Biology subjects

Chiu, C.-Y.

Publications and source records attributed to Chiu, C.-Y..

4 recordsLinked to original sources

bioRxiv2024

CORNICHON HOMOLOG 5-dependent ER export of membrane cargoes in phosphate-starved Arabidopsis root as revealed by membrane proteomic analysis

Developing plants tolerant of low phosphate (Pi) availability is essential to reduce reliance on fertilizers and achieve agricultural sustainability. One strategy is to enhance the endoplasmic reticulum (ER) export of cargoes associated with Pi starvation and their trafficking to final destinations. However, the mechanisms underlying this process are underexplored. We recently discovered that Arabidopsis thaliana CORNICHON HOMOLOG 5 (AtCNIH5) encodes a Pi deficiency-induced ER cargo receptor that regulates Pi homeostasis. To find potential membrane cargoes of AtCNIH5, we applied the UV-cleavable 4-hexylphenylazosulfonate (Azo)-solubilized microsomal protein extraction for iTRAQ-based proteomic analysis. We identified 4,317 proteins in Pi-limited Arabidopsis roots, with 372 upregulated and 106 downregulated proteins in cnih5. Besides PHOSPHATE TRANSPORTER 1 proteins (PHT1s), downregulation of the biosynthetic or modifying enzymes for cell wall polysaccharides, very long-chain fatty acids, and their derivative extracellular aliphatic compounds is over-represented. Using the yeast split-ubiquitin and the in-planta tripartite split-GFP assays, we verified the interaction of AtCNIH5 with various downregulated transporters in cnih5, including AtPHT1s, AtOCT1, AtURGT6, AtDTX21, and AtDTX35. In addition, we demonstrated that the C-terminal acidic residue of AtCNIH5 is required for interaction with AtOCT1 but not with AtPHT1;1 or AtDTX21, indicating distinct cargo selection mechanisms. More importantly, enhancing in-situ AtCNIH5 expression/activity enhances plant growth. By analogy with transcriptional factors that govern gene expression, we propose that AtCNIH5 acts as a low Pi-responsive hub to facilitate ER export of specific membrane cargoes, providing a potential engineering strategy to improve plant fitness under suboptimal Pi supply.

plant biology↗

bioRxiv2024

Phosphate Starvation-Induced CORNICHON HOMOLOG 5 as Endoplasmic Reticulum Cargo Receptor for PHT1 Transporters in Arabidopsis

Inorganic phosphate (Pi) is essential for plant growth and is acquired and distributed by the plasma membrane PHOSPHATE TRANSPORTER 1 proteins (PHT1s). Enhancing the abundance of PHT1s at the cell surface thus ensures plant productivity and sustainable agriculture. CORNICHON HOMOLOG proteins (CNIHs) are conserved eukaryotic cargo receptors that mediate the selective endoplasmic reticulum (ER) export of membrane proteins. In this study, we identified the Arabidopsis thaliana CNIH5 (AtCNIH5) as a Pi starvation-inducible gene, preferentially expressed in vascular tissues and outer root cell layers above the meristem. AtCNIH5 co-localizes to the AtSAR1A/AtSEC16A/AtSEC24A-labeled ER exit sites and interacts with AtPHT1;1. Loss of AtCNIH5 confers reduced shoot Pi levels under Pi sufficiency due to the reduced translocation of Pi from roots to shoots, as well as decreased Pi uptake under Pi deficiency. The cnih5 mutant exhibits decreased abundance of AtPHT1s but increased PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 (AtPHF1), which enables the ER exit of PHT1s. The cnih5 mutant also shows a lower plasma membrane targeting efficiency of split-GFP tagged-AtPHT1;1 in the root hair and the epidermis within the root transition/elongation zone. Consistently, dysfunctional AtCNIH5 exerts a suppressive effect on the growth of phf1 and alleviates Pi toxicity in the Pi overaccumulator pho2. However, the in vivo protein-protein interaction and degradation assays indicated that AtCNIH5 is not a direct target of AtPHO2. Our findings unveil that AtCNIH5 is a low Pi-responsive ER cargo receptor that interplays with AtPHF1 to promote the plasma membrane targeting of AtPHT1s in a cell-type-dependent manner.

plant biology↗

bioRxiv2021

Genomes of keystone Mortierella species lead to better in silico prediction of soil mycobiome functions from Taiwan's offshore islands

The ability to correlate the functional relationship between microbial communities and their environment is critical to understanding microbial ecology. There is emerging knowledge on island biogeography of microbes but how island characteristics influence functions of microbial community remain elusive. Here, we explored soil mycobiomes from nine islands adjacent to Taiwan using ITS2 amplicon sequencing. Geographical distances and island size were positively correlated to dissimilarity in mycobiomes, and we identified 56 zero-radius operational taxonomic units (zOTUs) that were ubiquitously present across all islands, and as few as five Mortierella zOTUs dominate more than half of mycobiomes. Correlation network analyses revealed that seven of the 45 hub species were part of the ubiquitous zOTUs belonging to Mortierella, Trichoderma, Aspergillus, Clonostachys and Staphylotrichum. We sequenced and annotated the genomes of seven Mortierella isolates, and comparative predictions of KEGG orthologues using PICRUSt2 database updated with new genomes increased sequence reads coverage by 62.9% at the genus level. In addition, genes associated with carbohydrate and lipid metabolisms were differentially abundant between islands which remained undetected in the original database. Predicted functional pathways were similar across islands despite their geographical separation, difference in differentially abundant genes and composition. Our approach demonstrated the incorporation of the key taxa genomic data can improve functional gene prediction results and can be readily applied to investigate other niches of interests.

genomics↗

bioRxiv2020

Reciprocal transplant experiment in lakes with disparate trophic states show resolution dependent partial functional redundancy

Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes with disparate trophic states and tracked changes in their microbial community and functional attributes for 6 weeks using high-throughput sequencing and functional approaches. The communities from both lakes were resistant to changes in composition after the reciprocal transplant, but their functions tended to become similar to the incubating lakes functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes, though with varying scales of similarity, suggesting partial functional redundancy. Furthermore, the entropy-based L-divergence measure quantified the scale of partial functional redundancy in the lakes surface and bottom waters. This study establishes and quantifies the scale of partial functional redundancy in the freshwater ecosystem through empirical investigation.

ecology↗