Molecular insights into RmcA-mediated c-di-GMP consumption: Linking redox potential to biofilm morphogenesis in Pseudomonas aeruginosa

The ability of many bacteria to form biofilms contributes to their resilience and makes infections more difficult to treat. Biofilm growth leads to the formation of internal oxygen gradients, creating hypoxic subzones where cellular reducing power accumulates, and metabolic activities can be limited. The pathogen Pseudomonas aeruginosa counteracts the redox imbalance in the hypoxic biofilm subzones by producing redox-active electron shuttles (phenazines) and by secreting extracellular matrix, leading to an increased surface area-to-volume ratio, which favors gas exchange. Matrix production is regulated by the second messenger bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP) in response to different environmental cues. RmcA (Redox modulator of c-di-GMP) from P. aeruginosa is a multidomain phosphodiesterase (PDE) that modulates c-di-GMP levels in response to phenazine availability. RmcA can also sense the fermentable carbon source arginine via a periplasmic domain, which is linked via a transmembrane domain to four cytoplasmic Per-Arnt-Sim (PAS) domains followed by a diguanylate cyclase (DGC) and a PDE domain. The biochemical characterization of the cytoplasmic portion of RmcA reported in this work shows that the PAS domain adjacent to the catalytic domain tunes RmcA PDE activity in a redox-dependent manner, by differentially controlling protein conformation in response to FAD or FADH2. This redox-dependent mechanism likely links the redox state of phenazines (via FAD/FADH2 ratio) to matrix production as indicated by a hyperwrinkling phenotype in a macrocolony biofilm assay. This study provides insights into the role of RmcA in transducing cellular redox information into a structural response of the biofilm at the population level. Conditions of resource (i.e. oxygen and nutrient) limitation arise during chronic infection, affecting the cellular redox state and promoting antibiotic tolerance. An understanding of the molecular linkages between condition sensing and biofilm structure is therefore of crucial importance from both biological and engineering standpoints.The authors would like to acknowledge Sapienza University of Rome [RM120172A7AD98EB to SR, RM1221815D52AB32 to APaiardini and AR12117A63EE6037; AR2221816C44C7B3 to CSR] for financial support. AUC experiments have received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101004806. We thank Patrick England of the Plateforme de Biophysique Moléculaire of the C2RT (Institut Pasteur) for fruitful discussion

Molecular Binding Mechanism of TtgR Repressor to Antibiotics and Antimicrobials

A disturbing phenomenon in contemporary medicine is the prevalence of multidrug-resistant pathogenic bacteria. Efflux pumps contribute strongly to this antimicrobial drug resistance, which leads to the subsequent failure of clinical treatments. The TtgR protein of Pseudomonas putida is a HTH-type transcriptional repressor that controls expression of the TtgABC efflux pump, which is the main contributor to resistance against several antimicrobials and toxic compounds in this microbe. One of the main strategies to modulate the bacterial resistance is the rational modification of the ligand binding target site. We report the design and characterization of four mutants-TtgRS77A, TtgRE78A, TtgRN110A and TtgRH114A - at the active ligand binding site. The biophysical characterization of the mutants, in the presence and in the absence of different antimicrobials, revealed that TtgRN110A is the variant with highest thermal stability, under any of the experimental conditions tested. EMSA experiments also showed a different dissociation pattern from the operator for TtgRN110A, in the presence of several antimicrobials, making it a key residue in the TtgR protein repression mechanism of the TtgABC efflux pump. We found that TtgRE78A stability is the most affected upon effector binding. We also probe that one mutation at the C-terminal half of helix-α4, TtgRS77A, provokes a severe protein structure distortion, demonstrating the important role of this residue in the overall protein structure and on the ligand binding site. The data provide new information and deepen the understanding of the TtgR-effector binding mechanism and consequently the TtgABC efflux pump regulation mechanism in Pseudomonas putida.This work was supported by Spanish Ministry of Economy and Competitiveness, National programme for Recruitment and Incorporation of Human Resources, Subprogramme: Ramon y Cajal RYC-2009-04570 and grant P11-CVI-7391 from Junta de Andalucía and EFDR (European Regional Development Fund)

Generating antiaromaticity in polycyclic conjugated hydrocarbons by thermally selective skeletal rearrangements at interfaces

Antiaromatic polycyclic conjugated hydrocarbons (PCHs) are attractive research targets because of their interesting structural, electronic and magnetic properties. Unlike aromatic compounds, the synthesis of antiaromatic PCHs is challenging because of their high reactivity and lack of stability, which stems from the small energy gap between their highest occupied and lowest unoccupied molecular orbitals. Here we describe a strategy for the introduction of antiaromatic units in PCHs via thermally selective intra- and intermolecular ring-rearrangement reactions of dibromomethylene-functionalized molecular precursors upon sublimation on a hot Au(111) metal surface, not available in solution chemistry. The synthetic value of these reactions is proven by the integration of pentalene segments into acene-based precursors, which undergo intramolecular ring rearrangement, and the formation of π-conjugated ladder polymers, linked through cyclobutadiene connections, due to ring-rearrangement and homocoupling reactions of indenofluorene-based precursors. The reaction products are investigated by scanning tunnelling microscopy and non-contact atomic force microscopy, and mechanistic insights are unveiled by computational studies. [Figure not available: see fulltext.] © 2023, The Author(s), under exclusive licence to Springer Nature Limited.This project has received funding from Comunidad de Madrid (projects QUIMTRONIC-CM (Y2018/NMT-4783) and NanoMagCost (P2018/NMT-4321)), an ERC Consolidator Grant (ELECNANO, 766555), ERC (SyG TOMATTO ERC-2020-951224) and Ministerio de Ciencia, Innovacion y Universidades (projects SpOrQuMat (PGC2018-098613-B-C21), CTQ2017-83531-R, PID2019-108532GB-I00, PID2020-114653RB-I00 and CTQ2016-81911-REDT). We acknowledge the support from the ‘(MAD2D-CM)-UCM’ and the ‘(MAD2D-CM)-IMDEA-Nanociencia’ projects funded by Comunidad de Madrid, by the Recovery, Transformation and Resilience Plan, and by NextGenerationEU from the European Union. IMDEA Nanociencia is appreciative of support from the ‘Severo Ochoa’ Programme for Centers of Excellence in R&D (MINECO, grant nos. SEV-2016-0686 and CEX2020-001039-S). Q.C., D.S.-P. and P.J. acknowledge funding support from the CzechNanoLab Research Infrastructure supported by MEYS CR (LM2023051) and GACR project no. 20-13692X. Computational resources were provided by the e-INFRA CZ project (ID 90140), supported by the Ministry of Education, Youth and Sports of the Czech Republic. A.S.-G. acknowledges funding from the ‘Ministerio de Universidades’ for the ‘Plan de Recuperación, Transformación y Resiliencia’ under Margarita Salas grant agreement CA1/RSUE/2021-00369. J.I.U. acknowledges the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 886314. We acknowledge B. Cirera for fruitful discussions.The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. The Fireball software package is available 458 at: https://github.com/fireball-QMD and PP-SPM software package can be downloaded at: https://github.com/Probe-Particle/ppafm#probe-particle-model.Peer reviewe

Determinación de la estabilidad de macro- y micro-agregados del suelo mediante una combinación de técnicas de tamizado en húmedo y difracción de rayos láser

Soil structural stability affects the profitability and sustainability of agricultural systems. Different-sized structural units have different stability mechanisms and respond differently to such external factors as rain, wind, irrigation and management. A comprehensive analysis of the soils structural stability requires its characterization at the macroand micro-aggregate scales. We determined the aggregate stability of 36 soils at the macro-aggregate scale using wetsieving methods and of 20 soils at the micro-aggregate scale using laser-ray diffraction techniques. All the tests gave consistent estimates of aggregate stability. Most soils were homogeneous and quite stable at the macro-aggregate level as determined by the "water stable aggregate" parameter, but differed significantly among them and were quite unstable at the micro-aggregate level as determined by the "mean weight diameter of micro-aggregates" parameter. Slaking induced by the fast wetting of aggregates was the main destabilizing mechanism in these soils (88% of the soils had slaking stability index values < 0.5), whereas most soils were quite tolerant to the mechanical shaking of aggregates (89% of the soils had stirring stability index values > 0.5). The combination of the macro- and micro-aggregate stability tests is a consistent way for describing the structural stability of the studied soils.La estabilidad estructural del suelo afecta a la rentabilidad y sostenibilidad de los agrosistemas. Los agregados de distintos tamaños son estabilizados por mecanismos diferentes, y responden de forma diferente frente a la lluvia, el viento, el riego y otras prácticas agronómicas. Un análisis completo de la estabilidad estructural de los suelos requiere su caracterización a nivel de macro- y micro-agregados. En este trabajo se ha determinado la estabilidad de macroagregados de 36 suelos mediante métodos de tamizado en húmedo, y la estabilidad de microagregados de 20 suelos mediante técnicas de difracción de rayos láser. Todos los ensayos estimaron de forma consistente la estabilidad de agregados. La mayoría de los suelos se comportaron homogéneamente y de forma bastante estable al nivel de macroagregados, de acuerdo con los valores del parámetro "agregados estables en agua", mientras que se comportaron de forma muy diferente y muy inestable al nivel de microagregados, de acuerdo a los valores del parámetro "diámetro medio ponderado de los microagregados". La desagregación inducida por la humectación rápida de los gregados (slaking) fue el mecanismo más desestabilizador en estos suelos (el 88% de los suelos presentó índices de estabilidad frente a slaking 0,5). La combinación de pruebas de estabilidad de macro- y micro-agregados es un procedimiento consistente y necesario para entender la estabilidad estructural de los suelos estudiados