Identification, expression, and characterization of a novel bacterial RGI lyase enzyme for the production of bio-functional fibers

A gene encoding a putative rhamnogalacturonan I (RGI) Lyase (EC 4.2.2.-) from Bacillus licheniformis (DSM13) was selected after a homology search and phylogenetic analysis and optimized with respect to codon usage. The designed gene was transformed into Pichia pastoris and the enzyme was produced in the eukaryotic host with a high titer in a 5 l bioreactor. The RGI Lyase was purified by Cu²⁺ affinity chromatography and 1.1 g pure enzyme was achieved pr. L. When the denatured protein was deglycosylated with EndoH, the molecular weight of the protein decreased to 65 kDa, which correlated with the predicted molecular weight of the mature RGI Lyase of 596 amino acids. By use of a statistical design approach, with potato rhamnogalacturonan as the substrate, the optimal reaction conditions for the RGI Lyase were established to be: 61 °C, pH 8.1, and 2 mM of both Ca²⁺ and Mn²⁺ (specific activity 18.4 U/mg; K_M 1.2 mg/ml). The addition of both Ca²⁺ and Mn²⁺ was essential for enzyme activity. The enzyme retained its catalytic activity at higher temperatures and the enzyme has a half life at 61 °C of 15 min. The work thus demonstrated the workability of in silico based screening coupled with a synthetic biology approach for gene synthesis for identification and production of a thermostable enzyme.     

The memory remains: application of historical DNA for scaling biodiversity loss

Few species worldwide have attracted as much attention in relation to conservation and sustainable management as Pacific salmon. Most populations have suffered significant reductions, many have disappeared, and even entire evolutionary significant units (ESUs) are believed to have been lost. Until now, no ‘smoking gun’ in terms of direct genetic evidence of the loss of a salmon ESU has been produced. In this issue of Molecular Ecology, Iwamoto et al. (2012) use microsatellite analysis of historical scale samples of Columbia River sockeye salmon (Oncorhynchus nerka) from 1924 ( Fig. 1 ) to ask the pertinent question: Do the historical samples contain salmon from extirpated populations or ESUs? They identified four genetic groups in the historical samples of which two were almost genetically identical to contemporary ESUs in the river, one showed genetic relationship with a third ESU, but one group was not related to any of the contemporary populations. In association with ecological data, the genetic results suggest that an early migrating Columbia River headwater sockeye salmon ESU has been extirpated. The study has significant importance for conservation and reestablishment of sockeye populations in the Columbia River, but also underpins the general significance of shifting baselines in conservation biology, and how to assess loss of genetic biodiversity. The results clearly illustrate the huge and versatile potential of using historical DNA in population and conservation genetics. Because of the extraordinarily plentiful historical samples and rapid advances in fish genomics, fishes are likely to spearhead future studies of temporal ecological and population genomics in non‐model organisms.

Figure 1 Open in figure viewer PowerPoint (a) Kokanee sampling site between Columbia and Windermere lakes on the upper Columbia River at Fairmont Hot Springs, British Columbia, Canada. (b) Bureau of Fisheries scale books that contained sockeye salmon (locally called ‘blueback’ salmon) scales collected from commercial fisheries during the 1920s in the lower Columbia River. (c) Kokanee on spawning beds in Kuskanax Creek, a tributary to Upper Arrow Lake, British Columbia. Photo credit Rick Gustafson and Jim Myers.     

Seasonal sea ice cover as principal driver of spatial and temporal variation in depth extension and annual production of kelp in Greenland

We studied the depth distribution and production of kelp along the Greenland coast spanning Arctic to sub‐Arctic conditions from 78 ºN to 64 ºN. This covers a wide range of sea ice conditions and water temperatures, with those presently realized in the south likely to move northwards in a warmer future. Kelp forests occurred along the entire latitudinal range, and their depth extension and production increased southwards presumably in response to longer annual ice‐free periods and higher water temperature. The depth limit of 10% kelp cover was 9–14 m at the northernmost sites (77–78 ºN) with only 94–133 ice‐free days per year, but extended to depths of 21–33 m further south (73 ºN–64 ºN) where >160 days per year were ice‐free, and annual production of Saccharina longicruris and S. latissima, measured as the size of the annual blade, ranged up to sevenfold among sites. The duration of the open‐water period, which integrates light and temperature conditions on an annual basis, was the best predictor (relative to summer water temperature) of kelp production along the latitude gradient, explaining up to 92% of the variation in depth extension and 80% of the variation in kelp production. In a decadal time series from a high Arctic site (74 ºN), inter‐annual variation in sea ice cover also explained a major part (up to 47%) of the variation in kelp production. Both spatial and temporal data sets thereby support the prediction that northern kelps will play a larger role in the coastal marine ecosystem in a warmer future as the length of the open‐water period increases. As kelps increase carbon‐flow and habitat diversity, an expansion of kelp forests may exert cascading effects on the coastal Arctic ecosystem.     

Present and past depth distribution of bladderwrack (Fucus vesiculosus) in the Baltic Sea

This study aimed to (1) assess the present depth distribution of Fucus vesiculosus in the Baltic Sea and evaluate differences between districts and (2) assess long-term and recent changes in depth distribution and evaluate reasons for such changes. This was done through compilation and analysis of existing data (3356 obs.). Depth limits were shallowest in the Kattegat, the Danish Belts and the Øresund (∼1.5 m on average), located at the entrance of the Baltic Sea and markedly deeper in the central and inner parts of the Baltic (up to ∼4.5 m on average). This increase in depth limits to some extent matched the decline in salinity and may in part be explained by reduced competition when species diversity decreases successively along the Baltic salinity gradient. In the central and inner Baltic Sea, Secchi depths explained part of the variation (16%) in depth limits and the majority (85%) of the variation in maximum attainable depth limits whereas at the entrance of the Baltic Secchi depths explained a negligible part of the variation (∼1%). In most districts, depth limits moved upwards during the 20th century. In many cases this happened during or shortly after the 1960s/1970s, and was most likely due to eutrophication.     

Transfer of Genetic Material between Pathogenic and Food-Borne Yeasts

Many pathogenic yeast species are asexual and therefore not involved in intra- or interspecies mating. However, high-frequency transfer of plasmid DNA was observed when pathogenic and food-borne yeasts were grown together. This property could play a crucial role in the spread of virulence and drug resistance factors among yeasts.