Biology subjects

Franklin, K.

Publications and source records attributed to Franklin, K..

3 recordsLinked to original sources

bioRxiv2026

Metaproteomics Reveals Functional Rewiring and Metabolic Limits in Synthetic Bacterial Consortia Degrading Complex Waste Oils

Elucidating the metabolic mechanisms underpinning complex hydrocarbon biodegradation by microbial consortia benefits from integration of community-level genomic and proteomic data. Here, we deployed a combined metagenomics and metaproteomic analysis to characterize functional dynamics within bacterial consortia enriched from hydrocarbon-contaminated soil, using military waste oil as the sole carbon source. Metagenomic profiling revealed a consortium dominated by Stenotrophomonas maltophilia alongside established hydrocarbon-degrading taxa including Pseudomonas fluorescens, Pseudomonas putida, and Delftia acidovorans. Quantitative label-free metaproteomics uncovered dynamic taxonomic restructuring and metabolic reorientation, with Delftia and Achromobacter proteins enriched during active degradation, indicating niche advantages under chronic contamination. Enzymatic mapping resolved expression of degradation pathways targeting aliphatic and aromatic substrates, with one specific consortium, BPS4, exhibiting preferential catabolism of catechol intermediates channeled toward the tricarboxylic acid cycle, supported by elevated protein abundance of oxidoreductases, dehydrogenases, and {beta}-oxidation enzymes. Gene ontology enrichment revealed heightened nitrogen cycling capacity, including upregulation of nitric oxide biosynthesis and nitrate reductase, suggesting adaptive nitrogen metabolism coupled to hydrocarbon mineralization. In-vitro batch-fed adaptation studies demonstrated limited improvements in degradation of recalcitrant fractions, particularly branched aliphatics and organophosphates, revealing intrinsic metabolic constraints within the consortium. These findings underscore the complementary utility of metaproteomic interrogation for resolving both population-level dynamics and functional metabolic capabilities, while highlighting fundamental limitations in expanding the degradative spectrum of enriched consortia through conventional adaptation strategies. This work establishes a foundation for rational ecological engineering of hydrocarbon-remediating consortia informed by metaproteomics. ImportanceWaste oils from transport and industry are complex and toxic mixtures that are difficult and expensive to treat using conventional chemical methods. Microorganisms offer a sustainable alternative, but their performance depends on how different species work together and where their metabolic limits lie. In this study, we show how advanced protein-based analysis using quantitative metaproteomics, can reveal microbial community activities whilst breaking down real-world waste oils. We enriched bacteria from contaminated soils and then identified the enzymes driving effective degradation. We investigated how communities reorganise under chemical stress, and why certain oil components remain resistant even after long-term adaptation. By uncovering both strengths and limitations of naturally enriched microbial consortia, this work provides practical insights for designing more reliable biological treatments for oil-based wastes and even contaminated environments, supporting greener approaches to pollution management and industrial waste recycling.

microbiology↗

bioRxiv2024

In-utero rescue of neurological dysfunction in a mouse model of Wiedemann-Steiner syndrome

Wiedemann-Steiner syndrome (WDSTS) is a rare genetic cause of intellectual disability primarily caused by heterozygous loss of function variants in the gene encoding the histone methyltransferase KMT2A. Prior studies have shown successful postnatal amelioration of disease phenotypes for Rett, Rubinstein-Taybi and Kabuki syndromes, related Mendelian disorders of the epigenetic machinery. To explore whether the neurological phenotype in WDSTS is treatable in-utero, we created a novel mouse model carrying a loss of function variant in between two loxP sites. Kmt2a+/LSL mice demonstrate core features of WDSTS including growth retardation, craniofacial abnormalities, and hypertrichosis as well as hippocampal memory defects. The neurological phenotypes show rescue upon restoration of KMT2A in-utero following breeding to a nestin-Cre. Together, our data provide a novel mouse model to explore the therapeutic window in WDSTS. Our work suggests that WDSTS has a window of opportunity extending at least until the mid-point of in-utero development, making WDSTS an ideal candidate for future therapeutic strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/604339v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1b913caorg.highwire.dtl.DTLVardef@1c23ce3org.highwire.dtl.DTLVardef@12b8a25org.highwire.dtl.DTLVardef@17a9a4e_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

genetics↗

bioRxiv2021

Effects of α-crystallin gene knockout on zebrafish lens development

The -crystallin small heat shock proteins contribute to the transparency and refractive properties of the vertebrate eye lens and prevent the protein aggregation that would otherwise produce lens cataracts, the leading cause of human blindness. There are conflicting data in the literature as to what role the -crystallins may play in early lens development. In this study, we used CRISPR gene editing to produce zebrafish lines with null mutations for each of the three -crystallin genes (cryaa, cryaba and cryabb). The absence of normal protein was confirmed by mass spectrometry, and lens phenotypes were assessed with differential interference contrast microscopy and histology. Loss of A-crystallin produced a variety of lens defects with varying severity in larval lenses at 3 and 4 dpf but little substantial change in normal fiber cell denucleation. Loss of either Ba- or full-length Bb-crystallin produced no substantial lens defects. Mutation of each -crystallin gene did not alter the mRNA levels of the remaining two, suggesting a lack of genetic compensation. These data confirm a developmental role for A-crystallin in lens development, but the range of phenotype severity suggests that its loss simply increases the chance for defects and that the protein is not essential. Our finding that cryaba and cryabb mutants lack noticeable lens defects is congruent with insubstantial transcript levels in lens epithelial and fiber cells. Future experiments can explore the molecular consequences of cryaa mutation and causes of lens defects in this null mutant, as well as the roles of other genes in lens development and function.

developmental biology↗