KEGG pathway analysis of <i>P</i>. <i>atrosepticum</i> genes up- and down-regulated in cross-protected cells compared to growing ones (p-value ≤0.05).

<p>KEGG pathway analysis of <i>P</i>. <i>atrosepticum</i> genes up- and down-regulated in cross-protected cells compared to growing ones (p-value ≤0.05).</p

Summary of RNA-seq reads mapping to reference genes.

<p>Summary of RNA-seq reads mapping to reference genes.</p

Modules and pathways of genes expressed differentially in <i>P</i>. <i>atrosepticum</i> during growth in nutrient rich medium and after the formation of cross-protected phenotype under starvation conditions.

<p>Manually assigned modules and pathways are marked with stars.</p

Cross-protective effect in <i>P</i>. <i>atrosepticum</i> SCRI1043 cells during starvation.

<p><i>Pba</i> cells of late log growth phase were transferred to carbon-deficient medium (primary stress). To elucidate the dynamics of the formation of cross-protected phenotype during starvation induced stress, <i>Pba</i> cells after 0, 4, 8, 24 and 48 h of starvation were subjected to secondary stresses: 50°C for 5 min (white columns), 2.5 mM H₂O₂ for 1 h (gray columns) or 20% NaCl for 1 h (black columns). Cells were plated prior to and right after secondary stresses. The survival of cells starving for 0, 4, 8, 24 and 48 h was assessed by the comparison of cell titer prior and after secondary stress factor exposure. Values are the average ± SD of three biological replicates.</p

Global Gene Expression Analysis of Cross-Protected Phenotype of <i>Pectobacterium atrosepticum</i>

<div><p>The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Under some of these conditions, bacteria encounter absence of nutrients and persist, acquiring new properties related to resistance to a variety of stress factors (cross-protection). Although many studies describe the phenomenon of cross-protection and several regulatory components that induce the formation of resistant cells were elucidated, the global comparison of the physiology of cross-protected phenotype and growing cells has not been performed. In our study, we took advantage of RNA-Seq technology to gain better insights into the physiology of cross-protected cells on the example of a harmful phytopathogen, <i>Pectobacterium atrosepticum</i> (<i>Pba</i>) that causes crop losses all over the world. The success of this bacterium in plant colonization is related to both its virulence potential and ability to persist effectively under various stress conditions (including nutrient deprivation) retaining the ability to infect plants afterwards. In our previous studies, we showed <i>Pba</i> to be advanced in applying different adaptive strategies that led to manifestation of cell resistance to multiple stress factors. In the present study, we determined the period necessary for the formation of cross-protected <i>Pba</i> phenotype under starvation conditions, and compare the transcriptome profiles of non-adapted growing cells and of adapted cells after the cross-protective effect has reached the maximal level. The obtained data were verified using qRT-PCR. Genes that were expressed differentially (DEGs) in two cell types were classified into functional groups and categories using different approaches. As a result, we portrayed physiological features that distinguish cross-protected phenotype from the growing cells.</p></div

Number of DEGs assigned to a particular pathway by means of GO, KEGG and manual classification using different databases.

<p>Number of DEGs assigned to a particular pathway by means of GO, KEGG and manual classification using different databases.</p

Verification of RNA-Seq data.

<p>Expression levels of genes in cross-protected <i>P</i>. <i>atrosepticum</i> cells determined by RNA-Seq (black columns) and qPCR (grey columns) respective to unstressed growing cells (equal to zero).</p

Additional file 2: of The genome-wide transcription response to telomerase deficiency in the thermotolerant yeast Hansenula polymorpha DL-1

Supplementary tables presenting the data on differential expression of H. polymorpha DL-1 genes. Table S1 Differential expression of H. polymorpha DL-1 genes classified into KEGG groups. Table S2. Expression levels of H. polymorpha DL-1 genes related to telomere maintenance. Table S3. Expression levels of H. polymorpha DL-1 genes relevant to autophagy. Table S4. Expression levels of H. polymorpha DL-1 genes relevant to cell architecture and intracellular traffic. Table S5. Expression levels of H. polymorpha DL-1 genes related to DNA damage checkpoint signaling, DNA replication and repair. Table S6. Expression levels of H. polymorpha DL-1 antioxidant system and heat shock genes. Table S7. Expression levels of H. polymorpha DL-1 genes involved in glycolysis, gluconeogensis and pyruvate metabolism. Table S8. Expression levels of H. polymorpha DL-1 pentose phosphate pathway genes. Table S9. Expression levels of H. polymorpha DL-1 tricarboxylic acids cycle genes. Table S10. Expression levels of H. polymorpha DL-1 genes encoding cytochrom c oxidase and related proteins. Table S11. Expression levels of H. polymorpha DL-1 genes encoding the NADH dehodrogenase subunits. Table S12. Expression levels of H. polymorpha DL-1 genes encoding the ATP synthase subunits. Table S13. Expression of homologs of telomerase deletion signature genes of Saccharomyces cerevisiae described in Nautiyal et al. (2002). (PDF 418 kb

Additional file 1: of Age-dependent neuroinflammation and cognitive decline in a novel Ala152Thr-Tau transgenic mouse model of PSP and AD

Supplemental material and results. (PDF 5946 kb