The N-end rule pathway targets protein degradation through the identity of the amino-terminal residue of specific protein substrates. Two components of this pathway in Arabidopsis thaliana, PROTEOLYSIS6 (PRT6) and arginyl-tRNA:protein arginyltransferase (ATE), were shown to regulate seed after-ripening, seedling sugar sensitivity, seedling lipid breakdown, and abscisic acid (ABA) sensitivity of germination. Sensitivity of prt6 mutant seeds to ABA inhibition of endosperm rupture reduced with after-ripening time, suggesting that seeds display a previously undescribed window of sensitivity to ABA. Reduced root growth of prt6 alleles and the ate1 ate2 double mutant was rescued by exogenous sucrose, and the breakdown of lipid bodies and seed-derived triacylglycerol was impaired in mutant seedlings, implicating the N-end rule pathway in control of seed oil mobilization. Epistasis analysis indicated that PRT6 control of germination and establishment, as exemplified by ABA and sugar sensitivity, as well as storage oil mobilization, occurs at least in part via transcription factors ABI3 and ABI5. The N-end rule pathway of protein turnover is therefore postulated to inactivate as-yet unidentified key component(s) of ABA signaling to influence the seed-to-seedling transition.abscisic acid ͉ aminoacyl tRNA protein transferase ͉ lipid bodies ͉ targeted protein degradation

Despite Arabidopsis thaliana's pre-eminence as a model organism, major questions remain regarding the geographic structure of its genetic variation due to the geographically incomplete sample set available for previous studies. Many of these questions are addressed here with an analysis of genome-wide variation at 10 loci in 475 individuals from 167 globally distributed populations, including many from critical but previously un-sampled regions. Rooted haplotype networks at three loci suggest that A. thaliana arose in the Caucasus region. Identification of large-scale metapopulations indicates clear east-west genetic structure, both within proposed Pleistocene refugia and post-Pleistocene colonized regions. The refugia themselves are genetically differentiated from one another and display elevated levels of within-population genetic diversity relative to recolonized areas. The timing of an inferred demographic expansion coincides with the Eemian interglacial (approximately 120,000 years ago). Taken together, these patterns are strongly suggestive of Pleistocene range dynamics. Spatial autocorrelation analyses indicate that isolation by distance is pervasive at all hierarchical levels, but that it is reduced in portions of Europe.

Population-based methods for the genetic mapping of adaptive traits and the analysis of natural selection require that the population structure and demographic history of a species are taken into account. We characterized geographic patterns of genetic variation in the model plant Arabidopsis thaliana by genotyping 115 genome-wide single nucleotide polymorphism (SNP) markers in 351 accessions from the whole species range using a matrix-assisted laser desorption/ionization time-of-flight assay, and by sequencing of nine unlinked short genomic regions in a subset of 64 accessions. The observed frequency distribution of SNPs is not consistent with a constant-size neutral model of sequence polymorphism due to an excess of rare polymorphisms. There is evidence for a significant population structure as indicated by differences in genetic diversity between geographic regions. Accessions from Central Asia have a low level of polymorphism and an increased level of genome-wide linkage disequilibrium (LD) relative to accessions from the Iberian Peninsula and Central Europe. Cluster analysis with the structure program grouped Eurasian accessions into K = 6 clusters. Accessions from the Iberian Peninsula and from Central Asia constitute distinct populations, whereas Central and Eastern European accessions represent admixed populations in which genomes were reshuffled by historical recombination events. These patterns likely result from a rapid postglacial recolonization of Eurasia from glacial refugial populations. Our analyses suggest that mapping populations for association or LD mapping should be chosen from regional rather than a species-wide sample or identified genetically as sets of individuals with similar average genetic distances.

Phase II of germination represents a key developmental stage of plant growth during which imbibed seeds either enter stage III of germination, completing the germination process via radicle protrusion, or remain dormant. In this study, we analyzed the influence of the peroxisomal ATP-binding cassette transporter COMATOSE (CTS) on the postimbibition seed transcriptome of Arabidopsis (Arabidopsis thaliana) and also investigated interactions between gibberellin (GA) and CTS function. A novel method for analysis of transcriptome datasets allowed visualization of developmental signatures of seeds, showing that cts-1 retains the capacity to after ripen, indicating a germination block late in phase II. Expression of the key GA biosynthetic genes GA3ox1 and 2 was greatly reduced in cts seeds and genetic analysis suggested that CTS was epistatic to RGL2, a germinationrepressing DELLA protein that is degraded by GA. Comparative analysis of seed transcriptome datasets indicated that specific cohorts of genes were influenced by GA and CTS. CTS function was required for expression of the flavonoid biosynthetic pathway. Confocal imaging demonstrated the exclusive accumulation of flavonoids in the epidermis of wild-type seeds. In contrast, flavonoids were absent from cts and kat2-1 mutant seeds, but accumulated following the application of sucrose, indicating an essential role for b-oxidation in inducing flavonoid biosynthetic genes. These results demonstrate that CTS functions very late in phase II of germination and that its function is required for the expression of specific gene sets related to an important biochemical pathway associated with seedling establishment and survival.

The European dogroses (Rosa sect. Caninae (DC.) Ser.) are characterized by a unique meiosis system ("canina-meiosis"), which controls the heterogamous development of tetraploid egg cells and haploid pollen grains resulting in a pentaploid somatic status. This permanent anorthoploidy is supposed to have originated by a hybridization event in the postglacial period. In this study we present molecular evidence by an analysis of nuclear ribosomal DNA data that dogroses are complex allopolyploids resulting from multiple hybridization events. As previously described, the nrITS-1 region does not undergo concerted evolution in dogroses. Thus, different ITS-1 sequences persist within single individuals. Secondary structure predictions do not point to the existence of pseudogenes within these ITS-1 types. Our data suggest that the pentaploid Caninae genome originated from different members of nondogroses and the now extinct Protocaninae.

A closer investigation of the DNA fractions involved in intraspecific genome size differences in this experimentally accessible species may provide information on the factors involved in stability and evolution of genome sizes.

Overall, the data show huge variation of germination and establishment among natural accessions of A. thaliana and might serve as a valuable source for further germination and plasticity studies.

COMATOSE (CTS), the Arabidopsis homologue of human Adrenoleukodystrophy protein (ALDP), is required for import of substrates for peroxisomal ␤-oxidation.A new allelic series and a homology model based on the bacterial ABC transporter, Sav1866, provide novel insights into structure-function relations of ABC subfamily D proteins. In contrast to ALDP, where the majority of mutations result in protein absence from the peroxisomal membrane, all CTS mutants produced stable protein. Mutation of conserved residues in the Walker A and B motifs in CTS nucleotide-binding domain (NBD) 1 resulted in a null phenotype but had little effect in NBD2, indicating that the NBDs are functionally distinct in vivo. Two alleles containing mutations in NBD1 outside the Walker motifs (E617K and C631Y) exhibited resistance to auxin precursors 2,4-dichlorophenoxybutyric acid (2,4-DB) and indole butyric acid (IBA) but were wild type in all other tests. The homology model predicted that the transmission interfaces are domain-swapped in CTS, and the differential effects of mutations in the conserved "EAA motif" of coupling helix 2 supported this prediction, consistent with distinct roles for each NBD. Our findings demonstrate that CTS functions can be separated by mutagenesis and the structural model provides a framework for interpretation of phenotypic data. INTRODUCTIONATP-binding cassette (ABC) transporters are ubiquitous, integral membrane proteins that mediate vectorial transport of a diverse range of molecules across membranes and consequently are involved in a wide variety of biological processes (Higgins, 1992;Rea, 2007). All ABC transporters share the same basic architecture, comprising two transmembrane domains (TMDs), each composed of several ␣-helices that are involved in substrate recognition and translocation across the lipid bilayer, and two nucleotide-binding domains (NBDs) that bind and hydrolyze ATP, providing the driving force for transport. In prokaryotes, these domains are usually present on separate polypeptides, whereas in eukaryotes, fusion of a TMD and NBD module to form a "half transporter," or indeed fusion of all modules to form a "full transporter" is more common. The past decade has seen the determination of high-resolution crystal structures for several isolated NBDs and, more recently, complete ABC transporters (reviewed in .The NBDs characteristically contain several highly conserved features common to nucleotide hydrolases, including the Walker A motif (GxxGxGKS/T, where x is any amino acid), forming the P-loop, which binds to the ␣-and ␤-phosphates of nucleotides, and the Walker B motif (⌽⌽⌽⌽DE, where ⌽ is hydrophobic), thought to coordinate the Mg 2ϩ ion or polarize the attacking water molecule (Walker et al., 1982;Hung et al., 1998;Schneider and Hunke, 1998;Hopfner et al., 2000). ABC transporters additionally contain the signature motif (LSGGQ), which contacts the ␥-phosphate of ATP; the Q-loop (or "lid") containing a glutamine residue, which interacts with ␥-phosphate through a water molecule; and the swi...