FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis.

Plant microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, it also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5'-3' RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). In mutants of FRY1 and the nuclear 5'-3' exonuclease genes XRN2 and XRN3, we find that a large number of 21-nt risiRNAs are generated through an endogenous siRNA biogenesis pathway. The production of risiRNAs correlates with pre-rRNA processing defects in these mutants. We also show that these risiRNAs are loaded into AGO1, causing reduced loading of miRNAs. This study reveals a previously unknown link between rRNA processing and miRNA accumulation

Combined Influences of Light and Nitrogen Enrichment on the Physiological Performance of a Golden Tide Alga (Sargassum horneri)

Sargassum golden tides (GT) are common in numerous coastal areas all over the world, and it adversely affects local marine life. Eutrophication is critical for Sargassum GT development. However, its physiological and ecological mechanism remains unclear. To investigate the responses of drifting Sargassum horneri, the species causing GT in the western Pacific, to light and enriched nitrogen, we set three light conditions (Low-light (LL), 10 μmol photons m−2 s−1; Middle-light (ML), 60 μmol photons m−2 s−1; and High-light (HL), 300 μmol photons m−2 s−1) and three nitrogen conditions (Natural seawater, the final concentration of N was 31.8 μmol L−1, including 30.5 μmol L−1 of NO3− and 1.3 μmol L−1 of NH4+; Enrichment of NO3−, final concentration of N was 200 μmol L−1; and Enrichment of NH4+, the final concentration of N was 200 μmol L−1), and grew the thalli under varying conditions for 10 days before determining the growth and utilization of carbon and nitrogen. Based on the accumulated data, the elevated light level led to a higher growth rate of alga. In the LL culture, the higher capacity for carbon utilization, which was reflected by the higher maximum photosynthetic carbon fixation rate (Vmax), resulted in the elevated growth rates of thalli in the nitrogen-enriched media as compared with the natural seawater. Furthermore, a higher growth rate was found in the enrichment of NH4+ despite a low affinity for inorganic carbon indicated by a higher value of the half-saturation constant (K0.5). In the ML treatment, an insignificant difference in growth rate was found in three nitrogen cultures, except for a slight increase in the enrichment of NH4+ than the enrichment of NO3−. In the HL treatment, compared with natural seawater culture, enrichment of NO3− or NH4+ accelerated the growth of alga, with no significant difference between the two nitrogen sources. Such enhancement in growth was related to the more photosynthetic carbon fixation, indicated by the higher value of Vmax and soluble carbohydrates content of alga cultured with NO3− and NH4+ enrichments. Additionally, the uptake and assimilation products of nitrogen, such as pigments and soluble proteins, remained unaffected by nitrogen source enrichment of NO3− or NH4+ at all three light levels. In conclusion, enrichment of NO3− and NH4+ exhibited different influences on the growth of S. horneri at different light levels, which was mainly associated with the capacity and efficiency of photosynthetic carbon utilization. At the HL level, both the enrichment of NO3− and NH4+ dramatically accelerate the growth of alga by stimulating the photosynthetic carbon fixation. Accordingly, we speculated that drifting S. horneri, exposed to HL level on the surface of the sea, were likely to develop rapidly to form GT in eutrophic oceanic areas with upwelled and river plume NO3− or NH4+ nutrients

Combined Influences of Light and Nitrogen Enrichment on the Physiological Performance of a Golden Tide Alga (<i>Sargassum horneri</i>)

Sargassum golden tides (GT) are common in numerous coastal areas all over the world, and it adversely affects local marine life. Eutrophication is critical for Sargassum GT development. However, its physiological and ecological mechanism remains unclear. To investigate the responses of drifting Sargassum horneri, the species causing GT in the western Pacific, to light and enriched nitrogen, we set three light conditions (Low-light (LL), 10 μmol photons m−2 s−1; Middle-light (ML), 60 μmol photons m−2 s−1; and High-light (HL), 300 μmol photons m−2 s−1) and three nitrogen conditions (Natural seawater, the final concentration of N was 31.8 μmol L−1, including 30.5 μmol L−1 of NO3− and 1.3 μmol L−1 of NH4+; Enrichment of NO3−, final concentration of N was 200 μmol L−1; and Enrichment of NH4+, the final concentration of N was 200 μmol L−1), and grew the thalli under varying conditions for 10 days before determining the growth and utilization of carbon and nitrogen. Based on the accumulated data, the elevated light level led to a higher growth rate of alga. In the LL culture, the higher capacity for carbon utilization, which was reflected by the higher maximum photosynthetic carbon fixation rate (Vmax), resulted in the elevated growth rates of thalli in the nitrogen-enriched media as compared with the natural seawater. Furthermore, a higher growth rate was found in the enrichment of NH4+ despite a low affinity for inorganic carbon indicated by a higher value of the half-saturation constant (K0.5). In the ML treatment, an insignificant difference in growth rate was found in three nitrogen cultures, except for a slight increase in the enrichment of NH4+ than the enrichment of NO3−. In the HL treatment, compared with natural seawater culture, enrichment of NO3− or NH4+ accelerated the growth of alga, with no significant difference between the two nitrogen sources. Such enhancement in growth was related to the more photosynthetic carbon fixation, indicated by the higher value of Vmax and soluble carbohydrates content of alga cultured with NO3− and NH4+ enrichments. Additionally, the uptake and assimilation products of nitrogen, such as pigments and soluble proteins, remained unaffected by nitrogen source enrichment of NO3− or NH4+ at all three light levels. In conclusion, enrichment of NO3− and NH4+ exhibited different influences on the growth of S. horneri at different light levels, which was mainly associated with the capacity and efficiency of photosynthetic carbon utilization. At the HL level, both the enrichment of NO3− and NH4+ dramatically accelerate the growth of alga by stimulating the photosynthetic carbon fixation. Accordingly, we speculated that drifting S. horneri, exposed to HL level on the surface of the sea, were likely to develop rapidly to form GT in eutrophic oceanic areas with upwelled and river plume NO3− or NH4+ nutrients

A Census of Nuclear Cyanobacterial Recruits in the Plant Kingdom

<div><p>The plastids and mitochondria of the eukaryotic cell are of endosymbiotic origin. These events occurred ~2 billion years ago and produced significant changes in the genomes of the host and the endosymbiont. Previous studies demonstrated that the invasion of land affected plastids and mitochondria differently and that the paths of mitochondrial integration differed between animals and plants. Other studies examined the reasons why a set of proteins remained encoded in the organelles and were not transferred to the nuclear genome. However, our understanding of the functional relations of the transferred genes is insufficient. In this paper, we report a high-throughput phylogenetic analysis to identify genes of cyanobacterial origin for plants of different levels of complexity: <i>Arabidopsis thaliana</i>, <i>Chlamydomonas reinhardtii</i>, <i>Physcomitrella patens</i>, <i>Populus trichocarpa</i>, <i>Selaginella moellendorffii</i>, <i>Sorghum bicolor</i>, <i>Oryza sativa</i>, and <i>Ostreococcus tauri</i>. Thus, a census of cyanobacterial gene recruits and a study of their function are presented to better understand the functional aspects of plastid symbiogenesis. From algae to angiosperms, the GO terms demonstrated a gradual expansion over functionally related genes in the nuclear genome, beginning with genes related to thylakoids and photosynthesis, followed by genes involved in metabolism, and finally with regulation-related genes, primarily in angiosperms. The results demonstrate that DNA is supplied to the nuclear genome on a permanent basis with no regard to function, and only what is needed is kept, which thereby expands on the GO space along the related genes.</p></div

Relative standard deviations of plastome measures.

<p>In contrast to plastids, the size of the plant chondriome (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120527#pone.0120527.g002" target="_blank">Fig. 2</a>) increased from algae to angiosperms, with lower variance in algae than in angiosperms (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120527#pone.0120527.t004" target="_blank">Table 4</a>). For angiosperms, the variance was higher in the number of protein-coding genes than for nonvascular land plants and algae. The coding region of the chondriome decreased from 52% in algae to 15% in angiosperms, but the variance remained similar. However, the number of proteins coded by the chondriome increased with an increasing variance. The number of structural RNAs of the mitochondria remained similar in all species. The amount of noncoding DNA increased in all three cellular organelles (nucleus, plastid, and mitochondria), but the size of coding DNA increased concurrently only in the nucleus (data not shown).</p><p>Relative standard deviations of plastome measures.</p

The average size in Mbps of the nuclear (orange), plastid (green) and mitochondrial (blue) genomes in phylogenetic groups.

<p>The plastome size remains similar in all the groups, whereas the chondriome seems to be inflating as plants are becoming more complex. The average genome size of gymnosperms is out of the scale due to the extremely large genome of Picea glauca, and the low number of species sequenced in the group.</p

The number of NUMTs in the species studied.

<p>The number of NUMTs in the species studied.</p

The number of NUPTs in the species studied.

<p>The number of NUPTs in the species studied.</p