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Role of RfaH in Yersinia enterocolitica O:3

ABSTRACT: To assess the effects of rfaH mutation on gene expression, RNA sequencing was carried out using the RNA extracted from rfaH mutant and wild type bacteria cultivated at both 22˚C and 37˚C. Additionally, to differentiate between genes affected directly by the rfaH mutation and those affected by the O-antigen negative phenotype, the Y. enterocolitica O:3 strain YeO3-R1 missing the O-antigen was included in the RNA-sequencing study. At RT-grown bacteria altogether 77 (45 up- and 32 down-regulated) differentially expressed genes were identified. At 37ºC, on the other hand, 44 genes were differentially expressed; 14 genes up- and 30 genes down-regulated. The RNA-sequencing data of YeO3-R1 was available only for bacteria grown at 22˚C and the comparison revealed that 22 of the 102 genes were similarly differentially expressed both in rfaH and YeO3-R1 mutants. To detect genes regulated directly or indirectly by Hfq, deep RNA-seq was performed with RNA isolated from Y. enterocolitica wild-type strain 6471/76 and the YeO3-hfq::Km strain. Total RNA was isolated from two biological replicas of bacteria grown in LB to logarithmic phase (OD600 = 0.6) at two different temperatures, RT and 37°C. knocking out of Hfq affected the transcription of 346 genes at RT and 541 genes at 37°C, i.e., ca. 8 and 12.5 % of the Y. enterocolitica genes, respectively. At RT, of the 346 genes 216 genes were down- and 132 up-regulated, and at 37°C, of the 541 genes, 96 were down- and 445 up-regulated. A total of 95 genes were differentially expressed both at RT and 37°C; 27 showed down- and 59 up-regulated. For 9 genes opposite changes took place depending on the growth temperature.

ORGANISM(S): Yersinia enterocolitica

PROVIDER: GSE66516 | GEO | 2015/03/04

SECONDARY ACCESSION(S): PRJNA277186

REPOSITORIES: GEO

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Role of RfaH in Yersinia enterocolitica O:3

Project description:To assess the effects of rfaH mutation on gene expression, RNA sequencing was carried out using the RNA extracted from rfaH mutant and wild type bacteria cultivated at both 22?C and 37?C. Additionally, to differentiate between genes affected directly by the rfaH mutation and those affected by the O-antigen negative phenotype, the Y. enterocolitica O:3 strain YeO3-R1 missing the O-antigen was included in the RNA-sequencing study. At RT-grown bacteria altogether 77 (45 up- and 32 down-regulated) differentially expressed genes were identified. At 37ºC, on the other hand, 44 genes were differentially expressed; 14 genes up- and 30 genes down-regulated. The RNA-sequencing data of YeO3-R1 was available only for bacteria grown at 22?C and the comparison revealed that 22 of the 102 genes were similarly differentially expressed both in rfaH and YeO3-R1 mutants. To detect genes regulated directly or indirectly by Hfq, deep RNA-seq was performed with RNA isolated from Y. enterocolitica wild-type strain 6471/76 and the YeO3-hfq::Km strain. Total RNA was isolated from two biological replicas of bacteria grown in LB to logarithmic phase (OD600 = 0.6) at two different temperatures, RT and 37°C. knocking out of Hfq affected the transcription of 346 genes at RT and 541 genes at 37°C, i.e., ca. 8 and 12.5 % of the Y. enterocolitica genes, respectively. At RT, of the 346 genes 216 genes were down- and 132 up-regulated, and at 37°C, of the 541 genes, 96 were down- and 445 up-regulated. A total of 95 genes were differentially expressed both at RT and 37°C; 27 showed down- and 59 up-regulated. For 9 genes opposite changes took place depending on the growth temperature. Bacterial RNA profiles of wild type, rfaH- and hfq- strains were generated using deep sequencing, in duplicates, under two growth temperatures (22°C and 37°C). The RNA-sequencing data of YeO3-R1 was generated only from bacteria grown at 22?C.

2015-03-04 | E-GEOD-66516 | biostudies-arrayexpress

Whole transcriptome sequencing of phage φR1-37 and its host Yersinia enterocolitica

Project description:RNA-sequencing was preformed from RNA isolated from bacteria infected with the bacteriophage. In order to reveal the phage-host interactions between φR1-37 and Yersinia enterocolitica throughout the phage infection cycle, both the transcriptomes were scrutinized during all the stages of infection.

2016-01-22 | GSE77068 | GEO

Role of YbeY in Yersinia enterocolitica O:3

Project description:In order to detect genes that are directly or indirectly affected by the inactivation of the ybeY gene the transcriptomes of the WT and ybeY bacteria grown at 22°C and 37°C were determined. The two temperatures were chosen since temperature is an important cue regulating the virulence genes. When comparing the WT and ybeY mutant strain transcriptomes of bacteria grown at 22°C we found changes in the expression of 350 genes in the ybeY bacteria, out of which 121 (34.6%) were up-regulated and 229 (65.4%) down-regulated. At 37°C 334 genes in the ybeY bacteria showed changes, out of which 48 (14.4%) were up-regulated and 286 (85.6%) down-regulated. Expression of 92 genes was changed at both temperatures, of these 92 genes, 12 were up- and 80 down-regulated.

2014-10-23 | GSE62601 | GEO

Transcriptomic analysis reveals the gene expression profiles and cellular functions regulated by the RcsB in Yersinia enterocolitica

Project description:A total of 132 differentially expressed genes (DEGs) regulated by the RcsB have been identified, of which 114 were up-regulated and 18 were down-regulated. Analyses of the GO annotation and KEGG enrichment led us to focus on the role of RcsB in the inhibition of chemotactic behavior, flagella biosynthesis and bacterial infection in Y. enterocolitica. Overall, the information provided in this study complements our understanding of Rcs phosphorelay in the regulation of Y. enterocolitica pathogenicity, and, simultaneously, provides clues to additional roles of the Rcs system in other members of family Enterobacteriaceae.

2020-04-27 | GSE149365 | GEO

Gene expression profiles of wild-type Yersinia pestis CO92 and its Braun lipoprotein mutant at flea and human temp

Project description:Braun/murein lipoprotein (Lpp) is one of the major outer membrane components of gram-negative bacteria belonging to the enterobacteriaceae family that that is involved in inflammatory responses and septic shock. We previously characterized a delta-lpp isogenic mutant of Yersinia pestis CO92 and found that this mutant was defective in surviving in macrophages and was attenuated in a mouse inhalation model of plague when compared to the highly virulent wild-type (WT) bacterium. To better understand how deletion of the lpp gene might affect Yersinia virulence, we performed global transcriptional profiling of the genes in the WT Y. pestis CO92 and its delta-lpp mutant by using microarrays. The organisms were cultured at both 26 and 37 degrees Celsius to simulate the flea vector and mammalian host environments, respectively. Our data revealed vastly different effects of lpp mutation on the transcriptomes of Y. pestis grown at 37 versus 26°C. While the absence of Lpp resulted mainly in the down-regulation of metabolic genes at 26°C, the Y. pestis CO92 lpp mutant cultured at 37°C exhibited profound alterations in stress response and virulence genes, compared to the WT bacterium. We further investigated one of the stress-related genes (htrA) down-regulated in the lpp mutant relative to WT Y. pestis, as HtrA was previously shown to be important for intracellular survival of Y. enterocolitica in macrophages. Indeed, complementation of the delta-lpp mutant with the htrA gene in trans restored intracellular survival of the Y. pestis lpp mutant. Our results support a role for Lpp in Y. pestis CO92 adapatation to the host environment, possibly via transcriptional activation of htrA.

2010-06-04 | GSE19840 | GEO

The effect of hfq on global gene expression and virulence in Neisseria gonorrhoeae

Project description:Hfq is an RNA chaperone, which functions as a pleiotropic regulator for RNA metabolism in bacteria. To characterize the role of Hfq in pathogenicity of Neisseria gonorrhoeae we generated a N. gonorrhoeae hfq mutant, MS11hfq.Transcriptional analysis using a custom-made N. gonorrhoeae microarray revealed that 369 open reading frames were differentially regulated in MS11hfq compared to the wild-type (wt) strain (202 were upregulated, 167 were downregulated).

2009-09-15 | GSE16046 | GEO

Transcriptomic analysis of differential epression of genes of HSC4 cells on treatment with SSTP1 in comparison to its inactive mutant SSTP2

Project description:RNA was isolated from HSC 4 cells after treatment with peptides SSTP1 and SSTP 2 using RNeasy mini kit (Qiagen) as per the manufacturer’s instruction and reverse transcribed to double-stranded cDNA. RNA-Seq analysis was done on Illumina platform to identify the target genes on treatment with SSTP1 in comparison with SSTP2, in HSC4 cells. Out of the 34 to 37 million reads obtained, 31 to 34 million reads per samples were mapped on the indexed Human reference genome GRCh38.p7. 208 up-regulated genes and 118 down-regulated genes were identified through differential gene expression analysis.The RNA-Seq results were validated by 12 up-regulated and four down-regulated genes by RT-PCR and q-PCR.

2021-04-23 | GSE173131 | GEO

Global post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB RNA

Project description:The control of amino acid synthesis and transport in bacteria has been well-investigated at the transcriptional level. The discovery of a small Hfq-dependent regulatory RNA, GcvB, added another layer of gene expression control at the post-transcriptional level. GcvB RNA has been shown to directly regulate multiple ABC transporters for amino acids in E. coli and Salmonella using a highly conserved G/U-rich domain, R1. To identify additional GcvB targets, we have combined a sRNA pulse-expression and microarray analysis of whole transcriptome changes with biocomputational target searches for C/A- rich target sites in Salmonella. Moreover, we have included GcvB mutant RNAs in our microarray approach providing a new target search approach by inactivating conserved domains or target interaction sites. This dual approach revealed further amino acid transporters and, in addition, genes involved in amino acid metabolism as consensus R1-dependent GcvB targets. Moreover, GcvB RNA seems to bind with at least two binding sites to an R1-independent target, the glycine transporter cycA. Using GFP reporter gene fusions we have now validated 21 GcvB targets which is best to our knowledge with ~1% of all Salmonella protein coding genes, the largest bacterial sRNA-controlled regulon. Intriguingly, GcvB rewires many primary control circuits and, thus, constitutes an important metabolic knot.

2011-07-01 | GSE26573 | GEO

Pseudomonas chlororaphis subsp. aureofaciens 30-84

Project description:Hfq regulated genes in Pseudomonas chlororaphis 30-84

| PRJNA213886 | ENA

Effect of short- and long-term morphine treatment on gene expression in the hypothalamus and pituitary

Project description:Addictive drugs including opioids activate signal transduction pathways that regulate gene expression in the brain. However, changes in CNS gene expression following morphine exposure are poorly understood. We studied the effect of short- and long-term morphine treatment on gene expression in the hypothalamus and pituitary using genome-wide DNA microarray and real-time reverse transcriptase polymerase chain reaction (RT-PCR) analyses. In the hypothalamus, we found that short-term morphine administration up-regulated (at least 2-fold) 39 genes and down-regulated six genes. Long-term morphine administration up-regulated 35 genes and down-regulated 51 hypothalamic genes. In the pituitary, we found that short-term morphine administration up-regulated (at least 2-fold) 110 genes and down-regulated 29 genes. Long-term morphine administration up-regulated 85 genes and down-regulated 37 pituitary genes. Strikingly, microarray analysis uncovered several genes involved in food intake (neuropeptide Y, agouti-related protein, and cocaine and amphetamine-regulated transcript) whose expression was strongly altered by morphine exposure in either the hypothalamus or pituitary. Subsequent RT-PCR analysis confirmed similar gene regulation of noteworthy genes in these regions. Finally, we found functional correlation between morphine-induced alterations in food intake and regulations of genes involved in this process. Changes in genes related to food intake may uncover new pathways related to some of the physiological effects of opioids. Keywords: Comparative treatment versus placebo

2008-10-01 | GSE9525 | GEO

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