biostudies-arrayexpressSang Sun YoonPseudomonas aeruginosa PAO1https://www.ebi.ac.uk/biostudies/studies/E-GEOD-34836Pseudomonas aeruginosa undergoes cell elongation and forms robust biofilms during anaerobic respiratory growth using nitrate (NO3-) as an alternative electron acceptor. Understanding the mechanism of cell shape change induced upon anaerobiosis is crucial to the development of effective treatments against P. aeruginosa biofilm infection. Anaerobic growth of PAO1 reached higher cell density in the presence of vitamin B12, an essential coenzyme of class II ribonucleotide reductase. In addition, cell morphology returned to a normal rod shape. These results suggest that vitamin B12, the production of which was suppressed during anaerobic growth, can restore cellular machineries for DNA replication and therefore facilitate better anaerobic growth of P. aeruginosa with normal cell division. We used microarray to elucidate the global gene expression profiles underlying vitamin B12-induced changes in bacterial cell shape and growth-associated properties. Gene expression profiles of PAO1 grown in LBN (LB+NO3-) or LBN supplemented with 1 microM vitamin B12 are compared.biostudies-arrayexpressSample Processing - Two different growth media, LBN and LBN+vitamin B12, are used to grow P. aeruginosa strain PAO1.Growth Protocol - Bacterial cells were grown anaerobically in LBN or LBN supplemented with 1 microM vitamin B12 for 12 hrs.Nucleic Acid Extraction - Total bacterial RNA was isolated from each of three independent cultures per growth condition. RNA was extracted using TRIzol reagent (Invitrogen, Burlington, ON) following the manufacturer’s instructions and extracted RNA was further purified by using an RNAeasy kit (Qiagen). Purified RNA samples were then pooled together and processed for downstream process.Hybridization - Following fragmentation and end-labeling, 5 ug of cDNA were hybridized for 16 hr at 50C on GeneChip P. aeruginosa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.Labeling - Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Prokaryote Target Preparation, P/N 702232 Rev. 2, Affymetrix).MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataAdditional FilesMAGE-TAB FilesArray DesignsFeature Extraction - The RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software (version1.1) was used to normalize the raw data. To reduce noise for the significance analysis, probe sets that were called Present by the MAS5 detection call in 100% of the samples were selected. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.Assay Data Transformation - ID_REF = <br>VALUE = log2 RMA signalImage Adquisition - GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7GMetabolomicsUnknownTranscriptomicsGenomicsProteomicsPseudomonas aeruginosa undergoes cell elongation and forms robust biofilms during anaerobic respiratory growth using nitrate (NO(3)(-)) as an alternative electron acceptor. Understanding the mechanism of cell shape change induced upon anaerobiosis is crucial to the development of effective treatments against P. aeruginosa biofilm infection. Here, we uncovered the molecular basis of anaerobiosis-triggered cell elongation and identified vitamin B(12) to be a molecule that can reinstate defective anaerobic growth of P. aeruginosa. The ratio of total cellular DNA content to protein content was significantly decreased in the PAO1 strain grown under anaerobic conditions, indicating that DNA replication is impaired during anaerobic growth. Anaerobic growth of PAO1 reached a higher cell density in the presence of vitamin B(12), an essential coenzyme of class II ribonucleotide reductase. In addition, cell morphology returned to a normal rod shape and transcription of stress-response genes was downregulated under the same anaerobic growth conditions. These results suggest that vitamin B(12), the production of which was suppressed during anaerobic growth, can restore cellular machineries for DNA replication and therefore facilitate better anaerobic growth of P. aeruginosa with normal cell division. Importantly, biofilm formation was substantially decreased when grown with vitamin B(12), further demonstrating that anaerobiosis-induced cell elongation is responsible for robust biofilm formation. Taken together, our data reveal mechanistic details of a morphological change that naturally occurs during anaerobic growth of P. aeruginosa and illustrates the ability of vitamin B(12) to modulate the biofilm-forming capacity of P. aeruginosa under such condition.transcription profiling by arrayPseudomonas aeruginosa PAO1Vitamin B12-mediated restoration of defective anaerobic growth leads to reduced biofilm formation in Pseudomonas aeruginosa.Lee KM, Go J, Yoon MY, Park Y, Kim SC, Yong DE, Yoon SSSang Sun YoonSang-Sun YoonfalseEffects of vitamin B12 on the gene expression of PAO1 under anaerobic growth conditionsPseudomonas aeruginosa undergoes cell elongation and forms robust biofilms during anaerobic respiratory growth using nitrate (NO3-) as an alternative electron acceptor. Understanding the mechanism of cell shape change induced upon anaerobiosis is crucial to the development of effective treatments against P. aeruginosa biofilm infection. Anaerobic growth of PAO1 reached higher cell density in the presence of vitamin B12, an essential coenzyme of class II ribonucleotide reductase. In addition, cell morphology returned to a normal rod shape. These results suggest that vitamin B12, the production of which was suppressed during anaerobic growth, can restore cellular machineries for DNA replication and therefore facilitate better anaerobic growth of P. aeruginosa with normal cell division. We used microarray to elucidate the global gene expression profiles underlying vitamin B12-induced changes in bacterial cell shape and growth-associated properties. Gene expression profiles of PAO1 grown in LBN (LB+NO3-) or LBN supplemented with 1 microM vitamin B12 are compared.2012-06-17T00:00:00Z2023-03-30T14:38:03.811Z2021-09-28T10:05:45ZE-GEOD-34836GSE3483622371376EFO_000276810.1128/IAI.06161-11