Biomineralization: a structural perspective

Biomineralization is an inherently structural subject; the structure of the mineral phase, the structure of the matrix composed of macromolecules and especially the structure of the interphase zone between them. Studies of the dynamics of mineral formation have revealed that a widespread strategy used by many organisms is to first form a disordered mineral phase. Only when it is in place and has adopted its appropriate shape, is it induced to crystallize. Matrix studies have highlighted the importance of a unique group of proteins that are rich in aspartic acid. These are involved in controlling mineral formation. Relating structure to function in mineralized tissues, often involves an understanding of mechanical properties in terms of not only the hierarchical structure of the tissue, but also the graded structure that varies from one location to another. Structure is thus in many respects the foundation upon which the field of biomineralization rests.     

Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins

Nuclear organization has been implicated in regulating gene activity. Recently, large developmentally regulated regions of the genome dynamically associated with the nuclear lamina have been identified. However, little is known about how these lamina-associated domains (LADs) are directed to the nuclear lamina. We use our tagged chromosomal insertion site system to identify small sequences from borders of fibroblast-specific variable LADs that are sufficient to target these ectopic sites to the nuclear periphery. We identify YY1 (Ying-Yang1) binding sites as enriched in relocating sequences. Knockdown of YY1 or lamin A/C, but not lamin A, led to a loss of lamina association. In addition, targeted recruitment of YY1 proteins facilitated ectopic LAD formation dependent on histone H3 lysine 27 trimethylation and histone H3 lysine di- and trimethylation. Our results also reveal that endogenous loci appear to be dependent on lamin A/C, YY1, H3K27me3, and H3K9me2/3 for maintenance of lamina-proximal positioning.     

Immunolocalization of lamins in the thick nuclear lamina of human synovial cells

While in the great majority of cells the nuclear lamina is not resolved as a distinct structure separating the chromatin from the nuclear envelope, a demonstrable nuclear lamina ("fibrous lamina") of 30 to 300 nm thickness, interposed between the inner nuclear membrane and the peripheral chromatin, is characteristic for certain types of cells of vertebrates and invertebrates. We have examined whether the thick (50-70 nm) fibrous lamina of human synovial cells from patients suffering from rheumatoid arthritis indeed contains the lamins found in the indiscernible lamina structures present in most normal cells. We have observed, by electron microscopic immunolocalization, that both the A and the B type lamins occur throughout the entire nuclear lamina of these cells and that this structure is also resistant to treatments with nucleases and high salt buffers. This shows that the thick fibrous lamina only seen in certain vertebrate cells is compositionally related to the "masked" nuclear lamina of most other cells which usually is identified only upon removal of the adjacent nuclear structures.     

From aquatic science to ecosystem health: a philosophical perspective

The development of an ecosystem (social, economic, environmental) approach to water management is traced from its origins in the Great Lakes of North America. The focus on health and integrity of ecosystems is an outgrowth of the Lamarckian concept of The Biosphere as a global system of matter, life, and mind. The driving forces behind the development of an ecosystem approach have been negative feedback from excessive demotechnic growth and faith that we can maintain a healthy relationship with Mother Earth.     

Mammalian DNA methyltransferases: a structural perspective

The methylation of mammalian DNA, primarily at CpG dinucleotides, has long been recognized to play a major role in controlling gene expression, among other functions. Given their importance, it is surprising how many basic questions remain to be answered about the proteins responsible for this methylation and for coordination with the parallel chromatin-marking system that operates at the level of histone modification. This article reviews recent studies on, and discusses the resulting biochemical and structural insights into, the DNA nucleotide methyltransferase (Dnmt) proteins 1, 3a, 3a2, 3b, and 3L.     

Nonsequence-specific DNA recognition: a structural perspective

Chromosomal proteins that form essential architectural components of chromatin bind and bend DNA with an intrinsic low degree of sequence preference. Comparisons made between two recently determined structures of high mobility group (HMG) protein-DNA complexes and other nonsequence-specific protein-DNA complexes reveal the structural basis of this important mode of DNA binding.     

Ran-dependent nuclear export mediators: a structural perspective

Nuclear export is an essential eukaryotic activity. It proceeds through nuclear pore complexes (NPCs) and is mediated by soluble receptors that shuttle between nucleus and cytoplasm. RanGTPase-dependent export mediators (exportins) constitute the largest class of these carriers and are functionally highly versatile. All of these exportins load their substrates in response to RanGTP binding in the nucleus and traverse NPCs as ternary RanGTP-exportin-cargo complexes to the cytoplasm, where GTP hydrolysis leads to export complex disassembly. The different exportins vary greatly in their substrate range. Recent structural studies of both protein- and RNA-specific exporters have illuminated how exportins bind their cargoes, how Ran triggers cargo loading and how export complexes are disassembled in the cytoplasm. Here, we review the current state of knowledge and highlight emerging principles as well as prevailing questions.     

Beta-lactam antibiotic resistance: a current structural perspective

Bacterial resistance to beta-lactam antibiotics can be achieved by any of three strategies: the production of beta-lactam-hydrolyzing beta-lactamase enzymes, the utilization of beta-lactam-insensitive cell wall transpeptidases, and the active expulsion of beta-lactam molecules from Gram-negative cells by way of efflux pumps. In recent years, structural biology has contributed significantly to the understanding of these processes and should prove invaluable in the design of drugs to combat beta-lactam resistance in the future.     

Desmosomes from a structural perspective

Desmosomes are cell-cell junctions responsible for maintaining the structural integrity of tissues by resisting shear forces. Defects result in diseases of mechanically challenged tissues such as skin and heart. The architectural design represents the key to understanding the strength and durability inherent to desmosomes. A number of different proteins contribute to this architecture, and X-ray crystallography has made considerable progress in defining the atomic structure of various isolated domains. Electron tomography has been used to determine the three-dimensional structure of intact desmosomes in situ. By combining information from X-ray crystallography, cell and molecular biology and electron tomography, it should ultimately be possible to deduce the specific protein interactions that define the mechanical properties of this important adhesive junction.     

Phenomics and lamins: from disease to therapy

Systematic correlation of phenotype with genotype is a key goal of the emerging field of phenomics, which is expected to help define complex diseases. Careful evaluation of phenotype-genotype associations in monogenic disorders, such as laminopathies, might provide new hypotheses to be tested with molecular and cellular studies and might also suggest potential new intervention strategies. For instance, evaluation of the clinical features of carriers of mutant LMNA in kindreds with familial partial lipodystrophy suggests rational, staged intervention using established pharmaceutical agents to prevent cardiovascular complications not just for patients with lipodystrophy but by extension for patients with the common metabolic syndrome. Careful non-invasive imaging shows phenotypic differences between partial lipodystrophy due to mutant LMNA and not due to mutant LMNA. Furthermore, hierarchical cluster analysis detects systematic relationships between organ involvement in laminopathies and mutation position in the LMNA genomic sequence. However, sometimes the same LMNA mutation can underlie markedly different clinical phenotypes; cellular and molecular experiments can help to explain the mechanistic basis for such differences. Finally, promising novel treatment modalities for laminopathies, such as farnesyl transferase inhibition and gene-based therapies, might help not only to illuminate mechanisms that link genotype to phenotype, but also to provide hope for patients suffering with laminopathies, since these treatments are designed to modulate key early or proximal steps in the pathogenesis of these disorders.     

Differential transport and integration into the nuclear lamina for lamins A, B, and C

Lamins A, B, and C are the major proteins of the mammalian nuclear lamina and have been well studied in BHK-21 cells. Using in vivo labelling, cell fractionation, and immunoprecipitation, we have found that lamins have different patterns of nuclear transport and solubility. Newly synthesized lamin A is translocated to the nucleus faster than lamin C or B. It is the most tightly bound lamin and cannot be extracted from the lamina by nonionic detergent or high-salt buffers. Lamins B and C migrate more slowly to the nucleus. Partitioning between cytoskeleton and detergent-soluble fractions shows that integration of lamins B and C is not completed before a 1-h chase. For lamin C this process is dependent upon protein synthesis and can be inhibited with cycloheximide. Even though lamins A and C are almost identical, lamin C is never firmly bound to the lamina and can be partially solubilized upon high-salt treatment.     

Partial cleavage of A-type lamins concurs with their total disintegration from the nuclear lamina during apoptosis

Although activated caspase 6 is capable of cleaving both A- and B-type lamins during apoptosis, the higher-order structure of the nuclear lamina may cause a differential breakdown of these two types of lamins. In order to obtain a better understanding of the dynamics and the consequences of the rapid, coordinated breakdown of the lamina complex, we applied the green fluorescent protein (GFP) technology in living cells, in which the fate of individual caspase cleavage fragments of A- and B-type lamins was examined. CHO-K1 cells were stably transfected with cDNA constructs encoding N-terminally GFP-labelled hybrids of lamin A, lamin Adelta10, lamin C or lamin B1. The course of the apoptotic process, induced by the kinase inhibitor staurosporine or by the proteasome inhibitor MG132, was monitored by digital imaging microscopy or confocal microscopy. Time-lapse recordings showed that parallel to DNA condensation N-terminally GFP-tagged A-type lamins became diffusely dispersed throughout the nucleoplasm and rapidly translocated to the cytoplasm. In contrast, the majority of GFP-lamin B1 signal remained localised at the nuclear periphery, even after extensive DNA condensation. Comparison of lamin B1-GFP signal with A-type lamin antibody staining in the same apoptotic cells confirmed the temporal differences between A- and B-type lamina dispersal. Immunoblotting revealed only a partial cleavage of A-type lamins and an almost complete cleavage of lamin B1 during apoptosis. In contrast to lamin B1 in normal cells, this cleaved lamin B1, which is apparently still associated with the nuclear membrane, can be completely extracted by methanol or ethanol. Fluorescence loss of intensity after photobleaching experiments showed that in apoptotic cells A-type lamin-GFP molecules diffuse almost freely in both nucleoplasm and cytoplasm, while the lamin B1-GFP fragments remain more stably associated with the nuclear membrane, which is confirmed by co-localisation immunofluorescence studies with a nucleoporin p62 antibody. Our results therefore clearly show a differential behaviour of A- and B-type lamins during apoptosis, suggesting not only distinct differences in the organisation of the lamina filaments, but also that caspase cleavage of only a small fraction of A-type lamins is needed for its complete disintegration.     

Ubiquitin family proteins and their relationship to the proteasome: a structural perspective

Many biological processes rely on targeted protein degradation, the dysregulation of which contributes to the pathogenesis of various diseases. Ubiquitin plays a well-established role in this process, in which the covalent attachment of polyubiquitin chains to protein substrates culminates in their degradation via the proteasome. The three-dimensional structural topology of ubiquitin is highly conserved as a domain found in a variety of proteins of diverse biological function. Some of these so-called "ubiquitin family proteins" have recently been shown to bind components of the 26S proteasome via their ubiquitin-like domains, thus implicating proteasome activity in pathways other than protein degradation. In this chapter, we provide a structural perspective of how the ubiquitin family of proteins interacts with the proteasome.     

Lipid-protein interactions in biological membranes: a structural perspective

Lipid molecules bound to membrane proteins are resolved in some high-resolution structures of membrane proteins. An analysis of these structures provides a framework within which to analyse the nature of lipid-protein interactions within membranes. Membrane proteins are surrounded by a shell or annulus of lipid molecules, equivalent to the solvent layer surrounding a water-soluble protein. The lipid bilayer extends right up to the membrane protein, with a uniform thickness around the protein. The surface of a membrane protein contains many shallow grooves and protrusions to which the fatty acyl chains of the surrounding lipids conform to provide tight packing into the membrane. An individual lipid molecule will remain in the annular shell around a protein for only a short period of time. Binding to the annular shell shows relatively little structural specificity. As well as the annular lipid, there is evidence for other lipid molecules bound between the transmembrane α-helices of the protein; these lipids are referred to as non-annular lipids. The average thickness of the hydrophobic domain of a membrane protein is about 29 Å, with a few proteins having significantly smaller or greater thicknesses than the average. Hydrophobic mismatch between a membrane protein and the surrounding lipid bilayer generally leads to only small changes in membrane thickness. Possible adaptations in the protein to minimise mismatch include tilting of the helices and rotation of side chains at the ends of the helices. Packing of transmembrane α-helices is dependent on the chain length of the surrounding phospholipids. The function of membrane proteins is dependent on the thickness of the surrounding lipid bilayer, sometimes on the presence of specific, usually anionic, phospholipids, and sometimes on the phase of the phospholipid.     

Lipid-protein interactions in biological membranes: a structural perspective

Lipid molecules bound to membrane proteins are resolved in some high-resolution structures of membrane proteins. An analysis of these structures provides a framework within which to analyse the nature of lipid-protein interactions within membranes. Membrane proteins are surrounded by a shell or annulus of lipid molecules, equivalent to the solvent layer surrounding a water-soluble protein. The lipid bilayer extends right up to the membrane protein, with a uniform thickness around the protein. The surface of a membrane protein contains many shallow grooves and protrusions to which the fatty acyl chains of the surrounding lipids conform to provide tight packing into the membrane. An individual lipid molecule will remain in the annular shell around a protein for only a short period of time. Binding to the annular shell shows relatively little structural specificity. As well as the annular lipid, there is evidence for other lipid molecules bound between the transmembrane alpha-helices of the protein; these lipids are referred to as non-annular lipids. The average thickness of the hydrophobic domain of a membrane protein is about 29 A, with a few proteins having significantly smaller or greater thicknesses than the average. Hydrophobic mismatch between a membrane protein and the surrounding lipid bilayer generally leads to only small changes in membrane thickness. Possible adaptations in the protein to minimise mismatch include tilting of the helices and rotation of side chains at the ends of the helices. Packing of transmembrane alpha-helices is dependent on the chain length of the surrounding phospholipids. The function of membrane proteins is dependent on the thickness of the surrounding lipid bilayer, sometimes on the presence of specific, usually anionic, phospholipids, and sometimes on the phase of the phospholipid.     

From Avicennia to Zizania: seed recalcitrance in perspective

BACKGROUND: Considered only in terms of tolerance of, or sensitivity to, desiccation (which is an oversimplification), orthodox seeds are those which tolerate dehydration and are storable in this condition, while highly recalcitrant seeds are damaged by loss of only a small proportion of water and are unstorable for practical purposes. Between these extremes, however, there may be a gradation of the responses to dehydration--and also to other factors--suggesting perhaps that seed behaviour might be best considered as constituting a continuum subtended by extreme orthodoxy and the highest degree of recalcitrance. As the characteristics of seeds of an increasing number of species are elucidated, non-orthodox seed behaviour is emerging as considerably more commonplace--and its basis far more complex--than previously suspected. SCOPE: Whatever the post-harvest responses of seeds of individual species may be, they are the outcome of the properties of pre-shedding development, and a full understanding of the subtleties of various degrees of non-orthodox behaviour must await the identification of, and interaction among, all the factors conferring extreme orthodoxy. Appreciation of the phenomenon of recalcitrance is confounded by intra- and interseasonal variability across species, as well as within individual species. However, recent evidence suggests that provenance is a pivotal factor in determining the degree of recalcitrant behaviour exhibited by seeds of individual species. Non-orthodox--and, in particular, recalcitrant--seed behaviour is not merely a matter of desiccation sensitivity: the primary basis is that the seeds are actively metabolic when they are shed, in contrast to orthodox types which are quiescent. This affects all aspects of the handling and storage of recalcitrant seeds. In the short to medium term, recalcitrant seeds should be stored in as hydrated a condition as when they are shed, and at the lowest temperature not diminishing vigour or viability. Such hydrated storage has attendant problems of fungal proliferation which, unless minimized, will inevitably and significantly affect seed quality. The life span of seeds in hydrated storage even under the best conditions is variable among species, but is curtailed (days to months), and various approaches attempting to extend non-orthodox seed longevity are discussed. Conservation of the genetic resources by means other than seed storage is then briefly considered, with detail on the potential for, and difficulties with, cryostorage highlighted. CONCLUSIONS: There appears to be little taxonomic relationship among species exhibiting the phenomenon of seed recalcitrance, suggesting that it is a derived trait, with tolerance having been lost a number of times. Although recalcitrant seededness is best represented in the mesic tropics, particularly among rainforest climax species, it does occur in cooler, drier and markedly seasonal habitats. The selective advantages of the trait are considered.