Analysis of global transcriptional changes in H. neptunium cells lacking the cell cycle regulatory genes pleC, divJ or divK
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PROVIDER: PRJNA554809 | ENA |
REPOSITORIES: ENA
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Project description:Within the bacterial phylum of the Alphaproteobacteria many species show complex life cycles. Proper regulation of these life cycles requires cell cycle regulation pathways, one of which is the so-called CtrA pathway. Key factors in the CtrA pathway are the histidine kinases PleC and DivJ (located at opposite poles in the cell) and the response regulator DivK. Within the Alphaproteobacteria, stalked budding bacteria are even more asymmetric than most other representatives. How they regulate their cell cycle has not been studied before. Here, we investigated the transcriptional profiles of Hyphomonas neptunium cells lacking either PleC, DivJ or DivK and compared their profiles to that of wildtype cells. We found that the changes upon deletion of DivJ, PleC and especially DivK were smaller than expected from related organisms.
2022-01-01 | GSE134343 | GEO
Project description:Within the bacterial phylum of the Alphaproteobacteria many species show complex life cycles. Proper regulation of these life cycles requires cell cycle regulation pathways, one of which is the so-called CtrA pathway. Key factors in the CtrA pathway are the histidine kinase CckA and the phosphotransferase ChpT, which are directly involved in cell cycle specific activation of the response regulator CtrA. Within the Alphaproteobacteria, stalked budding bacteria are even more asymmetric than most other representatives. How they regulate their cell cycle has not been studied before. Here, we investigated the transcriptional profiles of Hyphomonas neptunium cells depleted of CckA or ChpT and compared their profiles to that of wildtype cells. We identified that the essential proteins CckA and ChpT influence the transcription levels of multiple essential processes, such as cell division, as well as specific cell cycle regulated functions such as motility.
2022-01-01 | GSE134341 | GEO
Project description:Analysis of global transcriptional changes in H. neptunium cells depleted of the cell cycle regulators CckA or ChpT
| PRJNA554803 | ENA
Project description:Alphaproteobacteria stand out for their complex cell cycles, which are often regulated by the DivJ/PleC-DivK-DivL-CckA-ChpT-CtrA pathway. DivJ and PleC set up the polarity of the cell, thereby eventually leading to differential activation of the DNA-binding response regulator CtrA in the two nascent daughter cells. CtrA regulates replication and transcription of many genes, thereby ensuring that processes such as motility and cell division take place at the appropriate cell cycle stage. The cell cycle of the stalked budding alphaproteobacterium Hyphomonas neptunium culminates in an asymmetric cell division at the stalk-bud junction. Here, we investigate the role of the pathway from DivJ and PleC down to CtrA in this recently established model organism. Even though DivJ and PleC are localized to opposite poles, suggesting they are involved in polarity establishment inH. neptunium, DivJ, PleC and the other components of the upstream pathway (DivK and PleD) are not essential for cell cycle regulation. In contrast, the downstream part of the pathway starting from DivL is essential and involved in the regulation of important functions such as replication inhibition, cell division and motility, as shown by the identification of the (direct) regulon of CtrA. The overlap between the regulons of DivJ and PleC, DivK and CtrA is only partial, demonstrating that additional factors feeding into the pathway must be present in H. neptunium. Furthermore, unlike in other alphaproteobacteria, the regulation of CtrA throughout the cell cycle does not take place at the level of CtrA abundance in H. neptunium. All in all, the DivL-CckA-ChpT-CtrA pathway plays an essential role in the regulation of the complicated cell cycle ofH. neptunium, but several proteins feeding into CtrA remain undiscovered. The in-depth analysis of CtrA regulation in this stalked budding organism leads to hypotheses that might also hold in well-established model organisms such as Caulobacter crescentus.
2020-03-29 | GSE124953 | GEO
Project description:Hyphomonas neptunium proliferates by a unique budding mechanism in which daughter cells emerge from the end of a stalk‐like extension emanating from the mother cell body. Studies of this species have so far been hampered by the lack of a genetic system and of molecular tools allowing the regulated expression of target genes. Based on microarray analyses, this work identifies two H. neptunium promoters that are specifically activated by copper and zinc, respectively. Functional analyses show that they have low basal activity and a high dynamic range, thus meeting the requirements for use as a multi‐purpose expression system.
2014-11-24 | GSE62447 | GEO
Project description:Heavy metal-inducible gene expression in Hyphomonas neptunium
| PRJNA264144 | ENA
Project description:The equine endometrium exhibits characteristic morphological and functional changes during the estrous cycle controlled by the interplay of progesterone and estradiol. A microarray analysis of endometrial tissue samples derived from 5 time points of the estrous cycle (D0, D3, D8, D12, and D16) was performed to study the dynamics of endometrial gene expression. Endometrial biopsies were collected from five mares (Bavarian Warmblood) at the respective time points. Samples were divided and subjected to isolation of RNA for microarray analysis and analysis of tissue composition. Blood samples were collected to determine serum progesterone levels for every sample. Statistical analysis of microarray data revealed almost 10,000 differential probes corresponding to 4,996 differentially expressed genes. A cluster analysis based on gene expression profiles during the estrous cycle revealed 8 major gene expression profiles: mRNAs with highest levels 1) at D0, 2) from D0 to D3, 3) at D3, 4) from D3 to D8, 5) at D8, 6) from D8 to D12, 7) from D12 to D16, and 8) at D16. DAVID Functional Annotation Clustering revealed overrepresentation of distinct functional terms in different phases of the cycle, e.g. ‘extracellular matrix’ and ‘protein transport’ during estrus, ‘DNA replication and ‘cell cycle’ during early luteal phase, ‘endoplasmic reticulum’ and ‘protein transport’ in the luteal phase, and ‘inflammatory response’ in the late luteal and follicular phase. Expression of selected genes of the expression clusters was validated by quantitative Real-time PCR (qPCR). This study provides new insights into global changes of equine endometrial gene expression during the estrous cycle.
2012-10-23 | GSE39043 | GEO
Project description:Colorectal polypectomy is offten incompletely performed with high variability between endoscopists, resulting in interval cancer or repeated procedures. Current available scoring systems for polypectomy technique are lacking in different areas so the investigators developed the Global Polypectomy Assessment Tool (GPAT) which is an online video-based assessment tool for any colorectal polypectomy.
The goal of the study is to assess the validity of GPAT through demonstrating the inter-rater agreement (Fleiss Kappa (κ)). GPAT has 20 items, contains evidence-based statements to aid interpretation, calculates an overall quality score and a complexity score.
| 61454 | ecrin-mdr-crc
Project description:The equine endometrium exhibits characteristic morphological and functional changes during the estrous cycle controlled by the interplay of progesterone and estradiol. A microarray analysis of endometrial tissue samples derived from 5 time points of the estrous cycle (D0, D3, D8, D12, and D16) was performed to study the dynamics of endometrial gene expression. Endometrial biopsies were collected from five mares (Bavarian Warmblood) at the respective time points. Samples were divided and subjected to isolation of RNA for microarray analysis and analysis of tissue composition. Blood samples were collected to determine serum progesterone levels for every sample. Statistical analysis of microarray data revealed almost 10,000 differential probes corresponding to 4,996 differentially expressed genes. A cluster analysis based on gene expression profiles during the estrous cycle revealed 8 major gene expression profiles: mRNAs with highest levels 1) at D0, 2) from D0 to D3, 3) at D3, 4) from D3 to D8, 5) at D8, 6) from D8 to D12, 7) from D12 to D16, and 8) at D16. DAVID Functional Annotation Clustering revealed overrepresentation of distinct functional terms in different phases of the cycle, e.g. M-bM-^@M-^Xextracellular matrixM-bM-^@M-^Y and M-bM-^@M-^Xprotein transportM-bM-^@M-^Y during estrus, M-bM-^@M-^XDNA replication and M-bM-^@M-^Xcell cycleM-bM-^@M-^Y during early luteal phase, M-bM-^@M-^Xendoplasmic reticulumM-bM-^@M-^Y and M-bM-^@M-^Xprotein transportM-bM-^@M-^Y in the luteal phase, and M-bM-^@M-^Xinflammatory responseM-bM-^@M-^Y in the late luteal and follicular phase. Expression of selected genes of the expression clusters was validated by quantitative Real-time PCR (qPCR). This study provides new insights into global changes of equine endometrial gene expression during the estrous cycle. Equine endometrial tissue samples were collected at 5 time points during the sexual (estrous) cycle from 5 mares (5 biological replicates per time point) and analyzed with Agilent microarrays.
2012-10-23 | E-GEOD-39043 | biostudies-arrayexpress