Comparative Gene Expression and Physiological Analyses Reveal Molecular Mechanisms in Wound-Induced Spore Formation in the Edible Seaweed Nori

Overexpression of Rboh enhances inorganic carbon acquisition through coordinating with carbonic anhydrase in Pyropia yezoensis

Pyropia yezoensis is an important intertidal economic macroalgae, which is periodically affected by various stresses, such as the limitation of inorganic carbon (Ci) deficiency. Under such environment, the redox homeostasis within the cells of P. yezoensis is seriously affected, and the reactive oxygen species (ROS) signal transduction system would be activated to regulate the photosynthetic activity. Therefore, how P. yezoensis manage ROS to maintain effective photosynthetic carbon fixation has aroused great interest. Here, we characterize transformants overexpressing respiratory burst oxidase homolog (Rboh), an important gene that can actively produce ROS, at the levels of cellular physiology, biochemistry, and transcriptomics. Our data indicated the expression of Rboh significantly increased, accompanied by a significant upregulated expression of alpha-type carbonic anhydrase 3 (αCA3) and increased extracellular carbonic anhydrase activity in the Rboh overexpressing strains. Interestingly, compared with the wild type, the photosynthetic activity of transgenic strains was significantly higher under the low Ci and high light condition, implying that the ROS signal triggered by overexpression of Rboh was involved in regulating the Ci absorption and utilization in P. yezoensis when the Ci source was limited. In summary, this study provided evidence supporting the correlation between the ROS production and the Ci utilization under stress environments in P. yezoensis.

PhbZIP2 regulates photosynthesis-related genes in an intertidal macroalgae, Pyropia haitanensis, under stress

Intertidal macroalgae are important research subjects in stress biology. Basic region-leucine zipper transcription factors (bZIPs) play an important regulatory role in the expression of target genes under abiotic stress. We herein identified a bZIP2 gene PhbZIP2 to regulate abiotic stress tolerance in Pyropia haitanensis, a representative intertidal macroalgal species. Cloning and sequencing of the cDNA characterized a BRLZ structure and an α coiled-coil structure between amino acids and Expression of PhbZIP2 was detected to upregulate under both high temperature and salt stresses. A DAP-seq analysis revealed the PhbZIP2-binding motifs of (T/C)TCCA(C/G) and A (A/G)AAA (G/A), which differed from the conserved motifs in plants. Overexpression of PhbZIP2 was indicative of a high temperature and salt stress tolerances in transgenic Chlamydomonas reinhardtii. It was suggested that PhbZIP2 was probably involved in regulating expression of the photosynthetic-related genes and the response to the abiotic stresses in P. haitanensis, which provide new insights for elucidating efficient adaptation strategies of intertidal macroalgae.

ChIP-Based Nuclear DNA Isolation for Genome Sequencing in Pyropia to Remove Cytosol and Bacterial DNA Contamination

Contamination from cytosolic DNA (plastid and mitochondrion) and epiphytic bacteria is challenging the efficiency and accuracy of genome-wide analysis of nori-producing marine seaweed Pyropia yezoensis. Unlike bacteria and organellar DNA, Pyropia nuclear DNA is closely associated with histone proteins. In this study, we applied Chromatin Immunoprecipitation (ChIP) of histone H3 to isolate nuclear DNA, followed by high-throughput sequencing. More than 99.41% of ChIP-sequencing data were successfully aligned to the reference nuclear genome; this was remarkably higher than those from direct extraction and direct extraction data, in which 40.96% to 42.95% are from plastids. The proportion of data that were mapped to the bacterial database when using ChIP extraction was very low. Additionally, ChIP data can cover up to 89.00% of the nuclear genome, higher than direct extraction data at equal data size and comparable to the latter at equal sequencing depth. The uncovered regions from the three methods are mostly overlapping, suggesting that incomplete sequencing accounts for the missing data, rather than failed chromatin-antibody binding in the ChIP extraction method. This ChIP extraction method can successfully separate nuclear DNA from cytosolic DNA and bacterial DNA, thus overwhelmingly reducing the sequencing cost in a genome resequencing project and providing strictly purified reference data for genome assembly. The method's applicability to other macroalgae makes it a valuable contribution to the algal research community.

Histone acetylation functions in the wound-induced spore formation in nori

The red macroalgae Pyropia yezoensis is one of the most economically important marine crops. In the asexual reproduction process, released archeospores could provide secondary seedling resources in nori farming and be used to establish asexual seeding strategies. We previously found that wounds could induce the somatic cells in sectioned Pyropia thalli to develop into large number of asexual wound-induced spores (WIS) in a short time. Many genes involved in signaling pathways, cell division, cell wall remodeling, etc. exhibited transcriptional variation in this cell fate transition process. However, the regulatory mechanisms controlling gene transcription remain elusive. In this study, we found that suberoylanilide hydroxamic acid (SAHA), the inhibitor of histone deacetylase, strongly repressed WIS formation after wounding. The lack of a sharp increase in HDAC activity after wounding, as well as the hyperacetylated status of histone H3 and H4, were observed in SAHA-treated thalli fragments, thus confirming a histone deacetylation-related epigenetic mechanism of wound-induced cell fate reprogramming. Moreover, histone deacetylation is required in the whole process of WIS formation and release. We further compared the genome-wide transcriptional variations after SAHA treatment. SAHA-responsive genes were identified, including some transcriptional factors, chromatin remodeling complex proteins, protein kinases, etc. Transcription of RBOH genes was also altered by SAHA, and moreover, ROS signals in cut fragments were attenuated, both indicating that the ROS systematic signaling pathway is closely associated with histone deacetylation. Our findings provide insights into the biological significance of dynamic histone acetylation states in WIS formation in P. yezoensis.