Vertebrate evolution: turning heads

The skeleton of the neck and shoulders has undergone alterations during evolution, but muscle connectivity has not. A recent study suggests this is a result of neural crest cells defining attachment points and thus muscle connectivity.     

Nuclease colicins and their immunity proteins

It is more than 80 years since Gratia first described 'a remarkable antagonism between two strains of Escherichia coli'. Shown subsequently to be due to the action of proteins (or peptides) produced by one bacterium to kill closely related species with which it might be cohabiting, such bacteriocins have since been shown to be commonplace in the internecine warfare between bacteria. Bacteriocins have been studied primarily from the twin perspectives of how they shape microbial communities and how they penetrate bacteria to kill them. Here, we review the modes of action of a family of bacteriocins that cleave nucleic acid substrates in E. coli, known collectively as nuclease colicins, and the specific immunity (inhibitor) proteins that colicin-producing organisms make in order to avoid committing suicide. In a process akin to targeting in mitochondria, nuclease colicins engage in a variety of cellular associations in order to translocate their cytotoxic domains through the cell envelope to the cytoplasm. As well as informing on the process itself, the study of nuclease colicin import has also illuminated functional aspects of the host proteins they parasitize. We also review recent studies where nuclease colicins and their immunity proteins have been used as model systems for addressing fundamental problems in protein folding and protein-protein interactions, areas of biophysics that are intimately linked to the role of colicins in bacterial competition and to the import process itself.     

Vertebrate and invertebrate carotenoid-binding proteins

In invertebrates and vertebrates, carotenoids are ubiquitous colorants, antioxidants, and provitamin A compounds that must be absorbed from dietary sources and transported to target tissues where they are taken up and stabilized to perform their physiological functions. These processes occur in a specific and regulated manner mediated by high-affinity carotenoid-binding proteins. In this mini-review, we examine the published literature on carotenoid-binding proteins in vertebrate and invertebrate systems, and we report our initial purification and characterization of a novel lutein-binding protein isolated from liver of Japanese quail (Coturnix japonica).     

Vertebrate evolution: recent perspectives from fish

Recent progress in understanding the evolution of vertebrate genomes has been rapid, and previous notions that all such genomes could be regarded as equivalent in their gene content have been rendered outdated. This notion, often embodied in the representation that vertebrates possess four Hox complexes, still appears in contemporary textbooks of developmental biology. Recent data from the genomes of teleost fish show that this assumption is untrue and suggest that interesting situations might arise from the apparent proliferation of genes among fish.     

Reprint of: Virus-binding proteins and their roles in shrimp innate immunity

Disease outbreaks caused by viral pathogens constitute a major limitation to development of the shrimp aquaculture industry. Many research have been conducted to better understand how host shrimp respond to viral infections with the aim of using the gained knowledge to develop better strategies for disease management and control. One approach has been to study the interactions between host and viral proteins, and particularly host virus-binding proteins that might play an important role in the viral infection process. Within the past five years, increasing numbers of virus-binding proteins (VBPs) have been reported in shrimp. Characterization of these molecules has emphasized on their potential therapeutic applications by demonstrating their activities in inhibition of viral replication via in vivo neutralization assay. However, signaling to induce innate antiviral immune responses as a consequence of binding between viral proteins and VBPs remain to be fully elucidated.     

Vertebrate evolution: doubling and shuffling with a full deck

The number and role of whole-genome duplications in vertebrate evolution has intrigued evolutionary biologists since Ohno first proposed genome duplication as the force driving the 'big leap' in vertebrate morphological innovation. Attempts to resolve these issues have been thwarted by small and noisy datasets, and by lack of computational accuracy and statistical rigor. Recently, Ken Wolfe and colleagues presented a genome-scale, statistically rigorous analysis of evidence based on the spatial organization of duplicated genes, as well as estimates of duplication times. Their results provide the strongest evidence to date of large-scale duplication throughout the vertebrate genome, consistent with at least one whole-genome duplication.     

Vertebrate crystallins- from proteins to genes

A review of literature on tissue-specific proteins of the vertebrate eye lens and genes coding for these proteins is presented. Particular attention is paid to the most heterogeneous family of crystallins: beta- and gamma-crystallins, their nomenclature, and the structure of their genes. It is pointed out that mutations in gene coding for ubiquitous crystallins may be related to some forms of cataracts.     

Vertebrate cranial evolution: Contributions and conflict from the fossil record

In modern vertebrates, the craniofacial skeleton is complex, comprising cartilage and bone of the neurocranium, dermatocranium and splanchnocranium (and their derivatives), housing a range of sensory structures such as eyes, nasal and vestibulo-acoustic capsules, with the splanchnocranium including branchial arches, used in respiration and feeding. It is well understood that the skeleton derives from neural crest and mesoderm, while the sensory elements derive from ectodermal thickenings known as placodes. Recent research demonstrates that neural crest and placodes have an evolutionary history outside of vertebrates, while the vertebrate fossil record allows the sequence of the evolution of these various features to be understood. Stem-group vertebrates such as Metaspriggina walcotti (Burgess Shale, Middle Cambrian) possess eyes, paired nasal capsules and well-developed branchial arches, the latter derived from cranial neural crest in extant vertebrates, indicating that placodes and neural crest evolved over 500 million years ago. Since that time the vertebrate craniofacial skeleton has evolved, including different types of bone, of potential neural crest or mesodermal origin. One problematic part of the craniofacial skeleton concerns the evolution of the nasal organs, with evidence for both paired and unpaired nasal sacs being the primitive state for vertebrates.     

The mysterious RAMP proteins and their roles in small RNA-based immunity

A new class of prokaryotic RNA binding proteins called Repeat Associated Mysterious Proteins (RAMPs), has recently been identified. These proteins play key roles in a novel type immunity in which the DNA of the host organism (e.g. a prokaryote) has sequence segments corresponding to the sequences of potential viral invaders. The sequences embedded in the host DNA confer immunity by directing selective destruction of the nucleic acid of the virus using an RNA-based strategy. In this viral defense mechanism, RAMP proteins have multiple functional roles including endoribonucleotic cleavage and ribonucleoprotein particle assembly. RAMPs contain the classical RNA recognition motif (RRM), often in tandem, and a conserved glycine-rich segment (G-loop) near the carboxyl terminus. However, unlike RRMs that bind single-stranded RNA using their β-sheet surface, RAMPs make use of both sides of the RRM fold and interact with both single-stranded and structured RNA. The unique spatial arrangement of the two RRM folds, facilitated by a hallmark G-loop, is crucial to formation of a composite surface for recognition of specific RNA. Evidence for RNA-dependent oligomerization is also observed in some RAMP proteins that may serve as an important strategy to increase specificity.     

Vertebrate invaders and their ecological impacts in Chile

The South American country of Chile has been subjected to relatively few invasions in historic times. In comparison to the ca 610 vertebrate species found in continental Chile, only 24 species (3.9%) have invaded the country. Except for two bird and two or three mammal species that expanded their range and crossed the Andean Ranges from Argentina, the remaining 20 species were all introduced, or aided, by humans. Of the 24 invader species that currently occur in Chile, 11 (46%) were first introduced in central Chile, two (8%) in the northern part of the country, nine (38%) in the southern part, and two (8%) in Juan Fernández Archipelago. For ten (42%) of those species there is no information about their effects on the native flora, vegetation, or fauna. For eight species (33%), the information regarding the effects of the invaders is anecdotal. For six species (25%), there is adequate quantitative documentation available on their effects. Of a total of seven convincingly repo rted cases, two involve positive effects (increase in the prey base for native predators) and five have negative effects, of which three are on native vegetation and the remaining two on native fauna.     

Tests of 4 controlling-element systems of maize for mutator activity and their interaction with Mu mutator

The maize mutator system, Mu, behaves in a non-Mendelian manner that may be expected if it were an extremely active controlling-element system. To test this hypothesis, the maize controlling-element systems, a---dt---Dt, Ds---Ac (= MP), I---En, and r---cu---Fcu were tested for mutation activity. Ds---Ac and r---cu---Fcu tests were the only ones in which new mutants were induced, but at a frequency much lower than that found in Mu crosses. The mutation frequency in these controlling-element systems does not differ statistically from that found in control (Non-Mu) populations.

Tests also were made to determine if Mu will substitute for the regulatory element of any of the 4 conotrolling-element. All tests were negative, suggesting that, if Mu is a controlling-element system, it is a different one from those previously described.