Floral organogenesis of Chloranthus sessilifolius, with special emphasis on the morphological nature of the androecium of Chloranthus (Chloranthaceae)

 Floral organogenesis of Chloranthus sessilifolius K. F. Wu is described. The inflorescence primordium is dome-like in the beginning and then elongates, and bract primordia initiate almost decussately. Each floral primordium, arising from the axil of a bract, soon becomes a scale-like structure, with three primordia of androecial lobes originating from its abaxial part, and the gynoecial primordium in adaxial position. As the androecial lobes become more distinct, four thecae are already in differentiation, and the gynoecial primordium appears as a shallow disc. The androecial lobes do not extend their length until the thecae approach maturity and the stigma is differentiated. The androecial lobes are united at all the stages of development, and the entire androecium falls off as a unit at the end of anthesis. Based on these results, combined with published evidence from neobotany, palaeobotany and phylogenetic studies, the morphological nature of the androecium of Chloranthus is further discussed. Our studies support the viewpoint that the androecial structure of Chloranthus may have arisen by splitting of a single stamen with 2 marginal thecae. Received May 2, 2001 Accepted December 18, 2001     

Phylogeny of the Altingiaceae based on cpDNA matK, PY-IGS and nrDNA ITS sequences

 Phylogenetic relationships of the three genera of the family Altingiaceae, i.e., Altingia, Liquidambar and Semiliquidambar, based on matK sequences and the intergenic spacer between the psaA and ycf3 genes (PY-IGS) of cpDNA, and on the internal transcribed spacer (ITS) of nrDNA were studied. Phylogenetic trees based on the three data sets (matK, PY-IGS and ITS) were generated using Hamamelis japonica and Mytilaria laosensis (Hamamelidaceae), Cercidiphyllum japonicum (Cercidiphyllaceae), and Daphniphyllum calycinum (Daphniphyllaceae) as outgroups. The partition-homogeneity tests indicated that the three data sets and the combined data are homogeneous. A combined analysis also generated a strongly supported phylogeny. The phylogenetic trees show that the North American and western Asian species, L. styraciflua and L. orientalis, respectively, form a monophyletic group which is sister to the clade including all Asian species in the family. The genus Liquidambar is paraphyletic with Altingia and Semiliquidambar nested within. Phylogenetic analyses of the molecular data indicate that taxonomic reexamination of the generic delimitation in the Altingiaceae is needed. Received December 20, 2000 Accepted June 25, 2001     

Survival costs of reproduction vary with age in North American red squirrels

The costs of reproduction are expected to be higher under unfavourable conditions, so that breeding in years of low food supply should have important costs. In addition, the costs of reproduction may be contingent on the age of individuals, and young growing and old senescent individuals should suffer higher costs than the prime-age ones. We tested these predictions by investigating the costs of reproduction as a function of food availability and age in female North American red squirrels using the long-term data on survival and reproduction. We found that the costs of reproduction were independent of food supply, and we did not detect any trade-off between the current and future reproduction. We also did not detect any survival cost of reproduction for the prime-age females, but found evidence for survival costs in yearlings and old (6 years or above) females with successfully breeding individuals having a lower chance of survival compared with unsuccessful or non-breeding ones. These results supported our prediction that the costs of reproduction depended on the age of female red squirrels and were higher in young growing and old senescent individuals. Our study also indicated that, in contrast to large herbivores, heterogeneity in individual quality and viability selection in red squirrels do not affect the study of trade-offs and of the age variation in life-history traits.     

Microsecond Dynamics During the Binding-induced Folding of an Intrinsically Disordered Protein

Tau is an intrinsically disordered protein implicated in many neurodegenerative diseases. The repeat domain fragment of tau, tau-K18, is known to undergo a disorder to order transition in the presence of lipid micelles and vesicles, in which helices form in each of the repeat domains. Here, the mechanism of helical structure formation, induced by a phospholipid mimetic, sodium dodecyl sulfate (SDS) at sub-micellar concentrations, has been studied using multiple biophysical probes. A study of the conformational dynamics of the disordered state, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS) has indicated the presence of an intermediate state, I, in equilibrium with the unfolded state, U. The cooperative binding of the ligand (L), SDS, to I has been shown to induce the formation of a compact, helical intermediate (IL₅) within the dead time (∼37 µs) of a continuous flow mixer. Quantitative analysis of the PET-FCS data and the ensemble microsecond kinetic data, suggests that the mechanism of induction of helical structure can be described by a U ↔ I ↔ IL₅ ↔ FL₅ mechanism, in which the final helical state, FL₅, forms from IL₅ with a time constant of 50–200 µs. Finally, it has been shown that the helical conformation is an aggregation-competent state that can directly form amyloid fibrils.     

A Conservative Point Mutation in a Dynamic Antigen-binding Loop of Human Immunoglobulin λ6 Light Chain Promotes Pathologic Amyloid Formation

Immunoglobulin light chain (LC) amyloidosis (AL) is a life-threatening human disease wherein free mono-clonal LCs deposit in vital organs. To determine what makes some LCs amyloidogenic, we explored patient-based amyloidogenic and non-amyloidogenic recombinant LCs from the λ6 subtype prevalent in AL. Hydrogen-deuterium exchange mass spectrometry, structural stability, proteolysis, and amyloid growth studies revealed that the antigen-binding CDR1 loop is the least protected part in the variable domain of λ6 LC, particularly in the AL variant. N32T substitution in CRD1 is identified as a driver of amyloid formation. Substitution N32T increased the amyloidogenic propensity of CDR1 loop, decreased its protection in the native structure, and accelerated amyloid growth in the context of other AL substitutions. The destabilizing effects of N32T propagated across the molecule increasing its dynamics in regions ∼30 Å away from the substitution site. Such striking long-range effects of a conservative point substitution in a dynamic surface loop may be relevant to Ig function. Comparison of patient-derived and engineered proteins showed that N32T interactions with other substitution sites must contribute to amyloidosis. The results suggest that CDR1 is critical in amyloid formation by other λ6 LCs.     

Membrane Binding and Homodimerization of Atg16 Via Two Distinct Protein Regions is Essential for Autophagy in Yeast

Macroautophagy is a bulk degradation mechanism in eukaryotic cells. Efficiency of an essential step of this process in yeast, Atg8 lipidation, relies on the presence of Atg16, a subunit of the Atg12–Atg5-Atg16 complex acting as the E3-like enzyme in the ubiquitination-like reaction. A current view on the functional structure of Atg16 in the yeast S. cerevisiae comes from the two crystal structures that reveal the Atg5-interacting α-helix linked via a flexible linker to another α-helix of Atg16, which then assembles into a homodimer. This view does not explain the results of previous in vitro studies revealing Atg16-dependent deformations of membranes and liposome-binding of the Atg12–Atg5 conjugate upon addition of Atg16. Here we show that Atg16 acts as both a homodimerizing and peripheral membrane-binding polypeptide. These two characteristics are imposed by the two distinct regions that are disordered in the nascent protein. Atg16 binds to membranes in vivo via the amphipathic α-helix (amino acid residues 113–131) that has a coiled-coil-like propensity and a strong hydrophobic face for insertion into the membrane. The other protein region (residues 64–99) possesses a coiled-coil propensity, but not amphipathicity, and is dispensable for membrane anchoring of Atg16. This region acts as a Leu-zipper essential for formation of the Atg16 homodimer. Mutagenic disruption in either of these two distinct domains renders Atg16 proteins that, in contrast to wild type, completely fail to rescue the autophagy-defective phenotype of atg16Δ cells. Together, the results of this study yield a model for the molecular mechanism of Atg16 function in macroautophagy.     

Bifidobacteria-mediated immune system imprinting early in life

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Structure Basis for Shaping the Nse4 Protein by the Nse1 and Nse3 Dimer within the Smc5/6 Complex

The Smc5/6 complex facilitates chromosome replication and DNA break repair. Within this complex, a subcomplex composed of Nse1, Nse3 and Nse4 is thought to play multiple roles through DNA binding and regulating ATP-dependent activities of the complex. However, how the Nse1-Nse3-Nse4 subcomplex carries out these multiple functions remain unclear. To address this question, we determine the crystal structure of the Xenopus laevis Nse1-Nse3-Nse4 subcomplex at 1.7 Å resolution and examine how it interacts with DNA. Our structural analyses show that the Nse1-Nse3 dimer adopts a closed conformation and forms three interfaces with a segment of Nse4, forcing it into a Z-shaped conformation. The Nse1-Nse3-Nse4 structure provides an explanation for how the lung disease immunodeficiency and chromosome breakage syndrome-causing mutations could dislodge Nse4 from Nse1-Nse3. Our DNA binding and mutational analyses reveal that the N-terminal and the middle region of Nse4 contribute to DNA interaction and cell viability. Integrating our data with previous crosslink mass spectrometry data, we propose potential roles of the Nse1-Nse3-Nse4 complex in binding DNA within the Smc5/6 complex.     

Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1

Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.     

Mysterious bio-duck sound attributed to the Antarctic minke whale (Balaenoptera bonaerensis)

For decades, the bio-duck sound has been recorded in the Southern Ocean, but the animal producing it has remained a mystery. Heard mainly during austral winter in the Southern Ocean, this ubiquitous sound has been recorded in Antarctic waters and contemporaneously off the Australian west coast. Here, we present conclusive evidence that the bio-duck sound is produced by Antarctic minke whales (Balaenoptera bonaerensis). We analysed data from multi-sensor acoustic recording tags that included intense bio-duck sounds as well as singular downsweeps that have previously been attributed to this species. This finding allows the interpretation of a wealth of long-term acoustic recordings for this previously acoustically concealed species, which will improve our understanding of the distribution, abundance and behaviour of Antarctic minke whales. This is critical information for a species that inhabits a difficult to access sea-ice environment that is changing rapidly in some regions and has been the subject of contentious lethal sampling efforts and ongoing international legal action.