Crystalline layer in Drosophila melanogaster eggshell: arrangement of components as revealed by negative staining and reconstruction

Eggshell formation in Drosophila melanogaster is used as a model system in studies of cellular differentiation. A detailed knowledge of eggshell structure is necessary for this purpose and also to permit correlation of eggshell structure with function. Unique among the eggshell layers, the innermost chorionic layer (ICL) was investigated by means of transmission electron microscopy of thin sections and whole mounts, utilizing conventional fixation. LaNO₃ impregnation and negative staining with uranyl acetate. Whole mount face views of negatively stained ICLs were processed by means of optical and computer reconstruction. The ICL, which almost fully covers the oocyte, consists of 4 5 bilaminar sublayers with a total thickness of 400–500 Å. It appears to be formed by crystallites 1– μm in size, containing roughtly spherical molecules which are 30 Å in diameter approximately. Each unit cell probably includes 8 molecules and also distinct vacant spaces, differing in size, ICL may be involved in the exchange of the respiratory gases during embryogenesis.     

A database for G proteins and their interaction with GPCRs

Background

The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development.

Results

BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange.

Conclusions

As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.     

Analysis of Molecular Recognition Features (MoRFs) in membrane proteins

Molecular Recognition Features (MoRFs) are defined as short, intrinsically disordered regions in proteins that undergo disorder-to-order transition upon binding to their partners. As their name suggests, they are implicated in molecular recognition, which serves as the initial step for protein–protein interactions. Membrane proteins constitute approximately 30% of fully sequenced proteomes and are responsible for a wide variety of cellular functions. The aim of the current study was to identify and analyze MoRFs in membrane proteins. Two datasets of MoRFs, transmembrane and peripheral membrane protein MoRFs, were constructed from the Protein Data Bank, and sequence, structural and functional analysis was performed. Characterization of our datasets revealed their unique compositional biases and membrane protein MoRFs were categorized depending on their secondary structure after the interaction with their partners. Moreover, the position of transmembrane protein MoRFs in relation with the protein's topology was determined. Further studies were focused on functional analyses of MoRF-containing proteins and MoRFs' partners, associating them with protein binding, regulation and cell signaling, indicating half of them as putative hubs in protein–protein interaction networks. In conclusion, we provide insights into the disorder-based protein–protein interactions involving membrane proteins.     

The silkmoth eggshell as a natural amyloid shield for the safe development of insect oocyte and embryo: insights from studies of silkmoth chorion protein peptide-analogues of the B family

Silkmoth chorion is the major component of the silkmoth eggshell. The proteins that constitute more than 95% of its dry mass have remarkable mechanical and physicochemical properties forming a protective natural shield for the oocyte and the developing embryo from a wide range of environmental hazards. Peptide-analogues of the central conservative domain of the two major families of silkmoth chorion proteins, the A's and the B's, form amyloid fibrils under a variety of conditions, which prompted us to propose, 10 years ago, that silkmoth chorion is an amyloid with protective properties. Following our finding, a number of studies verified the existence of several functional amyloids. In this study, we designed, synthesized and studied two peptide-analogues of the central conservative domain of the B family of silkmoth chorion proteins, and we present experimental results, which show: (a) that the amyloidogenic properties of silkmoth chorion peptides are encoded into the tandemly repeating hexapeptides comprising the central domain of silkmoth chorion proteins, confirming our previous findings from peptide analogues of the A family of chorion proteins, and, (b) they suggest how silkmoth chorion proteins of the B family self-assemble in vivo, for the formation of the helicoidal architecture of silkmoth chorion.     

LepChorionDB,a database of Lepidopteran chorion proteins and a set of tools useful for the identification of chorion proteins in Lepidopteran proteomes

Chorion proteins of Lepidoptera have a tripartite structure, which consists of a central domain and two, more variable, flanking arms. The central domain is highly conserved and it is used for the classification of chorion proteins into two major classes, A and B. Annotated and unreviewed Lepidopteran chorion protein sequences are available in various databases. A database, named LepChorionDB, was constructed by searching 5 different protein databases using class A and B central domain-specific profile Hidden Markov Models (pHMMs), developed in this work. A total of 413 Lepidopteran chorion proteins from 9 moths and 1 butterfly species were retrieved. These data were enriched and organised in order to populate LepChorionDB, the first relational database, available on the web, containing Lepidopteran chorion proteins grouped in A and B classes. LepChorionDB may provide insights in future functional and evolutionary studies of Lepidopteran chorion proteins and thus, it will be a useful tool for the Lepidopteran scientific community and Lepidopteran genome annotators, since it also provides access to the two pHMMs developed in this work, which may be used to discriminate A and B class chorion proteins. LepChorionDB is freely available at http://bioinformatics.biol.uoa.gr/LepChorionDB.     

Ovarian activity and plasma sex steroid levels of Distichodus antonii in relation to environmental conditions in the upper basin of the Congo River

Distichodus antonii is an endemic fish species of the Congo River basin in which the stocks of wild populations are threatened by overfishing pressure. Knowledge of its reproductive biology would be useful in consideration of conservation and management options for the species. Therefore, this study investigated changes in ovarian activity and levels of steroid profiles in wild populations in relation to variation in temperature and rainfall. Adult females (n = 101, body weight of 3 183 ± 14.75 g, SE) were captured monthly over one year (2013–2014). Apart from evaluation of oocyte diameters and gonad developmental stages, gonado-, hepato-, lipososomatic indices (GSI, HSI, LSI) and plasma levels of sex steroids (testosterone-T, estradiol-17β-E2) were determined. The results suggested a synchronous development of oocytes with two annual reproductive seasons over the one-year study. Plasma T and E2 levels peaked during spawning periods likely reflecting active oogenesis. The highest values of morphosomatic indices were observed during the longest rainfall period in September, and were associated with high steroidogenic activity evidenced by increased E2 production. In addition, more vitellogenic oocytes (September and October) were observed during the latter season than during the short rainy season (in May).     

Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: application to complete genomes

Surface proteins in Gram-positive bacteria are frequently implicated in virulence. We have focused on a group of extracellular cell wall-attached proteins (CWPs), containing an LPXTG motif for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A hidden Markov model (HMM) approach for predicting the LPXTG-anchored cell wall proteins of Gram-positive bacteria was developed and compared against existing methods. The HMM model is parsimonious in terms of the number of freely estimated parameters, and it has proved to be very sensitive and specific in a training set of 55 experimentally verified LPXTG-anchored cell wall proteins as well as in reliable data sets of globular and transmembrane proteins. In order to identify such proteins in Gram-positive bacteria, a comprehensive analysis of 94 completely sequenced genomes has been performed. We identified, in total, 860 LPXTG-anchored cell wall proteins, a number that is significantly higher compared to those obtained by other available methods. Of these proteins, 237 are hypothetical proteins according to the annotation of SwissProt, and 88 had no homologs in the SwissProt database--this might be evidence that they are members of newly identified families of CWPs. The prediction tool, the database with the proteins identified in the genomes, and supplementary material are available online at http://bioinformatics.biol.uoa.gr/CW-PRED/.     

Invasion status of Florida bass Micropterus floridanus (Lesueur, 1822) in South Africa

Largemouth bass Micropterus salmoides are a popular North American angling species that was introduced into South Africa in 1928. To enhance the largemouth bass fisheries, Florida bass Micropterus floridanus were introduced into KwaZulu Natal, South Africa, in 1980. Knowledge on the status of M. floridanus in South Africa is required, because it lives longer and reaches larger sizes than M. salmoides, which may result in heightened impacts on native biota. Because M. floridanus are morphologically similar, but genetically distinct from M. salmoides, the distribution of this species was assessed by genetically screening 185 Micropterus sp. individuals sampled from 20 localities across South Africa using the mitochondrial ND2 gene. Individuals with mitochondrial DNA matching M. salmoides were recovered from 16 localities, whereas M. floridanus mitochondrial DNA was recovered from 13 localities. At nine localities (45%), the mitochondrial DNA of both species was detected. These results demonstrate M. floridanus dispersal to multiple sites across South Africa.     

Comparative analysis of the zeta-crystallin/quinone reductase gene in guinea pig and mouse

zeta-Crystallin is a novel nicotinamide adenine dinucleotide phosphate:quinone reductase, present at enzymatic levels in various tissues of different species, which is highly expressed in the lens of some hystricomorph rodents and camelids. We report here the complementary DNA (cDNA) cloning of zeta-crystallin from liver libraries in guinea pig (Cavia porcellus), where zeta-crystallin is highly expressed in the lens, and in the laboratory mouse (Mus musculus), where expression in the lens occurs only at enzymatic levels. A 5' untranslated sequence different from the one previously reported for the guinea pig lens cDNA was found in these clones. We also report the isolation of genomic clones including the complete guinea pig zeta-crystallin gene and the 5' region of this gene in mouse. These results show the presence of two promoters in the guinea pig zeta-crystallin gene, one responsible for expression at enzymatic levels and the other responsible for the high expression in the lens. The guinea pig lens promoter is not present in the mouse gene. This is the first example in which the recruitment of an enzyme as a lens crystallin can be explained by the acquisition of an alternative lens- specific promoter.      

Evidence for independent recruitment of zeta-crystallin/quinone reductase (CRYZ) as a crystallin in camelids and hystricomorph rodents

Zeta-crystallin/quinone reductase (CRYZ) is an NADPH oxidoreductase expressed at very high levels in the lenses of two groups of mammals: camelids and some hystricomorph rodents. It is also expressed at very low levels in all other species tested. Comparative analysis of the mechanisms mediating the high expression of this enzyme/crystallin in the lens of the Ilama (Lama guanacoe) and the guinea pig (Cavia porcellus) provided evidence for independent recruitment of this enzyme as a lens crystallin in both species and allowed us to elucidate for the first time the mechanism of lens recruitment of an enzyme- crystallin. The data presented here show that in both species such recruitment most likely occurred through the generation of new lens promoters from nonfunctional intron sequences by the accumulation of point mutations and/or small deletions and insertions. These results further support the idea that recruitment of CRYZ resulted from an adaptive process in which the high expression of CRYZ in the lens provides some selective advantage rather than from a purely neutral evolutionary process.