Biology subjects

Russ, D.

Publications and source records attributed to Russ, D..

9 recordsLinked to original sources

bioRxiv2026

Loss of MAX1 redirects, rather than delays, the leaf senescence program in lettuce

Background Strigolactones (SLs) regulate diverse aspects of plant development and have been implicated in promoting leaf senescence. However, senescence phenotypes associated with SL deficiency have not been consistently observed across species, suggesting that this function may be species- or context-dependent. Moreover, the contribution of endogenous SL biosynthesis to senescence in leafy vegetable crops remains unclear. Here, we investigated the role of the SL biosynthetic gene MORE AXILLARY GROWTH1 (MAX1) in dark-induced leaf senescence in lettuce (Lactuca sativa). Results We found that endogenous SL biosynthesis plays a major role in dark-induced senescence in lettuce. SL pathway genes were induced during dark storage, while exogenous GR24 accelerated senescence and lettuce MAX1 (LsMAX1) complemented the delayed-senescence phenotype of the Arabidopsis max1 mutant. Consistent with these findings, CRISPR/Cas9-generated Lsmax1 mutants exhibited a pronounced stay-green phenotype during prolonged darkness, accompanied by strongly reduced induction of key senescence-associated genes. Despite this delayed visible senescence, Lsmax1 retained a substantial transcriptional response to dark storage. Strikingly, loss of LsMAX1 did not simply weaken the wild-type senescence program, but redirected part of the response toward a distinct stress-associated transcriptional state that was largely absent from wild type. Loss of LsMAX1 did not affect vegetative rosette architecture, although increased branching emerged after bolting. Conclusions Our findings establish MAX1-dependent SL biosynthesis as an important regulator of leaf senescence in lettuce and reveal a role that extends beyond controlling the rate of senescence. Rather than simply delaying the wild-type program, loss of LsMAX1 alters the transcriptional trajectory of senescence, favoring an alternative stress-associated state during prolonged darkness. The strong stay-green phenotype without detectable changes to vegetative rosette architecture further highlights SL biosynthesis as a potential target for extending postharvest longevity in lettuce and other leafy crops.

plant biology↗

bioRxiv2026

Streptomyces enrichment in roots during drought is uncoupled from plant benefit and is driven by host suppression of iron uptake and immunity

Drought reshapes plant root microbiota, yet the mechanistic drivers and consequences of this observation remain unclear. We discovered that suppression of host immunity and iron homeostasis is required for Streptomyces enrichment in roots during drought across diverse soils. Genetic and physiological manipulation of these host pathways confirmed their requirement in modulating Streptomyces root enrichment. Drought-induced suppression of iron uptake was conserved across the [~]160 My monocot-eudicot divergence. Some Streptomyces strains enhanced plant growth and rescued iron uptake under drought. These benefits were uncoupled from Streptomyces root enrichment. They were instead shaped by intra-Streptomyces antagonism. We propose a two-step model: drought-driven down regulation of host iron and immune pathways enriches Streptomyces, while intra-genus dynamics fine-tune strain-level assembly and functional outcomes. Our data refine the idea that Streptomyces are enriched in roots during drought in response to a plant cry for help and consequently contribute to alleviation of this abiotic stress.

plant biology↗

bioRxiv2026

Specialization of independently acquired flagellar FliC proteins in plant-associated Sphingomonas balances swimming and immunogenicity

Plants monitor their environment for microbial invaders using pattern-recognition receptors that detect microbe-associated molecular patterns (MAMPs). Flagellin, the main component of bacterial flagellum, contains the flg22 epitope recognized by the plant immune receptor FLS2. Immune recognition can create an evolutionary conflict, requiring bacteria to balance flagellar function and immune evasion. Here, we show that plant-associated Sphingomonads resolve this constraint by partitioning two flagellar functions, motility and colonization, across two divergent and independently acquired flagellin genes. Comparative genomics revealed widespread coexistence of FliC proteins expressing either an immunogenic variant (FliC-H) or a non-immunogenic variant (FliC-L). The non-immunogenic FliC-L is necessary and sufficient for full directional swimming, whereas FliC-H is dispensable for swimming, but sufficient for full attachment and colonization. Flagellin expression patterns mirror these functions. Thus, FLS2 recognizes the flagellar variant required for colonization rather than motility, potentially restricting colonizing bacteria from entering internal leaf and root tissues.

plant biology↗

bioRxiv2024

An efflux pump family distributed across plant commensal bacteria conditions host- and organ-specific detoxfication of a host-specific glucosinolate

In nature, plants recruit a diverse microbial community, the plant microbiome, that is distinct from the surrounding soil community 1-4. To understand the forces that shape the plant microbiome we need to characterize the microbial traits that contribute to plant colonization. We used barcoded mutant libraries to identify bacterial genes that contribute to the colonization of a monocot and a eudicot host 5-7. We show that plant colonization is influenced by dozens of genes. While some of these colonization genes were shared between the two host plant species, most were highly specific, benefiting the colonization of a single host and organ. We characterized an efflux pump that specifically contributes to Arabidopsis shoot colonization. This efflux pump is prevalent across Pseudomonadota genomes, yet benefits the bacterial association with only a small subset of Arabidopsis thaliana accessions. Leveraging genomic diversity within Arabidopsis thaliana, we confirmed that specific glucosinolate breakdown products are detoxified by this family of efflux pumps. The broad prevalence of this efflux pump family suggests that its members contribute to protection of commensal bacteria from collateral damage of plant glucosinolate-based defense responses to herbivores and necrotrophic pathogens.

microbiology↗

bioRxiv2024

Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

microbiology↗

bioRxiv2022

Broader functions of TIR domains in Arabidopsis immunity

TIR domains are NAD-degrading enzymes that function during immune signaling in prokaryotes, plants, and animals. In plants, most TIR domains are incorporated into intracellular immune receptors. In Arabidopsis, TIR-derived small molecules bind and activate EDS1 heterodimers, which in turn activate RNLs, a class of cation channel-forming immune receptors. RNL activation drives cytoplasmic Ca2+ influx, transcriptional reprogramming, pathogen resistance and host cell death. We screened for mutants that suppress an RNL activation mimic allele and identified a TIR-containing immune receptor, SADR1. Despite functioning downstream of an auto-activated RNL, SADR1 is not required for defense signaling triggered by other tested TIR-containing immune receptors. SADR1 is required for defense signaling initiated by some trans-membrane pattern recognition receptors and contributes to the unbridled spread of cell death in lesion simulating disease 1. Together with RNLs, SADR1 regulates defense gene expression at infection site borders, likely in a non-autonomous manner. RNL mutants that cannot sustain this pattern of gene expression are unable to prevent disease spread beyond localized infection sites, suggesting that this pattern corresponds to a pathogen containment mechanism. SADR1 potentiates RNL-driven immune signaling partially through the activation of EDS1, but also partially independently of EDS1. We studied EDS1-independent TIR function using nicotinamide, an NADase inhibitor. We observed decreased defense induction from trans-membrane pattern recognition receptors and decreased calcium influx, pathogen growth restriction and host cell death following intracellular immune receptor activation. We demonstrate that TIR domains can potentiate calcium influx and defense and are thus broadly required for Arabidopsis immunity.

plant biology↗

bioRxiv2019

Escape mutations circumvent a tradeoff between resistance to beta-lactams and a beta-lactamase inhibitor

Beta-lactamase inhibitors are increasingly used to counteract microbial resistance to beta-lactam antibiotics mediated by beta-lactamase enzymes. These inhibitors compete with the beta-lactam drug for the same binding site of the beta-lactamase, thereby generating an inherent evolutionary tradeoff: enzyme mutations that increase its activity against the beta-lactam drug also increase its susceptibility towards the inhibitor. It is unclear how common and accessible are mutants that escape this adaptive tradeoff. Here, systematically constructing and phenotyping a deep mutant library of the ampC beta-lactamase gene of Escherichia coli, we identified escape mutations, which even in the presence of the enzyme inhibitor allow growth at beta-lactam concentrations far exceeding the native inhibitory levels of the wildtype strain. Importantly, while such escape mutations appear for combinations of avibactam with some beta-lactam drugs, for other drugs escape phenotypes are completely restricted. Amplicon sequencing of the selected mutant pool identified these escape mutations and showed that they are rare and drug specific. For the combination of avibactam with aztreonam, an escape phenotype was conferred via multiple substitutions in a single conserved amino acid (Tyr 150). In contrast, a different set of mutations showed an escape phenotype for cefepime, and no escape mutants appeared for piperacillin. The differential adaptive potential of ampC to combinations of avibactam and different beta-lactam drugs can help guide drug treatments that are more resilient to evolution of resistance.

microbiology↗

bioRxiv2018

M3C: A Monte Carlo reference-based consensus clustering algorithm

Genome-wide data is used to stratify patients into classes for precision medicine using clustering algorithms. A common problem in this area is selection of the number of clusters (K). The Monti consensus clustering algorithm is a widely used method which uses stability selection to estimate K. However, the method has bias towards higher values of K and yields high numbers of false positives. As a solution, we developed Monte Carlo reference-based consensus clustering (M3C), which is based on this algorithm. M3C simulates null distributions of stability scores for a range of K values thus enabling a comparison with real data to remove bias and statistically test for the presence of structure. M3C corrects the inherent bias of consensus clustering as demonstrated on simulated and real expression data from The Cancer Genome Atlas (TCGA). For testing M3C, we developed clusterlab, a new method for simulating multivariate Gaussian clusters.

bioinformatics↗

bioRxiv2017

The null additivity of multi-drug combinations

From natural ecology 1-4 to clinical therapy 5-8, cells are often exposed to mixtures of multiple drugs. Two competing null models are used to predict the combined effect of drugs: response additivity (Bliss) and dosage additivity (Loewe) 9-11. Here, noting that these models diverge with increased number of drugs, we contrast their predictions with measurements of Escherichia coli growth under combinations of up to 10 different antibiotics. As the number of drugs increases, Bliss maintains accuracy while Loewe systematically loses its predictive power. The total dosage required for growth inhibition, which Loewe predicts should be fixed, steadily increases with the number of drugs, following a square root scaling. This scaling is explained by an approximation to Bliss where, inspired by RA Fishers classical geometric model 12, dosages of independent drugs adds up as orthogonal vectors rather than linearly. This dose-orthogonality approximation provides results similar to Bliss, yet uses the dosage language as Loewe and is hence easier to implement and intuit. The rejection of dosage additivity in favor of effect additivity and dosage orthogonality provides a framework for understanding how multiple drugs and stressors add up in nature and the clinic.

systems biology↗