Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases

Xaa‐Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa‐Pro iminopeptide bond with a trans‐proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those that prefer longer oligopeptides are called aminopeptidases P. Though XPPs are strictly conserved in bacterial and archaeal species, the structural and sequence features that distinguish between prolidases and aminopeptidases P are not always clear. Here, we report 1.4 Å resolution crystal structure of a novel XPP from Deinococcus radiodurans (XPPdr). XPPdr forms a novel dimeric structure via unique dimer stabilization loops of N‐terminal domains such that their C‐terminal domains are placed far apart from each other. This novel dimerization is also the consequence of a different orientation of N‐terminal domain in XPPdr monomer than those in other known prolidases. The enzymatic assays show that it is a prolidase with broad substrate specificity. Our structural, mutational, and molecular dynamics simulation analyses show that the conserved Arg46 of N‐terminal domain is important for the dipeptide selectivity. Our BLAST search found XPPdr orthologs with conserved sequence motifs which correspond to unique structural features of XPPdr, thus identify a new subfamily of bacterial prolidases.     

Isolation and preliminary characterization of ferritin from clover seeds

Ferritin from clover (Trifolium subterraneum) seeds was isolated and characterized. It was shown to contain polypeptide units of 28–26.5 kDa. The apparent molecular mass of the native protein was 560 kDa. The average iron cores were 4 nm in diameter and contained 1300 iron atoms, with Fe:P = 4:1. Purified clover apoferritin was shown to be functional by means of iron uptake experiments. Plots of initial velocities of iron uptake (at pH 6.7) into clover and horse spleen apoferritins were found to have similar profiles.     

Formation and succession of alvar communities in the Baltic land uplift area

Calciphilous plant communities, soil and geomorphology along the gradient of elevation in land uplift area in the coast of western Estonia were described. In grazed areas, species rich alvar grassland is a final stage in successional sere. The differences in site history in various points of the transect were reflected by the variability of underlying deposits. When soils with different ages but having similar parent material were compared, some successional trends (decrease of the content of Ca, increase of the content of P and humus supply) became evident. Species composition of plant communities was determined mainly by local ecological conditions (moisture level, soil pH, also grazing) at any particular site. Differences between communities of the same association but with different successional age were negligible.     

Carbodithioate MeOBDCG for decreasing intracellular cadmium deposits in rats of different ages

The efficiency of chelating agents to remove aged intracellular deposits of cadmium in young and older rats was studied. The administration of the chelating agent sodiumN-(4-methoxybenzyl)-D-glucamine-N-carbodithioate monohydrate (MeOBDCG) 2 wk after a single intraperitoneal 115m Cd administration reduced the whole body, liver, and kidney retention in suckling rats to about 63, 42, and 71 percent and in older rats to 39, 17 and 76 percent of values obtained in respective controls. Chelation therapy was generally more effective in older than younger rats and the age-related effect was most pronounced in the liver. These results indicate that specific features of young organisms may significantly alter the effect of chelation treatment.     

Effects of N-free fertilization on ectomycorrhiza community structure in Norway spruce stands in Southern Sweden

The application of N-free fertilizer (i.e. lime combined with nutrients such as P, Ca, K and Mg) has been suggested as one way of compensating for nitrogen-caused eutrophication and losses of base cations due to atmospheric pollution. To study the effects of such a treatment on mycorrhizal fungi, fine-root samples were collected from the LFH-layer in four Norway spruce stands in southern Sweden. One stand was part of a larger experiment (Skogaby) and had four replicates. It was fertilized twice in 1988–89 (P:K:Ca:Mg:S 48:43:218:46:75 kg ha^-1), and sampling was carried out once yearly during 1991–93. The other three stands were fertilized once in 1988–89 (P:K:Ca:Mg:S|25:62:33:12:54 kg ha^-1) and sampled in 1992.Ectomycorrhizal fine-roots were classified into morphotypes on the basis of the structure and colours of their external hyphae and fungal mantle. The fungal biomass was estimated in 1992 using ergosterol analysis. In Skogaby, N-free fertilizer had no apparent effects on fungal biomass or on the total number of ECM types. Similar results were obtained for the other three stands. Previously reported 50% reductions in sporocarp production on the fertilized plots at Skogaby can probably be explained by a decrease in carbon allocation to the roots and by a decline in the abundance of a single morphotype which accounted for 3% of the total number of root tips, but ca. 30% of the sporocarp biomass in the control plots in the present study. It is concluded that moderate levels of N-free fertilization are not likely to drastically affect the community structure of the dominating ectomycorrhizal fungi. This result should be interpreted with some caution, however, since it remains to be determined whether the fertilizer treatments affect the function of the nutrient-absorbing soil mycelium of the mycorrhizal fungi.     

Sequence variation in four mitochondrial genes of the salmon louse Lepeophtheirus salmonis

A total of 210 Lepeophtheirus salmonis collected from 7 locations (Scotland, Russia, Canada, Japan and 3 locations in Norway), were screened for sequence variation in 4 mitochondrial genes; ATPase subunit 6 (A6), Cytochrome b oxidase subunit I (COI), Cytochrome b (Cyt b) and 16S rRNA. A high level of intraspecific variation was observed within all genes. The majority of polymorphisms were present in single individuals only, which resulted in a high number of private haplotypes within each gene. Little evidence of genetic differentiation was observed among the 3 Norwegian locations or between L. salmonis samples from Norway, Scotland and Russia. Pairwise FST values indicated that a weak degree of sub-division between L. salmonis sampled in Canada and the Northeast Atlantic might, however, exist. All samples collected in the Atlantic were highly different from the Japanese sample. It is suggested that the lack of genetic differentiation among lice samples from the North Atlantic is a result of extensive gene flow mediated by passive transport of L. salmonis larvae, and the migratory pattern of its salmonid hosts.     

Emergence and maintenance of infectious salmon anaemia virus (ISAV) in Europe: a new hypothesis

The present study describes the use of molecular methods in studying infectious salmon anaemia virus (ISAV), an important pathogen of farmed salmon in Norway, Scotland, the Faeroe Islands, Canada, USA and Chile. The nucleotide sequences of the haemagglutinin gene (HA) from 70 ISAV isolates have been analysed for phylogenetic relationship and the average mutation rate of nucleotide substitutions calculated. The isolates constitute 2 major groups, 1 European and 1 North American group. The isolate from Chile is closely related to the North American isolates. The European isolates can be further divided into 3 separate groups reflecting geographical distribution, time of collection, and transmission connected with farming activity. Based on existing information about infectious salmon anaemia (ISA) and new information emerging from the present study, it is hypothesised that: (1) ISAV is maintained in wild populations of trout and salmon in Europe; (2) it is transmitted between wild hosts mainly during their freshwater spawning phase in rivers; (3) wild salmonids, mainly trout, possibly carry benign wild-type ISAV isolates; (4) a change (mutation) in virulence probably results from deletions of amino acid segments from the highly polymorphic region (HPR) of benign wild-type isolates; (5) ISA emerges in farmed Atlantic salmon when mutated isolates are transmitted from wild salmonids or, following mutation of benign isolates, in farmed salmon after transmission from wild salmonids; (6) farming activity is an important factor in transmission of ISAV between farming sites in addition to transmission of ISAV from wild salmonids to farmed salmon; (7) transmission of ISAV from farmed to wild salmonids probably occurs less frequently than transmission from wild to farmed fish due to lower frequency of susceptible wild individuals; (8) the frequency of new outbreaks of ISA in farmed salmon probably reflects natural variation in the prevalence of ISAV in wild populations of salmonids.