Rosetta Stone proteins: "chance and necessity"?

A response to Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions by AJ Enright, CA Ouzounis. Genome Biology 2000, 2:research0034.1-0034.7     

Do telomeres ask checkpoint proteins: "gimme shelter-in"?

Telomeres are complicated structures designed to allow one thing and avoid another. They allow replication of chromosome ends, an issue mostly about telomerase, which we seem to understand (though details of its regulation are works in progress). Telomeres must also avoid being detected as DNA breaks. This is important for two reasons: DNA breaks activate checkpoints that cause arrest of cell division, and DNA breaks engage repair machinery. Clearly, normal telomeres neither activate cell cycle arrest nor allow themselves to be repaired; arrest blocks cell division, and repair fuses chromosomes.     

A Rosetta Stone for Nature’s Benefits to People

After a long incubation period, the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) is now underway. Underpinning all its activities is the IPBES Conceptual Framework (CF), a simplified model of the interactions between nature and people. Drawing on the legacy of previous large-scale environmental assessments, the CF goes further in explicitly embracing different disciplines and knowledge systems (including indigenous and local knowledge) in the co-construction of assessments of the state of the world’s biodiversity and the benefits it provides to humans. The CF can be thought of as a kind of “Rosetta Stone” that highlights commonalities between diverse value sets and seeks to facilitate crossdisciplinary and crosscultural understanding. We argue that the CF will contribute to the increasing trend towards interdisciplinarity in understanding and managing the environment. Rather than displacing disciplinary science, however, we believe that the CF will provide new contexts of discovery and policy applications for it.     

Will the transgenic mouse serve as a Rosetta Stone to glycoconjugate function?

The overwhelming diversity of oligosaccharide structures on glycoproteins and glycolipids is both the most fascinating and the most frustrating aspect of glycobiology. Moreover, a single protein may be variably glycosylated and thereby represented by multiple glycoforms. As envisioned, many modifications may serve no useful function while others are likely to be essential [1]; hence, experimental approaches to understand the biological basis for such complexity can be difficult to formulate. In a recent comprehensive review on oligosaccharide function [2], Varki concludes that oligosaccharides carry out a large number of biological roles and that while all theories are correct, exceptions to each can be found. Although a common theme to oligosaccharide function may never appear, crucial biological information can be observed to reside within various glycoforms. Examples include the glycoform-dependent mechanism of selectin function in mediating haemopoietic cell extravasation during inflammatory responses [3] and the clearance of particular glycoforms from serum by various glycoform-specific receptors [4–6]. Together, studies of glycosyltransferase biochemistry, naturally-occurring and experimentally-induced glycoform mutations, and the genetic basis for the production of glycoform complexity have allowed crucial steps in the biosynthesis of specific glycan structures to be reconstructed as they appear to occur in the endoplasmic reticulum and Golgi apparatus of intact cells [7]. With a significant foundation of biochemical knowledge achieved, genetic approaches are under way further to decipher the physiological roles encoded within the diverse and dynamic mammalian oligosaccharide repertoire.     

Is the unfolded state the Rosetta Stone of the protein folding problem?

Solving the protein folding problem is one of the most challenging tasks in the post genomic era. Identification of folding-initiation sites is very important in order to understand the protein folding mechanism. Detection of residual structure in unfolded proteins can yield important clues to the initiation sites in protein folding. A substantial number of studied proteins possess residual structure in hydrophobic regions clustered together in the protein core. These stable structures can work as seeds in the folding process. In addition, local preferences for secondary structure in the form of turns for beta-sheet initiation and helical turns for alpha-helix formation can guide the folding reaction. In this respect the unfolded states, studied at increasing structural resolution, can be the Rosetta Stone of the protein folding problem.     

Are membrane proteins "inside-out" proteins?

One of the central paradigms of structural biology is that membrane proteins are "inside-out" proteins, in that they have a core of polar residues surrounded by apolar residues. This is the reverse of the characteristics found in water-soluble proteins. We have decided to test this paradigm, now that sufficient numbers of transmembrane alpha-helical structures are accessible to statistical analysis. We have analyzed the correlation between accessibility and hydrophobicity of both individual residues and complete helices. Our analyses reveal that hydrophobicity of residues in a transmembrane helical bundle does not correlate with any preferred location and that the hydrophilic vector of a helix is a poor indicator of the solvent exposed face of a helix. Neither polar nor hydrophobic residues show any bias for the exterior or the interior of a transmembrane domain. As a control, analysis of water-soluble helical bundles performed in a similar manner has yielded clear correlations between hydrophobicity and accessibility. We therefore conclude that, based on the data set used, membrane proteins as "inside-out" proteins is an unfounded notion, suggesting that packing of alpha-helices in membranes is better understood by maximization of van der Waal's forces, rather than by a general segregation of hydrophobicities driven by lipid exclusion.     

Plasmid- and chromosome-encoded redundant and specific functions are involved in biosynthesis of the siderophore anguibactin in Vibrio anguillarum 775: a case of chance and necessity?

We report the identification of a novel chromosome cluster of genes in Vibrio anguillarum 775 that includes redundant functional homologues of the pJM1 plasmid-harbored genes angE and angC that are involved in anguibactin biosynthesis. We also identified in this cluster a chromosomal angA gene that is essential in anguibactin biosynthesis.     

Small heat shock proteins and α-crystallins: dynamic proteins with flexible functions

The small heat shock proteins (sHSPs) and the related α-crystallins (αCs) are virtually ubiquitous proteins that are strongly induced by a variety of stresses, but that also function constitutively in multiple cell types in many organisms. Extensive research has demonstrated that a majority of sHSPs and αCs can act as ATP-independent molecular chaperones by binding denaturing proteins and thereby protecting cells from damage due to irreversible protein aggregation. As a result of their diverse evolutionary history, their connection to inherited human diseases, and their novel protein dynamics, sHSPs and αCs are of significant interest to many areas of biology and biochemistry. However, it is increasingly clear that no single model is sufficient to describe the structure, function or mechanism of action of sHSPs and αCs. In this review, we discuss recent data that provide insight into the variety of structures of these proteins, their dynamic behavior, how they recognize substrates, and their many possible cellular roles.     

Anchoring proteins and cardiac sudden death: how and why?

Mutations in proteins responsible for ion transport in cardiac tissue can induce a destabilization of electrical function and provoke cardiac sudden death. Identification of a genetic anomaly in a French family that developed the syndrome of cardiac sudden death has revealed a crucial new element in normal cardiac electrical function : Ion channels need to be anchored to specific domains at the plasma membrane by an anchoring protein called ankyrin-B.     

The gap junction as a “Biological Rosetta Stone”: implications of evolution, stem cells to homeostatic regulation of health and disease in the Barker hypothesis

The discovery of the gap junction structure, its functions and the family of the “connexin” genes, has been basically ignored by the major biological disciplines. These connexin genes code for proteins that organize to form membrane-associated hemi-channels, “connexons”, co-join with the connexons of neighboring cells to form gap junctions. Gap junctions appeared in the early evolution of the metazoan. Their fundamental functions, (e.g., to synchronize electrotonic and metabolic functions of societies of cells, and to regulate cell proliferation, cell differentiation, and apoptosis), were accomplished via integrating the extra-cellular triggering of intra-cellular signaling, and therefore, regulating gene expression. These functions have been documented by genetic mutations of the connexin genes and by chemical modulation of gap junctions. Via genetic alteration of connexins in knock-out and transgenic mice, as well as inherited connexin mutations in various human syndromes, the gap junction has been shown to be directly linked to many normal cell functions and multiple diseases, such as birth defects, reproductive, neurological disorders, immune dysfunction and cancer. Specifically, the modulation of gap junctional intercellular communication (GJIC), either by increasing or decreasing its functions by non-mutagenic chemicals or by oncogenes or tumor suppressor genes in normal or “initiated” stem cells and their progenitor cells, can have a major impact on tumor promotion or cancer chemoprevention and chemotherapy. The overview of the roles of the gap junction in the evolution of the metazoan and its potential in understanding a “systems” view of human health and aging and the diseases of aging will be attempted.     

Inuit myopia: an environmentally induced "epidemic"?

Among Inuit less than 30 years old the prevalence of myopia is far in excess of that of their elders. This is especially true for females. There seems to be little, if any, genetic contribution to this "epidemic" of myopia in the young. The age and sex distribution indicates the likelihood of an environmental factor, probably cultural, being responsible for the current pattern. Other data implicate school attendance as a possible etiologic factor.