Amyloid fibrillogenesis: themes and variations

Recent progress has improved our knowledge of how proteins form amyloid fibrils. Both 'natively unfolded' and globular proteins have been shown to initiate fibrillization by adopting a partially structured conformation. Oligomeric prefibrillar intermediates have been extensively characterized with respect to their morphology and temporal evolution. Three-dimensional models obtained using biophysical and computational methods have provided information about fibril structure. All of these advances suggest common features of self-assembly pathways, with subtle variations accounting for differences among distinct amyloid fibrils.     

Evo-devo: variations on ancestral themes

Most animals evolved from a common ancestor, Urbilateria, which already had in place the developmental genetic networks for shaping body plans. Comparative genomics has revealed rather unexpectedly that many of the genes present in bilaterian animal ancestors were lost by individual phyla during evolution. Reconstruction of the archetypal developmental genomic tool-kit present in Urbilateria will help to elucidate the contribution of gene loss and developmental constraints to the evolution of animal body plans.     

Suppression mechanisms: themes from variations.

Suppressor analysis is a commonly used strategy to identify functional relationships between genes that might not have been revealed through other genetic or biochemical means. Many mechanisms that explain the phenomenon of genetic suppression have been described, but the wide variety of possible mechanisms can present a challenge to defining the relationship between a suppressor and the original gene. This article provides a broad framework for classifying suppression mechanisms and describes a series of genetic tests that can be applied to determine the most likely mechanism of suppression.     

RNA splicing: three themes with variations

We have isolated the four separate segments of chicken DNA which contain sequence homology to β tubulin. With the exception of a fifth region of DNA which appears to contain only a 5′ fragment of β gene, these four cloned sequences represent all of the β tubulin encoding DNA in the chicken. Each gene is very similar in structure, containing three or four small intervening sequences clustered in the 5′ portion of the coding region. Using RNAs prepared from a variety of cell lines and tissues, we have found five different mRNAs which carry β tubulin sequences, two of which are encoded by the same gene. Three of these mRNAs are unexpectedly long (between 3500 and 4000 bases). However, these large mRNAs do give authentic β tubulin translation products. Overall, we conclude that each of the four β tubulin genes is a functional gene which is expressed in a specific program during differentiation. These data strongly suggest that four β tubulins are necessary for proper microtubule function in vertebrates.     

RNA and protein folding: common themes and variations

Visualizing the navigation of an ensemble of unfolded molecules through the bumpy energy landscape in search of the native state gives a pictorial view of biomolecular folding. This picture, when combined with concepts in polymer theory, provides a unified theory of RNA and protein folding. Just as for proteins, the major folding free energy barrier for RNA scales sublinearly with the number of nucleotides, which allows us to extract the elusive prefactor for RNA folding. Several folding scenarios can be anticipated by considering variations in the energy landscape that depend on sequence, native topology, and external conditions. RNA and protein folding mechanism can be described by the kinetic partitioning mechanism (KPM) according to which a fraction (Phi) of molecules reaches the native state directly, whereas the remaining fraction gets kinetically trapped in metastable conformations. For two-state folders Phi approximately 1. Molecular chaperones are recruited to assist protein folding whenever Phi is small. We show that the iterative annealing mechanism, introduced to describe chaperonin-mediated folding, can be generalized to understand protein-assisted RNA folding. The major differences between the folding of proteins and RNA arise in the early stages of folding. For RNA, folding can only begin after the polyelectrolyte problem is solved, whereas protein collapse requires burial of hydrophobic residues. Cross-fertilization of ideas between the two fields should lead to an understanding of how RNA and proteins solve their folding problems.     

Centrosome positioning in polarized cells: Common themes and variations

The centrosome position is tightly regulated during the cell cycle and during differentiated cellular functions. Because centrosome organizes the microtubule network to coordinate both intracellular organization and cell signaling, centrosome positioning is crucial to determine either the axis of cell division, the direction of cell migration or the polarized immune response of lymphocytes. Since alteration of centrosome positioning seems to promote cell transformation and tumor spreading, the molecular mechanisms controlling centrosome movement in response to extracellular and intracellular cues are under intense investigation. Evolutionary conserved pathways involving polarity proteins and cytoskeletal rearrangements are emerging as common regulators of centrosome positioning in a wide variety of cellular contexts.     

Vertebrate floor-plate specification: variations on common themes

Situated at the ventral-most part of the vertebrate neural tube, the floor plate (FP) is an important signalling centre that controls the regional differentiation of neurons in the nervous system. It secretes guidance molecules that direct ventrally navigating axons crucial for the correct wiring of neuronal circuits. Although the function of the FP is well-conserved from fish to humans, discrepancies exists with respect to both the signalling system involved in FP induction, and the origin of the FP in various vertebrate species. Recent findings from the embryos of zebrafish, chicken and mouse provide insights that reconcile previous results and suggest common themes in vertebrate FP specification.     

Common themes and variations in serine protease autotransporters

The serine protease autotransporters of the Enterobacteriaceae (SPATEs) represent a group of large-sized, multi-domain exoproteins found only in pathogenic enteric bacteria. These proteins contain a highly conserved channel-forming C-terminal domain, which functions together with YaeT/Omp85 to facilitate secretion of the passenger domain to the cell surface. The C-terminal domain also mediates autoproteolytic cleavage, which releases the passenger from the bacterial cell. The passenger folds into a characteristic parallel beta-helical stalk-like structure with an N-terminal globular domain that performs serine proteolytic activity. Here, we review and discuss recent findings that have led to a better understanding of these unique features in this virulence protein family, including their biogenesis, structural architecture, sequence variation, sub-grouping, evolution and biochemical function.     

Common themes and variations in the rhodanese superfamily

The rhodanese homology domain is a ubiquitous fold found in several phylogenetically related proteins encoded by eubacterial, archeal, and eukaryotic genomes. Although rhodanese-like proteins share evolutionary relationships, analysis of their sequences highlights that they are so heterogeneous to form the rhodanese superfamily. The variability occurs at different levels including sequence, active site loop length, presence of a critical catalytic Cys residue, and domain arrangement. Even within the same genome, multiple genes encode rhodanese-like proteins presenting with variably arranged rhodanese domain(s): as single or tandem domain(s), or combined with other protein domain(s). Given the highly variable organization of the rhodanese domain(s) and the context where it is found, here we review the structural organization and function of the rhodanese-like proteins. The overview of the most recent findings about rhodanese allow us to depict a superfamily of versatile proteins relying on persulfide chemistry to accomplish cellular functions spanning from resistance to environmental threats, such as cyanide, and key cellular reactions related to sulfur metabolism and progression of cell cycle.     

Nodal signaling in early vertebrate embryos: themes and variations.

The nodal family of TGFbeta-related ligands have emerged as critical regulators of early vertebrate embryogenesis. Recent studies in mice, fish, and frogs of nodals and their intracellular transducers allow a comparison of how this signaling pathway is used in the patterning of early embryos of these different vertebrates.     

Glycosyltransferases and their products: cryptococcal variations on fungal themes

Glycosyltransferases are specific enzymes that catalyse the transfer of monosaccharide moieties to biological substrates, including proteins, lipids and carbohydrates. These enzymes are present from prokaryotes to humans, and their glycoconjugate products are often vital for survival of the organism. Many glycosyltransferases found in fungal pathogens such as Cryptococcus neoformans do not exist in mammalian systems, making them attractive potential targets for selectively toxic agents. In this article, we present the features of this diverse class of enzymes, and review the fungal glycosyltransferases that are involved in synthesis of the cell wall, the cryptococcal capsule, glycoproteins and glycolipids. We specifically focus on enzymes that have been identified or studied in C. neoformans, and we consider future directions for research on glycosyltransferases in the context of this opportunistic pathogen.     

The vertebrate social behavior network: evolutionary themes and variations

Based on a wide variety of data, it is now clear that birds and teleost (bony) fish possess a core "social behavior network" within the basal forebrain and midbrain that is homologous to the social behavior network of mammals. The nodes of this network are reciprocally connected, contain receptors for sex steroid hormones, and are involved in multiple forms of social behavior. Other hodological features and neuropeptide distributions are likewise very similar across taxa. This evolutionary conservation represents a boon for experiments on phenotypic behavioral variation, as the extraordinary social diversity of teleost fish and songbirds can now be used to generate broadly relevant insights into issues of brain function that are not particularly tractable in other vertebrate groups. Two such lines of research are presented here, each of which addresses functional variation within the network as it relates to divergent patterns of social behavior. In the first set of experiments, we have used a sexually polymorphic fish to demonstrate that natural selection can operate independently on hypothalamic neuroendocrine functions that are relevant for (1) gonadal regulation and (2) sex-typical behavioral modulation. In the second set of experiments, we have exploited the diversity of avian social organizations and ecologies to isolate species-typical group size as a quasi-independent variable. These experiments have shown that specific areas and peptidergic components of the social behavior network possess functional properties that evolve in parallel with divergence and convergence in sociality.     

Septin localization across kingdoms: three themes with variations

Septins are GTPases that form filaments in fungi and animals. In addition to their original role in cell division, septins have been shown to have roles in coordinating nuclear division, membrane trafficking and organizing the cytoskeleton. Many recent studies have examined subcellular localization of septins in a wide range of fungi and animals. Septin localization shows three patterns, which generally correspond to function across kingdoms. Septins that localize to projections shape and compartmentalize emerging growth. Septins that localize to partitions compartmentalize pre-existing cellular material. Septins that localize to the whole cell are involved in membrane trafficking and organizing the cytoskeleton and are most often in animals. The difference in localization pattern frequency between kingdoms will probably disappear as more septins are examined in diverse organisms and tissues.     

Distribution of hospital provision: policy themes and resource variations.

There has been much discussion in the past about the inequitable distribution of N.H.S. resources between different regions. This paper examines the distribution of hospital resources in terms of current revenue and beds in different specialties in eight regions (49 area health authorities). Variations between A.H.A.s are far more important than those between regions, and indeed they are so large (even in the acute specialties) that it is doubtful whether some A.H.A.s can be considered to be offering a comprehensive service. In the light of these findings the paper explores policy problems involved in trying to secure a more equitable distribution of N.H.S. resources at a time of financial stringency.     

Egg development in parthenogenetic nematodes: variations in meiosis and axis formation

In the well studied model nematode Caenorhabditis elegans entrance of the sperm induces an anterior-posterior polarity in the egg and determines the orientation of the primary embryonic axis. Subsequently, fusion of two haploid gamete nuclei results in a diploid zygote as a prerequisite for normal embryogenesis. Here we analyze the establishment of embryonic polarity and diploidy in the absence of sperm in three parthenogenetic nematode species from three different families, Diploscapter coronatus (Diploscapteridae), Acrobeloides nanus (Cephalobidae) and Plectus sp. (Plectidae). We find that they not only differ from C. elegans in these two aspects but also from each other, indicating variant solutions for the same developmental challenges and supporting the view that the parthenogenetic mode of reproduction has been acquired multiple times independently.     

Appalachian spring: variations on ancient gastro-entero-pancreatic themes in New World mammals

Studies of guinea pig genomic and/or cDNA clones encoding the gastro-entero-pancreatic (GEP) hormones--insulin, glucagon and pancreatic polypeptide--as well as portions of the insulin receptor, are described. Multiple clustered substitutions (localized rapid mutation acceptance) altering the biological properties of both insulin and glucagon have been revealed, but this does not appear to be the case with either pancreatic polypeptide or those regions of guinea pig insulin receptor cDNAs that have been examined thus far. These findings suggest that novel selective pressures operative in the New World environment, in which these animals evolved in isolation from Old World mammalian species, have led to altered solutions to problems related to the regulation of growth and carbohydrate metabolism.