Plastid signals remodel light signaling networks and are essential for efficient chloroplast biogenesis in Arabidopsis

Plastid signals are among the most potent regulators of genes that encode proteins active in photosynthesis. Plastid signals help coordinate the expression of the nuclear and chloroplast genomes and the expression of genes with the functional state of the chloroplast. Here, we report the isolation of new cryptochrome1 (cry1) alleles from a screen for Arabidopsis thaliana genomes uncoupled mutants, which have defects in plastid-to-nucleus signaling. We also report genetic experiments showing that a previously unidentified plastid signal converts multiple light signaling pathways that perceive distinct qualities of light from positive to negative regulators of some but not all photosynthesis-associated nuclear genes (PhANGs) and change the fluence rate response of PhANGs. At least part of this remodeling of light signaling networks involves converting HY5, a positive regulator of PhANGs, into a negative regulator of PhANGs. We also observed that mutants with defects in both plastid-to-nucleus and cry1 signaling exhibited severe chlorophyll deficiencies. These data show that the remodeling of light signaling networks by plastid signals is a mechanism that plants use to integrate signals describing the functional and developmental state of plastids with signals describing particular light environments when regulating PhANG expression and performing chloroplast biogenesis.     

Plastid biogenesis in embryonic pea leaf cells during early germination

Summary The ultrastructure of embryonic pea leaf cells was examined during the first 24 h of imbibition of dry seeds. Special attention was paid to plastids, which underwent two interesting interactions during this period. The first was a close physical association between the endoplasmic reticulum and plastids. The second was an association of numerous lipid bodies with the surface of plastids. The functional implications of these associations are considered.Abbreviations CCF conventional chemical fixation - ER endoplasmic reticulum - HPF-FS high-pressure freezing and freeze substitution Dedicated to Professor Eldon H. Newcomb in recognition of his contributions to cell biology     

Bayesian shadows of molecular mechanisms cast in the light of evolution

A great many carefully designed experiments will be required to fully understand biological mechanisms in atomic detail. A complementary approach is to use powerful statistical procedures to rapidly test numerous scientific hypotheses using vast numbers of protein sequences--the cell's own blueprints for specifying biological mechanisms. Bayesian inference of the evolutionary constraints imposed on functionally divergent proteins can reveal key components of the molecular machinery and thereby suggest likely mechanisms to test experimentally. This approach is demonstrated by considering how DNA polymerase clamp-loader AAA+ ATPases couple DNA recognition to ATP hydrolysis and clamp loading.     

Dispersal mode,seed shadows,and colonization patterns

This review assesses the state of our knowledge about comparative seed shadows. Using data presently available in the literature, I compare the slopes (on a log-linear scale) of seed shadows for plants with different morphologically characterized modes of dispersal. The seeds of many species have no evident morphological adaptation for dispersal and seem to achieve only short-distance dispersal. Seed shadows for herbaceous species with devices for wind have flatter slopes and more distant modes and maxima than those of ballists, which in turn exceed those with no special devices. Seed shadows for wind-dispersed trees and shrubs had similar or steeper slopes than those for vertebrate-dispersed species in this sample. Species with poor mechanisms for dispersal in space only sometimes had the capacity for better dispersal in time (dormancy). Although some species exhibited seed shadows sufficiently steep to be predicted to colonize new-habitat in a front or phalanx pattern, actual colonization patterns must reflect many other factors.     

Chloroplast biogenesis - Correlation between structure and function

Chloroplast biogenesis is a multistage process leading to fully differentiated and functionally mature plastids. Complex analysis of chloroplast biogenesis was performed on the structural and functional level of its organization during the photoperiodic plant growth after initial growth of seedlings in the darkness. We correlated, at the same time intervals, the structure of etioplasts transforming into mature chloroplasts with the changes in the photosynthetic protein levels (selected core and antenna proteins of PSI and PSII) and with the function of the photosynthetic apparatus in two plant species: bean (Phaseolus vulgaris L.) and pea (Pisum sativum L). We selected these plant species since we demonstrated previously that the mature chloroplasts differ in the thylakoid organization. We showed that the protein biosynthesis as well as photosynthetic complexes formation proceeds gradually in both plants in spite of periods of darkness. We found that both steady structural differentiation of the bean chloroplast and reformation of prolamellar bodies in pea were accompanied by a gradual increase of the photochemical activity in both species. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.     

Plastid division: evolution, mechanism and complexity

BACKGROUND: The continuity of chloroplasts is maintained by division of pre-existing chloroplasts. Chloroplasts originated as bacterial endosymbionts; however, the majority of bacterial division factors are absent from chloroplasts and the eukaryotic host has added several new components. For example, the ftsZ gene has been duplicated and modified, and the Min system has retained MinE and MinD but lost MinC, acquiring at least one new component ARC3. Further, the mechanism has evolved to include two members of the dynamin protein family, ARC5 and FZL, and plastid-dividing (PD) rings were most probably added by the eukaryotic host. SCOPE: Deciphering how the division of plastids is coordinated and controlled by nuclear-encoded factors is key to our understanding of this important biological process. Through a number of molecular-genetic and biochemical approaches, it is evident that FtsZ initiates plastid division where the coordinated action of MinD and MinE ensures correct FtsZ (Z)-ring placement. Although the classical FtsZ antagonist MinC does not exist in plants, ARC3 may fulfil this role. Together with other prokaryotic-derived proteins such as ARC6 and GC1 and key eukaryotic-derived proteins such as ARC5 and FZL, these proteins make up a sophisticated division machinery. The regulation of plastid division in a cellular context is largely unknown; however, recent microarray data shed light on this. Here the current understanding of the mechanism of chloroplast division in higher plants is reviewed with an emphasis on how recent findings are beginning to shape our understanding of the function and evolution of the components. CONCLUSIONS: Extrapolation from the mechanism of bacterial cell division provides valuable clues as to how the chloroplast division process is achieved in plant cells. However, it is becoming increasingly clear that the highly regulated mechanism of plastid division within the host cell has led to the evolution of features unique to the plastid division process.     

Plastid evolution: origins, diversity, trends

The amazing diversity of extant photosynthetic eukaryotes is largely a result of the presence of formerly free-living photosynthesizing organisms that have been sequestered by eukaryotic hosts and established as plastids in a process known as endosymbiosis. The evolutionary history of these endosymbiotic events was traditionally investigated by studying ultrastructural features and pigment characteristics but in recent years has been approached using molecular sequence data and gene trees. Two important developments, more detailed studies of members of the Cyanobacteria (from which plastids ultimately derive) and the availability of complete plastid genome sequences from a wide variety of plant and algal lineages, have allowed a more accurate reconstruction of plastid evolution.     

Peroxisome biogenesis and peroxisome biogenesis disorders

Peroxisome assembly in mammals requires more than 15 genes. Two isoforms of the peroxisome targeting signal type 1 (PTS1) receptor, Pex5pS and Pex5pL, are identified in mammals. Pex5pS and Pex5pL bind PTS1 proteins. Pex5pL, but not Pex5pS, directly interacts with the PTS2 receptor, Pex7p, carrying its cargo PTS2 protein in the cytosol. Pex5p carrying the cargos, PTS1 and PTS2, docks with the initial site Pex14p in a putative import machinery, subsequently translocating to other components such as Pex13p, Pex2p, Pex10p and Pex12p, whereby the matrix proteins are imported. The peroxins, Pex3p, Pex16p and Pex19p, function in the assembly of peroxisomal membrane vesicles that precedes the import of matrix proteins. Hence, peroxisomes may form de novo and do not have to arise from pre-existing, morphologically recognizable peroxisomes. Impaired peroxisome assembly causes peroxisome biogenesis disorders such as Zellweger syndrome.     

Evolution of Red Algal Plastid Genomes: Ancient Architectures,Introns, Horizontal Gene Transfer,and Taxonomic Utility of Plastid Markers

Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase – a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.     

Differences between glycogen biogenesis in fast- and slow-twitch rabbit muscle

Skeletal muscle glycogen is an essential energy substrate for muscular activity. The biochemical properties of the enzymes involved in de novo synthesis of glycogen were analysed in two types of rabbit skeletal muscle fiber (fast- and slow-twitch). Glycogen concentration was higher in fast-twitch muscle than in slow-twitch muscle, but the latter contained many more small intermediate-acceptor molecules that could act as glycogen synthase substrates. The enzymes involved in de novo synthesis of glycogen in fast-twitch muscle were strongly stimulated by Glc-6-P, but those in slow-twitch muscle were not.     

Plasmodesmata: structure, function and biogenesis

Plasmodesmata remain one of the outstanding mysteries in plant biology. In providing conduits for the exchange of small and large, informational molecules they are central to the growth, development and defence of all higher plants. In the past few years, strategies have been devised for the molecular dissection of plasmodesmal composition and function, and we are beginning to see how these enigmatic structures will become to be understood.