A comparison between two Escherichia coli K-12 MG1655 substrains possessing different swimming motility
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ABSTRACT:
PROVIDER: PRJNA694620 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13520672_1.fastq.gz | Fastqsanger.gz | |||
| SRR13520672_2.fastq.gz | Fastqsanger.gz | |||
| SRR13520673_1.fastq.gz | Fastqsanger.gz | |||
| SRR13520673_2.fastq.gz | Fastqsanger.gz | |||
| SRR13520674_1.fastq.gz | Fastqsanger.gz |
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Project description:Substrains in Escherichia coli K-12 MG1655 can possess various swimming motility, which is mostly resulted from different expression levels of flhDC. Here, we studied the swimming motility of two MG1655 substrains, CY562 and CY570. Our results showed that CY562 had no insertion at the promoter region of flhDC and possessed no swimming motility. In contrast, CY570 had an IS-element insertion at the promoter region of flhDC and showed a hyper-motile phenotype. Transcriptomic data suggest that expression of flhDC and the other known flagella genes was much lower in CY562 than that in CY570. Moreover, CY562 possessed higher expression levels for genes involved in stress response, especially acid-stress response, than CY570. Consistently, CY562 showed a higher survival rate under acid stress than CY570. Our data indicate that there are mechanisms conversely regulating motility and stress response in E. coli.
2021-11-15 | GSE165438 | GEO
Project description:We used NGS to find that the PilS-PilR two component system of P. aeruginosa controls the expression of many non-pilus related genes and has a role in regulating swimming motility
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Project description:The enteric pathogen Salmonella enterica serovar Typhimurium infects humans and animals. Invasion of intestinal epithelial cells is an important step in gut colonization. Both the Salmonella invasion-associated Type III Secretion System 1 (T3SS1) and motility are required for efficient invasion. The master regulator HilD induces expression of T3SS1 and flagella genes, thus coordinating expression of invasion and motility. Here we show that HilD also induces smooth swimming and that this is important for invasion of epithelial cells, in vitro and in vivo. HilD-induced bacteria express the chemotaxis receptor McpC, which suppresses tumbling and increases smooth swimming, even in the absence of exogenous ligands. mcpC is repressed by H-NS binding, which can be displaced by HilD. This is the first time that bacteria have been shown to use the smooth swimming phenotype in order to optimize invasion.
2020-11-02 | GSE156765 | GEO
Project description:Bacteria growing as surface-adherent biofilms are better able to withstand chemical and physical stresses than their unattached, planktonic counterparts. Using transcriptional profiling and quantitative PCR, we observed a previously uncharacterized gene, yjfO, to be upregulated during Escherichia coli MG1655 biofilm growth in a chemostat on serine-limited defined medium. A yjfO mutant, developed through targeted insertion mutagenesis, and a yjfO-complemented strain, were obtained for further characterization. While bacterial surface colonization levels (CFU/cm2) were similar in all three strains, the mutant strain exhibited reduced microcolony formation when observed in flow cells, and greatly enhanced flagellar motility on soft (0.3%) agar. Complementation of yjfO restored microcolony formation and flagellar motility to wild type levels. Cell surface hydrophobicity and twitching motility were unaffected by the presence or absence of yjfO. In contrast to the parent strain, biofilms from the mutant strain were less able to resist acid and peroxide stresses. yjfO had no significant effect on E. coli biofilm susceptibility to alkali or heat stress. Planktonic cultures from all three strains showed similar responses to these stresses. Regardless of the presence of yjfO, planktonic E. coli withstood alkali stress better than biofilm populations. Complementation of yjfO restored viability following exposure to peroxide stress, but did not restore acid resistance. Based on its influence on biofilm formation, stress response, and effects on motility, we propose renaming the uncharacterized gene, yjfO, as bsmA (biofilm stress and motility). Transcriptional profiling of duplicate biofilm and planktonic cultures of E. coli MG1655 grown in serine-limited MOPS minimal media.
2010-06-21 | E-GEOD-18362 | biostudies-arrayexpress
Project description:Transcriptome profiles were analyzed using the samples taken at the exponential and stationary phases during the cultivation of REL606 and MG1655 in LB medium. At the exponential growth phase, most highly expressed genes of B were those for replication, translation, or nucleotide transport and metabolism, while many of the K-12 genes were involved in cell motility, transcription, carbohydrate transport, or energy production. At the stationary phase, many of the genes highly expressed in B were for transport and metabolism of various amino acids and carbohydrates, whereas those in K-12 had functions related to cell motility, ribosomal subunit protein production, or energy generation. Many genes in REL606 and MG1655 showed highly distinct expression levels irrespective of growth conditions. Highly expressed genes in REL606 included those encoding enzymes for biosynthesis of L-arginine (argAGDECBHI) and branched-chain amino acid (ilvGMEDA), and those encoding a subunit of the L-arginine transporter (artJ), cytochrome b562 (cybC), subunits of the histidine ABC transporter (hisPJ), cytotoxins (hokED), outer membrane porin (ompF), L-arginine decarboxylase (speA), and cell division inhibitor (sulA). Highly expressed genes in MG1655 included those for chemotaxis (cheZYRWA, tap, trg, tsr), Lon protease (lon), C4-dicarboxylate-sensing histidine kinase (dcuS), chaperones (clpB, dnaK, groES, htpG, ibpA), the major subunit of type 1 fimbriae (fimA), a regulator of flagellar biosynthesis (flhC), glycerol-3-phosphate-dehydrogenase (glpABCD), glycerophosphoryl diester phosphodiesterase (glpQ), glycerol-3-phosphate transporter (glpT), hydrogenase 2 (hybCBO), outer membrane porins (nmpC, ompA, ompC), and galactitol transport and metabolism (gatYZC).
2009-09-28 | GSE13011 | GEO
Project description:The marine bacterium Photobacterium galatheae S2753 produces a group of cyclodepsipeptides, solonamides, which impede the virulence but not the survival of Staphylococcus aureus. Besides the invaluable antivirulence activity, little is known about the biosynthesis and physiological function of solonamides in the native producer. This study generated a solonamides-deficient mutant, Δsol, by in-frame deleting the sol gene, thereby identifying the core gene for solonamides biosynthesis. By annotation from antiSMASH, the biosynthetic pathway of solonamides in S2753 was also proposed. Mass spectrometry analysis of cell extracts found that deficiency of solonamides production influenced the production of several novel lipids, but not the overall secondary metabolite profile. Physiological comparison between Δsol and wild-type S2753 demonstrated that growth dynamics and biofilm formation of both strains were similar; however, Δsol displayed reduced swimming rings as compared to the wild-type. The swimming ring size of Δsol was restored to the level of wild-type strain by adding solonamide B, indicating that solonamide B influences regulate the swimming behavior of P. galatheae S2753. Proteomic analysis of the Δsol and wild-type found that eliminating solonamides influenced many cellular processes, including swimming-related proteins and that solonamides trigger the motility of S2753 likely by adjusting the cellular cyclic di-GMP concentration. In conclusion, our results revealed the biosynthetic pathway of solonamides and their ecological benefits to P. galatheae S2753 by enhancing the swimming velocity, likely by altering the motile physiology.
2022-08-17 | PXD031490 | Pride
Project description:Swimming performance correlates with fitness of Atlantic salmon in the wild and farm conditions. Variation of this trait in salmon populations is high. The study assessed relationship between two parameters of swimming performance: the ability to cope with moderate and maximum swimming efforts.
2021-04-23 | GSE173119 | GEO
Project description:Bacteria growing as surface-adherent biofilms are better able to withstand chemical and physical stresses than their unattached, planktonic counterparts. Using transcriptional profiling and quantitative PCR, we observed a previously uncharacterized gene, yjfO, to be upregulated during Escherichia coli MG1655 biofilm growth in a chemostat on serine-limited defined medium. A yjfO mutant, developed through targeted insertion mutagenesis, and a yjfO-complemented strain, were obtained for further characterization. While bacterial surface colonization levels (CFU/cm2) were similar in all three strains, the mutant strain exhibited reduced microcolony formation when observed in flow cells, and greatly enhanced flagellar motility on soft (0.3%) agar. Complementation of yjfO restored microcolony formation and flagellar motility to wild type levels. Cell surface hydrophobicity and twitching motility were unaffected by the presence or absence of yjfO. In contrast to the parent strain, biofilms from the mutant strain were less able to resist acid and peroxide stresses. yjfO had no significant effect on E. coli biofilm susceptibility to alkali or heat stress. Planktonic cultures from all three strains showed similar responses to these stresses. Regardless of the presence of yjfO, planktonic E. coli withstood alkali stress better than biofilm populations. Complementation of yjfO restored viability following exposure to peroxide stress, but did not restore acid resistance. Based on its influence on biofilm formation, stress response, and effects on motility, we propose renaming the uncharacterized gene, yjfO, as bsmA (biofilm stress and motility).
2009-10-17 | GSE18362 | GEO
Project description:Purpose: Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that undergoes swarming motility in response to semisolid conditions with amino acids as a nitrogen source. With a genome encoding hundreds of potential intergenic small RNAs (sRNAs), P. aeruginosa can easily adapt to different conditions and stresses. We previously identified 20 sRNAs dysregulated under swarming conditions and here provide phenotypic characterization for these sRNAs. Methods: Here, these sRNA were overexpressed in strain PAO1 and subjected to an array of phenotypic screens. Results: Overexpression of prrH resulted in decreased swimming motility, while a ∆prrH mutant had decreased cytotoxicity and increased pyoverdine production. Overexpression of the previously uncharacterized PA2952.1 resulted in decreased swarming and swimming motility, increased gentamicin and tobramycin resistance under swarming conditions, and increased trimethoprim susceptibility. RNA-Seq and proteomics were performed on the wildtype overexpressing PA2952.1 cf. the empty vector control under swarming conditions, and revealed the differential expression of 784 genes and differential abundance of 445 proteins. Amongst these were found 82 transcriptional regulators, two-component systems, sigma and anti-sigma factors. Downstream effectors included downregulated pili, dysregulated flagellar genes, the upregulated efflux pump MexGHI-OpmD, the upregulated arn operon, and downregulated DNA synthesis genes. Genes involved in iron and zinc uptake were also dysregulated, and certain pyoverdine and phenazine genes were upregulated. Conclusions: Overall, the sRNAs PA2952.1 and prrH appeared to be involved in regulating virulence-related programs in P. aeruginosa, including iron acquisition and motility.
2020-11-04 | GSE146765 | GEO
Project description:Intestinal calcium absorption is the sole pathway to supply calcium to the body and duodenum is the most efficient site of calcium absorption. Endurance exercise with moderate intensity significantly increased the intestinal calcium absorption. The unloaded non-impact excercise, such as swimming may enhance calcium absorption. However, the cellular and molecular mechanisms of this change have not been investigated. Thus, a genome-wide study by using microarray should reveal changes in the expression of several transporter genes in the intestinal absorptive cells of swimming excercised rats. Keywords: Gene expression; Comparative genomic hybridization Twelve rats were randomly divided into control and swimming groups. Swimming rats were initially trained for a week until they could swim non stop 1 hour/day. Swimming frequency was 5 days/week for 2 weeks. The age-matched control remained sedentary for 2 weeks in a swimming pool. At the end of the swimming protocol, the intestinal segments of rats were removed for total RNA extraction and microarray study.
2010-06-24 | E-GEOD-13499 | biostudies-arrayexpress