can contaminate crop plants, potentially using them as secondary hosts, which can lead to food-borne infection. Currently, little is known about the influence of the specific plant species on the success of bacterial colonization. As such, we compared the ability of the VTEC strain, E. coli O157:H7 'Sakai,' to colonize the roots and leaves of four leafy vegetables: spinach (Spinacia oleracea), lettuce (Lactuca sativa), vining green pea (Pisum sativum), and prickly lettuce (Lactuca serriola), a wild relative of domesticated lettuce. Also, to determine the drivers of the initial response on interaction with plant tissue, the whole transcriptome of E. coli O157:H7 Sakai was analyzed following exposure to plant extracts of varying complexity (spinach leaf lysates or root exudates, and leaf cell wall polysaccharides from spinach or lettuce). Plant extracts were used to reduce heterogeneity inherent in plant-microbe interactions and remove the effect of plant immunity. This dual approach provided information on the initial adaptive response of E. coli O157:H7 Sakai to the plant environment together with the influence of the living plant during bacterial establishment and colonization. Results showed that both the plant tissue type and the plant species strongly influence the short-term (1 h) transcriptional response to extracts as well as longer-term (10 days) plant colonization or persistence. We show that propagation temperature (37 vs. 18°C) has a major impact on the expression profile and therefore pre-adaptation of bacteria to a plant-relevant temperature is necessary to avoid misleading temperature-dependent wholescale gene-expression changes in response to plant material. For each of the plant extracts tested, the largest group of (annotated) differentially regulated genes were associated with metabolism. However, large-scale differences in the metabolic and biosynthetic pathways between treatment types indicate specificity in substrate utilization. Induction of stress-response genes reflected the apparent physiological status of the bacterial genes in each extract, as a result of glutamate-dependent acid resistance, nutrient stress, or translational stalling. A large proportion of differentially regulated genes are uncharacterized (annotated as hypothetical), which could indicate yet to be described functional roles associated with plant interaction for E. coli O157:H7 Sakai.

No MeSH data available.


Related in: MedlinePlus