Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.     

Microbial degradation and physico-chemical alteration of polyhydroxyalkanoates by a thermophilic <Emphasis Type="Italic">Streptomyces</Emphasis> sp.

A thermophilic Streptomyces sp. capable of degrading various aliphatic polyesters was isolated from a landfill site. The isolate, Streptomyces sp. BCC23167, demonstrated rapid aerobic degradation of several polyesters, including polyhydroxyalkanoate copolymers, poly(ɛ-caprolactone) and polybutylene succinate at 50°C and neutral pH. The degrading activity was repressed by glucose and cellobiose, but tolerant to repression by other carbon substrates. Degradation of a commercial poly[(R)-3-hydroxybutyrate-co-3-hydroxyhexanoate] (PHBHx) by Streptomyces sp. BCC23167 progressed from surface to bulk as suggested by the slight decrease in polymer molecular weight. Differential scanning calorimetry analysis of PHBHx film degradation by Streptomyces sp. BCC23167 showed that relative crystallinity of the film increased slightly in the early stage of degradation, followed by a marked decrease later on. The surface morphology of degraded films was analyzed by scanning electron microscopy, which showed altered surface structure consistent with the changes in crystallinity. The isolate is thus of potential for application in composting technology for bio-plastic degradation.     

Life cycle assessment of single use thermoform boxes made from polystyrene (PS), polylactic acid, (PLA), and PLA/starch: cradle to consumer gate

Purpose

Currently, the bio-based plastics have been drawing considerable attention from the packaging industry as a sustainable solution for replacing petroleum-based plastics in order to reduce the accumulation of plastic waste in the environment. This work has benchmarked the environmental impact of bio-based against petroleum-based plastics for single use boxes. In this paper, the cradle to consumer gate environmental impact data of these boxes was calculated and reported as part 1. End-of-life options of both bio- and petroleum-based boxes are an important subject which will be further studied for part 2. The energy sources in this work were taken from the Thailand energy database namely: Thai electricity grid mix (TEGM), Thai coal electricity (TCE), Thai natural gas combine cycle (TNGCC), and Thai coal integrated gasification combine cycle (TIGCC).

Methods

The materials studied were polystyrene (PS) derived from petroleum, polylactic acid (PLA) derived from corn, and PLA/cassava starch blend (PLA/starch). The tray with lid (herein after called box) was processed in a plastic manufacturing in Thailand using cast sheet extrusion and then thermoforming techniques. The functional unit is specified as 10,000 units of 8.0?×?10.0?×?2.5 cm of PS, PLA, and PLA/starch boxes which weigh 447.60, 597.60, and 549.56 kg, respectively. Three impact categories; namely global warming potential including direct greenhouse gas, and indirect land use change (LUC) emissions, acidification, and photochemical ozone formation are investigated. Finally, the normalization results including and excluding LUC consideration were compared and reported.

Results and discussion

The results from this study have shown that the total environmental impact including LUC emission of bio-based boxes were different when the various energy sources were supplied throughout the life cycle production stage. It can be seen that the PS box has lower environmental impact than PLA and PLA/starch boxes when TEGM, TCE, TNGCC, and TIGCC were used as energy supplied. LUC of renewable feedstocks, such as corn and cassava, were considered as the biggest impact of absolute scores of PLA and PLA/starch boxes. These results are consistent with Piemonte and Gironi (2010).

Conclusions

PLA and PLA/starch boxes give a slightly higher environmental impact than the PS box by 1.59 and 1.09 times, respectively, when LUC was not accounted in the absolute scores and clean energy TIGCC was used throughout the life cycle.     

Molecular paleontology: a biochemical model of the ancestral ribosome

Ancient components of the ribosome, inferred from a consensus of previous work, were constructed in silico, in vitro and in vivo. The resulting model of the ancestral ribosome presented here incorporates ∼20% of the extant 23S rRNA and fragments of five ribosomal proteins. We test hypotheses that ancestral rRNA can: (i) assume canonical 23S rRNA-like secondary structure, (ii) assume canonical tertiary structure and (iii) form native complexes with ribosomal protein fragments. Footprinting experiments support formation of predicted secondary and tertiary structure. Gel shift, spectroscopic and yeast three-hybrid assays show specific interactions between ancestral rRNA and ribosomal protein fragments, independent of other, more recent, components of the ribosome. This robustness suggests that the catalytic core of the ribosome is an ancient construct that has survived billions of years of evolution without major changes in structure. Collectively, the data here support a model in which ancestors of the large and small subunits originated and evolved independently of each other, with autonomous functionalities.