Ligophorus abditus n. sp. (Monogenea: Ancyrocephalidae) and other species of Ligophorus Euzet & Suriano, 1977 infecting the flathead grey mullet Mugil cephalus L. in the Sea of Japan and the Yellow Sea

As a result of the re-examination of museum slides and new material of monogeneans collected from Mugil cephalus L. in the Sea of Japan, the estuary of a river which flows into the Sea of Japan, the Yellow Sea (off Zhifu, at the boundary of the Bohai Sea) and the East China Sea (off the Ryukyu Islands), five species of Ligophorus Euzet & Suriano, 1977 were identified, one of which is new. The known species are L. chabaudi Euzet & Suriano, 1977, L. cheleus Rubtsova, Balbuena & Sarabeev, 2007, L. domnichi Rubtsova, Balbuena & Sarabeev, 2007 and L. pacificus Rubtsova, Balbuena & Sarabeev, 2007, which are reported from the Yellow Sea; in addition, L. domnichi is reported for the first time from the East China Sea. Ligophorus abditus n. sp., from the Sea of Japan, differs from its most similar congeners, L. pacificus and L. domnichi, in the shapes of the dorsal anchors and the accessory piece of the male copulatory organ. A comparison of all of the species of Ligophorus recovered from M. cephalus in the Sea of Japan was carried out using Principal Component Analysis, and their distribution and origin are discussed.     

Staphylococcal Phage 2638A endolysin is lytic for Staphylococcus aureus and harbors an inter-lytic-domain secondary translational start site

Staphylococcus aureus is a notorious pathogen highly successful at developing resistance to virtually all antibiotics to which it is exposed. Staphylococcal phage 2638A endolysin is a peptidoglycan hydrolase that is lytic for S. aureus when exposed externally, making it a new candidate antimicrobial. It shares a common protein organization with more than 40 other reported staphylococcal peptidoglycan hydrolases. There is an N-terminal M23 peptidase domain, a mid-protein amidase 2 domain (N-acetylmuramoyl-L-alanine amidase), and a C-terminal SH3b cell wall-binding domain. It is the first phage endolysin reported with a secondary translational start site in the inter-lytic-domain region between the peptidase and amidase domains. Deletion analysis indicates that the amidase domain confers most of the lytic activity and requires the full SH3b domain for maximal activity. Although it is common for one domain to demonstrate a dominant activity over the other, the 2638A endolysin is the first in this class of proteins to have a high-activity amidase domain (dominant over the N-terminal peptidase domain). The high activity amidase domain is an important finding in the quest for high-activity staphylolytic domains targeting novel peptidoglycan bonds.     

Identification of the nature of reading frame transitions observed in prokaryotic genomes

Our goal was to identify evolutionary conserved frame transitions in protein coding regions and to uncover an underlying functional role of these structural aberrations. We used the ab initio frameshift prediction program, GeneTack, to detect reading frame transitions in 206 991 genes (fs-genes) from 1106 complete prokaryotic genomes. We grouped 102 731 fs-genes into 19 430 clusters based on sequence similarity between protein products (fs-proteins) as well as conservation of predicted position of the frameshift and its direction. We identified 4010 pseudogene clusters and 146 clusters of fs-genes apparently using recoding (local deviation from using standard genetic code) due to possessing specific sequence motifs near frameshift positions. Particularly interesting was finding of a novel type of organization of the dnaX gene, where recoding is required for synthesis of the longer subunit, τ. We selected 20 clusters of predicted recoding candidates and designed a series of genetic constructs with a reporter gene or affinity tag whose expression would require a frameshift event. Expression of the constructs in Escherichia coli demonstrated enrichment of the set of candidates with sequences that trigger genuine programmed ribosomal frameshifting; we have experimentally confirmed four new families of programmed frameshifts.     

Perspectives and industrial potential of PGA selectivity and promiscuity

Penicillin G acylases (PGAs) are robust industrial catalysts used for biotransformation of β-lactams into key intermediates for chemical production of semi-synthetic β-lactam antibiotics by hydrolysis of natural penicillins. They are used also in reverse, kinetically controlled synthetic reactions for large-scale productions of these antibiotics from corresponding beta-lactam nuclei and activated acyl donors. Further biocatalytic applications of PGAs have recently been described: catalysis of peptide syntheses and the resolutions of racemic mixtures for the production of enantiopure active pharmaceutical ingredients that are based on enantioselective acylation or chiral hydrolysis. Moreover, PGAs rank among promiscuous enzymes because they also catalyze reactions such as trans-esterification, Markovnikov addition or Henry reaction. This particular biocatalytic versatility represents a driving force for the discovery of novel members of this enzyme family and further research into the catalytic potential of PGAs. This review deals with biocatalytic applications exploiting enantioselectivity and promiscuity of prokaryotic PGAs that have been recently reported. Biocatalytic applications are discussed and presented with reaction substrates converted into active compounds useful for the pharmaceutical industry.     

Changes in the curvature of sperm apical hooks in murine rodents

Sperm apical hooks in murine rodents play an important role in sperm competition. Apical hooks are more curved and longer in species with relatively larger testes, that is in species with a higher risk of sperm competition. The sperm can form aggregations, ‘trains’, that can move faster than individual sperm, thus reaching the egg earlier as was observed in Apodemus sylvaticus. The apical hook plays an important role for train formation. This study focuses on the changes in the curvature of sperm apical hooks during the final stages of spermiogenesis and stages before fertilization (sperm-life span). Apical hook curvatures of field mice (A. agrarius and A. sylvaticus) vary significantly between dormant and active sperm. In contrast, there are no significant differences among the stages in the eastern house mouse. Since there are high ranges of angle values in all stages, the mean angles of apical hook curvature are not appropriate for evaluating risk of sperm competiton. The ranges of angle values point to a level of flexibility of the apical hooks. The lengths of sperm hooks in individual species do not change during particular stages. The length and flexibility of the sperm apical hooks are important for the formation of sperm aggregations, thus these sperm characters indicate the risk of sperm competition and the sperm strategies in murine rodents.     

Immobilization of histidine-tagged proteins on monodisperse metallochelation liposomes: Preparation and study of their structure

Liposomes represent a biocompatible platform for the construction of self-assembling proteoliposomes using nickel or zinc metallochelation. Potential applications of such structures consist in the development of new biocompatible vaccination nanoparticles and drug delivery nanoparticle systems. Here, we describe the design and construction of a flow-through ultrafiltration cell suitable for the preparation of monodisperse liposomes enabled for metallochelation and, hence, the formation of proteoliposomes. The linkage of the cell with a fast protein liquid chromatography system facilitates automation of the procedure, which fits the criteria for upscaling. Proof-of-concept experiments are performed using a mixture of egg phosphatidyl choline and nickel-chelating lipid DOGS–NTA–Ni (1,2-dioleoyl-sn-glycero-3-{[N(5-amino-1-carboxypentyl)iminodiacetic acid]succinyl}(nickel salt)) to formulate proteoliposomes with proteins attached by metallochelation, including histidine (His)-tagged recombinant green fluorescent protein and rgp120 (derived from HIV-1 Env). These model proteoliposomes are characterized by gel permeation chromatography and by dynamic light scattering. Transmission electron microscopy and immunogold staining are used to characterize surface-bound proteins, revealing the tendency of rgp120 to form microdomains on liposome surfaces. These microdomains possess a two-dimensional crystal-like structure that is seen more precisely by atomic force microscopy.     

Mutations of human cytochrome P450 reductase differentially modulate heme oxygenase-1 activity and oligomerization

Genetic variations in POR, encoding NADPH-cytochrome P450 oxidoreductase (CYPOR), can diminish the function of numerous cytochromes P450, and also have the potential to block degradation of heme by heme oxygenase-1 (HO-1). Purified full-length human CYPOR, HO-1, and biliverdin reductase were reconstituted in lipid vesicles and assayed for NADPH-dependent conversion of heme to bilirubin. Naturally-occurring human CYPOR variants queried were: WT, A115V, Y181D, P228L, M263V, A287P, R457H, Y459H, and V492E. All CYPOR variants exhibited decreased bilirubin production relative to WT, with a lower apparent affinity of the CYPOR–HO-1 complex than WT. Addition of FMN or FAD partially restored the activities of Y181D, Y459H, and V492E. When mixed with WT CYPOR, only the Y181D CYPOR variant inhibited heme degradation by sequestering HO-1, whereas Y459H and V492E were unable to inhibit HO-1 activity suggesting that CYPOR variants might have differential binding affinities with redox partners. Titrating the CYPOR–HO-1 complex revealed that the optimal CYPOR:HO-1 ratio for activity was 1:2, lending evidence in support of productive HO-1 oligomerization, with higher ratios of CYPOR:HO-1 showing decreased activity. In conclusion, human POR mutations, shown to impact P450 activities, also result in varying degrees of diminished HO-1 activity, which may further complicate CYPOR deficiency.