Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.07.02.662759

DcaP-Family Porins are Required for Carboxylic Acid Catabolism in Acinetobacter baumannii

Noel, H.·Winkelman, J.·Palmer, L. D.
View original source ↗Export metadata ↓

Abstract

Acinetobacter baumannii is a pathogen of concern and a leading cause of multidrug-resistant healthcare-associated infections. The A. baumannii outer membrane is a barrier to antimicrobials and host defenses but must also allow essential nutrients to permeate. Here, we investigate the functional importance of the putative DcaP-family outer membrane porins, which include a proposed vaccine target in A. baumannii. All A. baumannii genomes surveyed encode multiple DcaP family porins, which we classify in four classes based on protein sequence phylogeny (DcaP1-4). DcaP proteins encoded by species in other genera could not be mapped to these DcaP classes and phylogenetic analysis suggests DcaP1-4 proteins diversified within Acinetobacter. Phenotypic array assays and additional experiments show that the DcaP proteins were necessary for growth on multiple di- and tri-carboxylic acids as sole carbon sources, including citric acid and tricarballylic acid. Specifically, DcaP3 was required; however, DcaP1, DcaP2, and DcaP4 were all able to complement the total dcaP knockout to varying degrees, suggesting partial functional overlap. Finally, a mutant lacking all DcaP proteins was attenuated in the liver and spleen in a mouse model of bloodstream infection and complemented by expression of DcaP3. However, a {Delta}dcaP3 mutant had no defect, demonstrating functional redundancy among DcaP proteins during infection. These findings provide insight on how A. baumannii acquires nutrients through the outer membrane barrier and show DcaP proteins are important during infection in specific host niches, validating their potential as a therapeutic target.

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Noel, H., Winkelman, J., Palmer, L. D.. 2025-07-02. DcaP-Family Porins are Required for Carboxylic Acid Catabolism in Acinetobacter baumannii. https://doi.org/10.1101/2025.07.02.662759

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗
bioRxiv2026

The iron-binding siderophore enterobactin is required for the response of multi-drug resistant Klebsiella pneumoniae to zinc limitation

To persist during infection Klebsiella pneumoniae must overcome nutrient iron and zinc limitation imposed by the host immune system through a process called nutritional immunity. Secreted small molecule siderophores are a major virulence determinant of Klebsiella pneumoniae pathogenesis and are presumed to overcome nutritional immunity by binding iron for bacterial acquisition. In this work, we set out to identify how a multi-drug resistant K. pneumoniae grows in zinc limited environments. Using unbiased transcriptomics, proteomics, and an arrayed transposon screen, we identified that synthesis and uptake of the siderophore enterobactin is required to allow for growth in low zinc conditions. Iron-specific chelators did not replicate this phenotype and addition of supplemental iron through heme in growth media could not complement severe growth defects of enterobactin mutant K. pneumoniae experiencing zinc limitation. Finally, zinc starvation induced enterobactin production independent of the canonical zinc uptake regulator (Zur) transcription factor suggesting an unidentified regulatory mechanism by which Gram-negative pathogens may respond to zinc stress. Together, these studies expand the role of enterobactin beyond iron regulation and highlight a previously unreported link between iron and zinc homeostasis in Klebsiella pneumoniae.

microbiology↗
bioRxiv2026

A microbiota-derived protease links phage susceptibility to host epithelial responses

Bacteriophages are major ecological drivers of gut microbial ecology, yet whether bacterial mechanisms that determine phage susceptibility have consequences for the mammalian host remains poorly understood. Here, we identify dipeptidyl peptidase 11 (Dpp11a), the predominant active serine protease of the prevalent gut commensal Phocaeicola vulgatus, as an unexpected bacterial defence factor. Dpp11a protects against environmental proteases and confers resistance to bacteriophage infection. Metatranscriptomic analyses further reveal increased expression of both dpp11a and P. vulgatus-associated phage transcripts in ulcerative colitis stool samples, indicating that both components of this interaction are transcriptionally active in disease-associated human microbiomes. Using the microfluidic gut-on-a-chip co-culture model HuMiX, we show that the absence of Dpp11 is accompanied by altered epithelial tight-junction remodelling during phage-bacterial infection. Together, our findings reveal that the consequences of bacterial phage defence can extend beyond phage-bacterium interactions to the mammalian epithelium.

microbiology↗