Fluorescence Anisotropy Reveals Order and Disorder of Protein Domains in the Nuclear Pore Complex

We present a new approach for studying individual protein domains within the nuclear pore complex (NPC) using fluorescence polarization microscopy. The NPC is a large macromolecular complex, the size and complexity of which presents experimental challenges. Using fluorescence anisotropy and exploiting the symmetry of the NPC and its organization in the nuclear envelope, we have resolved order and disorder of individual protein domains. Fluorescently tagging specific domains of individual nucleoporins revealed both rigid and flexible domains: the tips of the FG domains are disordered, whereas the NPC-anchored domains are ordered. Our technique allows the collection of structural information in vivo, providing the ability to probe the organization of protein domains within the NPC. This has particular relevance for the FG domain nucleoporins, which are crucial for nucleocytoplasmic transport.     

Genetic variability of the frameshift region in IS911 transposable elements from Escherichia coli clinical isolates

The IS911 bacterial transposable element has been analyzed for its mechanism of transposition and for the way it controls the expression of its genes by programmed -1 translational frameshifting. In the present study the prevalence of IS911 has been determined in the Enterobacteriaceae family and in other Gram-negative bacilli. Three variants, found in Escherichia coli clinical isolates and having mutations in the region implicated in frameshifting, were functionally characterized. All three were altered in their frameshifting and transposition abilities, suggesting that the frameshift region of IS911 may constitute a target for mutations reducing the transposition frequency of this mobile element in natural populations of E. coli.     

Mass tag-assisted identification of naturally processed HLA class II-presented meningococcal peptides recognized by CD4+ T lymphocytes

The meningococcal class I outer membrane protein porin A plays an important role in the development of T cell-dependent protective immunity against meningococcal serogroup B infection and is therefore a major component of candidate meningococcal vaccines. T cell epitopes from porin A are poorly characterized because of weak in vitro memory T cell responses against purified Ag and strain variation. We applied a novel strategy to identify relevant naturally processed and MHC class II-presented porin A epitopes, based on stable isotope labeling of Ag. Human immature HLA-DR1-positive dendritic cells were used for optimal uptake and MHC class II processing of (14)N- and (15)N-labeled isoforms of the neisserial porin A serosubtype P1.5-2,10 in bacterial outer membrane vesicles. HLA-DR1 bound peptides, obtained after 48 h of Ag processing, contained typical spectral doublets in mass spectrometry that could easily be assigned to four porin A regions, expressed at diverging densities ( approximately 30-4000 copies/per cell). Epitopes from two of these regions are recognized by HLA-DR1-restricted CD4(+) T cell lines and are conserved among different serosubtypes of meningococcal porin A. This mass tag-assisted approach provides a useful methodology for rapid identification of MHC class II presented bacterial CD4(+) T cell epitopes relevant for vaccine development.     

Invertebrate data predict an early emergence of vertebrate fibrillar collagen clades and an anti-incest model

Fibrillar collagens are involved in the formation of striated fibrils and are present from the first multicellular animals, sponges, to humans. Recently, a new evolutionary model for fibrillar collagens has been suggested (Boot-Handford, R. P., Tuckwell, D. S., Plumb, D. A., Farrington Rock, C., and Poulsom, R. (2003) J. Biol. Chem. 278, 31067-31077). In this model, a rare genomic event leads to the formation of the founder vertebrate fibrillar collagen gene prior to the early vertebrate genome duplications and the radiation of the vertebrate fibrillar collagen clades (A, B, and C). Here, we present the modular structure of the fibrillar collagen chains present in different invertebrates from the protostome Anopheles gambiae to the chordate Ciona intestinalis. From their modular structure and the use of a triple helix instead of C-propeptide sequences in phylogenetic analyses, we were able to show that the divergence of A and B clades arose early during evolution because alpha chains related to these clades are present in protostomes. Moreover, the event leading to the divergence of B and C clades from a founder gene arose before the appearance of vertebrates; altogether these data contradict the Boot-Handford model. Moreover, they indicate that all the key steps required for the formation of fibrils of variable structure and functionality arose step by step during invertebrate evolution.     

Rho controls actin cytoskeletal assembly in renal epithelial cells during ATP depletion and recovery

Actincytoskeletal disruption is a hallmark of ischemic injury and ATPdepletion in a number of cell types, including renal epithelial cells.We manipulated Rho GTPase signaling by transfection and microinjectionin LLC-PK proximal tubule epithelial cells and observed actincytoskeletal organization following ATP depletion or recovery byconfocal microscopy and quantitative image analysis. ATP depletionresulted in disruption of stress fibers, cortical F-actin, and apicalactin bundles. Constitutively active RhoV14 prevented disruption ofstress fibers and cortical F-actin during ATP depletion and enhancedthe rate of stress fiber reassembly during recovery. Conversely, theRho inhibitor C3 or dominant negative RhoN19 prevented recovery ofF-actin assemblies upon repletion. Actin bundles in the apicalmicrovilli and cytosolic F-actin were not affected by Rho signaling.Assembly of vinculin and paxillin into focal adhesions was disrupted byATP depletion, and constitutively active RhoV14, although protectingstress fibers from disassembly, did not prevent dispersion of vinculinand paxillin, resulting in uncoupling of stress fiber and focaladhesion assembly. We propose that ATP depletion causes Rhoinactivation during ischemia and that recovery of normalcellular architecture and function requires Rho.

     

Does photosynthetic acclimation to elevated CO2 increase photosynthetic nitrogen-use efficiency? A study of three native UK grassland species in open-top chambers

1. The photosynthetic response to elevated CO₂ and nutrient stress was investigated in Agrostis capillaris, Lolium perenne and Trifolium repens grown in an open-top chamber facility for 2 years under two nutrient regimes. Acclimation was evaluated by measuring the response of light-saturated photosynthesis to changes in the substomatal CO₂ concentration.
2. Growth at elevated CO₂ resulted in reductions in apparent Rubisco activity in vivo in all three species, which were associated with reductions of total leaf nitrogen content on a unit area basis for A. capillaris and L. perenne . Despite this acclimation, photosynthesis was significantly higher at elevated CO₂ for T. repens and A. capillaris , the latter exhibiting the greatest increase of carbon uptake at the lowest nutrient supply.
3. The photosynthetic nitrogen-use efficiency (the rate of carbon assimilation per unit leaf nitrogen) increased at elevated CO₂, not purely owing to higher values of photosynthesis at elevated CO₂, but also as a result of lower leaf nitrogen contents.
4. Contrary to most previous studies, this investigation indicates that elevated CO₂ can stimulate photosynthesis under a severely limited nutrient supply. Changes in photosynthetic nitrogen-use efficiency may be a critical determinant of competition within low nutrient ecosystems and low input agricultural systems.