Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.03.16.532963

The Cucumber Kinome: genome-wide, identification, characterisation and expression analysis of the Cucumis sativus protein kinases in response to Powdery Mildew, Alternaria Leaf Spot and Root-Knot Nematode

Costa, F. C. L.·Aono, A. H.·Silva, E. M. d. A.·Pereira, W. A.
View original source ↗Export metadata ↓

Abstract

It is widely known that protein kinases (PKs) play a fundamental role in regulating various metabolic processes in plants, from development to response to the environment. However, a detailed characterization of this superfamily is still lacking for several species, such as cucumber (Cucumis sativus), especially regarding their involvement in the response to Powdery Mildew (PM) caused by Podosphaera xanthii. This study aimed to characterize the cucumber PK family, shedding light on its genomic distribution, classification, and expression patterns triggered by P. xanthii. The hidden Markov models (HMMs) analysis uncovered 835 PKs in the cucumber kinome, distributed across its seven chromosomes, and categorized into 20 distinct groups and 123 families, with the RLK group being the most abundant. Evidence of tandem duplication of PK genes was also observed, enriching our understanding of cucumber PKs. To investigate the expression profiles of PK genes in cucumber, we analyzed the transcription levels of all 835 PK genes in RNA-seq data from leaves of resistant and susceptible cultivars of cucumber to P. xanthii, which were artificially inoculated. Depending on the treatment, DEGs ranged from 319 to 1,690, with PK DEGs ranging from 8 to 105. The number of PK DEGs varied between the different contrasts analyzed. Notably, we observed a greater number of PK DEGs in susceptible genotypes when challenged by the pathogen. Our findings indicate the role of specific cucumber PKs in regulating metabolic processes in the context of plant-pathogen interactions and pave the way for further research into the intricate mechanisms underlying cucumber responses to Powdery Mildew. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/532963v3_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@11340b8org.highwire.dtl.DTLVardef@fe1896org.highwire.dtl.DTLVardef@5de8org.highwire.dtl.DTLVardef@1564d0_HPS_FORMAT_FIGEXP M_FIG C_FIG

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Costa, F. C. L., Aono, A. H., Silva, E. M. d. A., Pereira, W. A.. 2023-03-20. The Cucumber Kinome: genome-wide, identification, characterisation and expression analysis of the Cucumis sativus protein kinases in response to Powdery Mildew, Alternaria Leaf Spot and Root-Knot Nematode. https://doi.org/10.1101/2023.03.16.532963

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

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗
bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗
bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗