Genome-wide identification and expression analysis reveal potential functions of the MTP gene family in Moso bamboo (Phyllostachys edulis (Carrière) J.Houz.)

Abstract

As an important economic forest species, Moso bamboo (Phyllostachys edulis) possesses significant ecological and economic value. However, the intensification of environmental pollution has heightened concerns regarding the impact of heavy metal stress on the growth and ecological functions of Moso bamboo. The MTP (Metal Tolerance Protein) gene family, also referred to as the CDF (Cation Diffusion Facilitator) gene family, consists of integral membrane transporters that facilitate the translocation of metal ions across plant membranes. By sequestering cytoplasmic divalent cations into vacuoles or other endomembrane compartments, MTPs effectively mitigate metal toxicity and maintain ionic homeostasis. Nevertheless, the genomic repertoire, expression landscape and biological roles of MTP genes in Moso bamboo remain largely uncharacterized. We conducted a genome-wide scan that identified 16 non-redundant MTP loci within the Moso bamboo genome. Phylogenetic reconstruction classified the bamboo MTP complement into four distinct clades that are evolutionarily conserved across land plants. Comprehensive in-silico characterization, including conserved motif profiling, exon-intron architecture, chromosomal distribution, cis-regulatory element composition and micro-synteny analyses, revealed both conserved lineage-specific features and segmental duplication events that have shaped this gene family. Time-course expression mining of RNA-seq datasets using STEM algorithms indicated that selected MTP paralogues are dynamically co-expressed during the rapid elongation phase of bamboo shoots, implicating this family in both developmental and stress-responsive processes. Homology-based tertiary modeling recapitulated the canonical CDF fold, with signature zinc-binding and cation-transporting motifs positioned within the transmembrane helices, thereby providing structural insights into ion selectivity and efflux mechanisms. Protein–protein interaction networks and transcription-factor binding-site enrichment further predicted a core regulatory module centered on five hub MTPs. Subcellular localization of GFP fusions in transgenic Nicotiana benthamiana confirmed plasma membrane residency for the investigated isoforms. Collectively, these findings provide the first integrated framework for understanding the classification, structural properties and putative physiological functions of the MTP family in Moso bamboo, establishing a molecular basis for future genetic improvements in bamboo resilience to heavy-metal stress.