Novel α-L-Fucosidases from a Soil Metagenome for Production of Fucosylated Human Milk Oligosaccharides

This paper describes the discovery of novel α-L-fucosidases and evaluation of their potential to catalyse the transglycosylation reaction leading to production of fucosylated human milk oligosaccharides. Seven novel α-L-fucosidase-encoding genes were identified by functional screening of a soil-derived metagenome library and expressed in E. coli as recombinant 6xHis-tagged proteins. All seven fucosidases belong to glycosyl hydrolase family 29 (GH 29). Six of the seven α-L-fucosidases were substrate-inhibited, moderately thermostable and most hydrolytically active in the pH range 6–7, when tested with para-nitrophenyl-α-L-fucopyranoside (pNP-Fuc) as the substrate. In contrast, one fucosidase (Mfuc6) exhibited a high pH optimum and an unusual sigmoidal kinetics towards pNP-Fuc substrate. When tested for trans-fucosylation activity using pNP-Fuc as donor, most of the enzymes were able to transfer fucose to pNP-Fuc (self-condensation) or to lactose. With the α-L-fucosidase from Thermotoga maritima and the metagenome-derived Mfuc5, different fucosyllactose variants including the principal fucosylated HMO 2’-fucosyllactose were synthesised in yields of up to ~6.4%. Mfuc5 was able to release fucose from xyloglucan and could also use it as a fucosyl-donor for synthesis of fucosyllactose. This is the first study describing the use of glycosyl hydrolases for the synthesis of genuine fucosylated human milk oligosaccharides.     

Effect of floral display on reproductive success in terrestrial orchids

Almost one-third of all species in the familyOrchidaceae offer no reward to insect pollinators. In the absence of a reward, floral display (number of flowers), may be the most important component of insect attraction but the role of floral display in capsule production of both deceptive (nectarless) and rewarding (nectariferous) orchids has not yet been satisfactorily explored. Based on our theoretical considerations, we propose and test here the following hypotheses: (i) deceptive species flower earlier than rewarding ones, (ii) reproductive success in deceptive species is lower than that in rewarding ones, (iii) reproductive success is independent of the number of flowers in the inflorescence in both deceptive and rewarding orchids. Our data supported hypotheses (i) and (ii). In 9 out of our 12 populations of deceptive species and in 10 out of 12 populations of rewarding species we found support for our hypothesis (iii).     

Is the colour dimorphism inDactylorhiza sambucina maintained by differential seed viability instead of frequency-dependent selection?

The European rewardless, bee-pollinated orchidDactylorhiza sambucina commonly produces yellow-flowered and purple-flowered individuals in frequencies that range from balanced (per population) to very unbalanced, with parts of the species’ range entirely monochromatic. We studied male and female reproductive success of the two morphs in 22 populations in the Czech Republic, relating it to morph frequency, population size and density, and presence and abundance of yellow and purple co-flowering nectar-providing species visited by the same bee species. Cumulative abundances of yellow nectar-producing co-flowering species (of which, on average,Primula veris made up 56%) had a negative effect on male reproductive success of the yellow morph, and spectral analyses showed that to bumblebees the colours ofP. veris and yellowD. sambucina are different, permitting ready visual discrimination. The cumulative abundance of purple co-flowering species had no significant effect on morph reproductive success. Morph frequencies were unrelated to reproductive success and population size, and there was no evidence of frequency-dependent selection except in one highly unbalanced population. Density of flowering conspecifics was negatively correlated with male reproductive success of the purple morph. Seed mass, viability, and germination success depended on whether seeds resulted from outcrossed or selfed matings and on morph colour. Selfed seeds and seeds produced by the yellow morph from yellow × yellow and yellow × purple crosses had zero germination (after three months), providing the first hint that differential vegetative fitness, rather than differential reproductive fitness via pollinator selection, may explain morph frequencies inD. sambucina.     

Drivers of vegetative dormancy across herbaceous perennial plant species

Vegetative dormancy, that is the temporary absence of aboveground growth for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life‐history costs of sprouting, and of dormancy. Short‐lived and mycoheterotrophic species have higher proportions of dormant plants than long‐lived species and species with other nutritional modes. Foliage loss is associated with higher future dormancy levels, suggesting that carbon limitation promotes dormancy. Maximum dormancy duration is shorter under higher precipitation and at higher latitudes, the latter suggesting an important role for competition or herbivory. Study length affects estimates of some demographic parameters. Our results identify life historical and environmental drivers of dormancy. We also highlight the evolutionary importance of the little understood costs of sprouting and growth, latitudinal stress gradients and mixed nutritional modes.     

Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks

Bacteria use protein phosphorylation to regulate all kinds of physiological processes. Protein phosphorylation plays a role in several key steps of the infection process of bacterial pathogens, such as adhesion to the host, triggering and regulation of pathogenic functions as well as biochemical warfare; scrambling the host signaling cascades and impairing its defense mechanisms. Recent phosphoproteomic studies indicate that the bacterial protein phosphorylation networks could be more complex than initially expected, comprising promiscuous kinases that regulate several distinct cellular functions by phosphorylating different protein substrates. Recent advances in protein labeling with stable isotopes in the field of quantitative mass spectrometry phosphoproteomics will enable us to chart the global phosphorylation networks and to understand the implication of protein phosphorylation in cellular regulation on the systems scale. For the study of bacterial pathogens, in particular, this research avenue will enable us to dissect phosphorylation-related events during different stages of infection and stimulate our efforts to find inhibitors for key kinases and phosphatases implicated therein.     

NetPhosBac – A predictor for Ser/Thr phosphorylation sites in bacterial proteins

There is ample evidence for the involvement of protein phosphorylation on serine/threonine/tyrosine in bacterial signaling and regulation, but very few exact phosphorylation sites have been experimentally determined. Recently, gel‐free high accuracy MS studies reported over 150 phosphorylation sites in two bacterial model organisms Bacillus subtilis and Escherichia coli. Interestingly, the analysis of these phosphorylation sites revealed that most of them are not characteristic for eukaryotic‐type protein kinases, which explains the poor performance of eukaryotic data‐trained phosphorylation predictors on bacterial systems. We used these large bacterial datasets and neural network algorithms to create the first bacteria‐specific protein phosphorylation predictor: NetPhosBac. With respect to predicting bacterial phosphorylation sites, NetPhosBac significantly outperformed all benchmark predictors. Moreover, NetPhosBac predictions of phosphorylation sites in E. coli proteins were experimentally verified on protein and site‐specific levels. In conclusion, NetPhosBac clearly illustrates the advantage of taxa‐specific predictors and we hope it will provide a useful asset to the microbiological community.     

Environmental determinants of genetic diversity in Caragana microphylla (Fabaceae) in northern China

Non‐rewarding orchids rely on various ruses to attract their pollinators. One of the most common is for them to resemble flowers sought by insects as food sources. This can range from generalized food deception to the mimicry of specific sympatric food plants. We investigated the basis of pollinator deception in the European food‐deceptive orchid Traunsteinera globosa, which has unusually compact flowerheads resembling those of sympatric rewarding species of Knautia and Scabiosa (Dipsacaceae), and Valeriana (Caprifoliaceae). Visual signals of T. globosa are similar in both fly and bee vision models to those of the sympatric food plants used in the choice experiments, but scent signals are divergent. Field experiments conducted in Austria and the Czech Republic showed that both naive and experienced (with respect to visitation of T. globosa) insect species approached the orchids at the same rate as food plants, but direct contact with orchid flowers was taxon specific. Flies were most easily duped into probing the orchid, and, in doing so, frequently received and deposited pollinaria, whereas most bees and butterflies avoided landing on orchid flowers. We conclude that T. globosa is a mimic of a guild of fly‐pollinated plants, but the ecological dependence of the orchid on its models remains to be fully tested. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 269–294.