Proteome analysis of grape skins during ripening

The characterization of proteins isolated from skin tissue is apparently an essential parameter for understanding grape ripening as this tissue contains the key compounds for wine quality. It has been particularly difficult to extract proteins from skins for analysis by two-dimensional electrophoresis gels and, therefore, a protocol for this purpose has been adapted. The focus was on the evolution of the proteome profile of grape skin during maturation. Proteome maps obtained at three stages of ripening were compared to assess the extent to which protein distribution differs in grape skin during ripening. The comparative analysis shows that numerous soluble skin proteins evolve during ripening and reveal specific distributions at different stages. Proteins involved in photosynthesis, carbohydrate metabolisms, and stress response are identified as being over-expressed at the beginning of colour-change. The end of colour-change is characterized by the over-expression of proteins involved in anthocyanin synthesis and, at harvest, the dominant proteins are involved in defence mechanisms. In particular, increases in the abundance of different chitinase and beta-1,3-glucanase isoforms were found as the berry ripens. This observation can be correlated with the increase of the activities of both of these enzymes during skin ripening. The differences observed in proteome maps clearly show that significant metabolic changes occur in grape skin during this crucial phase of ripening. This comparative analysis provides more detailed characterization of the fruit ripening process.     

A Cryptic Cytoplasmic Male Sterility Unveils a Possible Gynodioecious Past for Arabidopsis thaliana

Gynodioecy, the coexistence of hermaphrodites and females (i.e. male-sterile plants) in natural plant populations, most often results from polymorphism at genetic loci involved in a particular interaction between the nuclear and cytoplasmic genetic compartments (cytonuclear epistasis): cytoplasmic male sterility (CMS). Although CMS clearly contributes to the coevolution of involved nuclear loci and cytoplasmic genomes in gynodioecious species, the occurrence of CMS genetic factors in the absence of sexual polymorphism (cryptic CMS) is not easily detected and rarely taken in consideration. We found cryptic CMS in the model plant Arabidopsis thaliana after crossing distantly related accessions, Sha and Mr-0. Male sterility resulted from an interaction between the Sha cytoplasm and two Mr-0 genomic regions located on chromosome 1 and chromosome 3. Additional accessions with either nuclear sterility maintainers or sterilizing cytoplasms were identified from crosses with either Sha or Mr-0. By comparing two very closely related cytoplasms with different male-sterility inducing abilities, we identified a novel mitochondrial ORF, named orf117Sha, that is most likely the sterilizing factor of the Sha cytoplasm. The presence of orf117Sha was investigated in worldwide natural accessions. It was found mainly associated with a single chlorotype in accessions belonging to a clade predominantly originating from Central Asia. More than one-third of accessions from this clade carried orf117Sha, indicating that the sterilizing-inducing cytoplasm had spread in this lineage. We also report the coexistence of the sterilizing cytoplasm with a non-sterilizing cytoplasm at a small, local scale in a natural population; in addition a correlation between cytotype and nuclear haplotype was detected in this population. Our results suggest that this CMS system induced sexual polymorphism in A. thaliana populations, at the time when the species was mainly outcrossing.     

Comprehensive Linkage and Association Analyses Identify Haplotype, Near to the TNFSF15 Gene, Significantly Associated with Spondyloarthritis

Spondyloarthritis (SpA) is a chronic inflammatory disorder with a strong genetic predisposition dominated by the role of HLA-B27. However, the contribution of other genes to the disease susceptibility has been clearly demonstrated. We previously reported significant evidence of linkage of SpA to chromosome 9q31–34. The current study aimed to characterize this locus, named SPA2. First, we performed a fine linkage mapping of SPA2 (24 cM) with 28 microsatellite markers in 149 multiplex families, which allowed us to reduce the area of investigation to an 18 cM (13 Mb) locus delimited by the markers D9S279 and D9S112. Second, we constructed a linkage disequilibrium (LD) map of this region with 1,536 tag single-nucleotide polymorphisms (SNPs) in 136 families (263 patients). The association was assessed using a transmission disequilibrium test. One tag SNP, rs4979459, yielded a significant P-value (4.9×10⁻⁵). Third, we performed an extension association study with rs4979459 and 30 surrounding SNPs in LD with it, in 287 families (668 patients), and in a sample of 139 cases and 163 controls. Strong association was observed in both familial and case/control datasets for several SNPs. In the replication study, carried with 8 SNPs in an independent sample of 232 cases and 149 controls, one SNP, rs6478105, yielded a nominal P-value<3×10⁻². Pooled case/control study (371 cases and 312 controls) as well as combined analysis of extension and replication data showed very significant association (P<5×10⁻⁴) for 6 of the 8 latter markers (rs7849556, rs10817669, rs10759734, rs6478105, rs10982396, and rs10733612). Finally, haplotype association investigations identified a strongly associated haplotype (P<8.8×10⁻⁵) consisting of these 6 SNPs and located in the direct vicinity of the TNFSF15 gene. In conclusion, we have identified within the SPA2 locus a haplotype strongly associated with predisposition to SpA which is located near to TNFSF15, one of the major candidate genes in this region.     

TBC1D14 regulates autophagy via the TRAPP complex and ATG9 traffic

Macroautophagy requires membrane trafficking and remodelling to form the autophagosome and deliver its contents to lysosomes for degradation. We have previously identified the TBC domain‐containing protein, TBC1D14, as a negative regulator of autophagy that controls delivery of membranes from RAB11‐positive recycling endosomes to forming autophagosomes. In this study, we identify the TRAPP complex, a multi‐subunit tethering complex and GEF for RAB1, as an interactor of TBC1D14. TBC1D14 binds to the TRAPP complex via an N‐terminal 103 amino acid region, and overexpression of this region inhibits both autophagy and secretory traffic. TRAPPC8, the mammalian orthologue of a yeast autophagy‐specific TRAPP subunit, forms part of a mammalian TRAPPIII‐like complex and both this complex and TBC1D14 are needed for RAB1 activation. TRAPPC8 modulates autophagy and secretory trafficking and is required for TBC1D14 to bind TRAPPIII. Importantly, TBC1D14 and TRAPPIII regulate ATG9 trafficking independently of ULK1. We propose a model whereby TBC1D14 and TRAPPIII regulate a constitutive trafficking step from peripheral recycling endosomes to the early Golgi, maintaining the cycling pool of ATG9 required for initiation of autophagy.     

Does the presence of grassy strips and landscape grain affect the spatial distribution of aphids and their carabid predators?

• 1 We investigated, over the course of 2 years, the spatial distribution and abundance of two species of aphid, Metopolophium dirhodum and Sitobion avenae, and predatory species of carabid. This was undertaken in 24 wheat fields in ‘coarse‐grain’ and ‘fine‐grain’ landscapes in western France. A greater percentage of the latter landscape was covered by hedgerows and grassland and the total area covered by fields and the average size of the fields were smaller.
• 2 The effects on aphid abundance of the distance from field margins, the presence of grassy strips and carabid abundance were determined in both landscapes.
• 3 Both aphid species were more abundant in the ‘fine‐grain’ landscape, which may have been a result of the higher density of semi‐natural elements. In both types of landscape, the total numbers of aphids were negatively correlated with the distance from the field margin. This may have been because aphids were dispersing from overwintering sites in field margins. The abundance of M. dirhodum was strongly negatively correlated with the presence of grassy strips in the ‘coarse‐grain’ landscape, although there were no such significant correlations for either of the aphid species in the ‘fine‐grain’ landscape.
• 4 Aphid and carabid abundances were negatively correlated in the ‘fine‐grain’ and positively in ‘coarse‐grain’ landscape.
• 5 The results obtained in the present study emphasize the importance of semi‐natural areas in agricultural landscapes in shaping the spatial distribution of aphids and carabid beetles, their natural enemies, at different spatial scales.

     

Multilevel Control of Organelle DNA Sequence Length in Plants

We have compared the length of noncoding organelle DNA spacers in a broad sample of plant species characterized by different life history traits to test hypotheses regarding the nature of the mechanisms driving changes in their size. We first demonstrate that the spacers do not evolve at random in size but have experienced directional evolutionary trends during plant diversification. We then study the relationships between spacer lengths and other molecular features and various species attributes by taking into account population genetic processes acting within cell lineages. Comparative techniques are used to test these relationships while controlling for species phylogenetic relatedness. The results indicate that spacer length depends on mode of organelle transmission, on population genetic structure, on nucleotide content, on rates of molecular evolution, and on life history traits, in conformity with predictions based on a model of intracellular competition among replicating organelle genomes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Crystal structure of an HD‐GYP domain cyclic‐di‐GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre

Bis‐(3′,5′) cyclic di‐guanylate (c‐di‐GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c‐di‐GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD‐GYP domains. Here, we have determined the structure of an enzymatically active HD‐GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c‐di‐GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c‐di‐GMP. This structure completes the picture of all domains involved in c‐di‐GMP metabolism and reveals that the HD‐GYP family splits into two distinct subgroups containing bi‐ and trinuclear metal centres.     

Dispersal mood revealed by shifts from routine to direct flights in the meadow brown butterfly Maniola jurtina

A comprehensive mechanistic approach to dispersal requires the translation of the whole mobility register of the target organism into movement rules that could subsequently be used to model its displacements. According to the optimality paradigm, this procedure implies a cost–benefit analysis of mobility patterns taking into account not only movements, but also their external context and the internal state of the moving individuals. Using this framework, we detected a ‘dispersal mood’ in some individuals of the meadow brown butterfly Maniola jurtina. These adopted a direct flight strategy, which was topologically different from the previously documented foray search strategy. Those individuals that used the direct flight strategy moved straighter as soon as they left the habitat and avoided heading back to their patch of origin, which is the best inter‐patch search strategy when dispersal risks and costs are high. The direct flight strategy was conditional to sex: females used it twice as much as males. We suggest that this sex bias was due to female investment in offspring, which is maximized by male avoidance and spatial bet hedging. Inter‐patch dispersal of gravid females is crucial for the persistence of M. jurtina populations in spatially and temporally unpredictable environments.     

Diet shifts by adult flightless dung beetles Circellium bacchus,revealed using DNA metabarcoding,reflect complex life histories

Oecologia - Life history changes may change resource use. Such shifts are not well understood in the dung beetles, despite recognised differences in larval and adult feeding ability. We use the...     

Development and composition of the seeds of nine genotypes of the Medicago truncatula species complex.

The seed development and composition of Medicago truncatula Gaertn., the new model plant for grain legumes, was studied using nine genotypes of the species complex: M. truncatula-Medicago littoralis (M. truncatula). The seed development of M. truncatula was very similar to that of other legumes, the only notable exception being the presence, in the mature seed, of an endosperm layer that is absent in grain legumes. During early embryogenesis and until mid-maturation, transient storage of starch occurred in the seed coat and embryo. This temporary storage probably contributed to the early development of the embryo and reserve synthesis. During maturation the synthesis and accumulation of proteins and oil took place at quasi-constant rates. Conversely oligosaccharides, mainly stachyose, were synthesised only during late maturation and at the beginning of desiccation. Proteins represented the major class of storage compounds and their average amino acid composition was found to be very close to that of pea and robust in various environmental conditions. Similar compositions between the two species and other grain legumes were also found for the fatty acids and the soluble sugars; most of these characters varied depending on the various environmental conditions used for seed production. All these similarities fully justify the use of M. truncatula as a model plant for genomic approaches to grain legume improvement. The major difference between M. truncatula seeds and European grain legume seeds resides in the nature of their carbon storage namely triacylglycerides for M. truncatula and starch for pea and faba bean.