Biology subjects

Escudero-Martinez, C.

Publications and source records attributed to Escudero-Martinez, C..

7 recordsLinked to original sources

bioRxiv2026

Towards a comprehensive chemical and genetic tool library for rhamnogalacturonan-II oligosaccharides and exploitation

Rhamnogalacturonan-II (RG-II) is considered the most complex glycan in nature. It forms part of an intricate network of complex glycans in the plant cell wall where it plays a critical role in plant growth, development and defence. It has been identified as an important nutrient source for the human gut microbiota (HGM), a key modulator of human health and disease status. Increasing evidence also suggests that RG-II can modulate plant-microbe interactions. Given its importance and potential, detailed studies of RG-IIs structure-function relationships and metabolism are required to underpin future crop-improvement strategies and to harness its benefits for plant and human health. Progress in this field is however hampered by RG-IIs structural complexity and limited access to enabling tools, in particular chemically defined RG-II-derived oligosaccharide (CDRO) substructures. Achieving targeted, efficient, and scalable production of CDROs remains a significant challenge and is indeed one of the major reasons why RG-II and glycomic research in general, significantly lag behind genomic and proteomic research. Here, we have genetically engineered as well as screened a diverse set of genetic strains, including transposon (Tn) mutants of the prominent model human gut microbe Bacteroides thetaiotaomicron (B. theta) and its gut and plant-associated relatives for new CDRO-generating and/or RG-II-utilising strains. Several CDROs, some of which had never been produced before by any other means (including chemical synthesis), where generated and characterised by a combination of high-resolution mass spectrometry (MS), enzymatic profiling and 2D-NMR. In addition to expanding the CDRO toolbox, we identified key genetic strains that will serve as a base or platform for the production of an unprecedented amount of CDROs covering the complexity and diversity of chemical modifications in RG-II. CDROs were later exploited to gain new insights into the microbial metabolism of RG-II in the human gut, revealing key aspects of its chemical structure that drive or limit its metabolism in B. theta. Notably, we generated new evidence in support of an alternative operational paradigm for polysaccharide utilisation systems that are widespread in the Bacteroidota phylum. We confirmed the presence of pathways for the metabolism of RG-II and/or RG-II core sugars D-apiose (D-Apif), and 3-deoxy-D-manno-2-octulosonic acid (D-Kdo) in aerobic plant-associated microbes including fungi and Flavobacterium spp., highlighting their potential to be exploited as cost-effective alternatives to B. theta for the generation of CDROs.

biochemistry↗

bioRxiv2025

Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interaction

O_LIDeciphering the root exudate-driven interplay between plants and the rhizosphere microbiota is essential for understanding plant adaptation to the environment and future-proofing crop production. However, sampling root exudates and rhizosphere soil remains challenging due to the low throughput and destructive nature of the process. C_LIO_LIWe used the staple crop barley [Hordeum vulgare] as a model to benchmark different sampling approaches for simultaneous exudation and microbiota profiling of soil-grown plants. C_LIO_LIExudate profiles and total dissolved organic carbon exudation rates were consistent across different sampling approaches, whereas root biomass, root morphology measurements, and organic nitrogen exudation varied. C_LIO_LIHigh-throughput amplicon sequencing and quantitative PCR (qPCR) of phylogenetic markers and nitrogen cycle-selected genes revealed a protocol-specific footprint in the composition and abundance of rhizosphere bacterial and fungal microbiota. Yet, on average, 75% of microbes enriched in, and differentiating between, barley rhizosphere and unplanted soil controls were recovered across all the sampling approaches evaluated. C_LIO_LIOur results demonstrated that, under the tested conditions, different sampling approaches produced comparable microbiota and exudation patterns, enabling the integrated study of root exudation and microbial profiles from the same plant. The observed differences across sampling approaches must be considered according to the experimental scope. C_LI

plant biology↗

bioRxiv2021

IDENTIFYING PLANT GENES SHAPING MICROBIOTA COMPOSITION IN THE BARLEY RHIZOSPHERE

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plants capacity of shaping rhizosphere microbes.

plant biology↗

bioRxiv2019

A cereal aphid effector promotes barley susceptibility in a species-specific manner through suppression of defence gene expression.

Aphids secrete diverse repertoires of effectors into their hosts to promote the infestation process. While \"omics\"-approaches facilitated the identification and comparison of effector repertoires from a number of aphid species, the functional characterization of these proteins has been limited to dicot (model) plants. The bird cherry-oat aphid Rhopalosiphum padi is a pest of cereal crops, including barley. Here, we extended efforts to characterize aphid effectors with regards to their role in promoting susceptibility to the R. padi-barley interaction. We selected 3 R. padi effectors based on sequences similarity to previously characterized M. persicae effectors and assessed their subcellular localisation, expression, and role in promoting plant susceptibility. Expression of R. padi effectors RpC002 and Rp1 in transgenic barley lines enhanced plant susceptibility to R. padi but not M. persicae, for which barley is a poor host. Characterization of Rp1 transgenic barley lines revealed reduced gene expression of plant hormone signalling genes relevant to plant-aphid interactions, indicating this effector enhances susceptibility by suppressing plant defences in barley. Our data suggests that some aphid effectors specifically function when expressed in host species, and feature activities that benefit their corresponding aphid species.

plant biology↗

bioRxiv2018

Non-host and poor-host resistance against aphids may reside in different plant cell layers depending on the plant species-aphid species interaction

Aphids are phloem-feeding insects that cause economic losses to crops globally. Whilst aphid interactions with susceptible plants and partially resistant genotypes have been well characterised with regards to aphid probing and feeding behaviour, the interactions with non-natural host species are not well understood. Using aphid choice assays with the broad host range pest Myzus persicae and the cereal pest Rhopalosiphum padi we show that about 10% of aphids settle on non-/poor-host species over a 24h time period. We used the Electrical Penetration Graph technique to assess aphid probing and feeding behaviour during the non-/poor-host interactions. In the Arabidopsis non-host interaction with the cereal pest R. padi aphids were unable to reach and feed from the phloem, with resistance likely residing in the mesophyll cell layer. In the barley poor-host interaction with M. persicae, resistance is likely phloem-based as aphids were able to reach the phloem but ingestion was reduced compared with the host interaction. Overall our data suggests that plant resistance to aphids in non-host and poor-host interactions with these aphid species likely resides in different plant cell layers. Future work will take into account specific cell layers where resistances are based to dissect the underlying mechanisms and gain a better understanding of how we may improve crop resistance to aphids.

ecology↗

bioRxiv2018

Extensive Myzus cerasi transcriptional changes associated with detoxification genes upon primary to secondary host alternation

Aphids are phloem-feeding insects that cause yield losses to crops globally. These insects feature complex life cycles, which in the case of many agriculturally important species involves the use of primary and secondary host plant species. Whilst host alternation between primary and secondary host can occur in the field depending on host availability and the environment, aphid populations maintained as laboratory stocks generally are kept under conditions that allow asexual reproduction by parthenogenesis on secondary hosts. Here, we used Myzus cerasi (black cherry aphid) to assess aphid transcriptional differences between populations collected from primary hosts in the field and those adapted to secondary hosts under controlled environment conditions. Adaptation experiments of M. cerasi collected from local cherry tress to reported secondary host species resulted in low survival rates. Moreover, aphids were unable to survive on secondary host Land cress, unless first adapted to another secondary host, cleavers. Transcriptome analyses of populations collected from primary host cherry in the field and the two secondary host plant species in a controlled environment showed extensive transcriptional plasticity to a change in host environment, with predominantly genes involved in redox reactions differentially regulated. Most of the differentially expressed genes across the M. cerasi populations from the different host environments were duplicated and we found evidence for differential exon usage. In contrast, we observed only limited transcriptional to a change in secondary host plant species.

genomics↗

bioRxiv2018

Shared transcriptional control and disparate gain and loss of aphid parasitism genes and loci acquired via horizontal gene transfer

BackgroundAphids are a diverse group of taxa that contain hundreds of agronomically important species, which vary in their host range and pathogenicity. However, the genome evolution underlying agriculturally important aphid traits is not well understood.\n\nResultsWe generated highly-contiguous draft genome assemblies for two aphid species: the narrow host range Myzus cerasi, and the cereal specialist Rhopalosiphum padi. Using a de novo gene prediction pipeline on both these genome assemblies, and those of three related species (Acyrthosiphon pisum, D. noxia and M. persicae), we show that aphid genomes consistently encode similar gene numbers, and in the case of A. pisum, fewer and larger genes than previously reported. We compare gene content, gene duplication, synteny, horizontal gene transfer events, and putative effector repertoires between these five species to understand the genome evolution of globally important plant parasites.\n\nAphid genomes show signs of relatively distant gene duplication, and substantial, relatively recent, gene birth, and are characterized by disparate gain and loss of genes acquired by horizontal gene transfer (HGT). Such HGT events account for approximately 1% of loci, and contribute to the protein-coding content of aphid species analysed. Putative effector repertoires, originating from duplicated loci, putative HGT events and other loci, have an unusual genomic organisation and evolutionary history. We identify a highly conserved effector-pair that is tightly genetically-linked in all aphid species. In R. padi, this effector pair is tightly transcriptionally-linked, and shares a transcriptional control mechanism with a subset of approximately 50 other putative effectors distributed across the genome.\n\nConclusionsThis study extends our current knowledge on the evolution of aphid genomes and reveals evidence for a shared control mechanism, which underlies effector expression, and ultimately plant parasitism.

genomics↗