The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers

BACKGROUND: The rhomboid family of polytopic membrane proteins shows a level of evolutionary conservation unique among membrane proteins. They are present in nearly all the sequenced genomes of archaea, bacteria and eukaryotes, with the exception of several species with small genomes. On the basis of experimental studies with the developmental regulator rhomboid from Drosophila and the AarA protein from the bacterium Providencia stuartii, the rhomboids are thought to be intramembrane serine proteases whose signaling function is conserved in eukaryotes and prokaryotes. RESULTS: Phylogenetic tree analysis carried out using several independent methods for tree constructions and the corresponding statistical tests suggests that, despite its broad distribution in all three superkingdoms, the rhomboid family was not present in the last universal common ancestor of extant life forms. Instead, we propose that rhomboids evolved in bacteria and have been acquired by archaea and eukaryotes through several independent horizontal gene transfers. In eukaryotes, two distinct, ancient acquisitions apparently gave rise to the two major subfamilies, typified by rhomboid and PARL (presenilins-associated rhomboid-like protein), respectively. Subsequent evolution of the rhomboid family in eukaryotes proceeded by multiple duplications and functional diversification through the addition of extra transmembrane helices and other domains in different orientations relative to the conserved core that harbors the protease activity. CONCLUSIONS: Although the near-universal presence of the rhomboid family in bacteria, archaea and eukaryotes appears to suggest that this protein is part of the heritage of the last universal common ancestor, phylogenetic tree analysis indicates a likely bacterial origin with subsequent dissemination by horizontal gene transfer. This emphasizes the importance of explicit phylogenetic analysis for the reconstruction of ancestral life forms. A hypothetical scenario for the origin of intracellular membrane proteases from membrane transporters is proposed

Patterns of intron gain and conservation in eukaryotic genes

<p>Abstract</p> <p>Background:</p> <p>The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction of which share position in distant taxa, such as plants and animals. Depending on the methods and data sets used, researchers have reached opposite conclusions on the causes of the high fraction of shared introns in orthologous genes from distant eukaryotes. Some studies conclude that shared intron positions reflect, almost entirely, a remarkable evolutionary conservation, whereas others attribute it to parallel gain of introns. To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions.</p> <p>Results:</p> <p>We developed a probabilistic model of evolution that allows for variability of intron gain and loss rates over branches of the phylogenetic tree, individual genes, and individual sites. Applying this model to an extended set of conserved eukaryotic genes, we find that parallel gain, on average, accounts for only ~8% of the shared intron positions. However, the distribution of parallel gains over the phylogenetic tree of eukaryotes is highly non-uniform. There are, practically, no parallel gains in closely related lineages, whereas for distant lineages, such as animals and plants, parallel gains appear to contribute up to 20% of the shared intron positions. In accord with these findings, we estimated that ancestral introns have a high probability to be retained in extant genomes, and conversely, that a substantial fraction of extant introns have retained their positions since the early stages of eukaryotic evolution. In addition, the density of sites that are available for intron insertion is estimated to be, approximately, one in seven basepairs.</p> <p>Conclusion:</p> <p>We obtained robust estimates of the contribution of parallel gain to the observed sharing of intron positions between eukaryotic species separated by different evolutionary distances. The results indicate that, although the contribution of parallel gains varies across the phylogenetic tree, the high level of intron position sharing is due, primarily, to evolutionary conservation. Accordingly, numerous introns appear to persist in the same position over hundreds of millions of years of evolution. This is compatible with recent observations of a negative correlation between the rate of intron gain and coding sequence evolution rate of a gene, suggesting that at least some of the introns are functionally relevant.</p

Unique PFK regulatory property from some mosquito vectors of disease, and from Drosophila melanogaster

Effect of F2, 6BP on Aedes aegypti PFK activity. PFK activity was measured at pH = 7.4, 1 mM F6P, 5 mM ATP at several F2, 6BP concentrations (0.01–50 μM). Values are the means ± SEM of three independent experiments. (TIF 466 kb

Molecular biological studies on neuropeptides of the adipokinetic hormone/red pigment-concentrating hormone family and the neuroparsin family in the arthropod sister groups of insects and crustaceans

Includes abstract.Includes bibliographical references.This study describes the identification of three novel precursor transcripts which includes the adipokinetic hormone (AKH) / red pigment-concentrating hormone (RPCH) and the neuroparsin (NP) from the South African spiny lobster, Jasus lalandii, the RPCH and the RPCH receptor (RPCHR) from the water flea D. pulex and the NP from the southern green stinkbug, Nezara viridula. The study also investigates the localisation and expression profiles of the AKH/RPCH and NP transcripts within crustaceans and insects

Prapovijesno sojeničko naselje Bijeli Vir kod metkovića

U ovom radu obrađuju se keramički nalazi iz Bijeloga Vira kod Metkovića. Kontekst nalaza (slučajni nalaz prilikom kopanja kanala za navodnjavanje) kao i sačuvani arheološki ostaci (keramika, kost, kućni lijep, ostaci drva), jasno ukazuju da je na tom mjestu postojalo sojeničko naselje. Na osnovi analize keramičkih ulomaka (tehnologija, tipologija i analogije) i uz nepoznanicu o nastanku i prestanku života u tom naselju, ipak se može dati jedan određen vremenski raspon trajanja toga naselja, i to od kraja srednjega brončanoga doba, tj. Br c2 do u razvijeno željezno doba, tj. Ha d2/Ha d3

Functional Characterization of Hypertrehalosemic Hormone Receptor in Relation to Hemolymph Trehalose and to Oxidative Stress in the Cockroach Blattella germanica

Hypertrehalosemic hormone (HTH) is a peptide hormone that belongs to the adipokinetic hormone/red pigment concentrating hormone (AKH/RPCH) family, which exerts pleiotropic actions related to catabolic reaction and stress response. AKH peptides have been demonstrated to participate in stress response including oxidative stress in several insects. In order to study the signaling pathway of HTH involved in anti-oxidative stress, we have characterized a HIH receptor cDNA in Blattella germanica (Blage-HTHR) in structural and in functional terms using RNA interference (RNAi). Blage-HTHR is expressed in various female adult tissues (brain–CC–CA, ventral nerve cord, midgut, fat body, oviduct), but maximal expression is observed in the fat body. RNAi-mediated knockdown of Blage-HTHR expression results in a significantly lower level of hemolymph trehalose, even though HTH is exogenously administered. Paraquat elicits lethal oxidative stress in B. germanica, and co-injection of paraquat and HTH reduces this detrimental effect and extends the median survival time. Interestingly, the “rescue” effect of HTH on mortality caused by paraquat is diminished in specimens with depleted expression of Blage-HTH and Blage-HTHR. Finally, lipid peroxidation in the hemolymph increases 4 h after paraquat treatment, in comparison with control specimens or with HTH-treated specimens. However, lipid peroxidation induced by paraquat was not “rescued” by HTH in Blage-HTH and Blage-HTHR knockdown specimens. Our results demonstrate that HTH acts as a stress hormone mediating anti-oxidative protection in B. germanica, and that its receptor, Blage-HTHR, is essential for this action

Three-dimensional incompressible Navier-Stokes computations of internal flows

Several incompressible Navier-Stokes solution methods for obtaining steady and unsteady solutions are discussed. Special attention is given to internal flows which involve distinctly different features from external flows. The characterisitcs of the flow solvers employing the method of pseudocompressibility and a fractional step method are briefly described. This discussion is limited to a primitive variable formulation in generalized curvilinear coordinates. Computed results include simple test cases and internal flow in the Space Shuttle main engine hot-gas manifold

A Drosophila melanogaster H3.3 cDNA encodes a histone variant identical with the vertebrate H3.3

A cDNA encoding an H3.3 histone variant in Drosophila melanogaster predicts a protein with an amino acid (aa) sequence identical with that in vertebrates. The D. melanogaster H3.3 nucleotide (nt) sequence has diverged significantly from that of both the H3.3 gene of vertebrates and the H3.1 gene of D. melanogaster, largely through third nt changes in its codons. The perfect H3.3 aa sequence conservation between organisms as phylogenetically divergent as vertebrates and flies suggests that the H3.3 histone variant itself is an important structural component of chromatin, apart from the value of its replication-independent expression pattern. Keywords: Conserved proteins, amino acid sequence homologies, chromatin, bacteriophage λ library, invertebrat