Transcriptome-Wide Characterization of the PPR Gene Family Reveals Stable Plastid-Targeted PPR Expression Alongside Reduced Photosystem II Performance in HLB-Affected Persian Lime

Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), severely impairs photosynthesis and chloroplast function in citrus. However, Persian lime (Citrus latifolia) exhibits remarkable tolerance, maintaining productivity despite infection. Pentatricopeptide repeat (PPR) proteins regulate organellar RNA metabolism and are essential for chloroplast function. Here, we investigated whether plastid-targeted PPR regulatory networks are transcriptionally altered during CLas infection. We combined transcriptome-wide identification of PPR proteins, prediction of chloroplast RNA targets, gene expression analyses, and chlorophyll a fluorescence measurements. A total of 515 PPR proteins were identified, with 30.5% predicted to localize to plastids. Predicted RNA targets included chloroplast genes involved in transcription and photosynthesis, such as ycf2, rpoC1, psbB, and psbC. Despite this extensive predicted regulatory network, neither plastid-targeted PPR genes nor their chloroplast targets showed differential expression between HLB-positive and HLB-negative leaves. In contrast, infected leaves exhibited reduced Fv/Fm, PIabs, and electron transport efficiency, although the characteristic OJIP transient remained largely preserved, indicating maintenance of PSII structural organization. These findings suggest that constitutive plastid PPR regulatory mechanisms remain stable during CLas infection and may contribute to the chloroplast resilience underlying HLB tolerance in Persian lime.