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Farinha, A.

Publications and source records attributed to Farinha, A..

5 recordsLinked to original sources

Control of cell division by an Acinetobacter baumannii protein with a novel nucleotidyl-cyclase-like fold

The antibiotic-resistant pathogen Acinetobacter baumannii has diverged from model {psi}-proteobacteria in fundamental ways, complicating the development of new antimicrobial strategies. A major area of divergence is cell division. A. baumannii lacks several widely conserved division enzymes, such as FtsEX, and instead possesses a suite of atypical gene products with no similarity to well-characterized proteins. Key among these is AdvA, which we previously identified by Tn-seq as essential for A. baumannii division and fluoroquinolone resistance. The protein comprises an N-terminal transmembrane/periplasmic region connected to a C-terminal unannotated cytoplasmic domain, and most advA transposon insertions were lethal unless they occurred within the linker between these regions. The roles of AdvA in cell division and the basis for these positional transposon effects were unclear. Here, we combine mutagenesis with fluorescence localization, two-hybrid, and structural analyses to define how AdvA domains function in assembling and activating the A. baumannii divisome. AdvA depletion profoundly disrupts divisome construction at Z-rings. This dependence reflects numerous interactions with divisome proteins, with AdvAs N-terminal region binding multiple components and cytoplasmic domain binding one, the early protein ZipA. In addition, we identified substitutions in FtsB and FtsW that suppress AdvA essentiality, consistent with a role in divisome activation as well as recruitment. Finally, we determined the structure of the cytoplasmic domain, revealing a novel adenylyl/guanylyl cyclase-like fold that lacks canonical catalytic and dimerization sites and instead features a positively charged tip key to fluoroquinolone resistance and a C-terminal helix essential to division. The critical C-terminal structure helps explain the positional transposon effects and facilitated identification of a distant homolog in Pseudomonas aeruginosa. These results reveal a new control protein governing bacterial division that could be exploited to combat nosocomial infections. ImportanceThe multidrug-resistant sepsis pathogen Acinetobacter baumannii poses an urgent threat to public health. Fundamental features of its cell cycle, such as how it controls cell division, are not well understood, but this information could lead to improved antimicrobial strategies. We demonstrate that a protein (AdvA) bearing a previously unrecognized structure has a critical role in cell division and fluoroquinolone antibiotic resistance in the pathogen. The structure resembles the nucleotide cyclase class of enzymes, but it has lost the typical catalytic properties and instead uses novel sites to enable assembly and activation of the cell division machine. The novel fold is found in other pathogens such as Pseudomonas aeruginosa, in which it is also connected to drug resistance and cell division. This work opens new avenues to understand and interrupt cell division in multidrug-resistant hospital-acquired bacteria.

microbiology↗

NADES as Biocompatible Media for Thermally Stable RNA Molecules

The inherently low thermal stability of RNA poses operational, accessibility, and financial challenges for RNA research and RNA-based technologies. Natural deep eutectic solvents (NADES) have been shown to enhance the stability of various macromolecules, including DNA and protein. This study explores NADES as alternative storage media for RNA preservation and evaluates their biocompatibility in human cells. In vitro-transcribed mRNA was stored in various NADES at temperatures ranging from 4-50 {degrees}C, and the integrity was assessed by quantifying its translatability, represented by protein-expressing cells. NADES effectively preserved RNA integrity, retaining over 50% of its translatability for at least four months at room temperature (21 {degrees}C) and 48 hours at 50 {degrees}C, in comparison to -80 {degrees}C storage. Notably, the preservation efficacy remained unaffected by temperature fluctuations. Furthermore, the selected NADES concentrations maintained [~] 99% cell viability, demonstrating their biocompatibility. These findings establish NADES as efficient, biocompatible RNA storage media, enabling stable storage and transport at ambient and extreme temperatures while withstanding sudden fluctuations. This enhanced stability simplifies and expands the accessibility of RNA-based applications. Additionally, the biocompatibility of NADES supports their potential use in RNA-based biomedical applications.

pharmacology and toxicology↗

IL-1β-driven NF-κB transcription of ACE2 as a Mechanism of Macrophage Infection by SARS-CoV-2

Coronavirus disease 2019 (COVID-19), caused by infection with the enveloped RNA betacoronavirus, SARS-CoV-2, led to a global pandemic involving over 7 million deaths. Macrophage inflammatory responses impact COVID-19 severity; however, it is unclear whether macrophages are infected by SARS-CoV-2. We sought to identify mechanisms regulating macrophage expression of ACE2, the primary receptor for SARS-CoV-2, and to determine if macrophages are susceptible to productive infection. We developed a humanized ACE2 (hACE2) mouse whereby hACE2 cDNA was cloned into the mouse ACE2 locus under control of the native promoter. We validated the susceptibility of hACE2 mice to SARS-CoV-2 infection relative to wild-type mice and an established K18-hACE2 model of acute fulminating disease. Intranasal exposure to SARS-CoV-2 led to pulmonary consolidations with cellular infiltrate, edema, and hemorrhage, consistent with pneumonia, yet unlike the K18-hACE2 model, hACE2 mice survived and maintained stable weight. Infected hACE2 mice also exhibited a unique plasma chemokine, cytokine, and growth factor inflammatory signature relative to K18-hACE2 mice. Infected hACE2 mice demonstrated evidence of viral replication in infiltrating lung macrophages, and infection of macrophages in vitro revealed a transcriptional profile indicative of altered RNA and ribosomal processing machinery as well as activated cellular antiviral defense. Macrophage IL-1{beta}-driven NF-{kappa}B transcription of ACE2 was an important mechanism of dynamic ACE2 upregulation, promoting macrophage susceptibility to infection. Experimental models of COVID-19 that make use of native hACE2 expression will allow for mechanistic insight into factors that can either promote host resilience or increase susceptibility to worsening severity of infection.

immunology↗

Essential gene analysis in Acinetobacter baumannii by high-density transposon mutagenesis and CRISPR interference

Acinetobacter baumannii is a poorly understood bacterium capable of life-threatening infections in hospitals. Few antibiotics remain effective against this highly resistant pathogen. Developing rationally-designed antimicrobials that can target A. baumannii requires improved knowledge of the proteins that carry out essential processes allowing growth of the organism. Unfortunately, studying essential genes has been challenging using traditional techniques, which usually require time-consuming recombination-based genetic manipulations. Here, we performed saturating mutagenesis with dual transposon systems to identify essential genes in A. baumannii and we developed a CRISPR-interference (CRISPRi) system for facile analysis of these genes. We show that the CRISPRi system enables efficient transcriptional silencing in A. baumannii. Using these tools, we confirmed the essentiality of the novel cell division protein AdvA and discovered a previously uncharacterized AraC-family transcription factor (ACX60_RS03245) that is necessary for growth. In addition, we show that capsule biosynthesis is a conditionally essential process, with mutations in late-acting steps causing toxicity in strain ATCC 17978 that can be bypassed by blocking early-acting steps or activating the BfmRS stress response. These results open new avenues for analysis of essential pathways in A. baumannii. ImportanceNew approaches are urgently needed to control A. baumannii, one of the most drug resistant pathogens known. To facilitate the development of novel targets that allow inhibition of the pathogen, we performed a large-scale identification of genes whose products the bacterium needs for growth. We also developed a CRISPR-based gene knockdown tool that operates efficiently in A. baumannii, allowing rapid analysis of these essential genes. We used these methods to define multiple processes vital to the bacterium, including a previously uncharacterized gene-regulatory factor and export of a protective polymeric capsule. These tools will enhance our ability to investigate processes critical for the essential biology of this challenging hospital-acquired pathogen.

microbiology↗

Antibiotic hypersensitivity signatures identify targets for attack in the Acinetobacter baumannii cell envelope

Acinetobacter baumannii is an opportunistic pathogen that is a critical, high-priority target for new antibiotic development. Clearing of A. baumannii requires relatively high doses of antibiotics across the spectrum, primarily due to its protective cell envelope. Many of the proteins that support envelope integrity and modulate drug action are uncharacterized, largely because there is an absence of orthologs for several proteins that perform essential envelope-associated processes, impeding progress on this front. To identify targets that can synergize with current antibiotics, we performed an exhaustive analysis of A. baumannii mutants causing hypersensitivity to a multitude of antibiotic treatments. By examining mutants with antibiotic hypersensitivity profiles that parallel mutations in proteins of known function, we show that the function of poorly annotated proteins can be predicted and used to identify candidate missing link proteins in essential A. baumannii processes. Using this strategy, we uncovered multiple uncharacterized proteins with critical roles in cell division or cell elongation, and revealed that a predicted cell wall D,D-endopeptidase has an unappreciated function in lipooligosaccharide synthesis. Moreover, we provide a genetic strategy that uses hypersensitivity signatures to predict drug synergies, allowing the identification of {beta}-lactams that work cooperatively based on the cell wall assembly machineries that they preferentially target. These data reveal multiple pathways critical for envelope growth in A. baumannii that can be targeted in combination strategies for attacking the pathogen.

microbiology↗