Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT

Abstract

Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na+/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.

Phenazine biosynthesis protein MoPhzF regulates appressorium formation and host infection through canonical metabolic and noncanonical signaling function in Magnaporthe oryzae

“…Previous studies have suggested that Candida parapsilosis , Schizosaccharomyces pombe , and Nesidiocoris tenuis all acquired PhzF homologs from bacteria via HGT (Fitzpatrick et al ., 2008; Ferguson et al ., 2021). HGT is a natural biological process that facilitates the exchange of genetic material between distantly related lineages, which allows organisms to acquire novel traits and exploit unexplored resources (Bublitz et al ., 2019; Li et al ., 2022). For instance, Thinopyrum elongatum gained Fusarium head blight resistance gene Fhb7 through HGT from an endophytic Epichloë species, which confers broad resistance to Fusarium species by detoxifying trichothecenes (Wang et al ., 2020).…”

“…The top 200 database hits ( E ‐value < E‐70, bit‐score > 230) were downloaded by B lastp search. The phylogeny construction was conducted using the neighbor‐joining method and 1000 bootstrap replicates (with bootstrap values in black showing on respective branches; Li et al ., 2022). The resulting tree was midpoint rooted, and the tree layout was further edited using M ega 5.2 (Xia et al ., 2021).…”

Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints

“…In the HS treatments of Plagia, only chlorophyte-related OTUs seemed to withstand the scrubber effluent pressure, because their richness and relative abundances remained unchanged, in agreement with microscopy observations (Genitsaris et al, 2023). Genome mining has identified numerous gene entries coding resistance to several sources of pollution in chlorophyte genomes (Li et al, 2022).…”

Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota

“…Horizontal gene transfer (HGT), or the interchange of genetic material across phylogenetic clades, is thought to be an efficient strategy for dispersing reproductive fitness for prokaryotic and eukaryotic cells (Huang, 2013;Daubin and Szöllősi, 2016;Li et al, 2022). Employing transmitting mobile genetic elements (MGEs) like plasmids, viruses, transposons, and gene transfer agents (GTA, tailed phage-like entities capable of packing and transferring random pieces of the host genome) as well as by direct absorption and assimilation of naked DNA by homologous or unauthorized recombination, new genes are transferred through HGT (Thomas and Nielsen, 2005;Lang and Beatty, 2007).…”