Biology subjects

Bigler, L.

Publications and source records attributed to Bigler, L..

7 recordsLinked to original sources

bioRxiv2024

Discovery of chemical marker for maidong (roots of Ophiopogon japonicus and Liriope spicata): a feature-based molecular networking approach

BackgroundDried tuberous roots of Ophiopogon japonicus and Liriope spicata are collectively used as maidong medicine in China for the same clinical efficacy-nourish yin and generate fluids, moisten lung and clear heart fire. Extensive cultivation of these species has necessitated the need for stringent quality control measures. To guide quality control efforts effectively, a comprehensive understanding of metabolomic profiles of maidong is essential. MethodsMetabolomic profiling was conducted using ultra-high performance liquid chromatography coupled to a timsTOF Pro hybrid quadrupole-time-of-flight mass spectrometer employing trapped ion mobility spectrometry. Data interpretation was enhanced through feature-based molecular networking (FBMN), uni- and multivariate data analysis (MVDA), and in silico annotation. ResultsThe present study showcases a holistic overview of the metabolomic diversity and variation among maidong derived from different origins. Steroidal saponins and homoisoflavonoids were recognized as predominant chemical classes. Ophiopogon japonicus predominantly exhibited a variety of homoisoflavonoids, whereas Liriope spicata was characterized by a diversity of steroidal saponins. Characteristic metabolites among maidong derived from four origins were highlighted. Annotations of 58 metabolites revealed significant inter-species discrimination, with 6 and 36 metabolites critical for regional differentiation in Liriope spicata and Ophiopogon japonicus, respectively. ConclusionThe current approach effectively discriminated maidong from different origins, and facilitated the selection of chemical markers for quality assessment. This approach supports the advancement of quality control strategies for botanical medicines, particularly those derived from multiple origins, ensuring a more rigorous chemical marker selection for botanical medicines.

plant biology↗

bioRxiv2024

Histidine limitation causes alteration in the TOR network and plant development

Plant growth depends on growth regulators, nutrient availability, and amino acids levels. The TOR (Target of Rapamycin) network senses these parameters and influences cell wall formation and expansion accordingly. Cell wall integrity and structures are surveyed and modified by a complex array of cell wall integrity sensors, including LRR-extensins (LRXs), that function as hormone receptors and help to compact cell walls. Expressing the Arabidopsis root-hair specific LRX1 without the extensin domain, which anchors the protein to the cell wall, has a negative effect on root hair development. The mechanism of this negative effect was investigated by a suppressor screen, which led to the identification of a sune (suppressor of dominant-negative LRX1) mutant collection. The sune82 mutant was identified as an allele of HISN2 which encodes an enzyme essential for histidine biosynthesis. The sune82 mutation leads to reduced accumulation of histidine, and this influences the TOR network. The sune82 mutant reflects the impact of the TOR network on cell wall formation processes involving LRX proteins. It also represents an excellent tool to study the effects of reduced histidine levels on plant development, as it is a rare example of a viable partial loss-of-function allele in an essential biosynthetic pathway. HighlightPartial loss of function of HISN2 in sune82 results in a significant reduction in histidine content, which subsequently alters the TOR network.

cell biology↗

bioRxiv2023

From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicted. Here we developed a knowledge-guided bioinformatic pipeline to solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and focused on iron-scavenging pyoverdines as model metabolites. Our pipeline predicted 188 chemically different pyoverdines with nearly 100% structural accuracy and the presence of 94 distinct receptor groups required for the uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet overlooked diversity of siderophores (151 new structures) and receptors (91 new groups). Our approach, combining feature sequence with phylogenetic approaches, is extendable to other metabolites and microbial genera, and thus emerges as powerful tool to reconstruct bacterial secondary metabolism pathways based on sequence data. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/564663v5_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1dedad4org.highwire.dtl.DTLVardef@1f0a39eorg.highwire.dtl.DTLVardef@185e345org.highwire.dtl.DTLVardef@10beec6_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2023

Antimicrobial activity of iron-depriving pyoverdines against human opportunistic pathogens

The global rise of antibiotic resistance calls for new drugs against bacterial pathogens. A common approach is to search for natural compounds deployed by microbes to inhibit competitors. Here we show that the iron chelating pyoverdines, siderophores produced by environmental Pseudomonas spp., have strong antibacterial properties by inducing iron starvation and growth arrest in pathogens. A screen of 320 natural Pseudomonas isolates used against 12 human pathogens uncovered several pyoverdines with particularly high antibacterial properties and distinct chemical characteristics. The most potent pyoverdine effectively reduced growth of the pathogens Acinetobacter baumannii, Klebsiella pneumoniae and Staphylococcus aureus in a concentration- and iron-dependent manner. Pyoverdine increased survival of infected Galleria mellonella host larvae, and showed low toxicity for the host, mammalian cell lines, and erythrocytes. Furthermore, experimental evolution combined with whole-genome sequencing revealed reduced potentials for resistance evolution compared to an antibiotic. Thus, pyoverdines from environmental strains have the potential to become a new class of sustainable antibacterials against specific human pathogens.

microbiology↗

bioRxiv2023

Screening of leaf extraction and storage conditions for eco-metabolomics studies

Mass spectrometry-based plant metabolomics is frequently used to identify novel natural products or study the effect of specific treatments on a plants metabolism. Reliable sample handling is required to avoid artifacts, which is why most protocols mandate shock freezing of plant tissue in liquid nitrogen and an uninterrupted cooling chain. However, the logistical challenges of this approach make it infeasible for many ecological studies. Especially for research in the tropics, permanent cooling poses a challenge, which is why many of those studies use dried leaf tissue instead. We screened a total of ten extraction and storage approaches for plant metabolites extracted from maize leaf tissue across two cropping seasons to develop a methodology for agroecological studies in logistically challenging tropical locations. All methods were evaluated based on changes in the metabolite profile across a 2-month storage period at different temperatures with the goal of reproducing the metabolite profile of the living plant as closely as possible. We show that our newly developed on-site liquid-liquid extraction protocol provides a good compromise between sample replicability, extraction efficiency, material logistics, and metabolite profile stability. We further discuss alternative methods which showed promising results and feasibility of on-site sample handling for field studies. HighlightWe developed an on-site metabolite extraction method for leaf tissue samples from field studies in challenging logistical circumstances. We highlight extract stability and reproducibility compared to frozen or dried tissue.

plant biology↗

bioRxiv2020

A Volatile Signal Controls Virulence in the Plant Pathogen Pseudomonas syringae pv. syringae and a Strategy for Infection Control in Organic Farming

Pseudomonas syringae is an important pathogen of many agriculturally valuable crops. Among the various pathovars described P. syringae pv. syringae (Pss) has a particularly wide host range, infecting primarily woody and herbaceous host plants. The ability of Pss to cause bacterial apical necrosis of mango trees is dependent on the production of the antimetabolite toxin mangotoxin. The production of this toxin was shown to be regulated by a self-produced signaling molecule. In this study, we determined the structure of the Pss signal molecule belonging to the recently described family of diazeniumdiolate communication molecules. Employing a targeted mass spectrometry-based approach, we provide experimental evidence that the major signal produced by Pss is the volatile compound leudiazen, which controls mangotoxin production and virulence in a detached tomato leaflet infection model. Experimental results demonstrate that KMnO4 solution inactivates leudiazen and that treatment of infected leaves with KMnO4 abolishes necrosis. This strategy represents the first example of chemically degrading a signaling molecule to interfere with bacterial communication. The application of KMnO4 solution, which is regulatorily approved in organic farming, may constitute an environmentally friendly strategy to control Pss infections.

microbiology↗

bioRxiv2017

Type III CRISPR-Cas systems generate cyclic oligoadenylate second messengers to activate Csm6 RNases

In many prokaryotes, type III CRISPR-Cas systems detect and degrade invasive genetic elements by an RNA-guided, RNA-targeting multisubunit interference complex that possesses dual RNase and DNase activities. The CRISPR-associated protein Csm6 additionally contributes to interference by functioning as a standalone ribonuclease that degrades invader RNA transcripts, but the mechanism linking invader sensing to Csm6 activity is not understood. Here we show that Csm6 proteins are activated through a second messenger generated by the type III interference complex. Upon target RNA binding by the type III interference complex, the Cas10 subunit converts ATP into a cyclic oligoadenylate product, which allosterically activates Csm6 by binding to its CARF domain. CARF domain mutations that abolish allosteric activation inhibit Csm6 activity in vivo, and mutations in the Cas10 Palm domain phenocopy loss of Csm6. Together, these results point to a hitherto unprecedented mechanism for regulation of CRISPR interference that bears striking conceptual similarity to oligoadenylate signalling in mammalian innate immunity.

biochemistry↗