Organelle DNA degradation contributes to the efficient use of phosphate in seed plants

Mitochondria and chloroplasts (plastids) both harbour extranuclear DNA that originates from the ancestral endosymbiotic bacteria. These organelle DNAs (orgDNAs) encode limited genetic information but are highly abundant, with multiple copies in vegetative tissues, such as mature leaves. Abundant orgDNA constitutes a substantial pool of organic phosphate along with RNA in chloroplasts, which could potentially contribute to phosphate recycling when it is degraded and relocated. However, whether orgDNA is degraded nucleolytically in leaves remains unclear. In this study, we revealed the prevailing mechanism in which organelle exonuclease DPD1 degrades abundant orgDNA during leaf senescence. The DPD1 degradation system is conserved in seed plants and, more remarkably, we found that it was correlated with the efficient use of phosphate when plants were exposed to nutrient-deficient conditions. The loss of DPD1 compromised both the relocation of phosphorus to upper tissues and the response to phosphate starvation, resulting in reduced plant fitness. Our findings highlighted that DNA is also an internal phosphate-rich reservoir retained in organelles since their endosymbiotic origin

The Plant Organelles Database 2 (PODB2): An Updated Resource Containing Movie Data of Plant Organelle Dynamics

The Plant Organelles Database (PODB) was launched in 2006 and provides imaging data of plant organelles, protocols for plant organelle research and external links to relevant websites. To provide comprehensive information on plant organelle dynamics and accommodate movie files that contain time-lapse images and 3D structure rotations, PODB was updated to the next version, PODB2 (http://podb.nibb.ac.jp/Organellome). PODB2 contains movie data submitted directly by plant researchers and can be freely downloaded. Through this organelle movie database, users can examine the dynamics of organelles of interest, including their movement, division, subcellular positioning and behavior, in response to external stimuli. In addition, the user interface for access and submission has been enhanced. PODB2 contains all of the information included in PODB, and the volume of data and protocols deposited in the PODB2 continues to grow steadily. Moreover, a new website, Plant Organelles World (http://podb.nibb.ac.jp/Organellome/PODBworld/en/index.html), which is based on PODB2, was recently launched as an educational tool to engage members of the non-scientific community such as students and school teachers. Plant Organelles World is written in layman's terms, and technical terms were avoided where possible. We would appreciate contributions of data from all plant researchers to enhance the usefulness of PODB2 and Plant Organelles World

Electronic structure of Kondo lattice compounds YbNi3X9 (X = Al, Ga) studied by hard x-ray spectroscopy

We have performed hard x-ray photoemission spectroscopy (HAXPES) for Yb-based Kondo lattice compounds; an antiferromagnetic heavy-fermion system YbNi3Al9 and a valence fluctuation system YbNi3Ga9. The Yb 3d5/2 spectra of YbNi3Ga9 showed both Yb2+ and Yb3+-derived structures indicating strong valence fluctuation, and the intensity of Yb2+ (Yb3+) structures gradually increased (decreased) on cooling. The Yb 3d5/2 spectra of YbNi3Al9 mostly consisted of Yb3+-derived structures and showed little temperature dependence. The Yb valences of YbNi3Ga9 and YbNi3Al9 at 22 K were evaluated to be 2.43 and 2.97, respectively. Based on the results of the Ni 2p and valence-band HAXPES spectra together with soft x-ray valence-band spectra, we described that the difference of physical properties of YbNi3X9 (X= Al, Ga) is derived from the differences of the 4f-hole level relative to the Fermi level (EF) and Ni 3d density of states at EF. The HAXPES results on the Yb valences were consistent with those obtained by x-ray absorption spectroscopy using the partial fluorescence yield mode and resonant x-ray emission spectroscopy at the Yb L3 edge

Effect of dormancy on the development of phloem fiber clusters

The development of phloem fibers was investigated in poplars grown under artificially fixed conditions and under an artificially shortened annual cycle system that includes a dormancy phase. The phloem tissues in these trees formed two- or three-layer fiber clusters; however, clusters in trees that underwent periodic dormancy were larger than those in trees that did not. Individual fibers were also larger in the former than in the latter, as assessed on transverse sections. Differences were most pronounced in the radial diameter of fibers in the layer nearest the cambium. These results suggest that dormancy affects both the size of fiber clusters and the diameter of individual fibers. Furthermore, these results imply that dormancy affects the development of phloem fibers, and that the shortened annual cycle system is a useful model for investigating phloem development caused by dormancy repetition

Quantification of polyphosphate: different sensitivities to short-chain polyphosphate using enzymatic and colorimetric methods as revealed by ion chromatography

Polyphosphate is ubiquitous and has a variety of biochemical functions. Among polyphosphate quantification methods, an enzymatic assay using Escherichia coli polyphosphate kinase (PPK), in which polyphosphate is converted to adenosine 5′-triphosphate and quantified by luciferase assay, is the most specific and most sensitive. However, chain-length specificity of the assay has not been analyzed in detail so far. Ion chromatography equipped with an on-line hydroxide eluent generator enabled us to analyze polyphosphate up to 50 inorganic phosphate (Pi) residues, and we employed this method to investigate the chain-length specificity of PPK in this study. Several fractions of short-chain polyphosphate were prepared by electrophoresis, and the chain-length distribution was analyzed before and after 1–6 h PPK reaction by ion chromatography. Polyphosphates longer than 23 Pi residues were processed by PPK completely after 1 h incubation, but complete processing of those between 11 and 22 Pi residues required 6 h incubation. Limited processing of polyphosphates of 10 Pi residues or shorter were observed even after 6 h incubation. Metachromasy of Toluidine blue O, an alternative method for polyphosphate quantification, showed broader chain-length specificity although it was not as sensitive as the enzymatic assay. Combination of these two methods would be practically applicable to analysis of polyphosphate dynamics in living organisms

Experimental Study of Intra-Ring Anatomical Variation in <i>Populus alba</i> L. with Respect to Changes in Temperature and Day-Length Conditions

There are various studies on annual ring structural variations in plants grown in the field under varying meteorological statistics. However, related experimental approach is limited, hitherto. In this study, complete artificial conditions with growth chambers were adopted to evaluate the influence of day length and temperature on intra-ring structure formation. The basic artificial growing conditions have been previously reported as “shortened annual cycle system”, which consisted of the following three stages mimicking seasons approximately: Stage 1, spring/summer; Stage 2, autumn; and Stage 3, winter. This system shortens an annual cycle of Populus alba to 5 months. In this study, Stage 2 was modified in two ways: one was a condition in which the temperature was fixed and the day length was gradually shortened, and the other was a condition with a fixed day length and gradually lowered temperature. In the former condition, the cell wall of fibers thickened from the middle of the ring, and the vessel diameter became smaller from the same position. The wood in the latter condition appeared more natural in terms of wall thickness and vessel shape; however, the thickness of the wall reduced in the starting position of Stage 2. It may have been caused by the shortage of material for cell production under a high temperature but a short day length