Comment[ArrayExpressAccession]	E-GEOD-43376
MAGE-TAB Version	1.1						
Public Release Date	2016-01-08
Investigation Title	Cell wall-deficient Mycoplasma hominis represses biofilm formation of uropathogenic Escherichia coli.						
Comment[Submitted Name]	Cell wall-deficient Mycoplasma hominis represses biofilm formation of uropathogenic Escherichia coli.
Experiment Description	The features of Mycoplasma in human organ such lung and urinary tract are enigmatic.  Here, the role of M. hominis in regard to biofilm formation of uropathogenic Escherichia coli (UPEC) strain CFT073 was investigated. Although M. hominis were inferred to not impact on UPEC bacterial fitness including growth and productions of signaling molecules as autoinducer-2 (AI-2) and indole, we found that the presence of M. hominis dramatically decreased biofilm formation of UPEC CFT073 as well as slightly repressed attachment and cytotoxicity of that.  Importantly, this activity was observed on UPEC strain specifically, not enterohemorrhagic E. coli (EHEC) strain that exists on intestine.  Whole-transcriptome profiling and quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed PhoPQ system and anti-termination protein (encoded by ybcQ) participates on the reduction of biofilm formation by M. hominis (corroborated by qRT-PCR). Furthermore, collaborating with previous report that toxin-antitoxin (TA) system involved in biofilm formation, M. hominis increased on the transcriptions of toxin genes including hha (toxin gene in Hha-TomB TA system) and pasT (toxin part in PasT-PasI TA system).  Hence, we propose that one possible role of M. hominis is to influence bacterial biofilm formation in urinary tract. Only fourteen genes were induced (2.5-fold) by the presence of M. hominis in Uropathogenic Escherichia coli (UPEC) biofilm cells. Among upregulated genes, ybcQ (encodes anti-termination protein Q homolog) and phoP/phoQ (encode DNA-binding response regulators in two-component regulatory system), were induced by the presence of M. hominis. Two-condition experiment, UPEC CFT073 alone vs. UPEC CFT073 with Mycoplasma hominis PG21 (10^5 ccu/ml). For preparing the total RNA, UPEC CFT073 cells were grown at 37°C in biofilm cells on glass wool with or without M. hominis for 24 h.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Kim	Oh	Choi	Kim			
Person First Name	Younghoon	Sangnam	Nag-Jin	Younghoon			
Person Email	ykeys2584@jbnu.ac.kr						
Person Affiliation	Chonbuk National University						
Person Phone	82-10-4135-2584						
Person Address	Department of Animal Science, Chonbuk National University, 567 Baekje-Daero, Deokjin-Gu, Jeonju, South Korea						
Person Roles	submitter						
Protocol Name	P-GSE43376-1	P-GSE43376-5	P-GSE43376-6	P-GSE43376-2	P-GSE43376-3	P-GSE43376-4	P-GSE43376-7
Protocol Description	The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring 7.3.1 (Agilent Technologies, USA). The averages of normalized ratios were calculated by dividing the average of normalized test channel intensity by the average of normalized control channel intensity. ID_REF =  VALUE = average normalized log2 ratios of Cy5/Cy3 representing test/control	Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for CosR-knockdown) or Cy3-dUTP (for the wild type).	Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).	For infection with M. hominis, UPEC biofilms were cultured on glass wool with or without M. hominis (10^5 ccu/ml)	UPEC biofilms were formed on glass wool with or without M. hominis (10^5 ccu/ml) using overnight cultures to inoculate 250 ml of 1/5 diluted LB medium with 10 g of glass wool (Corning Glass Works). After incubation for 24 h with shaking (250 rpm), biofilm cells were prepared by rinsing and sonicating the glass wool in sterile 0.85% NaCl solution at 0°C.	After culturing UPEC CFT073 cells, bacterial cells were distrupted with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) and Rnase free-DNase I treatment (Qiagen)	The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Comment[SecondaryAccession]	GSE43376						
Comment[GEOReleaseDate]	2016-01-08						
Comment[ArrayExpressSubmissionDate]	2013-01-09						
Comment[GEOLastUpdateDate]	2016-01-08						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-43376.sdrf.txt