Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners

YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell.     

Fungal transformation of selenium and tellurium located in a volcanogenic sulfide deposit

Microbial reduction of soluble selenium (Se) or tellurium (Te) species results in immobilization as elemental forms and this process has been employed in soil bioremediation. However, little is known of direct and indirect fungal interactions with Se-/Te-bearing ores. In this research, the ability of Phoma glomerata to effect transformation of selenite and tellurite was investigated including interaction with Se and Te present in sulfide ores from the Kisgruva Proterozoic volcanogenic deposit. Phoma glomerata could precipitate elemental Se and Te as nanoparticles, intracellularly and extracellularly, when grown with selenite or tellurite. The nanoparticles possessed various surface capping molecules, with formation being influenced by extracellular polymeric substances. The presence of sulfide ore also affected the production of exopolysaccharide and protein. Although differences were undetectable in gross Se and Te ore levels before and after fungal interaction using X-ray fluorescence, laser ablation inductively coupled plasma mass spectrometry of polished flat ore surfaces revealed that P. glomerata could effect changes in Se/Te distribution and concentration indicating Se/Te enrichment in the biomass. These findings provide further understanding of fungal roles in metalloid transformations and are relevant to the geomicrobiology of environmental metalloid cycling as well as informing applied approaches for Se and Te immobilization, biorecovery or bioremediation.     

Molecular identification of <Emphasis Type="Italic">Ammonia</Emphasis> and <Emphasis Type="Italic">Elphidium</Emphasis> species (Foraminifera,Rotaliida) from the Kiel Fjord (SW Baltic Sea) with rDNA sequences

Ammonia and Elphidium collected in the Kiel Fjord for the present study were first identified on morphological bases as Ammonia beccarii (Linné, 1758) and Elphidium excavatum (Terquem, 1876). Phylogenetic analyses based on partial SSU rDNA and LSU rDNA sequences show that Ammonia specimens sampled in the Kiel Fjord belong to the phylotype T6, which has a disjunct distribution (Wadden and Baltic Seas/China and Japan) and has been identified as Ammonia aomoriensis (Asano, 1951). Partial SSU rDNA sequence analyses indicate that Elphidium specimens from the Kiel Fjord belong to the clade E. excavatum, confirming the morphological identification. This clade can be further divided in three subclades. Kiel Fjord Elphidium belong to two of these subclades and were identified morphologically as the subspecies E. excavatum excavatum (Terquem, 1876) and E. e. clavatum Cushman, 1930.     

Performance and molecular evaluation of an anaerobic system with suspended biomass for treating wastewater with high fat content after enzymatic hydrolysis

The effect of a lipase-rich fungal enzymatic preparation, produced by a Penicillium sp. during solid-state fermentation, was evaluated in an anaerobic digester treating dairy wastewater with 1200 mg of oil and grease/L. The oil and grease hydrolysis step was carried out with 0.1% (w/v) of solid enzymatic preparation at 30 °C for 24 h, and resulted in a final free acid concentration eight times higher than the initial value. The digester operated in sequential batches of 48 h at 30 °C for 245 days, and had high chemical oxygen demand (COD) removal efficiencies (around 90%) when fed with pre-hydrolyzed wastewater. However, when the pre-hydrolysis step was removed, the anaerobic digester performed poorly (with an average COD removal of 32%), as the oil and grease accumulated in the biomass and effluent oil and grease concentration increased throughout the operational period. PCR-DGGE analysis of the Bacteria and Archaea domains revealed remarkable differences in the microbial profiles in trials conducted with and without the pre-hydrolysis step, indicating that differences observed in overall parameters were intrinsically related to the microbial diversity of the anaerobic sludge.     

Probing impact of active site residue mutations on stability and activity of Neisseria polysaccharea amylosucrase

The amylosucrase from Neisseria polysaccharea is a transglucosidase from the GH13 family of glycoside-hydrolases that naturally catalyzes the synthesis of α-glucans from the widely available donor sucrose. Interestingly, natural molecular evolution has modeled a dense hydrogen bond network at subsite −1 responsible for the specific recognition of sucrose and conversely, it has loosened interactions at the subsite +1 creating a highly promiscuous subsite +1. The residues forming these subsites are considered to be likely involved in the activity as well as the overall stability of the enzyme. To assess their role, a structure-based approach was followed to reshape the subsite −1. A strategy based on stability change predictions, using the FoldX algorithm, was considered to identify the best candidates for site-directed mutagenesis and guide the construction of a small targeted library. A miniaturized purification protocol was developed and both mutant stability and substrate promiscuity were explored. A range of 8°C between extreme melting temperature values was observed and some variants were able to synthesize series of oligosaccharides with distributions differing from that of the parental enzyme. The crucial role of subsite −1 was thus highlighted and the biocatalysts generated can now be considered as starting points for further engineering purposes.