Axial protocadherin is a mediator of prenotochord cell sorting in Xenopus

Prenotochord cell sorting is regarded as one of the first cell sorting events in early chordate development. We recently demonstrated that this sorting event occurs in vitro, although the mediator of this activity remains unidentified. Herein, we report the isolation of a full-length cDNA clone of Axial protocadherin (AXPC), the homologue of human protocadherin-1 (PCD1). AXPC encodes a transmembrane protein (AXPC) that is expressed exclusively in the notochord at the neurula stage and in the pronephros, somites, heart, optic vesicle, otic vesicle, and distinct parts of the brain at the tailbud stage. Cell dissociation and reaggregation assays and in vivo microinjection experiments demonstrated that cells overexpressing a membrane-tethered form of AXPC (MT-AXPC) acquired the same adhesive properties as prenotochord cells. Moreover, microinjection of either mRNA encoding the dominant negative form of AXPC (DN-AXPC) or morpholino oligonucleotides interferes with the sorting activity of prenotochord cells and normal axis formation. This study suggests that AXPC is necessary and sufficient for prenotochord cell sorting in the gastrulating embryo, and may also mediate sorting events later in development.     

Early Tertiary out-of-India dispersal of Crypteroniaceae: evidence from phylogeny and molecular dating

Abstract.— Pylogenetic analyses and molecular dating estimates based on chloroplast DNA sequences were used to establish the relationships of the southern and Southeast Asian Crypteroniaceae and elucidate their biogeographic history. Maximum parsimony and likelihood analyses of rbc L sequences suggested that Crypteroniaceae should be restricted to Crypteronia , Axinandra , and Dactylocladus and that Crypteroniaceae, so defined, are sister to a clade formed by three small African taxa (Oliniaceae, Penaeaceae, and Rhynchocalycaceae) and the monotypic Central and South American Alzateaceae. Three molecular dating approaches (maximum-likelihood under a molecular clock, Langley-Fitch, and penalized-likelihood) were used to infer the age of Crypteroniaceae using both paleobotanic and geologic calibrations. Comparisons among these three methods revealed significant lineage effects in rbc L sequences. Clock-independent dating estimates suggested that divergence of Crypteroniaceae from its African and South American relatives coincided with the breakup of Gondwana, and that India likely served as a "raft" transporting Crypteroniaceae to Asia, with later expansion to Southeast Asia. To our knowledge, Crypteroniaceae are the first plant group for which the out-of-India hypothesis is well corroborated by molecular-based estimates of divergence times.     

A novel two-step mechanism for removal of a mitochondrial signal sequence involves the mAAA complex and the putative rhomboid protease Pcp1

The yeast protein cytochrome c peroxidase (Ccp1) is nuclearly encoded and imported into the mitochondrial intermembrane space, where it is involved in degradation of reactive oxygen species. It is known, that Ccp1 is synthesised as a precursor with a N-terminal pre-sequence, that is proteolytically removed during transport of the protein. Here we present evidence for a new processing pathway, involving novel signal peptidase activities. The mAAA protease subunits Yta10 (Afg3) and Yta12 (Rca1) were identified both to be essential for the first processing step. In addition, the Pcp1 (Ygr101w) gene product was found to be required for the second processing step, yielding the mature Ccp1 protein. The newly identified Pcp1 protein belongs to the rhomboid-GlpG superfamily of putative intramembrane peptidases. Inactivation of the protease motifs in mAAA and Pcp1 blocks the respective steps of proteolysis. A model of coupled Ccp1 transport and N-terminal processing by the mAAA complex and Pcp1 is discussed. Similar processing mechanisms may exist, because the mAAA subunits and the newly identified Pcp1 protein belong to ubiquitous protein families.     

Prediction of human protein function from post-translational modifications and localization features

We have developed an entirely sequence-based method that identifies and integrates relevant features that can be used to assign proteins of unknown function to functional classes, and enzyme categories for enzymes. We show that strategies for the elucidation of protein function may benefit from a number of functional attributes that are more directly related to the linear sequence of amino acids, and hence easier to predict, than protein structure. These attributes include features associated with post-translational modifications and protein sorting, but also much simpler aspects such as the length, isoelectric point and composition of the polypeptide chain.     

Rafts in adult peripheral nerve myelin contain major structural myelin proteins and myelin and lymphocyte protein (MAL) and CD59 as specific markers

The myelin and lymphocyte protein (MAL) proteolipid is localized in central and peripheral compact myelin membranes, as well as in apical membranes of particular polarized cells. In this study, we addressed the question whether MAL and other peripheral myelin proteins are sorted and targeted to myelin membranes using mechanisms similar to those observed in polarized epithelial cells. To investigate the presence of raft-mediated sorting pathways in Schwann cells, we have isolated and analysed their composition in myelin membranes. Here, we show that rafts are present in adult human and rat peripheral compact myelin membranes and contain MAL, the GPI-anchored protein CD59, and substantial amounts of the PMP22 and P0. Colocalization studies show that CD59, and MAL have an almost identical expression pattern within compact myelin. Moreover, immuno-electron microscopy revealed that MAL, besides its localization in compact myelin, is also localized to Schmidt-Lanterman incisures. Taken together, our results demonstrate the presence of detergent-insoluble glycolipid-enriched complexes (DIGs) in different compartments of myelin membranes and indicate an important role for DIG-mediated transport mechanisms in the maintenance of the adult myelin sheath.     

How LCA studies deal with uncertainty

In recent years many workers have examined the implications of various sources of uncertainty for the reliability of Life Cycle Assessment (LCA). Indeed, the International Standardization Organization (ISO) has recognised the relevance of this work by including several cautionary statements in the ISO 14040 series of standards. However, in practice, there is a risk that the significance of these uncertainties for the results of an LCA could be overlooked as practitioners strive to complete studies on time and within budget. This paper presents the findings of a survey of LCA studies we made to determine the extent to which the problem of uncertainty had been dealt with in practice. This survey revealed that the significance of the limitations on the reliability of LCA results given in the standards has not been fully appreciated by practitioners. We conclude that the standards need to be revised to ensure that LCA studies include at least a qualitative discussion on all relevant aspects of uncertainty.     

Predicting protein subcellular localisation from amino acid sequence information

Predicting the subcellular localisation of proteins is an important part of the elucidation of their functions and interactions. Here, the amino acid sequence motifs that direct proteins to their proper subcellular compartment are surveyed, different methods for localisation prediction are discussed, and some benchmarks for the more commonly used predictors are presented.     

Cellular patterning of the vertebrate embryo

Recent studies show that cell dispersal is a widespread phenomenon in the development of early vertebrate embryos. These cell movements coincide with major decisions for the spatial organization of the embryo, and they parallel genetic patterning events. For example, in the central nervous system, cell dispersal is first mainly anterior–posterior and subsequently dorsal–ventral. Thus, genes expressed in signaling centers of the embryo probably control cell movements, tightly linking cellular and genetic patterning. Cell dispersal might be important for the correct positioning of cells and tissues involved in intercellular signaling. The emergence of cell dispersal at the onset of vertebrate evolution indicates a shift from early, lineage-based cellular patterning in small embryos to late, movement-based cellular patterning of polyclones in large embryos. The conservation of the same basic body plan by invertebrate and vertebrate chordates suggests that evolution of the embryonic period preceding the phylotypic stage was by intercalary co-option of basic cell activities present in the ancestral metazoan cell.     

Features of influenza HA required for apical sorting differ from those required for association with DRMs or MAL

The influenza virus hemagglutinin (HA) is sorted to the apical membrane in polarized epithelial cells and associates with detergent-resistant membranes (DRMs). By systematic mutagenesis of the transmembrane residues, we show that hemagglutinin requires 10 contiguous transmembrane amino acids to enter detergent-resistant membranes and that the surface of the trimeric hemagglutinin transmembrane domain facing the lipid environment as well as that facing the interior of the trimer is important for stable association with detergent-resistant membranes. However, association with detergent-resistant membranes was not required for apical sorting. MAL/VIP17 is a protein that is required for apical transport and a small fraction of hemagglutinin co-precipitates with MAL. Mutations that prevented HA from being isolated in detergent-resistant membranes decreased co-precipitation with MAL. The hemagglutinin and MAL that co-precipitated were contained in a detergent-resistant vesicle. However, most of the co-precipitation of newly synthesized hemagglutinin with MAL occurred only after the majority of hemagglutinin reached the cell surface. Both the timing and the limited extent of co-precipitation suggest that the majority of vesicles containing hemagglutinin and MAL are not the detergent-resistant membrane transport intermediates carrying hemagglutinin from the TGN to the apical surface.     

PtdIns(3,5)P2 is required for delivery of endocytic cargo into the multivesicular body

The endocytic pathway transports cargo from the plasma membrane to early endosomes, where certain cargoes are sorted to the late endosome/multivesicular body. Biosynthetic cargo destined for the lysosome is also trafficked through the multivesicular body. Once delivered to the multivesicular body, cargo destined for the interior of the lysosome is selectively sorted into vesicles that bud into the lumen of the multivesicular body. These vesicles are released into the lumen of the lysosome upon the fusion of the multivesicular body and lysosomal limiting membranes. The yeast protein Fab1, which catalyzes the production of phosphatidylinositol (3,5) bisphosphate [PtdIns(3,5)P₂], is necessary for proper sorting of biosynthetic cargo in the multivesicular body. Utilizing an endocytosis screen, we isolated a novel allele of FAB1 that contains a point mutation in the lipid kinase domain. Characterization of this allele revealed reduced PtdIns(3,5)P₂ production, altered vacuole morphology, and biosynthetic protein sorting defects. We also found that endocytosis of the plasma membrane protein Ste3 is partially blocked downstream of the internalization step, and that delivery of the dye FM4-64 to the vacuole is delayed in fab1 mutants. Additionally, Ste3 is not efficiently sorted into multivesicular body vesicles in fab1 mutants and instead localizes to the vacuolar limiting membrane. These data show that PtdIns(3,5)P₂ is necessary for proper trafficking and sorting of endocytic cargo through the late endosome/multivesicular body.