Pool sequencing of natural HLA-DR,DQ, and DP ligands reveals detailed peptide motifs,constraints of processing,and general rules

We have approached the problem of MHC class II ligand motifs by pool sequencing natural peptides eluted from HLA-DR, DQ, and DP molecules. The results indicate surprisingly clear patterns, although not quite as clear as with natural class I ligands. The most striking feature is a highly dominant Proline at position 2. We interpret this to be a consequence of aminopeptidase N-like activity in processing. Another general aspect is the existence of three to four hydrophobic or aromatic anchors, whereby the first and the last are separated by five to eight residues. The peptide motifs for HLA-DR1, DR5, DQ7, and DPw4 are allele-specific and differ by spacing and occupancy of anchors. The anchors tend to be flanked by clusters of charged residues, and small residues, especially Ala, are frequent in the motif centers. These detailed motifs allow one to interpret most previous (DR-) motifs as fitting one or more of the anchors or conserved clusters. The relative motif symmetry suggests the possibility of bidirectional binding of peptides in the class II groove.     

Paracuaria hispanica n. sp. (Nematoda: Acuariidae), a stomach parasite of the pyrenean desman Galemys pyrenaicus Geoffr. (Insectivora: Talpidae), with a redefinition of the genus Paracuaria Rao, 1951

Adult and fourth-stage larvae of Paracuaria hispanica n. sp., from the stomach of the Pyrenean desman Galemys pyrenaicus Geoffroy (Insectivora: Talpidae) in northern and central Spain, are described. The new species differs from the other members of the genus Paracuaria (P. adunca and P. soricis), among other morphological details, in its smaller body and spicule sizes, the presence of a cuticular ring around the tip of the female tail, and the existence of lateral alae running longitudinally along its body from the cervical region to the tail. In view of the latter feature, the genus Paracuaria is redefined. The fourth stage larva of the new species is distinguished from that of P. adunca by its monocuspid deirids. P. hispanica occurred in 45% of the 20 host specimens examined.     

Two related low-temperature-inducible genes of Arabidopsis encode proteins showing high homology to 14-3-3 proteins,a family of putative kinase regulators

We have isolated two Rare Cold-Inducible (RCI1 and RCI2) cDNAs by screening a cDNA library prepared from cold-acclimated etiolated seedlings of Arabidopsis thaliana with a subtracted probe. RNA-blot hybridizations revealed that the expression of both RCI1 and RCI2 genes is induced by low temperature independently of the plant organ or the developmental stage considered. However, RCI1 mRNA accumulates faster and at higher levels than the RCI2 one indicating that these genes have differential responsiveness to cold stress. Additionally, when plants are returned to room temperature, RCI1 mRNA decreases faster than RCI2. In contrast to most of the cold-inducible plant genes characterized, the expression of RCI1 and RCI2 is not induced by ABA or water stress. The nucleotide sequences of RCI1 and RCI2 cDNAs predict two acidic polypeptides of 255 and 251 amino acids with molecular weights of 29 and 28 kDa respectively. The alignment of these polypeptides indicates that they have 181 identical amino acids suggesting that the corresponding genes have a common origin. Sequence comparisons reveal no similarities between the RCI proteins and any other cold-regulated plant protein so far described. Instead, they demonstrate that the RCI proteins are highly homologous to a family of proteins, known as 14-3-3 proteins, which are thought to be involved in the regulation of multifunctional protein kinases.     

Molecular characterization of a fourth isoform of the catalytic subunit of protein phosphatase 2A from Arabidopsis thaliana

We have recently reported the existence of multiple isoforms of the catalytic subunit of protein phosphatase 2A (PP2A) in Arabidopsis thaliana and the molecular cloning of cDNAs encoding three of these proteins (PP2A-1, PP2A-2, PP2A-3). The reported cDNA encoding PP2A-3 was truncated at the 5 terminus, lacking a short fragment of the N-terminal coding sequence. We have now isolated a near full-length cDNA encoding the entire PP2A-3 protein (313 residues). The clone includes 188 nucleotides of 5-untranslated region, where a 44 bp long poly(GA) track is found. We also describe the cloning of a cDNA encoding a fourth isoform of PP2A (PP2A-4). The polypeptide contains 313 residues being 98% identical to PP2A-3 and only 80% identical to both PP2A-1 and PP2A-2. The mRNA for PP2A-4 is 1.4 kb in length and, although predominantly expressed in roots, it is also found in other organs. It is concluded that in A. thaliana the isoforms of PP2A can be grouped in two extremely conserved subfamilies.     

Expression of sunflower low-molecular-weight heat-shock proteins during embryogenesis and persistence after germination: localization and possible functional implications

We isolated and sequenced Ha hsp 17.9, a DNA complementary (cDNA) of dry-seed stored mRNA that encodes a low-molecular-weight heat-shock protein (LMW HSP). Sequence analysis identified Ha hsp17.9, and the previously reported Ha hsp17.6, as cDNAs encoding proteins (HSP17.6 and HSP17.9) which belong to different families of cytoplasmic LMW HSPs. Using specific antibodies we observed differential expression of both proteins during zygotic embryogenesis under controlled environment, and a remarkable persistence of these LMW HSPs during germination. Immuno-blot analysis of HSP17.9 proteins in two-dimensional gels revealed that the polypeptides expressed in embryos were indistinguishable from LMW HSPs expressed in vegetative tissues in response to water deficit; but they appeared different from homologeous proteins expressed in response to thermal-stress. Tissue-print immunolocalization experiments showed that HSP17.9 and HSP17.6 were homogeneously distributed in every tissue of desiccation-tolerant dry seeds and young seedlings under non-stress conditions. These results demonstrate developmental regulation of specific, cytoplasmic, plant LMW HSPs, suggesting also their involvement in water-stress tolerance.     

Expression of the BnmNAP subfamily of napin genes coincides with the induction of Brassica microspore embryogenesis

Brassica napus cv. Topas microspores can be diverted from pollen development toward haploid embryo formation in culture by subjecting them to a heat stress treatment. We show that this switch in developmental pathways is accompanied by the induction of high levels of napin seed storage protein gene expression. Changes in the plant growth or microspore culture conditions were not by themselves sufficient to induce napin gene expression. Specific members of the napin multigene family were cloned from a cDNA library prepared from microspores that had been induced to undergo embryogenesis. The majority of napin clones represented three members (BnmNAP2, BnmNAP3 and BnmNAP4) that, along with a previously isolated napin genomic clone (BngNAP1), constitute the highly conserved BnmNAP subfamily of napin genes. Both RNA gel blot analysis, using a subfamily-specific probe, and histochemical analysis of transgenic plants expressing a BngNAP1 promoter--glucuronidase gene fusion demonstrated that the BnmNAP subfamily is expressed in embryogenic microspores as well as during subsequent stages of microsporic embryo development.     

Isolation of the facA (acetyl-CoA synthetase) gene of Phycomyces blakesleeanus

A 5.6 kb DNA fragment from the fungus Phycomyces blakesleeanus has been cloned and sequenced. The fragment contains a gene that probably codes for the enzyme acetyl-coenzyme A synthetase (facA). The amino acid sequence deduced for the P. blakesleeanns protein is highly homologous to those of acetyl-coA-synthetases from other organisms. When placed under the control of a constitutive promoter from Aspergillus nidulans, the cloned gene complemented a facA mutation of this organism. In P. blakesleeanns, the expression of facA is induced by acetate.     

A simple model for estimating the contribution of nitrogen mineralization to the nitrogen supply of crops from a stabilized pool of soil organic matter and recent organic input

A simple model was developed to estimate the contribution of nitrogen (N) mineralization to the N supply of crops. In this model the soil organic matter is divided into active and passive pools. Annual soil mineralization of N is derived from the active pool. The active pool comprises stabilized and labile soil organic N. The stabilized N is built up from accumulated inputs of fresh organic N during a crop rotation but the labile N is a fraction of total N added, which mineralizes faster than the stabilized N. The passive pool is considered to have no participation in the mineralization process. Mineralization rates of labile and stabilized soil organic N from different crop residues decomposing in soil were derived from the literature and were described by the first-order rate equation dN/dt =-K*N, where N is the mineralizable organic N from crop residues andK is a constant. The data were groupedK ₁ by short-term (0–1 year) andK ₂ by long-term (0–10 years) incubation. Because the range of variation inK ₂ was smaller than inK ₁ we felt justified in using an average value to derive N mineralization from the stabilized pool. The use of a constant rate ofK ₁ was avoided so net N mineralization during the first year after addition is derived directly from the labile N in the crop residues. The model was applied to four Chilean agro-ecosystems, using daily averages of soil temperature and moisture. The N losses by leaching were also calculated. The N mineralization varied between 30 and 130 kg N ha^–1 yr^–1 depending on organic N inputs. Nitrogen losses by leaching in a poorly structured soil were estimated to be about 10% of total N mineralized. The model could explain the large differences in N- mineralization as measured by the potential N mineralization at the four sites studied. However, when grassland was present in the crop rotation, the model underestimated the results obtained from potential mineralization.