Metagenomic and metatranscriptomic analyses reveal uncharted microbial constituents responsible for polyhydroxybutyrate biodegradation in coastal waters.

Polyhydroxybutyrate (PHB) has attracted attention as a representative polymer for biodegradable plastics produced by microorganisms. Since information regarding the fate of PHB released into the environment is limited, it is necessary to identify them based on metagenomic information. We estimated the PHB biodegradability in coastal water samples collected from 15 near shore sites around Japan using oxygen consumption as an indicator in laboratory-scale incubation experiments and conducted 16S rRNA gene-based microbial community profiling.

Design of RGDS Peptide-Immobilized Self-Assembling β-Strand Peptide from Barnacle Protein.

We designed three types of RGD-containing barnacle adhesive proteins using self-assembling peptides. In the present study, three types of RGD-containing peptides were synthesized by solid-phase peptide synthesis, and the secondary structures of these peptides were analyzed by CD and FT-IR spectroscopy. The mechanical properties of peptide hydrogels were characterized by a rheometer.

Purification, Cloning, Functional Expression, Structure, and Characterization of a Thermostable β-Mannanase from B168 and Its Efficiency in Production of Mannooligosaccharides from Coffee Wastes.

Highly thermostable β-mannanase, belonging to glycoside hydrolase family 5 subfamily 7, was purified from the culture supernatant of B168 and the cDNA of its transcript was cloned. The recombinant enzyme showed maximal activity at pH 4.5 and 85 °C.

GH30 Glucuronoxylan-Specific Xylanase from Streptomyces turgidiscabies C56.

Endoxylanases are important enzymes in bioenergy research because they specifically hydrolyze xylan, the predominant polysaccharide in the hemicellulose fraction of lignocellulosic biomass. For effective biomass utilization, it is important to understand the mechanism of substrate recognition by these enzymes. Recent studies have shown that the substrate specificities of bacterial and fungal endoxylanases classified into glycoside hydrolase family 30 (GH30) were quite different.

Vanadium-Binding Ability of Nucleoside Diphosphate Kinase from the Vanadium-Rich Fan Worm, Pseudopotamilla occelata.

Polychaete fan worms and ascidians accumulate high levels of vanadium ions. Several vanadiumbinding proteins, known as vanabins, have been found in ascidians. However, no vanadium-binding factors have been isolated from the fan worm.

Amyloid-like conformation and interaction for the self-assembly in barnacle underwater cement.

Barnacles are unique marine sessile crustaceans and permanently attach to various foreign surfaces during most of their lifespan. The protein complex secreted from their body and used to attach their calcareous shell to almost all surfaces in water has long fascinated us because we have limited technology with which to attach materials in water. Unraveling the mechanism of underwater attachment by barnacles is thus important for interface science, for the understanding of the biology and physiology of barnacles, and for the development of technology to prevent fouling.

Mini-review: barnacle adhesives and adhesion.

Barnacles are intriguing, not only with respect to their importance as fouling organisms, but also in terms of the mechanism of underwater adhesion, which provides a platform for biomimetic and bioinspired research. These aspects have prompted questions regarding how adult barnacles attach to surfaces under water. The multidisciplinary and interdisciplinary nature of the studies makes an overview covering all aspects challenging.

Significance of the conformation of building blocks in curing of barnacle underwater adhesive.

Barnacles are a unique sessile crustacean that attach irreversibly and firmly to foreign underwater surfaces. Its biological underwater adhesive is a peculiar extracellular multi-protein complex. Here we characterize one of the two major proteins, a 52 kDa protein found in the barnacle cement complex.

Advenella faeciporci sp. nov., a nitrite-denitrifying bacterium isolated from nitrifying-denitrifying activated sludge collected from a laboratory-scale bioreactor treating piggery wastewater.

Strain M-07(T) was isolated from nitrifying-denitrifying activated sludge treating piggery wastewater. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain M-07(T) belonged to the genus Advenella. 16S rRNA gene sequence similarity between M-07(T) and Advenella incenata CCUG 45225(T), Advenella mimigardefordensis DPN7(T) and Advenella kashmirensis WT001(T) was 96.

Absence of cross-linking via trans-glutaminase in barnacle cement and redefinition of the cement.

Balanomorphan barnacles attach their calcareous bases to a variety of substrata, including others of the same species, through secretion of an underwater adhesive, commonly referred to as cement. In this multi-functional process of underwater attachment, curing of the adhesive is crucial for the formation of a secure attachment. To date, there has been no direct evidence presented to suggest the involvement of cross-linking or polymerization in the cement curing process, despite the emergence of this hypothesis in the recent literature.

Sequence variation of Vanabin2-like vanadium-binding proteins in blood cells of the vanadium-accumulating ascidian Ascidia sydneiensis samea.

The blood cells of ascidians accumulate extremely high levels of the transition metal vanadium. We previously isolated four vanadium-binding proteins (Vanabins 1-4) and a homologous protein (VanabinP) from the vanadium-rich ascidian Ascidia sydneiensis samea. In the present study, we identified cDNAs encoding five different Vanabin2-related proteins in A.

Underwater adhesive of marine organisms as the vital link between biological science and material science.

Marine sessile organisms naturally attach themselves to diverse materials in water by a technique that has so far remained unreproducible. Recent studies on the holdfast of marine sessile organisms have revealed natural concepts that are currently beyond our understanding with respect to the molecular design and macroscopic range. The combination of valuable and practical natural design of biotic adhesives as biomolecular materials, together with continuing efforts towards mimetic design, hold the promise of revolution for future materials.

Characterization of a novel vanadium-binding protein (VBP-129) from blood plasma of the vanadium-rich ascidian Ascidia sydneiensis samea.

The ascidians, the so-called sea squirts, accumulate high levels of vanadium, a transition metal. Since Henze first observed this physiologically unusual phenomenon about one hundred years ago, it has attracted interdisciplinary attention from chemists, physiologists, and biochemists. The maximum concentration of vanadium in ascidians can reach 350 mM, and most of the vanadium ions are stored in the +3 oxidation state in the vacuoles of vanadium-accumulating blood cells known as vanadocytes.

Calcite-specific coupling protein in barnacle underwater cement.

The barnacle relies for its attachment to underwater foreign substrata on the formation of a multiprotein complex called cement. The 20 kDa cement protein is a component of Megabalanus rosa cement, although its specific function in underwater attachment has not, until now, been known. The recombinant form of the protein expressed in bacteria was purified in soluble form under physiological conditions, and confirmed to retain almost the same structure as that of the native protein.

Identification and functional characterization of a novel barnacle cement protein.

Barnacle attachment to various foreign materials in water is guided by an extracellular multiprotein complex. A 19 kDa cement protein was purified from the Megabalanus rosa cement, and its cDNA was cloned and sequenced. The gene was expressed only in the basal portion of the animal, where the histologically identified cement gland is located.

Self-assembling peptide inspired by a barnacle underwater adhesive protein.

An underwater bioadhesive generally comprises a multiprotein complex that provides a molecular basis for self-assembly. We report here a new class of self-assembling peptide inspired by a 20 kDa barnacle cement protein. Studies on the chemically synthesized 24-residue peptide have revealed that (1) it underwent irreversible self-assembly upon the addition of salt, (2) the self-assembly was started at a salt concentration close to that of seawater with noncovalent intermolecular interactions, (3) the self-assembled material resembled a macroscopic membrane of interwoven nanofilaments, (4) incubation in an alkaline pH range formed the intramolecular disulfide bond of a peptide molecule, thus triggering a conformation change of the molecule, and (5) conformational change of the building block promoted the formation of a nanofiber, resulting in the display of a three-dimensional meshlike mesoscopic structure with defined pores having a diameter of approximately 200 nm.

Glutathione transferases with vanadium-binding activity isolated from the vanadium-rich ascidian Ascidia sydneiensis samea.

Some ascidians accumulate vanadium in vanadocytes, which are vanadium-containing blood cells, at high levels and with high selectivity. However, the mechanism and physiological significance of vanadium accumulation remain unknown. In this study, we isolated novel proteins with a striking homology to glutathione transferases (GSTs), designated AsGST-I and AsGST-II, from the digestive system of the vanadium-accumulating ascidian Ascidia sydneiensis samea, in which the digestive system is thought to be involved in vanadium uptake.

VanabinP, a novel vanadium-binding protein in the blood plasma of an ascidian, Ascidia sydneiensis samea.

Some ascidians accumulate high levels of the transition metal vanadium in their blood cells. The process of vanadium accumulation has not yet been elucidated. In this report, we describe the isolation and cDNA cloning of a novel vanadium-binding protein, designated as VanabinP, from the blood plasma of the vanadium-rich ascidian, Ascidia sydneiensis samea.

Purification and characterization of ferredoxin-NADP+ reductase encoded by Bacillus subtilis yumC.

From Bacillus subtilis cell extracts, ferredoxin-NADP+ reductase (FNR) was purified to homogeneity and found to be the yumC gene product by N-terminal amino acid sequencing. YumC is a approximately 94-kDa homodimeric protein with one molecule of non-covalently bound FAD per subunit. In a diaphorase assay with 2,6-dichlorophenol-indophenol as electron acceptor, the affinity for NADPH was much higher than that for NADH, with Km values of 0.

Expressed sequence tag analysis of vanadocytes in a vanadium-rich ascidian, Ascidia sydneiensis samea.

Some species in the family Ascidiidae accumulate vanadium at concentrations in excess of 350 mM, which corresponds to about 10(7) times higher than that in seawater. In these species signet ring cells, with a single huge vacuole in which vanadium ion is contained, function as vanadium-accumulating cells, vanadocytes. To investigate the mechanism underlying this phenomenon, we performed an expressed sequence tag (EST) analysis of a complementary DNA library from vanadocytes of a vanadium-rich ascidian, Ascidia sydneiensis samea.