Transcriptomic Analysis of Two Homologous Salmonella Serogroup C1-specific Genes (SC0368 and SC0595)
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ABSTRACT:
PROVIDER: PRJNA471831 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7178090.fastq.gz | Fastqsanger.gz | |||
| SRR7178091.fastq.gz | Fastqsanger.gz | |||
| SRR7178092.fastq.gz | Fastqsanger.gz | |||
| SRR7178093.fastq.gz | Fastqsanger.gz | |||
| SRR7178084.fastq.gz | Fastqsanger.gz |
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Project description:Purpose:To reveal the function and relationship of the two homologous Salmonella serogroup C1-specific genes (SC0368 and SC0595 in SC). Methods: RNA was isolated from late exponential phase bacteria cultures of wild-type and mutants grown in LB medium. Three biological replicates were carried out per sample. RNA sample was sequenced with Illumina HiSeq 2500 System. DESeq2 method was used to calculate the differentially expressed genes. qRT–PCR were used to validate RNA-seq result. Results: The RNA sequencing yielded more than 28 million reads for 12 samples, and 98.83-99.58% of the high-quality reads were mapped to the reference genome sequence, covering more than 4500 genes in the Salmonella genome. According to the DEGseq analysis software, 76, 78, and 217 genes were considered differentially expressed compared to the wild-type (<2-fold changes, FDR< 0.05) in mutant strains △0368, △0595, and △0368△0595, respectively. RT–qPCR results of 18 selected genes were highly consistent with the RNAseq results. Conclusions: Combination of biological analyses and RNA-Seq of in-frame deletion mutants, experimental evidence for the possible involvement of SC0368 and SC0595 in regulation of motility, LPS synthesis, growth, virulence, and serotype conversion is provided.
2021-07-14 | GSE114577 | GEO
Project description:BackgroundSalmonella is a major bacterial pathogen associated with a large number of outbreaks of foodborne diseases. Many highly virulent serovars that cause human illness belong to Salmonella serogroup C1, and Salmonella ser. Choleraesuis is a prominent cause of invasive infections in Asia. Comparative genomic analysis in our previous study showed that two homologous genes, SC0368 and SC0595 in Salmonella ser. Choleraesuis were unique to serogroup C1. In this study, two single-deletion mutants (Δ0368 and Δ0595) and one double-deletion mutant (Δ0368Δ0595) were constructed based on the genome. All these mutants and the wild-type strain were subjected to RNA-Seq analysis to reveal functional relationships of the two serogroup C1-specific genes.ResultsData from RNA-Seq indicated that deletion of SC0368 resulted in defects in motility through repression of σ28 in flagellar regulation Class 3. Consistent with RNA-Seq data, results from transmission electron microcopy (TEM) showed that flagella were not present in △0368 and △0368△0595 mutants resulting in both swimming and swarming defects. Interestingly, the growth rates of two non-motile mutants △0368 and △0368△0595 were significantly greater than the wild-type, which may be associated with up-regulation of genes encoding cytochromes, enhancing bacterial proliferation. Moreover, the △0595 mutant was significantly more invasive in Caco-2 cells as shown by bacterial enumeration assays, and the expression of lipopolysaccharide (LPS) core synthesis-related genes (rfaB, rfaI, rfaQ, rfaY, rfaK, rfaZ) was down-regulated only in the △0368△0595 mutant. In addition, this study also speculated that these two genes might be contributing to serotype conversion for Salmonella C1 serogroup based on their apparent roles in biosynthesis of LPS and the flagella.ConclusionA combination of biological and transcriptomic (RNA-Seq) analyses has shown that the SC0368 and SC0595 genes are involved in biosynthesis of flagella and complete LPS, as well as in bacterial growth and virulence. Such information will aid to revealing the role of these specific genes in bacterial physiology and evolution within the serogroup C1.
| S-EPMC8259012 | biostudies-literature
Project description:These experiment were performed to show a serogroup conversion in Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 WT = A1552 was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (2 ug each) from strain VCO139-Kan was added after 24h and the cells grwon further for 24h. The VCO139-Kan strain is a MO10 derivative (both O139 serogroup) which harbors a Kanamycin cassette in the O139 region (as part of the operon between wbfA and wbfB w/o own promotor) for better selection. Transformants were selected on LB+Kan plates. Two groups of transformants were gained: Group I had a full exchange of the O1 region by the O139 region (clones serogroup-converted: SGC#1-3); the crossovers for the homologous recombination event had occurred within or upstream of the gmhD gene and in most instances within or downstream of the homolog gene of VC0271. This implies an exchange of an at least 33 kb spanning O1 genomic region by more than 42 kb of the O139 region. Group II had only half of the O139 region transfered and therefore half of the O1 region kept (clones HSGC#4-6). We analyzed their genotype and found that all of them had undergone a homologous recombination event with one crossover in or upstream of the gmhD gene and the second one inside the VC0254 and IS1358 gene. The transformation experiment was done three independent times (I - III). Three clones from group I and group II were selected from each experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Strain Name: -III for experimental replicates (transformation); clones #1 -#3 full region exchanged; clones #4-#6 half region exchanged. Two MA replicates for each clone Keywords: genotyping_design, array CGH
2007-04-25 | GSE5120 | GEO
Project description:These experiment were performed to show a serogroup conversion in Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 WT = A1552 was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (2 ug each) from strain VCO139-Kan was added after 24h and the cells grwon further for 24h. The VCO139-Kan strain is a MO10 derivative (both O139 serogroup) which harbors a Kanamycin cassette in the O139 region (as part of the operon between wbfA and wbfB w/o own promotor) for better selection. Transformants were selected on LB+Kan plates. Two groups of transformants were gained: Group I had a full exchange of the O1 region by the O139 region (clones serogroup-converted: SGC#1-3); the crossovers for the homologous recombination event had occurred within or upstream of the gmhD gene and in most instances within or downstream of the homolog gene of VC0271. This implies an exchange of an at least 33 kb spanning O1 genomic region by more than 42 kb of the O139 region. Group II had only half of the O139 region transfered and therefore half of the O1 region kept (clones HSGC#4-6). We analyzed their genotype and found that all of them had undergone a homologous recombination event with one crossover in or upstream of the gmhD gene and the second one inside the VC0254 and IS1358 gene. The transformation experiment was done three independent times (I - III). Three clones from group I and group II were selected from each experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone.
2007-08-01 | E-SMDB-3574 | biostudies-arrayexpress
Project description:These experiments were performed to show a serogroup conversion in Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 WT = A1552 was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (2 ug each) from strain VC73-orf6/7-Kan-A was added after 24h and the cells grown further for 24h. The VC73-orf6/7-Kan-A strain is a ATCC25873 derivative (both O37 serogroup) which harbors a Kanamycin cassette in the O37 region (as part of the operon between orf6 and orf7 w/o own promotor) for better selection. Transformants were selected on LB+Kan plates. Three clones were selected from each experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone. Comparison of A1552 versus VC73-orf6/7-Kan-A is shown as control. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design
2007-04-26 | GSE5935 | GEO
Project description:Analysis of gene expression patterns at single cell level of C1-sgControl, C1-sgEED and C1-sgKMT2D cells.
2022-04-26 | GSE201441 | GEO
Project description:These experiments were performed to show a serogroup conversion of Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 El Tor (A1552) was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (4 ug each) from strain MO10, an O139 serogroup strain, was added after 24h and the cells were further grown for 24h. After detachment from the crab shell fragments, bacteria were poured into soft-agar and overlaid onto LB plates. Mukerjee's El Tor phage V (a gift of Dr. M.S. Islam) was dropped onto the surface of the bacteria containing soft-agar. The plaques formed by killing non-transformed A1552 cells possessed resistant clones which were picked and further selected for opaque morphotype and agglutination by O139-specific antiserum. Four clones were selected from each independent experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone. Strain Names: ApO139#2 / ApO139#4 / ApO139#6 / ApO139#8 are four clones analyzed after the first experiment; AIIpO139#3 / AIIpO139#4 / AIIpO139#5 / AIIpO139#6 are four clones analyzed after the second independent experiment. Two MA replicates for each clone were done. CGHs of A1552 versus MO10 are provided as control. Keywords: array CGH
2007-04-25 | GSE5302 | GEO
Project description:These experiments were performed to show a serogroup conversion of Vibrio cholerae from O1 to 37. For this purpose, V. cholerae O1 El Tor (A1552) was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (4 ug each) from strain ATCC25872, an O37 serogroup strain, was added after 24h and the cells were further grown for 24h. After detachment from the crab shell fragments, bacteria were poured into soft-agar and overlaid onto LB plates. Mukerjee's El Tor phage III (a gift of Dr. M.S. Islam) was dropped onto the surface of the bacteria containing soft-agar. The plaques formed by killing non-transformed A1552 cells possessed resistant clones which were picked and further selected by non-agglutination with O1-specific antiserum. One to four clones were selected from each independent experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone. Strain Names: AIpO37#1 / AIpO37#4 / AIpO37#6 / AIpO37#8 are clones analyzed from the first experiment; AIIpO37#9 / AIIpO37#13 / AIIpO37#16 are clones analyzed from the second independent experiment; AIIIpO37#9A is a clone analyzed from the third independent experiment; AIVpO37#1A / AIVpO37#3A / AIVpO37#4A / AIVpO37#8A are clones analyzed from the fourth independent experiment. Two MA replicates per clone were done. CGHs of A1552 versus ATCC25872 are provided as control. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design
2007-04-25 | GSE5934 | GEO
Project description:These experiments were performed to show a serogroup conversion of Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 El Tor (A1552) was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (4 ug each) from strain MO10, an O139 serogroup strain, was added after 24h and the cells were further grown for 24h. After detachment from the crab shell fragments, bacteria were poured into soft-agar and overlaid onto LB plates. Mukerjees El Tor phage V (a gift of Dr. M.S. Islam) was dropped onto the surface of the bacteria containing soft-agar. The plaques formed by killing non-transformed A1552 cells possessed resistant clones which were picked and further selected for opaque morphotype and agglutination by O139-specific antiserum. Four clones were selected from each independent experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone. Strain Names: AIIIpO139#1 / AIIIpO139#3 / AIIIpO139#4 / AIIIpO139#5 are four clones analyzed after the second experiment; AIVpO139#2 / AIVpO139#4 / AIVpO139#5 / AIVpO139#8 are four clones analyzed after the fourth independent experiment. Two MA replicates for each clone were done. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: all_pairs, array CGH
2007-04-26 | GSE5933 | GEO
Project description:The purposes of this study are to compare euploid B. napus cv. “Oro” and the C1 nullisomics transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Leaves mRNA profiles of 30-day-old euploid B. napus cv. “Oro” and the C1 nullisomics were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods. qRT–PCR validation was performed. Results: After the high-throughput sequencing, each sample generated 7.2G Clean data on average and the 44.6-53.8 million clean reads were generated. Our study represents detailed analysis of leaves transcriptomes in euploid B. napus and nullisomic, with biologic replicates, generated by RNA-seq technology for comparative investigations of expression profiles. Our results show that Dose complementary effect exists between highly homologous genes, and partial loss of C subgenomic chromosome will lead to increased expression of A genome.
2021-07-24 | GSE180585 | GEO