RtmR is a membrane-embedded RRM-family RNA-binding protein that regulates biofilm formation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1287783 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The animal symbiont Vibrio fischeri has served as a model organism for molecular processes underlying bacterial group behaviors, including quorum sensing and biofilm development. Here, using a genetic approach to identify negative regulators of biofilm formation in V. fischeri, we identified a membrane-bound RNA-binding protein, RtmR (VF_2432), that acts as an inhibitor of the symbiosis polysaccharide (SYP) biofilm. Membrane localization of the protein seems to be required for protein stability, as truncation of the transmembrane helices led to an inability to detect the protein. The conserved RNP1 and RNP2 motifs in RtmR’s cytoplasmic RNA recognition motif (RRM) domain are required for function, and we demonstrate binding to RNA substrates. Identification of RtmR RNA ligands was conducted with a CLIP-seq approach that revealed a large interactome. One transcript identified was that of the biofilm regulatory histidine kinase RscS. We found that RtmR biofilm inhibition depends on RscS activity and that RtmR negatively regulates levels of RscS. Overall, this work characterizes a novel type of bacterial RNA-binding protein.
2025-07-09 | GSE301959 | GEO
Project description:rs10-01_rrm - quadruple rrm experience - What is the role of the RRM protein family in plants? Plants were grown on soil in controlled environment under LD (16 h light/8 h dark) and the rosette leaves (8-leaf stage seedlings) were collected for RNA preparation. Keywords: normal vs transgenic comparison 2 dye-swap - CATMA arrays
2011-04-16 | E-GEOD-21701 | biostudies-arrayexpress
Project description:rs10-01_rrm - quadruple rrm experience - What is the role of the RRM protein family in plants? Plants were grown on soil in controlled environment under LD (16 h light/8 h dark) and the rosette leaves (8-leaf stage seedlings) were collected for RNA preparation. Keywords: normal vs transgenic comparison
2011-04-16 | GSE21701 | GEO
Project description:Screening of genes regulated between two grapevine genotypes (the Carignan and the RRM) during early inflorescence development
2009-12-08 | E-MEXP-1950 | biostudies-arrayexpress
Project description:membrane distillation biofilm Raw sequence reads
| PRJNA481855 | ENA
Project description:RNA-binding proteins (RBPs) are central players in determining the life cycle of RNA molecules. These proteins are often modular in arrangement, featuring multiple RNA-binding domains, to enhance RNA recognition and functionality. How these multiple RNA-binding domains within individual RBPs work in concert to recognize mRNA targets is still poorly studied. In the model fungus Ustilago maydis, the multi-RRM domain protein Rrm4 plays a key role in mediating the long-distance mRNA transport on the cytoplasmic surface of early endosomes, thereby precisely regulating spatiotemporal gene expression. Rrm4 contains three RNA-recognition motifs (RRMs), organized in an ELAV-like pattern: a tandem RRM domain (RRM1,2) and a separate third RRM domain (RRM3). Utilizing Rrm4 variants with mutations in the RRM domains, we conducted a differential iCLIP analysis to dissect the RNA recognition code of individual RRM domains. Our study reveals that Rrm4 exhibits two binding mode: (i) a one-to-one interaction where the third RRM domain alone binds RNAs by recognizing the shot UAUG motif. (ii) an intricate composite binding mode where all three RRM domains cooperatively bind RNA. Improtantly, our finding demonstrates that it is not the simple one-to-one interaction but rather the complex cooperative binding mode, involving all three RRM domains, is critical for Rrm4 function in maintaining the unipolar growth of the fungal hyphae.
2026-02-18 | GSE273495 | GEO
Project description:RNA-binding proteins (RBPs) are central players in determining the life cycle of RNA molecules. These proteins are often modular in arrangement, featuring multiple RNA-binding domains, to enhance RNA recognition and functionality. How these multiple RNA-binding domains within individual RBPs work in concert to recognize mRNA targets is still poorly studied. In the model fungus Ustilago maydis, the multi-RRM domain protein Rrm4 plays a key role in mediating the long-distance mRNA transport on the cytoplasmic surface of early endosomes, thereby precisely regulating spatiotemporal gene expression. Rrm4 contains three RNA-recognition motifs (RRMs), organized in an ELAV-like pattern: a tandem RRM domain (RRM1,2) and a separate third RRM domain (RRM3). Utilizing Rrm4 variants with mutations in the RRM domains, we conducted a differential iCLIP analysis to dissect the RNA recognition code of individual RRM domains. Our study reveals that Rrm4 exhibits two binding mode: (i) a one-to-one interaction where the third RRM domain alone binds RNAs by recognizing the shot UAUG motif. (ii) an intricate composite binding mode where all three RRM domains cooperatively bind RNA. Improtantly, our finding demonstrates that it is not the simple one-to-one interaction but rather the complex cooperative binding mode, involving all three RRM domains, is critical for Rrm4 function in maintaining the unipolar growth of the fungal hyphae.
2026-02-18 | GSE288123 | GEO
Project description:Methane-based denitrification kinetics and syntrophy in a membrane biofilm reactor at low methane pressure
| PRJEB33776 | ENA
Project description:Cotton fiber is actually unicellular trichome, therefor its length is really hard to be modified but very meaningful to fiber quality and yield. We have reported the function of the second RRM domain of Oryza sativa FCA in rice cell size regulation. Data shows it is highly conserved across dicotyledonous and monocotyledonous plants. Here we provide evidence showing that the second RRM domain of Brassica napus FCA worked in Gossypium hirsutum, leading to the enlargement of multiple types of cells, such as pollen, cotyledon petiole and cotton fiber. In the transgenic cotton, the length of unicellular cotton fiber increased by about 10% and fiber yield per plant also showed a dramatic increase, ranging from 35% to 66%, over the control. Thus, this RRM domain may be an ancient and common cell size regulator and has great economic value on cotton industry. FCA encodes a strong promoter of the transition to flowering in Arabidopsis thaliana, which contains two RRM (RNA recognition motif) domain and a WW protein interaction domain (Macknight et al., 1997). We have previously found that cell size and yield of rice (Oryza sativa) can be increased by ectopic expression of the first RRM domain of OsFCA (Hong et al., 2007). The second RRM domain of OsFCA can also increase cell size (Attia et al., 2005), suggesting OsFCA-RRMs each play a role in homeostatic cell size regulation. We designate them as Oryza sativa cell size RRM 1 (Os-csRRM1) and Oryza sativa cell size RRM 2 (Os-csRRM2), respectively. Both of them exhibit a high degree of evolutionary conservation in plant. For Os-csRRM2, significant homology was observed in Triticum aestivum (90% identity), Hordeum vulgare (90% identity), Lolium perenne (82% identity), Zea mays (81% identity),Ricinus communis (76% identity), Vitis vinifera (68% identity), Arabidopsis thaliana (68% identity) and Brassica napus (64% identity) (Fig. 1). The high degree of conservation suggests that this RRM domain might have similar function in different plants. Indeed, we observed that overexpression of Bn-csRRM2 also increased the cell size of B. napus (unpublished data). As cotton fiber length is a key factor in cotton yield and quality, we investigated whether this attribute could be enhanced by constitutive expression of Bn-csRRM2. Transgenic and wild-type cotton were grown in same condition. The leaves of 25 day and 45 day plants were harvested for microarray analysis. RNA samples were isolated from 3 biological replications using TRIzol (Invitrogen) as described by the manufacturer. Microarray analyses were carried out using Agilent Cotton Gene Expression Microarray (G2519F-022523). Microarrays were scanned on Agilent Technologies Scanner G2505C and data points were extracted using Agilent Feature Extraction software (Version 10.7.1.1). Comparisons were made between transgenic samples and their corresponding wild-type samples.
2011-12-31 | E-GEOD-26445 | biostudies-arrayexpress
Project description:Dairy biofilm formation on filtration membrane used in a bioreactor Raw sequence reads
| PRJNA450825 | ENA