Structural and Biochemical Analyses of Glycoside Hydrolase Family 26 β-Mannanase from a Symbiotic Protist of the Termite Reticulitermes speratus

Termites and their symbiotic protists have established a prominent dual lignocellulolytic system, which can be applied to the biorefinery process. One of the major components of lignocellulose from conifers is glucomannan, which comprises a heterogeneous combination of β-1,4-linked mannose and glucose. Mannanases are known to hydrolyze the internal linkage of the glucomannan backbone, but the specific mechanism by which they recognize and accommodate heteropolysaccharides is currently unclear. Here, we report biochemical and structural analyses of glycoside hydrolase family 26 mannanase C (RsMan26C) from a symbiotic protist of the termite Reticulitermes speratus. RsMan26C was characterized based on its catalytic efficiency toward glucomannan, compared with pure mannan. The crystal structure of RsMan26C complexed with gluco-manno-oligosaccharide(s) explained its specificities for glucose and mannose at subsites −5 and −2, respectively, in addition to accommodation of both glucose and mannose at subsites −3 and −4. RsMan26C has a long open cleft with a hydrophobic platform of Trp⁹⁴ at subsite −5, facilitating enzyme binding to polysaccharides. Notably, a unique oxidized Met⁸⁵ specifically interacts with the equatorial O-2 of glucose at subsite −3. Our results collectively indicate that specific recognition and accommodation of glucose at the distal negative subsites confers efficient degradation of the heteropolysaccharide by mannanase.     

Sampling the rarest: threatened beetles in boreal forest biodiversity inventories

Presence or absence of threatened species in samples is information that is widely used in designing and implementing conservation actions. We explored the effectiveness of beetle (Coleoptera) inventories and contribution of different sampling methods in revealing occurrences of threatened and near threatened species in boreal forests. The number of species caught using traps in a particular area proved to be a useful indicator of the representativeness of data, the relationship between total number of species and the number of threatened and near threatened species being almost exponential. Samples containing less than 200 trapped species (or 2000 individuals) are almost useless in surveying threatened and near threatened species. The probability of finding such species increases considerably when the number of trapped species exceeds 400. Window traps attached directly on the trunks of dead trees proved to be the most efficient sampling method in trapping threatened beetles, whereas many other standard methods gave relatively poor results. We suggest that the best alternative in surveying threatened species in boreal forests is a combination of intensive direct searching and trunk window traps. Finding threatened beetles with rigorous probability requires very large sample sizes, even if the most effective sampling methods are used. For example, ranking 10 boreal forest areas to be protected according to the occurrence of threatened species with some reliability may require trapping of over 100000 beetle individuals. Collecting and identifying these large samples routinely in conservation actions is not feasible, which means that shortcuts (indicators etc.) are necessary. However, a lot of good-quality inventories with appropriate sampling efforts are needed before these shortcuts can be identified and elaborated. Such inventories are also crucial for the improvement of the classification of threatened species and full assessment on how past forest management has eventually affected the biota.     

Diverse population trajectories among coexisting species of subarctic forest moths

Records of 232 moth species spanning 26 years (total catch of ca. 230,000 specimens), obtained by continuous light-trapping in Kevo, northernmost subarctic Finland, were used to examine the hypothesis that life-history traits and taxonomic position contribute to both relative abundance and temporal variability of Lepidoptera. Species with detritophagous or moss-feeding larvae, species hibernating in the larval stage, and species pupating during the first half of the growing season were over-represented among 42 species classified as abundant during the entire sampling period. The coefficients of variation in annual catches of species hibernating as eggs averaged 1.7 times higher than those of species hibernating as larvae or pupae. Time-series analysis demonstrated that periodicity in fluctuations of annual catches is generally independent of life-history traits and taxonomic affinities of the species. Moreover, closely related species with similar life-history traits often show different population dynamics, undermining the phylogenetic constraints hypothesis. Species with the shortest (1 year) time lag in the action of negative feedback processes on population growth exhibit the largest magnitude of fluctuations. Our analyses revealed that only a few consistent patterns in the population dynamics of herbivorous moths can be deduced from life-history characteristics of the species. Moreover, the diversity of population behaviour in one moth assemblage challenges any conventional wisdom suggesting predictable patterns. Our results raise several questions about perceptions and paradigms in insect population dynamics and stress the need for research on detritivorous insect population dynamics, as well as the need for more assemblage-wide studies using common trapping methods to provide comparative data on related and unrelated species with different life-history traits.     

Specific recognition of the collagen triple helix by chaperone HSP47. II. The HSP47-binding structural motif in collagens and related proteins

The endoplasmic reticulum-resident chaperone heat-shock protein 47 (HSP47) plays an essential role in procollagen biosynthesis. The function of HSP47 relies on its specific interaction with correctly folded triple-helical regions comprised of Gly-Xaa-Yaa repeats, and Arg residues at Yaa positions have been shown to be important for this interaction. The amino acid at the Yaa position (Yaa(-3)) in the N-terminal-adjoining triplet containing the critical Arg (defined as Arg(0)) was also suggested to be directly recognized by HSP47 (Koide, T., Asada, S., Takahara, Y., Nishikawa, Y., Nagata, K., and Kitagawa, K. (2006) J. Biol. Chem. 281, 3432-3438). Based on this finding, we examined the relationship between the structure of Yaa(-3) and HSP47 binding using synthetic collagenous peptides. The results obtained indicated that the structure of Yaa(-3) determined the binding affinity for HSP47. Maximal binding was observed when Yaa(-3) was Thr. Moreover, the required relative spatial arrangement of these key residues in the triple helix was analyzed by taking advantage of heterotrimeric collagen-model peptides, each of which contains one Thr(-3) and one Arg(0). The results revealed that HSP47 recognizes the Yaa(-3) and Arg(0) residues only when they are on the same peptide strand. Taken together, the data obtained led us to define the HSP47-binding structural epitope in the collagen triple helix and also define the HSP47-binding motif in the primary structure. A motif search against human protein database predicted candidate clients for this molecular chaperone. The search result indicated that not all collagen family proteins require the chaperoning by HSP47.     

Temperature acclimation of photosynthesis: mechanisms involved in the changes in temperature dependence of photosynthetic rate

Growth temperature alters temperature dependence of the photosynthetic rate (temperature acclimation). In many species, the optimal temperature that maximizes the photosynthetic rate increases with increasing growth temperature. In this minireview, mechanisms involved in changes in the photosynthesis-temperature curve are discussed. Based on the biochemical model of photosynthesis, change in the photosynthesis-temperature curve is attributable to four factors: intercellular CO2 concentration, activation energy of the maximum rate of RuBP (ribulose-1,5-bisphosphate) carboxylation (Vc max), activation energy of the rate of RuBP regeneration (Jmax), and the ratio of Jmax to Vc max. In the survey, every species increased the activation energy of Vc max with increasing growth temperature. Other factors changed with growth temperature, but their responses were different among species. Among these factors, activation energy of Vc max may be the most important for the shift of optimal temperature of photosynthesis at ambient CO2 concentrations. Physiological and biochemical causes for the change in these parameters are discussed.     

Structure of the human galanin receptor 2 bound to galanin and Gq reveals the basis of ligand specificity and how binding affects the G-protein interface

Galanin is a neuropeptide expressed in the central and peripheral nervous systems, where it regulates various processes including neuroendocrine release, cognition, and nerve regeneration. Three G-protein coupled receptors (GPCRs) for galanin have been discovered, which is the focus of efforts to treat diseases including Alzheimer’s disease, anxiety, and addiction. To understand the basis of the ligand preferences of the receptors and to assist structure-based drug design, we used cryo-electron microscopy (cryo-EM) to solve the molecular structure of GALR2 bound to galanin and a cognate heterotrimeric G-protein, providing a molecular view of the neuropeptide binding site. Mutant proteins were assayed to help reveal the basis of ligand specificity, and structural comparison between the activated GALR2 and inactive hβ₂AR was used to relate galanin binding to the movements of transmembrane (TM) helices and the G-protein interface.

Galanin is a neuropeptide expressed in the central and peripheral nervous systems, where it regulates various processes including neuroendocrine release, cognition, and nerve regeneration. This cryo-electron microscopy study shows how galanin interacts with one of its three human receptor proteins, GALR2, and reveals the basis of the selectivity of this GPCR for Gq.     

Ontogenetic diet shift, feeding rhythm, and daily ration of juvenile yellowfin goby Acanthogobius flavimanus on a tidal mudflat in the Tama River estuary, central Japan

To ascertain the feeding habits of benthic juvenile yellowfin goby Acanthogobius flavimanus, the gut contents of 599 specimens (15–41 mm in standard length, SL), collected on a tidal mudflat in the Tama River estuary throughout the diel cycle, were examined. The major prey items changed from harpacticoid copepods to errant and sedentary polychaetes at ca. 20 mm SL. Prey width increased with fish size. Fish of 26–28 mm SL fed mainly from sunset to morning, with highest feeding intensity during twilight hours and/or high tide. Based on the gut evacuation rate estimated from a forced feeding experiment in the laboratory and data for the diel change of mean gut-content volume in the field, the daily ration of juvenile yellowfin goby (26–28 mm SL) was calculated to be 13.8 mm³ fish⁻¹ day⁻¹. This volume is approximately equivalent to 3.9 individuals of the errant polychaete Ceratonereis erythraeensis (9.7 mm in body length, BL) or 8.1 individuals of the sedentary polychaete Prionospio japonica (14.8 mm BL), both species occurring abundantly on the mudflat during the study.     

New Year’s greetings 2020 from the Journal of Plant Research

Journal of Plant Research -     

New year’s greetings 2019 from the Journal of Plant Research

Journal of Plant Research -