ALBERT

Beschreibung: Two-component regulatory systems are commonly used by bacteria to coordinate intracellular responses with environmental cues. These systems are composed of functional protein pairs consisting of a sensor histidine kinase and cognate response regulator. In contrast to the well-studied Caulobacter crescentus system, which carries dozens of these pairs, the streamlined bacterial endosymbiont Wolbachia pipientis encodes only two pairs: CckA/CtrA and PleC/PleD. Here, we used bioinformatic tools to compare characterized two-component system relays from C. crescentus , the related Anaplasmataceae species Anaplasma phagocytophilum and Ehrlichia chaffeensis , and 12 sequenced Wolbachia strains. We found the core protein pairs and a subset of interacting partners to be highly conserved within Wolbachia and these other Anaplasmataceae. Genes involved in two-component signaling were positioned differently within the various Wolbachia genomes, whereas the local context of each gene was conserved. Unlike Anaplasma and Ehrlichia , Wolbachia two-component genes were more consistently found clustered with metabolic genes. The domain architecture and key functional residues standard for two-component system proteins were well-conserved in Wolbachia , although residues that specify cognate pairing diverged substantially from other Anaplasmataceae. These findings indicate that Wolbachia two-component signaling pairs share considerable functional overlap with other α-proteobacterial systems, whereas their divergence suggests the potential for regulatory differences and cross-talk.

Beschreibung: Non-LTR retrotransposons are an important class of mobile elements that insert into host DNA by target-primed reverse transcription (TPRT). Non-LTR retrotransposons must bind to their mRNA, recognize and cleave their target DNA, and perform TPRT at the site of DNA cleavage. As DNA binding and cleavage are such central parts of the integration reaction, a better understanding of the endonuclease encoded by non-LTR retrotransposons is needed. This paper explores the R2 endonuclease domain from Bombyx mori using in vitro studies and in silico modeling. Mutations in conserved sequences located across the putative PD-(D/E)XK endonuclease domain reduced DNA cleavage, DNA binding and TPRT. A mutation at the beginning of the first α-helix of the modeled endonuclease obliterated DNA cleavage and greatly reduced DNA binding. It also reduced TPRT when tested on pre-cleaved DNA substrates. The catalytic K was located to a non-canonical position within the second α-helix. A mutation located after the fourth β-strand reduced DNA binding and cleavage. The motifs that showed impaired activity form an extensive basic region. The R2 biochemical and structural data are compared and contrasted with that of two other well characterized PD-(D/E)XK endonucleases, restriction endonucleases and archaeal Holliday junction resolvases.

Beschreibung: The requirement of vitamins for core metabolic processes creates a unique set of pressures for arthropods subsisting on nutrient-limited diets. While endosymbiotic bacteria carried by arthropods have been widely implicated in vitamin provisioning, the underlying molecular mechanisms are not well understood. To address this issue, standardized predictive assessment of vitamin metabolism was performed in 50 endosymbionts of insects and arachnids. The results predicted that arthropod endosymbionts overall have little capacity for complete de novo biosynthesis of conventional or active vitamin forms. Partial biosynthesis pathways were commonly predicted, suggesting a substantial role in vitamin provisioning. Neither taxonomic relationships between host and symbiont, nor the mode of host-symbiont interaction were clear predictors of endosymbiont vitamin pathway capacity. Endosymbiont genome size and the synthetic capacity of nonsymbiont taxonomic relatives were more reliable predictors. We developed a new software application that also predicted that last-step conversion of intermediates into active vitamin forms may contribute further to vitamin biosynthesis by endosymbionts. Most instances of predicted vitamin conversion were paralleled by predictions of vitamin use. This is consistent with achievement of provisioning in some cases through upregulation of pathways that were retained for endosymbiont benefit. The predicted absence of other enzyme classes further suggests a baseline of vitamin requirement by the majority of endosymbionts, as well as some instances of putative mutualism. Adaptation of this workflow to analysis of other organisms and metabolic pathways will provide new routes for considering the molecular basis for symbiosis on a comprehensive scale.

Beschreibung: Using the data from over 8000 wells augmented by seismic and thermal response information, a comparison of McMurray Formation (Cretaceous) and Grosmont C member (Devonian) thermal recovery reservoirs of northeastern Alberta is provided along with a discussion of reservoir performance to date. Fluvial-estuarine McMurray Formation reservoirs perform best where bitumen-charged homogeneous lenticular sandstones at least 20 metres thick are found. These deposits are relatively rare as the formation is characterized by endemic heterogeneity mainly in the form of inclined heterolithic stratification (IHS). Most of the best McMurray steam-assisted gravity drainage (SAGD) reservoirs appear to be currently on-line and produce approximately 113 000 m 3 /day of bitumen from fourteen projects. Platform carbonate Grosmont C successions are blanket deposits 32–35 metres thick, with bitumen columns typically 15–24 metres thick, and are characterized by consistent reservoir properties facilitated by pervasive multi-scale fracturing. Although no reserves have yet to be assigned to Alberta’s bitumen-bearing carbonates by the province, recent pilot results derived from cyclic steam stimulation (CSS) operations suggest that Grosmont C reservoir performance could ultimately prove to be competitive with superior McMurray SAGD reservoirs. Under current technological and economic conditions, McMurray SAGD reservoirs appear incapable of providing the 15.9 billion m 3 of in-situ bitumen reserves (59% of Canada’s total oil reserves) ascribed to this formation by the province of Alberta as only circa 6 billion m 3 of oil-in place appears to reside within optimal reservoirs (i.e. those reservoirs at least 20 metres thick with average porosity and oil saturation values of 33% and 80%, respectively). Barring future technological breakthroughs and, or, economic improvements, future commercial development of both the Grosmont C and other carbonate reservoirs might be needed to make up for some of the potential reserve shortfall associated with McMurray Formation SAGD reservoirs.