An effort to make sense of antisense transcription in bacteria

Analysis of bacterial transcriptomes have shown the existence of a genome-wide process of overlapping transcription due to the presence of antisense RNAs, as well as mRNAs that overlapped in their entire length or in some portion of the 5′- and 3′-UTR regions. The biological advantages of such overlapping transcription are unclear but may play important regulatory roles at the level of transcription, RNA stability and translation. In a recent report, the human pathogen Staphylococcus aureus is observed to generate genome-wide overlapping transcription in the same bacterial cells leading to a collection of short RNA fragments generated by the endoribonuclease III, RNase III. This processing appears most prominently in Gram-positive bacteria. The implications of both the use of pervasive overlapping transcription and the processing of these double stranded templates into short RNAs are explored and the consequences discussed. © 2012 Landes Bioscience.This research was supported by grants ERA-NET Pathogenomics (PIM2010EPA-00606), BIO2008-05284-C02, BIO2011- 30503-C02 and BFU2011-23222 from Spanish Ministry of Economy and Competitiveness.A.T.-A. is recipient of “Ramon y Cajal” contracts from the Spanish Ministry of Science and Innovation. This research was supported by grants ERA-NET Pathogenomics (PIM2010EPA-00606), BIO2008-05284-C02, BIO2011-30503-C02 and BFU2011-23222 from Spanish Ministry of Economy and CompetitivenessPeer Reviewe

Bacterial biofilm functionalization through Bap amyloid engineering

Biofilm engineering has emerged as a controllable way to fabricate living structures with programmable functionalities. The amyloidogenic proteins comprising the biofilms can be engineered to create self-assembling extracellular functionalized surfaces. In this regard, facultative amyloids, which play a dual role in biofilm formation by acting as adhesins in their native conformation and as matrix scaffolds when they polymerize into amyloid-like fibrillar structures, are interesting candidates. Here, we report the use of the facultative amyloid-like Bap protein of Staphylococcus aureus as a tool to decorate the extracellular biofilm matrix or the bacterial cell surface with a battery of functional domains or proteins. We demonstrate that the localization of the functional tags can be change by simply modulating the pH of the medium. Using Bap features, we build a tool for trapping and covalent immobilizing molecules at bacterial cell surface or at the biofilm matrix based on the SpyTag/SpyCatcher system. Finally, we show that the cell wall of several Gram-positive bacteria could be functionalized through the external addition of the recombinant engineered Bap-amyloid domain. Overall, this work shows a simple and modulable system for biofilm functionalization based on the facultative protein Bap. © 2022, The Author(s).This research was supported by grants from the Spanish Ministry of Science and Technology RTI2018-096011-B-I00 to J.V. and PID2020-113494RB-I00 to IL. L.M.-C. was supported by the predoctoral program of the Universidad Pública de Navarra

Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarray

UPNa. Instituto de Agrobiotecnología. Laboratorio de Biofilms MicrobianosIncluye 7 ficheros de datosBackground: High-density oligonucleotide microarray is an appropriate technology for genomic analysis, and is particulary useful in the generation of transcriptional maps, ChIP-on-chip studies and re-sequencing of the genome. Transcriptome analysis of tiling microarray data facilitates the discovery of novel transcripts and the assessment of differential expression in diverse experimental conditions. Although new technologies such as next-generation sequencing have appeared, microarrays might still be useful for the study of small genomes or for the analysis of genomic regions with custom microarrays due to their lower price and good accuracy in expression quantification. Results: Here, we propose a novel wavelet-based method, named ZCL (zero-crossing lines), for the combined denoising and segmentation of tiling signals. The denoising is performed with the classical SUREshrink method and the detection of transcriptionally active regions is based on the computation of the Continuous Wavelet Transform (CWT). In particular, the detection of the transitions is implemented as the thresholding of the zero-crossing lines. The algorithm described has been applied to the public Saccharomyces cerevisiae dataset and it has been compared with two well-known algorithms: pseudo-median sliding window (PMSW) and the structural change model (SCM). As a proof-of-principle, we applied the ZCL algorithm to the analysis of the custom tiling microarray hybridization results of a S. aureus mutant deficient in the sigma B transcription factor. The challenge was to identify those transcripts whose expression decreases in the absence of sigma B. Conclusions: The proposed method archives the best performance in terms of positive predictive value (PPV) while its sensitivity is similar to the other algorithms used for the comparison. The computation time needed to process the transcriptional signals is low as compared with model-based methods and in the same range to those based on the use of filters. Automatic parameter selection has been incorporated and moreover, it can be easily adapted to a parallel implementation. We can conclude that the proposed method is well suited for the analysis of tiling signals, in which transcriptional activity is often hidden in the noise. Finally, the quantification and differential expression analysis of S. aureus dataset have demonstrated the valuable utility of this novel device to the biological analysis of the S. aureus transcriptome.This work was supported by the Spanish Torres-Quevedo fellowship [PTQ-08-03-07769] to VS. ATA and AMB were supported by Spanish Ministry of Science and Innovation ‘Ramón y Cajal’ contracts. This work was supported by the Spanish Ministry of Science and Innovation Grants BIO2008-05284-C02-01, BFU2011-23222, ERA-NET Pathogenomics PIM2010EPA-00606 and the agreement between ‘Fundación para la Investigación médica aplicada’ (FIMA) and the ’UTE project CIMA’

Estudio funcional y estructural de la región B de Bap y su rol en el desarrollo de biofilms en S.aureus

Trabajo presentado en la X Reunión de Microbiología Molecular, celebrada en Segovia del 9 al 11 de junio de 2014.Peer Reviewe

Evaluation of Surface Microtopography Engineered by Direct Laser Interference for Bacterial Anti-Biofouling

© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Modification of the biomaterial surface topography is a promising strategy to prevent bacterial adhesion and biofilm formation. In this study, we use direct laser interference patterning (DLIP) to modify polystyrene surface topography at sub-micrometer scale. The results revealed that three-dimensional micrometer structures have a profound impact on bacterial adhesion. Thus, line- and pillar-like patterns enhanced S. aureus adhesion, whereas complex lamella microtopography reduced S. aureus adhesion in static and continuous flow culture conditions. Interestingly, lamella-like textured surfaces retained the capacity to inhibit S. aureus adhesion both when the surface is coated with human serum proteins and when the material is implanted subcutaneously in a foreign-body associated infection model.J. Valle was supported by Spanish Ministry of Science and Innovation “Ramón y Cajal” contract. This research was supported by grants AGL2011-23954 and BIO2011-30503-C02-02 from the Spanish Ministry of Economy and Competitivity and IIQ14066. RI1 from Innovation Department of the Government of Navarra. A. Lasagni, D. Langhenirich, and R. Helbig thank the Deutsche Forschungsgemeinschaft (DFG) for the financial support of the project “Mechanically stable anti-adhesive polymer surfaces” (LA-2513 4-1).Peer Reviewe

Las islas de patogenicidad de Saphylococcus aureus son capaces de controlar factores de virulencia cromosómicos

Trabajo presentado en la X Reunión de Microbiología Molecular, celebrada en Segovia del 9 al 11 de junio de 2014.Staphylococcus aureus es una importante bacteria patógena, debido a la enorme variedad de infecciones que es capaz de producir. La enorme versatilidad de S. aureus se debe a su habilidad para persistir y multiplicarse en diferentes ambientes junto con su capacidad para producir una gran variedad de factores de virulencia, algunos de las cuales están codificadas en elementos genéticos móviles (EGMs), como bacteriófagos e islas de patogenicidad (SaPI) (1). Sobre el 90% de las cepas de S. aureus aisladas de infecciones humanas están pigmentadas. Staphyloxanthin (STX) es un carotenoide considerado como factor de virulencia, ya que contribuye a la evasión del sistema inmune. Por otro lado, la N-acetiltransferasa (GNAT) está implicada en resistencia a antibióticos. En este trabajo describimos como las SaPIs son capaces de regular la producción de factores de virulencia como son STX y GNAT.Peer Reviewe